Road to the MCAT

OFFICE OF PREMEDICAL PROGRAMS

ROADMAP TO THE MCAT Tracking MCAT content in your natural and behavioral science courses.

University of Dayton

MCAT Mapping

Introduction:

One of the main criteria for selection of students to medical school is their performance on the Medical College Admission Test (MCAT). In 2015, the MCAT will change significantly, for the first time since 1991. The modifications reflect changes in both health care and an ever-­‐evolving body of medical knowledge. MCAT 2015 will include a new section focusing on the psychological, social and biological foundations of behavior. The exam will test ways these areas influence various factors such as perception, reactions and behavior, as well as psychological, social and cultural differences that influence well-­‐being. The MCAT also includes a critical analysis and reasoning skills section, which will test students’ ability to analyze, evaluate and apply information. Finally, two natural science sections will test concepts typically taught in introductory biology, general and organic chemistry, biochemistry and physics.

Recently the Association of American Medical Colleges (AAMC) released two documents to help institutions plan for these changes and develop course content which reflects the identified content areas of the new MCAT. The Preview Guide for MCAT 2015 provides a blueprint for the exam in that it describes the exam’s content and format and discusses the exam’s conceptual framework. The “Course-­‐Mapping Tool” provides the MCAT content and skills contained in an Excel spreadsheet so that specific topics and subtopics can be identified as being covered or not covered in specific courses.

The Office of Premedical Programs has recently completed a course-­‐mapping project in which content areas from MCAT 2015 were identified as being covered in specific University of Dayton courses. The following documents were developed as a result of this project involving faculty from the Departments of Biology, Chemistry, Physics, Psychology, and Sociology, Anthropology and Social Work. These faculty members were provided the MCAT course-­‐mapping tool and were asked to identify within their courses where specific MCAT content areas are covered. The results of these analyses were compiled by the Office of Premedical Programs.

Specifically, the following MCAT sections were included in this course-­‐mapping project:

• Biological and Biochemical Foundations of Living Systems.

• Chemical and Physical Foundations of Biological Systems.

• Psychological, Social, and Biological Foundations of Behavior.

The fourth section of the MCAT is titled Critical Analysis and Reasoning Skills (CARS). It includes passages and questions to test the student’s ability to comprehend. Passages are excerpted from authentic materials found in a variety of books, journals and magazines, often from disciplines in the social sciences and humanities. The CARS section is NOT included in this

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course mapping since it tests comprehension and not knowledge typically covered in a specific course.

The first document, titled “Course Listing with Associated Topics,” (page 4) lists courses from the natural and behavioral science departments along with identified MCAT content areas covered in each of these classes. It is expected that this document will be helpful to students and faculty. Students will be able to track and archive materials relevant to the MCAT as they complete these courses. They can also go back over course materials later and pull and archive these portions of the courses. Clearly, these materials will later be helpful for students as they organize and plan their study schedule for the exam.

Faculty may find it useful to use this document to identify areas of focus in their courses and identify to students that these areas are typically included in the MCAT. Faculty often look for MCAT content areas to include in their exams as well.

The second document is titled “Topic List with Associated Courses”(page 136). It provides a comprehensive listing of all of the content categories in the three identified sections of the MCAT. For each content category, specific courses are listed that include one or more topics or subtopics in that content category. The degree to which a specific topic is covered in a particular course will vary greatly and it is important that the reader look at the more detailed description of content in any given course in the main “Course Listing with Associated Topics” section.

This compilation is not intended to be the sole resource for preparation for the MCAT. Instead it is intended as a useful tool to assist in organizing and archiving MCAT-­‐related course materials and to help students begin their MCAT study as they are introduced to relevant materials, building a personal portfolio of these materials throughout their undergraduate studies.

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Topic List with Associated Courses

This document is a list of the main University of Dayton courses from the natural and behavioral sciences that include content from the MCAT 2015 exam. For each identified course, there is a list of topics typically covered in that course.

Table of Contents BIOLOGY CHEMISTRY PHYSICS PSYCHOLOGY SOCIOLOGY and ANTHROPOLOGY

Page 5 68 97 100 129

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BIOLOGY BIO 151 & BIO 151L Amino Acids ● Description ○ Absolute configuration at the position ○ Amino acids as dipolar ions ○ Classifications ■ Acidic or basic ■ Hydrophobic or hydrophilic ● Reactions ○ Sulfur linkage for cysteine and cysteine ○ Peptide linkage: polypeptides and proteins ○ Hydrolysis Protein Structure ● Structure ○ 1° structure of proteins ○ 2° structure of proteins ○ 3° structure of proteins; role of proline, cystine, hydrophobic bonding ○ 4° structure of proteins ● Conformational stability ○ Denaturing and folding ○ Hydrophobic interactions ● Separation techniques ○ Electrophoresis Non-­‐Enzymatic Protein Function ● Binding ● Immune system ● Motors Enzyme Structure and Function ● Function of enzymes in catalyzing biological reaction ● Reduction of activation energy ● Substrates and enzyme specificity ● Induced-­‐fit Model ● Mechanism of catalysis ○ Cofactors ○ Coenzyme ● Effects of local conditions on enzyme activity Control of Enzyme Activity ● Kinetics

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○ General (catalysis) ○ Cooperativity ● Feedback regulation ● Inhibition – types ○ Competitive ○ Non-­‐competitive ● Regulatory enzymes ○ Allosteric enzymes ○ Covalently-­‐modified enzymes ○ Zymogen Nucleic Acid Structure and Function ● Description ● Nucleotides and nucleosides ○ Sugar phosphate backbone ○ Pyrimidine, purine residues ● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure ● Base pairing specificity: A with T, G with C ● Function in transmission of genetic information ● DNA denaturation, reannealing, hybridization DNA Replication ● Mechanism of replication: separation of strands, specific coupling of free nucleic acids ● Semi-­‐conservative nature of replication ● Specific enzymes involved in replication ● Origins of replication, multiple origins in eukaryotes ● Replicating the ends of DNA molecules Repair of DNA ● Repair during replication ● Repair of mutations Genetic Code ● Central Dogma: DNA → RNA → protein ● The triplet code ● Codon-­‐anticodon relationship ● Degenerate code, wobble pairing ● Missense, nonsense codons ● Initiation, termination codons ● Messenger RNA (mRNA) Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA)

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● Mechanism of transcription ● mRNA processing in eukaryotes, introns, exons ● Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNA (snRNAs) ● Functional and evolutionary importance of introns Translation ● Roles of mRNA, tRNA, rRNA ● Role and structure of ribosomes ● Initiation, termination co-­‐factors ● Post-­‐translational modification of proteins Eukaryotic Chromosome Organization ● Chromosomal proteins ● Single copy vs. repetitive DNA ● Supercoiling ● Heterochromatin vs. euchromatin ● Telomeres, centromeres Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-­‐Monod Model ● Gene repression in bacteria ● Positive control in bacteria Control of Gene Expression in Eukaryotes ● Transcriptional regulation ● DNA binding proteins, transcription factors ● Gene amplification and duplication ● Post-­‐transcriptional control, basic concept of splicing (introns, exons) ● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes ● Regulation of chromatin structure ● DNA methylation ● Role of non-­‐coding RNAs Recombinant DNA and Biotechnology ● Gene cloning ● Restriction enzymes ● DNA libraries ● Generation of cDNA ● Hybridization ● Expressing cloned genes ● Polymerase Chain Reaction

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● ● ● ● ● ●

Gel Electrophoresis and Southern Blotting DNA sequencing Analyzing gene expression Determining gene function Stem cells Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture ● Safety and ethics of DNA technology Evidence that DNA is Genetic Material Mendelian Concepts ● Phenotype and genotype ● Gene ● Locus ● Allele: single and multiple ● Homozygosity and heterozygosity ● Wild-­‐type ● Recessiveness ● Complete dominance ● Co-­‐dominance ● Incomplete dominance ● Hybridization: viability ● Gene pool Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis ● Important differences between meiosis and mitosis ● Segregation of genes ○ Independent assortment ○ Linkage ○ Recombination ■ Single crossovers ■ Double crossovers ■ Synaptonemal complex ■ Tetrad ○ Sex-­‐linked characteristics ○ Very few genes on Y chromosome ○ Sex determination ○ Cytoplasmic/extranuclear inheritance ● Mutation

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○ General concept of mutation — error in DNA sequence ○ Types of mutations: random, translation error, transcription error, base substitution, inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation ○ Inborn errors of metabolism ○ Relationship of mutagens to carcinogens ● Genetic drift ● Synapsis or crossing-­‐over mechanism for increasing genetic diversity Analytic Methods ● Test cross ● Gene mapping: crossover frequencies Principles of Bioenergetics ● Bioenergetics/thermodynamics ○ Free energy/Keq ■ Equilibrium constant ■ Relationship of the equilibrium constant and ΔG° ○ Concentration ○ Endothermic/exothermic reactions ○ Free energy: G ○ Spontaneous reactions and ΔG° ● Phosphoryl group transfers and ATP ○ ATP hydrolysis ΔG << 0 ○ ATP group transfers ● Biological oxidation-­‐reduction ○ Half-­‐reactions ○ Soluble electron carriers ○ Flavoproteins Carbohydrates ● Description ○ Nomenclature and classification, common names ○ Absolute configuration ○ Cyclic structure and conformations of hexoses ○ Epimers and anomers ● Hydrolysis of the glycoside linkage ● Monosaccharides

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● Disaccharides ● Polysaccharides Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway ● Glycolysis (aerobic), substrates and products ○ Feeder pathways: glycogen, starch metabolism ● Fermentation (anaerobic glycolysis) ● Gluconeogenesis ● Net molecular and energetic results of respiration processes Principles of Metabolic Regulation ● Regulation of metabolic pathways ○ Maintenance of a dynamic steady state ● Regulation of glycolysis and gluconeogenesis ● Metabolism of glycogen ● Regulation of glycogen synthesis and breakdown ○ Allosteric and hormonal control ● Analysis of metabolic control Citric Acid Cycle ● Acetyl-­‐CoA production ● Reactions of the cycle, substrates and products ● Regulation of the cycle ● Net molecular and energetic results of respiration processes Metabolism of Fatty Acids and Proteins ● Description of fatty acids ● Oxidation of fatty acids ○ Saturated fats ○ Unsaturated fats ● Ketone bodies ● Anabolism of fats

Oxidative Phosphorylation ● Electron transport chain and oxidative phosphorylation, substrates and products, general features of the pathway ● Electron transfer in mitochondria ○ NADH, NADPH ○ Flavoproteins ○ Cytochromes ● ATP synthase, chemiosmotic coupling ○ Proton motive force ● Net molecular and energetic results of respiration processes ● Regulation of oxidative phosphorylation

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● Mitochondria, apoptosis, oxidative stress Hormonal Regulation and Integration of Metabolism ● Higher level integration of hormone structure and function ● Tissue specific metabolism ● Hormonal regulation of fuel metabolism ● Obesity and regulation of body mass Plasma Membrane ● General function in cell containment ● Composition of membranes ○ Lipid components ■ Phospholipids (and phosphatids) ■ Steroids ■ Waxes ○ Protein components ○ Fluid mosaic model ● Membrane dynamics ● Solute transport across membranes ○ Thermodynamic considerations ○ Osmosis ■ Colligative properties, osmotic pressure ○ Passive transport ○ Active transport ■ Sodium/potassium pump ● Membrane channels ● Membrane potential ● Membrane receptors ● Exocytosis and endocytosis ● Intercellular junctions ○ Gap junctions ○ Tight junctions ○ Desmosomes Membrane-­‐Bound Organelles and Defining Characteristics of Eukaryotic Cells ● Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles, ● mitotic division ● Nucleus ○ Compartmentalization, storage of genetic information ○ Nucleolus: location and function

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○ Nuclear envelope, nuclear pores ● Mitochondria ○ Site of ATP production ○ Inner and outer membrane structure ○ Self-­‐replication ● Lysosomes: membrane-­‐bound vesicles containing hydrolytic enzymes ● Endoplasmic reticulum ○ Rough and smooth components ○ Rough endoplasmic reticulum site of ribosomes ○ Double membrane structure ○ Role in membrane biosynthesis ○ Role in biosynthesis of secreted proteins ● Golgi apparatus: general structure and role in packaging and secretion ● Peroxisomes: organelles that collect peroxides Cytoskeleton ● General function in cell support and movement ● Microfilaments: composition and role in cleavage and contractility ● Microtubules: composition and role in support and transport ● Intermediate filaments, role in support ● Composition and function of cilia and flagella ● Centrioles, microtubule organizing centers Tissues Formed From Eukaryotic Cells ● Epithelial cells ● Connective tissue cells Cell Theory ● History and development ● Impact on biology Classification and Structure of Prokaryotic Cells ● Prokaryotic domains ○ Archaea ○ Bacteria ● Major classifications of bacteria by shape ○ Bacilli (rod-­‐shaped) ○ Spirilli (spiral shaped) ○ Cocci (spherical) ● Lack of nuclear membrane and mitotic apparatus

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● Lack of typical eukaryotic organelles ● Presence of cell wall in bacteria ● Flagellar propulsion, mechanism Growth and Physiology of Prokaryotic Cells ● Reproduction by fission ● High degree of genetic adaptability, acquisition of antibiotic resistance ● Exponential growth ● Existence of anaerobic and aerobic variants ● Parasitic and symbiotic ● Chemotaxis Genetics of Prokaryotic Cells ● Existence of plasmids, extragenomic DNA ● Transformation: incorporation into bacterial genome of DNA fragments from external medium ● Conjugation ● Transposons (also present in eukaryotic cells) Virus Structure ● General structural characteristics (nucleic acid and protein, enveloped and nonenveloped) ● Lack organelles and nucleus ● Structural aspects of typical bacteriophage ● Genomic content-­‐-­‐RNA or DNA ● Size relative to bacteria and eukaryotic cells Viral Life Cycle ● Self-­‐replicating biological units that must reproduce within specific host cell ● Generalized phage and animal virus life cycles ○ Attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic ○ material ○ Use of host synthetic mechanism to replicate viral components ○ Self-­‐assembly and release of new viral particles ● Transduction: transfer of genetic material by viruses ● Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV ● Prions and viroids: subviral particles Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase,

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interphase ● Mitotic structures ○ Centrioles, asters, spindles ○ Chromatids, centromeres, kinetochores ○ Nuclear membrane breakdown and reorganization ○ Mechanisms of chromosome movement ● Phases of cell cycle: G0, G1, S, G2, M ● Growth arrest ● Control of cell cycle ● Loss of cell cycle controls in cancer cells Biosignalling ● Apoptosis Biosignalling ● Gated ion channels ○ Voltage gated ○ Ligand gated ● Receptor enzymes ● G protein-­‐coupled receptors Lipids ● Description; structure ○ Steroids

Nucleotides and Nucleic Acids ● Nucleotides and nucleosides: composition ○ Sugar phosphate backbone ○ Pyrimidine, purine residues ● Deoxyribonucleic acid: DNA, double helix ● Chemistry ● Other functions Enzymes ● Classification by reaction type ● Mechanism ○ Substrates and enzyme specificity ○ Induced-­‐fit model ○ Cofactors, coenzymes and vitamins ● Kinetics ○ General (catalysis) ○ Cooperativity ○ Effects of local conditions on enzyme activity ● Inhibition

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● Regulatory enzymes ○ Allosteric ○ Covalently modified

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BIO152 & BIO 152L Mendelian Concepts ● Phenotype and genotype ● Gene ● Locus ● Allele: single and multiple ● Homozygosity and heterozygosity ● Wild-­‐type ● Recessiveness ● Complete dominance ● Co-­‐dominance ● Incomplete dominance, leakage, penetrance, expressivity ● Hybridization: viability ● Gene pool Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis ● Important differences between meiosis and mitosis ● Segregation of genes ○ Independent assortment ○ Linkage ○ Recombination ■ Single crossovers ■ Double crossovers ■ Synaptonemal complex ■ Tetrad ○ Sex-­‐linked characteristics ○ Very few genes on Y chromosome ○ Sex determination ○ Cytoplasmic/extranuclear inheritance ● Mutation ○ General concept of mutation — error in DNA sequence ○ Types of mutations: random, translation error, transcription error, base substitution, inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation ○ Inborn errors of metabolism ○ Relationship of mutagens to carcinogens ● Genetic drift ● Synapsis or crossing-­‐over mechanism for increasing genetic

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diversity Analytic Methods ● Hardy–Weinberg Principle ● Test cross ● Gene mapping: crossover frequencies ● Biometry: statistical methods Evolution ● Natural selection ○ Fitness concept ○ Selection by differential reproduction ○ Concepts of natural and group selection ○ Evolutionary success as increase in percent representation in the gene pool of the next ○ generation ● Speciation ○ Polymorphism ○ Adaptation and specialization ○ Inbreeding ○ Outbreeding ○ Bottlenecks ● Evolutionary time as measured by gradual random changes in genome Reproductive System ● Gametogenesis by meiosis ● Ovum and sperm ○ Differences in formation ○ Differences in morphology ○ Relative contribution to next generation ● Reproductive sequence: fertilization, implantation, development, birth Embryogenesis ● Stages of early development (order and general features of each) ○ Fertilization ○ Cleavage ○ Blastula formation ○ Gastrulation ■ First cell movements ■ Formation of primary germ layers (endoderm,

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mesoderm, ectoderm) ○ Neurulation ● Major structures arising out of primary germ layers ● Neural crest ● Environment–gene interaction in development Mechanisms of Development ● Cell specialization ○ Determination ○ Differentiation ○ Tissue types ● Cell–cell communication in development ● Cell migration ● Pluripotency: stem cells ● Gene regulation in development ● Programmed cell death ● Existence of regenerative capacity in various species ● Senescence and aging Nervous System: Structure and Function (BIO 152) ● Major Functions ○ High level control and integration of body systems ○ Adaptive capability to external influences ● Organization of vertebrate nervous system ● Sensor and effector neurons ● Sympathetic and parasympathetic nervous systems: antagonistic control ● Reflexes ○ Feedback loop, reflex arc ○ Role of spinal cord and supraspinal circuits ● Integration with endocrine system: feedback control Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at cell, tissue, and organ level ● Definitions of endocrine gland, hormone ● Major endocrine glands: names, locations, products ● Major types of hormones ● Neuroendrocrinology ― relation between neurons and hormonal systems Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action

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● Transport of hormones: blood supply ● Specificity of hormones: target tissue ● Integration with nervous system: feedback control regulation by second messengers Respiratory System ● General function ○ Gas exchange, thermoregulation ○ Protection against disease: particulate matter ● Structure of lungs and alveoli ● Breathing mechanisms ○ Diaphragm, rib cage, differential pressure ○ Resiliency and surface tension effects ● Thermoregulation: nasal and tracheal capillary beds; evaporation, panting ● Particulate filtration: nasal hairs, mucus/cilia system in lungs ● Alveolar gas exchange ○ Diffusion, differential partial pressure ○ Henry’s Law ● pH control ● Regulation by nervous control ○ CO2 sensitivity Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of metabolic waste ● Role in thermoregulation ● Four-­‐chambered heart: structure and function ● Endothelial cells ● Systolic and diastolic pressure ● Pulmonary and systemic circulation ● Arterial and venous systems (arteries, arterioles, venules, veins) ○ Structural and functional differences ○ Pressure and flow characteristics ● Capillary beds ○ Mechanisms of gas and solute exchange ○ Mechanism of heat exchange ○ Source of peripheral resistance ● Composition of blood

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○ Plasma, chemicals, blood cells ○ Erythrocyte production and destruction; spleen, bone marrow ○ Regulation of plasma volume ● Coagulation, clotting mechanisms ● Oxygen transport by blood ○ Hemoglobin, hematocrit ○ Oxygen content ○ Oxygen affinity ○ Oxygen transport by blood; modification of oxygen affinity ● Carbon dioxide transport and level in blood ● Nervous and endocrine control Lymphatic System ● Structure of lymphatic system ● Major functions ○ Equalization of fluid distribution ○ Transport of proteins and large glycerides ○ Production of lymphocytes involved in immune reactions ○ Return of materials to the blood

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BIO 301

Mendelian Concepts ● Phenotype and genotype ● Gene ● Locus ● Allele: single and multiple ● Homozygosity and heterozygosity ● Wild-­‐type ● Recessiveness ● Complete dominance ● Co-­‐dominance ● Incomplete dominance, leakage, penetrance, expressivity ● Hybridization: viability ● Gene pool

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BIO 312 & BIO 312L Amino Acids ● Description ○ Absolute configuration at the position ○ Amino acids as dipolar ions ○ Classifications ■ Acidic or basic ■ Hydrophobic or hydrophilic ● Reactions ○ Sulfur linkage for cysteine and cysteine ○ Peptide linkage: polypeptides and proteins ○ Hydrolysis Protein Structure ● Structure ○ 1° structure of proteins ○ 2° structure of proteins ○ 3° structure of proteins; role of proline, cystine, hydrophobic bonding ○ 4° structure of proteins ● Conformational stability ○ Denaturing and folding ○ Hydrophobic interactions ○ Solvation layer (entropy) ● Separation techniques ○ Isoelectric point ○ Electrophoresis Non-­‐Enzymatic Protein Function ● Binding ● Immune system ● Motors Nucleic Acid Structure and Function ● Description ● Nucleotides and nucleosides ○ Sugar phosphate backbone ○ Pyrimidine, purine residues ● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure ● Base pairing specificity: A with T, G with C ● Function in transmission of genetic information ● DNA denaturation, reannealing, hybridization DNA Replication

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● Mechanism of replication: separation of strands, specific coupling of free nucleic acids ● Semi-­‐conservative nature of replication ● Specific enzymes involved in replication ● Origins of replication, multiple origins in eukaryotes ● Replicating the ends of DNA molecules Repair of DNA ● Repair during replication ● Repair of mutations Genetic Code ● Central Dogma: DNA → RNA → protein ● The triplet code ● Codon-­‐anticodon relationship ● Degenerate code, wobble pairing ● Missense, nonsense codons ● Initiation, termination codons ● Messenger RNA (mRNA) Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA) ● Mechanism of transcription ● mRNA processing in eukaryotes, introns, exons ● Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNA (snRNAs) ● Functional and evolutionary importance of introns Translation ● Roles of mRNA, tRNA, rRNA ● Role and structure of ribosomes ● Initiation, termination co-­‐factors ● Post-­‐translational modification of proteins Eukaryotic Chromosome Organization ● Chromosomal proteins ● Single copy vs. repetitive DNA ● Supercoiling ● Heterochromatin vs. euchromatin ● Telomeres, centromeres Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-­‐Monod Model ● Gene repression in bacteria ● Positive control in bacteria

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Control of Gene Expression in Eukaryotes ● Transcriptional regulation ● DNA binding proteins, transcription factors ● Gene amplification and duplication ● Post-­‐transcriptional control, basic concept of splicing (introns, exons) ● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes ● Regulation of chromatin structure ● DNA methylation ● Role of non-­‐coding RNAs Recombinant DNA and Biotechnology ● Gene cloning ● Restriction enzymes ● DNA libraries ● Generation of cDNA ● Hybridization ● Expressing cloned genes ● Polymerase Chain Reaction ● Gel Electrophoresis and Southern Blotting ● DNA sequencing ● Analyzing gene expression ● Determining gene function ● Stem cells ● Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture ● Safety and ethics of DNA technology Evidence that DNA is Genetic Material Mendelian Concepts ● Phenotype and genotype ● Gene ● Locus ● Allele: single and multiple ● Homozygosity and heterozygosity ● Wild-­‐type ● Recessiveness ● Complete dominance ● Co-­‐dominance

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● Incomplete dominance, leakage, penetrance, expressivity ● Hybridization: viability ● Gene pool Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis ● Important differences between meiosis and mitosis ● Segregation of genes ○ Independent assortment ○ Linkage ○ Recombination ■ Single crossovers ■ Double crossovers ■ Synaptonemal complex ■ Tetrad ○ Sex-­‐linked characteristics ○ Very few genes on Y chromosome ○ Sex determination ○ Cytoplasmic/extranuclear inheritance ● Mutation ○ General concept of mutation — error in DNA sequence ○ Types of mutations: random, translation error, transcription error, base substitution, inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation ○ Inborn errors of metabolism ○ Relationship of mutagens to carcinogens ● Genetic drift ● Synapsis or crossing-­‐over mechanism for increasing genetic diversity Analytic Methods ● Hardy–Weinberg Principle ● Test cross ● Gene mapping: crossover frequencies ● Biometry: statistical methods Evolution ● Natural selection ○ Fitness concept ○ Selection by differential reproduction

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○ Concepts of natural and group selection ○ Evolutionary success as increase in percent representation in the gene pool of the next ○ generation ● Speciation ○ Polymorphism ○ Adaptation and specialization ○ Inbreeding ○ Outbreeding ○ Bottlenecks ● Evolutionary time as measured by gradual random changes in genome Genetics of Prokaryotic Cells (BIO 312L) ● Existence of plasmids, extragenomic DNA ● Transformation: incorporation into bacterial genome of DNA fragments from external medium ● Conjugation ● Transposons (also present in eukaryotic cells) Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase, interphase ● Mitotic structures ○ Centrioles, asters, spindles ○ Chromatids, centromeres, kinetochores ○ Nuclear membrane breakdown and reorganization ○ Mechanisms of chromosome movement ● Phases of cell cycle: G0, G1, S, G2, M ● Growth arrest ● Control of cell cycle ● Loss of cell cycle controls in cancer cells Biosignalling ● Gated ion channels ○ Voltage gated ○ Ligand gated ● Receptor enzymes ● G protein-­‐coupled receptors Nucleotides and Nucleic Acids ● Nucleotides and nucleosides: composition ○ Sugar phosphate backbone

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○ Pyrimidine, purine residues ● Deoxyribonucleic acid: DNA, double helix ● Chemistry ● Other functions Enzymes ● Classification by reaction type ● Mechanism ○ Substrates and enzyme specificity ○ Active site model ○ Induced-­‐fit model ○ Cofactors, coenzymes and vitamins ● Kinetics ○ General (catalysis) ○ Michaelis-­‐Menten ○ Cooperativity ○ Effects of local conditions on enzyme activity ● Inhibition ● Regulatory enzymes ○ Allosteric ● Covalently modified

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BIO 403 & BIO 403L Hormonal Regulation and Integration of Metabolism ● Higher level integration of hormone structure and function ● Tissue specific metabolism ● Hormonal regulation of fuel metabolism ● Obesity and regulation of body mass Plasma Membrane ● General function in cell containment ● Composition of membranes ○ Lipid components ■ Phospholipids (and phosphatids) ■ Steroids ■ Waxes ○ Protein components ○ Fluid mosaic model ● Membrane dynamics ● Solute transport across membranes ○ Thermodynamic considerations ○ Osmosis ■ Colligative properties, osmotic pressure ○ Passive transport ○ Active transport ■ Sodium/potassium pump ● Membrane channels ● Membrane potential ● Membrane receptors ● Exocytosis and endocytosis ● Intercellular junctions ○ Gap junctions ○ Tight junctions ○ Desmosomes ○ Nerve Cell ● Cell body: site of nucleus, organelles ● Dendrites: branched extensions of cell body ● Axon: structure and function ● Myelin sheath, Schwann cells, insulation of axon ● Nodes of Ranvier: propagation of nerve impulse along axon ● Synapse: site of impulse propagation between cells ● Synaptic activity: transmitter molecules

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● Resting potential: electrochemical gradient ● Action potential ○ Threshold, all-­‐or-­‐none ○ Sodium/potassium pump ● Excitatory and inhibitory nerve fibers: summation, frequency of firing ● Glial cells, neuroglia Electrochemistry ● Concentration cell: direction of electron flow, Nernst equation Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at cell, tissue, and organ level ● Definitions of endocrine gland, hormone ● Major endocrine glands: names, locations, products ● Major types of hormones ● Neuroendrocrinology ― relation between neurons and hormonal systems Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action ● Transport of hormones: blood supply ● Specificity of hormones: target tissue ● Integration with nervous system: feedback control regulation by second messengers Respiratory System ● General function ○ Gas exchange, thermoregulation ○ Protection against disease: particulate matter ● Structure of lungs and alveoli ● Breathing mechanisms ○ Diaphragm, rib cage, differential pressure ○ Resiliency and surface tension effects ● Thermoregulation: nasal and tracheal capillary beds; evaporation, panting ● Particulate filtration: nasal hairs, mucus/cilia system in lungs ● Alveolar gas exchange ○ Diffusion, differential partial pressure ○ Henry’s Law ● pH control

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● Regulation by nervous control ● CO2 sensitivity Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of metabolic waste ● Role in thermoregulation ● Four-­‐chambered heart: structure and function ● Endothelial cells ● Systolic and diastolic pressure ● Pulmonary and systemic circulation ● Arterial and venous systems (arteries, arterioles, venules, veins) ○ Structural and functional differences ○ Pressure and flow characteristics ● Capillary beds ○ Mechanisms of gas and solute exchange ○ Mechanism of heat exchange ○ Source of peripheral resistance ● Composition of blood ○ Plasma, chemicals, blood cells ○ Erythrocyte production and destruction; spleen, bone marrow ○ Regulation of plasma volume ● Coagulation, clotting mechanisms ● Oxygen transport by blood ○ Hemoglobin, hematocrit ○ Oxygen content ○ Oxygen affinity ○ Oxygen transport by blood; modification of oxygen affinity ● Carbon dioxide transport and level in blood ● Nervous and endocrine control Lymphatic System ● Structure of lymphatic system ● Major functions ○ Equalization of fluid distribution ○ Transport of proteins and large glycerides ○ Production of lymphocytes involved in immune

30

reactions ● Return of materials to the blood Digestive System ● Ingestion ○ Saliva as lubrication and source of enzymes ○ Ingestion, esophagus, transport function ● Stomach ○ Storage and churning of food ○ Low pH, gastric juice, mucal protection against self-­‐ destruction ○ Production of digestive enzymes, site of digestion ○ Structure (gross) ● Liver ○ Structural relationship of liver within gastrointestinal system ○ Production of bile ○ Role in blood glucose regulation, detoxification ● Bile ○ Storage in gall bladder ○ Function ● Pancreas ○ Production of enzymes ○ Transport of enzymes to small intestine ● Small Intestine ○ Absorption of food molecules and water ○ Function and structure of villi ○ Production of enzymes, site of digestion ○ Neutralization of stomach acid ○ Structure (anatomic subdivisions) ● Large Intestine ○ Absorption of water ○ Bacterial flora ○ Structure (gross) ● Rectum: storage and elimination of waste, feces ● Muscular control ○ Peristalsis ● Endocrine control ○ Hormones ○ Target tissues

31

● Nervous control: the enteric nervous system Excretory System ● Roles in homeostasis ○ Blood pressure ○ Osmoregulation ○ Acid-­‐base balance ○ Removal of soluble nitrogenous waste ● Kidney structure ○ Cortex ○ Medulla ● Nephron structure ○ Glomerulus ○ Bowman’s capsule ○ Proximal tubule ○ Loop of Henle ○ Distal tubule ○ Collecting duct ● Formation of urine ○ Glomerular filtration ○ Secretion and reabsorption of solutes ○ Concentration of urine ○ Counter-­‐current multiplier mechanism ● Storage and elimination: ureter, bladder, urethra ● Osmoregulation: capillary reabsorption of H2O, amino acids, glucose, ions ● Muscular control: sphincter muscle Reproductive System ● Male and female reproductive structures and their functions ○ Gonads ○ Genitalia ○ Differences between male and female structures ● Hormonal control of reproduction ○ Male and female sexual development ○ Female reproductive cycle ○ Pregnancy, parturition, lactation ● Integration with nervous control Muscle System ● Important functions ○ Support: mobility

32

○ Peripheral circulatory assistance ○ Thermoregulation (shivering reflex) ● Structure of three basic muscle types: striated, smooth, cardiac ● Muscle structure and control of contraction ○ T-­‐tubule system ○ Contractile apparatus ○ Sarcoplasmic reticulum ○ Fiber type ○ Contractile velocity of different muscle types ● Regulation of cardiac muscle contraction ● Oxygen debt: fatigue ● Nervous control ○ Motor neurons ○ Neuromuscular junction, motor end plates ○ Sympathetic and parasympathetic innervation ○ Voluntary and involuntary muscles Specialized Cell-­‐Muscle Cell ● Structural characteristics of striated, smooth, and cardiac muscle ● Abundant mitochondria in red muscle cells: ATP source ● Organization of contractile elements: actin and myosin filaments, crossbridges, sliding filament model ● Sarcomeres: “I” and “A” bands, “M” and “Z” lines, “H” zone ● Presence of troponin and tropomyosin ● Calcium regulation of contraction Skin System ● Structure ○ Layer differentiation, cell types ○ Relative impermeability to water ● Functions in homeostasis and osmoregulation ● Functions in thermoregulation ○ Hair, erectile musculature ○ Fat layer for insulation ○ Sweat glands, location in dermis ○ Vasoconstriction and vasodilation in surface capillaries ● Physical protection ○ Nails, calluses, hair

33

○ Protection against abrasion, disease organisms ● Hormonal control: sweating, vasodilation, and vasoconstriction Circulatory System ● Arterial and venous systems; pressure and flow characteristics Enzymes ● Classification by reaction type ● Mechanism ○ Substrates and enzyme specificity ○ Active site model ○ Induced-­‐fit model ○ Cofactors, coenzymes and vitamins ● Kinetics ○ General (catalysis) ○ Michaelis-­‐Menten ○ Cooperativity ○ Effects of local conditions on enzyme activity ● Inhibition ● Regulatory enzymes ○ Allosteric ○ Covalently modified Memory ● Changes in synaptic connections underlie memory and learning ○ Neural plasticity ○ Memory and learning ● Long-­‐term potentiation Emotion ● The role of biological processes in perceiving emotion ○ The role of the limbic system in emotion ○ Emotion and the autonomic nervous system

34

BIO 411 & BIO 411L Non-­‐Enzymatic Protein Function ● Binding ● Immune system ● Motors Enzyme Structure and Function ● Function of enzymes in catalyzing biological reactions Control of Enzyme Activity ● Kinetics ○ General (catalysis) ● Feedback regulation Repair of DNA ● Repair during replication ● Repair of mutations Genetic Code ● Central Dogma: DNA → RNA → protein ● Messenger RNA (mRNA) Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-­‐Monod Model ● Gene repression in bacteria ● Positive control in bacteria Control of Gene Expression in Eukaryotes ● Transcriptional regulation Recombinant DNA and Biotechnology ● Gene cloning ● Restriction enzymes ● DNA libraries ● DNA sequencing ● Analyzing gene expression ● Determining gene function Principles of Bioenergetics ● Bioenergetics/thermodynamics ○ Free energy/Keq ■ Equilibrium constant ■ Relationship of the equilibrium constant and ΔG° ○ Concentration ■ Le Châtelier’s Principle ○ Endothermic/exothermic reactions ○ Free energy: G ○ Spontaneous reactions and ΔG°

35

● Phosphoryl group transfers and ATP ○ ATP hydrolysis ΔG << 0 ○ ATP group transfers ● Biological oxidation-­‐reduction ○ Half-­‐reactions ○ Soluble electron carriers ○ Flavoproteins Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway ● Glycolysis (aerobic), substrates and products ○ Feeder pathways: glycogen, starch metabolism ● Fermentation (anaerobic glycolysis) ● Gluconeogenesis ● Pentose phosphate pathway ● Net molecular and energetic results of respiration processes Principles of Metabolic Regulation ● Regulation of metabolic pathways ○ Maintenance of a dynamic steady state ● Regulation of glycolysis and gluconeogenesis ● Analysis of metabolic control Citric Acid Cycle ● Acetyl-­‐CoA production ● Reactions of the cycle, substrates and products ● Regulation of the cycle ● Net molecular and energetic results of respiration processes Metabolism of Fatty Acids and Proteins ● Description of fatty acids ● Oxidation of fatty acids ○ Saturated fats ○ Unsaturated fats ● Metabolism of proteins Oxidative Phosphorylation ● Electron transport chain and oxidative phosphorylation, substrates and products, general features of the pathway ● Electron transfer in mitochondria ○ NADH, NADPH ○ Flavoproteins ○ Cytochromes ● ATP synthase, chemiosmotic coupling ○ Proton motive force ● Net molecular and energetic results of respiration processes

36

● Regulation of oxidative phosphorylation Plasma Membrane ● General function in cell containment ● Composition of membranes ○ Lipid components ■ Phospholipids (and phosphatids) ■ Steroids ■ Waxes ○ Protein components ○ Fluid mosaic model ● Membrane dynamics ● Solute transport across membranes ○ Thermodynamic considerations ○ Osmosis ■ Colligative properties, osmotic pressure ○ Passive transport ○ Active transport ■ Sodium/potassium pump ● Membrane channels ● Membrane potential ● Membrane receptors Cell Theory ● History and development ● Impact on biology Classification and Structure of Prokaryotic Cells ● Prokaryotic domains ○ Archaea ○ Bacteria ● Major classifications of bacteria by shape ○ Bacilli (rod-­‐shaped) ○ Spirilli (spiral shaped) ○ Cocci (spherical) ● Lack of nuclear membrane and mitotic apparatus ● Lack of typical eukaryotic organelles ● Presence of cell wall in bacteria ● Flagellar propulsion, mechanism Growth and Physiology of Prokaryotic Cells ● Reproduction by fission ● High degree of genetic adaptability, acquisition of antibiotic

37

resistance ● Exponential growth ● Existence of anaerobic and aerobic variants ● Parasitic and symbiotic ● Chemotaxis Genetics of Prokaryotic Cells ● Existence of plasmids, extragenomic DNA ● Transformation: incorporation into bacterial genome of DNA fragments from external medium ● Conjugation ● Transposons (also present in eukaryotic cells) Virus Structure ● General structural characteristics (nucleic acid and protein, enveloped and nonenveloped) ● Lack organelles and nucleus ● Structural aspects of typical bacteriophage ● Genomic content-­‐-­‐RNA or DNA ● Size relative to bacteria and eukaryotic cells Viral Life Cycle ● Self-­‐replicating biological units that must reproduce within specific host cell ● Generalized phage and animal virus life cycles ○ Attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic ○ material ○ Use of host synthetic mechanism to replicate viral components ○ Self-­‐assembly and release of new viral particles ● Transduction: transfer of genetic material by viruses ● Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV ● Prions and viroids: subviral particles Lipids ● Description; structure ○ Steroids Enzymes ● Inhibition ● Regulatory enzymes ○ Allosteric ○ Covalently modified

38

BIO 415

Nerve Cell ● Cell body: site of nucleus, organelles ● Dendrites: branched extensions of cell body ● Axon: structure and function ● Myelin sheath, Schwann cells, insulation of axon ● Nodes of Ranvier: propagation of nerve impulse along axon ● Synapse: site of impulse propagation between cells ● Synaptic activity: transmitter molecules ● Resting potential: electrochemical gradient ● Action potential ○ Threshold, all-­‐or-­‐none ○ Sodium/potassium pump ● Excitatory and inhibitory nerve fibers: summation, frequency of firing ● Glial cells, neuroglia Specialized Cell -­‐ Nerve Cell ● Myelin sheath, Schwann cells, insulation of axon ● Nodes of Ranvier: propagation of nerve impulse along axon Sensory Processing ● Sensation ○ Thresholds ○ Weber’s Law ○ Signal detection theory ○ Sensory adaptation ● Sensory receptors ○ Sensory pathways ● Types of sensory receptors Vision ● Structure and function of the eye ● Visual processing ○ Visual pathways in the brain ○ Parallel processing ● Feature detection Hearing ● Auditory processing ○ Auditory pathways in the brain ● Sensory reception by hair cells Other Senses ● Somatosensation ○ Pain perception 39

● Taste ○ Taste buds/chemoreceptors that detect specific chemicals ● Smell ○ Olfactory cells/chemoreceptors that detect specific chemicals ○ Pheromones ○ Olfactory pathways in the brain ● Kinesthetic sense ● Vestibular sense Cognition ● Information-­‐processing model ● Cognitive development ○ Piaget’s stages of cognitive development ○ Cognitive changes in late adulthood ○ Role of culture in cognitive development ○ Influence of heredity and environment on cognitive development ● Biological factors that affect cognition ● Problem solving and decision making ○ Types of problem solving ○ Barriers to effective problem solving ○ Approaches to problem solving ○ Heuristics, biases, intuition, and emotion ■ Overconfidence and belief perseverance ● Intellectual functioning ○ Multiple definitions of intelligence ○ Influence of heredity and environment on intelligence ● Variations in intellectual ability Consciousness ● States of consciousness ○ Alertness ○ Sleep ■ Stages of sleep ■ Sleep cycles and changes to sleep cycles ■ Sleep and circadian rhythms ■ Dreaming ■ Sleep disorders ○ Hypnosis and meditation

40

● Consciousness altering drugs ○ Types of consciousness altering drugs and their effects on the nervous system and behavior ● Drug addiction and the reward pathway in the brain Memory ● Encoding ○ Process of encoding information ○ Processes that aid in encoding memories ● Storage ○ Types of memory storage (e.g., sensory, working, long-­‐term) ○ Semantic networks and spreading activation ● Retrieval ○ Recall, recognition, and relearning ○ Retrieval cues ○ The role of emotion in retrieving memories ● Forgetting ○ Aging and memory ○ Memory dysfunctions (e.g., Alzheimer’s disease, Korsakoff’s syndrome) ○ Decay ○ Interference ○ Memory construction and source monitoring ● Changes in synaptic connections underlie memory and learning ○ Neural plasticity ○ Memory and learning ● Long-­‐term potentiation Language ● Theories of language development (e.g., learning, Nativist, Interactionist) ● Influence of language on cognition ● Different brain areas control language and speech Emotion ● Three components of emotion (i.e., cognitive, physiological, behavioral) ● Universal emotions (e.g., fear, anger, happiness, surprise, joy, disgust, sadness)

41

● Adaptive role of emotion ● Theories of emotion ○ James-­‐Lange theory ○ Cannon-­‐Bard theory ○ Schachter-­‐Singer theory ● The role of biological processes in perceiving emotion ○ Generation and experience of emotions involve many brain regions ○ The role of the limbic system in emotion ○ Emotional experiences can be stored as memories that can be recalled by similar ○ circumstances ○ Prefrontal cortex is critical for emotional experience, and is also important in ○ temperament and decision making ○ Emotion and the autonomic nervous system ● Physiological markers of emotion (signatures of emotion) Stress ● The nature of stress ○ Appraisal ○ Different types of stressors (e.g., cataclysmic events, personal, etc.) ○ Effects of stress on psychological functions ● Stress outcomes/response to stressors ○ Physiological ○ Emotional ○ Behavioral ● Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)

Biological Bases of Behavior ● The nervous system ○ Neurons ■ The reflex arc ○ Neurotransmitters ○ Peripheral nervous system ○ Central nervous system ■ The brain ○ The brainstem ○ The cerebellum

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○ The diencephalon ○ The cerebrum ○ Control of voluntary movement in the cerebral cortex ○ Information processing in the cerebral cortex ○ Lateralization of cortical functions ○ Methods of studying the brain ● Neurons communicate and influence behavior ● Influence of neurotransmitters on behavior ● The endocrine system ○ Components of the endocrine system ○ Effects of the endocrine system on behavior ● Behavioral genetics ○ Genes, temperament, and heredity ○ Adaptive value of traits and behaviors ○ Interaction between heredity and environmental influences ● Genetic and environmental factors contribute to the development of behaviors ○ Experience and behavior ○ Regulatory genes and behavior ○ Genetically based behavioral variation in natural populations ● Human physiological development ○ Prenatal development ○ Motor development ● Developmental changes in adolescence Associative Learning ● Classical conditioning ○ Neutral, conditioned, and unconditioned stimuli ○ Conditioned and unconditioned response ○ Processes: acquisition, extinction, spontaneous recovery, generalization, discrimination ● Operant conditioning ○ Processes of shaping and extinction ○ Types of reinforcement: positive, negative, primary, conditional ○ Reinforcement schedules: fixed-­‐ratio, variable-­‐ratio,

43

fixed-­‐interval, variable-­‐interval ○ Punishment ○ Escape and avoidance learning ● Cognitive processes that affect associative learning ● Biological factors that affect associative learning ○ Innate behaviors are developmentally fixed ○ Learned behaviors are modified based on experiences ○ Development of learned behaviors

44

BIO 427

Non-­‐Enzymatic Protein Function ● Binding ● Immune system ● Motors Immune System ● Innate (non-­‐specific) vs. adaptive (specific) immunity ● Adaptive immune system cells ○ T-­‐lymphocytes ○ B-­‐lymphocytes ● Innate immune system cells ○ Macrophages ○ Phagocytes ● Concept of antigen and antibody ● Antigen presentation ● Clonal selection ● Antigen-­‐antibody recognition ● Structure of antibody molecule ● Recognition of self vs. non-­‐self, autoimmune diseases ● Major histocompatibility complex

45

BIO 440

Amino Acids ● Description ○ Absolute configuration at the position ○ Amino acids as dipolar ions ○ Classifications ■ Acidic or basic ■ Hydrophobic or hydrophilic ● Reactions ○ Sulfur linkage for cysteine and cysteine ○ Peptide linkage: polypeptides and proteins ○ Hydrolysis Protein Structure ● Structure ○ 1° structure of proteins ○ 2° structure of proteins ○ 3° structure of proteins; role of proline, cystine, hydrophobic bonding ○ 4° structure of proteins ● Conformational stability ○ Denaturing and folding ○ Hydrophobic interactions ○ Solvation layer (entropy) ● Separation techniques ○ Isoelectric point ○ Electrophoresis DNA Replication ● Mechanism of replication: separation of strands, specific coupling of free nucleic acids ● Semi-­‐conservative nature of replication ● Specific enzymes involved in replication ● Origins of replication, multiple origins in eukaryotes ● Replicating the ends of DNA molecules Repair of DNA ● Repair during replication ● Repair of mutations Plasma Membrane ● General function in cell containment ● Composition of membranes ○ Lipid components ■ Phospholipids (and phosphatids)

46

■ Steroids ■ Waxes ○ Protein components ○ Fluid mosaic model ● Membrane dynamics ● Solute transport across membranes ○ Thermodynamic considerations ○ Osmosis ■ Colligative properties, osmotic pressure ○ Passive transport ○ Active transport ■ Sodium/potassium pump ● Membrane channels ● Membrane potential ● Membrane receptors ● Exocytosis and endocytosis ● Intercellular junctions ○ Gap junctions ○ Tight junctions ○ Desmosomes Membrane-­‐Bound Organelles and Defining Characteristics of Eukaryotic Cells ● Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles, ● mitotic division ● Nucleus ○ Compartmentalization, storage of genetic information ○ Nucleolus: location and function ○ Nuclear envelope, nuclear pores ● Mitochondria ○ Site of ATP production ○ Inner and outer membrane structure ○ Self-­‐replication ● Lysosomes: membrane-­‐bound vesicles containing hydrolytic enzymes ● Endoplasmic reticulum ○ Rough and smooth components ○ Rough endoplasmic reticulum site of ribosomes ○ Double membrane structure

47

○ Role in membrane biosynthesis ○ Role in biosynthesis of secreted proteins ● Golgi apparatus: general structure and role in packaging and secretion ● Peroxisomes: organelles that collect peroxides Cytoskeleton ● General function in cell support and movement ● Microfilaments: composition and role in cleavage and contractility ● Microtubules: composition and role in support and transport ● Intermediate filaments, role in support ● Composition and function of cilia and flagella ● Centrioles, microtubule organizing centers Tissues Formed From Eukaryotic Cells ● Epithelial cells ● Connective tissue cells Cell Theory ● History and development ● Impact on biology Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase, interphase ● Mitotic structures ○ Centrioles, asters, spindles ○ Chromatids, centromeres, kinetochores ○ Nuclear membrane breakdown and reorganization ○ Mechanisms of chromosome movement ● Phases of cell cycle: G0, G1, S, G2, M ● Growth arrest ● Control of cell cycle ● Loss of cell cycle controls in cancer cells Biosignalling ● Oncogenes, apoptosis Biosignalling ● Gated ion channels ○ Voltage gated ○ Ligand gated ● Receptor enzymes ● G protein-­‐coupled receptors Specialized Cell-­‐Muscle Cell

48

● Structural characteristics of striated, smooth, and cardiac muscle ● Abundant mitochondria in red muscle cells: ATP source ● Organization of contractile elements: actin and myosin filaments, crossbridges, sliding filament model ● Sarcomeres: “I” and “A” bands, “M” and “Z” lines, “H” zone ● Presence of troponin and tropomyosin ● Calcium regulation of contraction

49

BIO 442 & 442L

Protein Structure ● Separation techniques ○ Isoelectric point ○ Electrophoresis Non-­‐Enzymatic Protein Function ● Motors Enzyme Structure and Function ● Substrates and enzyme specificity Nucleic Acid Structure and Function ● Function in transmission of genetic information Genetic Code ● Central Dogma: DNA → RNA → protein ● Messenger RNA (mRNA) Transcription ● Mechanism of transcription ● mRNA processing in eukaryotes, introns, exons Translation ● Post-­‐translational modification of proteins Eukaryotic Chromosome Organization ● Chromosomal proteins ● Heterochromatin vs. euchromatin ● Telomeres, centromeres Control of Gene Expression in Eukaryotes ● Transcriptional regulation ● DNA binding proteins, transcription factors ● Post-­‐transcriptional control, basic concept of splicing (introns, exons) ● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes ● Regulation of chromatin structure ● DNA methylation Recombinant DNA and Biotechnology ● Gene cloning ● Restriction enzymes ● DNA libraries ● Generation of cDNA ● Hybridization ● Expressing cloned genes ● Polymerase Chain Reaction ● Gel Electrophoresis and Southern Blotting 50

● ● ● ● ●

DNA sequencing Analyzing gene expression Determining gene function Stem cells Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture ● Safety and ethics of DNA technology Mendelian Concepts ● Phenotype and genotype ● Gene ● Homozygosity and heterozygosity ● Wild-­‐type ● Recessiveness Meiosis and Other Factors Affecting Genetic Variability ● Important differences between meiosis and mitosis ● Segregation of genes ○ Recombination ■ Single crossovers ■ Double crossovers ■ Synaptonemal complex ■ Tetrad ○ Sex-­‐linked characteristics ● Mutation ○ General concept of mutation — error in DNA sequence ● Synapsis or crossing-­‐over mechanism for increasing genetic diversity Plasma Membrane ● Membrane receptors Membrane-­‐Bound Organelles and Defining Characteristics of Eukaryotic Cells ● Nucleus ○ Compartmentalization, storage of genetic information ○ Nucleolus: location and function ○ Nuclear envelope, nuclear pores

Cytoskeleton ● General function in cell support and movement

51

● Microfilaments: composition and role in cleavage and contractility ● Microtubules: composition and role in support and transport ● Intermediate filaments, role in support ● Composition and function of cilia and flagella ● Centrioles, microtubule organizing centers Tissues Formed From Eukaryotic Cells ● Epithelial cells ● Connective tissue cells Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase, interphase ● Mitotic structures ○ Centrioles, asters, spindles ○ Chromatids, centromeres, kinetochores ○ Nuclear membrane breakdown and reorganization ○ Mechanisms of chromosome movement ● Phases of cell cycle: G0, G1, S, G2, M ● Growth arrest ● Control of cell cycle ● Loss of cell cycle controls in cancer cells Biosignalling ● apoptosis Reproductive System ● Gametogenesis by meiosis ● Ovum and sperm ○ Differences in formation ○ Differences in morphology ○ Relative contribution to next generation ● Reproductive sequence: fertilization, implantation, development, birth Embryogenesis ● Stages of early development (order and general features of each) ○ Fertilization ○ Cleavage ○ Blastula formation ○ Gastrulation ■ First cell movements ■ Formation of primary germ layers (endoderm,

52

mesoderm, ectoderm) ○ Neurulation ● Major structures arising out of primary germ layers ● Neural crest ● Environment–gene interaction in development Mechanisms of Development ● Cell specialization ○ Determination ○ Differentiation ○ Tissue types ● Cell–cell communication in development ● Cell migration ● Pluripotency: stem cells ● Gene regulation in development ● Programmed cell death Nervous System: Structure and Function •

• • • •

•

Major Functions o High level control and integration of body systems o Adaptive capability to external influences Organization of vertebrate nervous system Sensor and effector neurons Sympathetic and parasympathetic nervous systems: antagonistic control Reflexes o Feedback loop, reflex arc o Role of spinal cord and supraspinal circuits Integration with endocrine system: feedback control

Nerve Cell • • • • • • • • •

• •

Cell body: site of nucleus, organelles Dendrites: branched extensions of cell body Axon: structure and function Myelin sheath, Schwann cells, insulation of axon Nodes of Ranvier: propagation of nerve impulse along axon Synapse: site of impulse propagation between cells Synaptic activity: transmitter molecules Resting potential: electrochemical gradient Action potential o Threshold, all-­‐or-­‐none o Sodium/potassium pump Excitatory and inhibitory nerve fibers: summation, frequency of firing Glial cells, neuroglia

Biosignalling •

Receptor enzymes

53

•

G protein-­‐coupled receptors

Endocrine System: Hormones and Their Sources ● Major endocrine glands: names, locations, products Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action ● Transport of hormones: blood supply Respiratory System ● General function ○ Gas exchange, thermoregulation ○ Protection against disease: particulate matter ● Structure of lungs and alveoli ● Breathing mechanisms ○ Diaphragm, rib cage, differential pressure ○ Resiliency and surface tension effects ● Thermoregulation: nasal and tracheal capillary beds; evaporation, panting ● Particulate filtration: nasal hairs, mucus/cilia system in lungs Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of metabolic waste ● Four-­‐chambered heart: structure and function ● Endothelial cells ● Systolic and diastolic pressure ● Pulmonary and systemic circulation ● Arterial and venous systems (arteries, arterioles, venules, veins) ○ Structural and functional differences ○ Pressure and flow characteristics ● Composition of blood ○ Plasma, chemicals, blood cells ○ Erythrocyte production and destruction; spleen, bone marrow ○ Regulation of plasma volume Lymphatic System ● Major functions ○ Equalization of fluid distribution ○ Transport of proteins and large glycerides ○ Production of lymphocytes involved in immune reactions

54

Immune System ● Adaptive immune system cells ○ T-­‐lymphocytes ○ B-­‐lymphocytes ● Innate immune system cells ○ Macrophages ○ Phagocytes ● Concept of antigen and antibody ● Structure of antibody molecule Digestive System ● Ingestion ○ Saliva as lubrication and source of enzymes ○ Ingestion, esophagus, transport function ● Stomach ○ Storage and churning of food ○ Low pH, gastric juice, mucal protection against self-­‐ destruction ○ Production of digestive enzymes, site of digestion ○ Structure (gross) ● Liver ○ Structural relationship of liver within gastrointestinal system ○ Production of bile ○ Role in blood glucose regulation, detoxification ● Bile ○ Storage in gall bladder ○ Function ● Pancreas ○ Production of enzymes ○ Transport of enzymes to small intestine ● Small Intestine ○ Absorption of food molecules and water ○ Function and structure of villi ○ Production of enzymes, site of digestion ○ Neutralization of stomach acid ○ Structure (anatomic subdivisions) ● Large Intestine ○ Absorption of water ○ Bacterial flora

55

○ Structure (gross) ● Rectum: storage and elimination of waste, feces ● Endocrine control ○ Hormones ○ Target tissues ● Nervous control: the enteric nervous system Excretory System ● Roles in homeostasis ○ Blood pressure ○ Osmoregulation ○ Acid-­‐base balance ○ Removal of soluble nitrogenous waste ● Kidney structure ○ Cortex ○ Medulla ● Nephron structure ○ Glomerulus ○ Bowman’s capsule ○ Proximal tubule ○ Loop of Henle ○ Distal tubule ○ Collecting duct ● Storage and elimination: ureter, bladder, urethra Reproductive System ● Male and female reproductive structures and their functions ○ Gonads ○ Genitalia ○ Differences between male and female structures ● Hormonal control of reproduction ○ Male and female sexual development ○ Female reproductive cycle ○ Pregnancy, parturition, lactation Skeletal System ● Functions ○ Structural rigidity and support ○ Calcium storage ○ Physical protection ● Skeletal structure ○ Specialization of bone types, structures

56

○ Joint structures ○ Endoskeleton vs. exoskeleton ● Bone structure ○ Calcium/protein matrix ○ Cellular composition of bone ● Cartilage: structure and function ● Ligaments, tendons ● Endocrine control Skin System ● Structure ○ Layer differentiation, cell types ○ Relative impermeability to water ● Functions in thermoregulation ○ Hair, erectile musculature ○ Fat layer for insulation ○ Sweat glands, location in dermis ○ Vasoconstriction and vasodilation in surface capillaries ● Physical protection ○ Nails, calluses, hair ○ Protection against abrasion, disease organisms Specialized Cell -­‐ Nerve Cell ● Myelin sheath Geometrical Optics •

Optical Instruments, including the human eye

Stoichiometry • • •

Molecular weight Metric units commonly used in the context of chemistry Description of composition by percent mass

Solubility •

Units of concentration (e.g., molarity)

Separations and Purifications •

Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography ! Size-­‐exclusion ! Ion-­‐exchange ! Affinity o Racemic mixtures, separation of enantiomers

Non-­‐Enzymatic Protein Function

57

•

Motors

Vision •

Structure and function of the eye

Other Senses •

Smell o Olfactory cells/chemoreceptors that detect specific chemicals o Olfactory pathways in the brain

Biological Bases of Behavior •

The nervous system o Neurons ! The reflex arc o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain

Psychological Disorders •

Biological bases of nervous system disorders o Alzheimer’s disease o Parkinson’s disease o Stem cell-­‐based therapy to regenerate neurons in CNS

58

BIO 462

Protein Structure ● Structure ○ 1° structure of proteins ○ 2° structure of proteins ○ 3° structure of proteins; role of proline, cystine, hydrophobic bonding ○ 4° structure of proteins ● Conformational stability ○ Denaturing and folding ○ Hydrophobic interactions ○ Solvation layer (entropy) ● Separation techniques ○ Isoelectric point ○ Electrophoresis Enzyme Structure and Function ● Function of enzymes in catalyzing biological reactions ● Enzyme classification by reaction type ● Reduction of activation energy ● Substrates and enzyme specificity ● Active Site Model ● Induced-­‐fit Model ● Mechanism of catalysis ○ Cofactors ○ Coenzymes ○ Water-­‐soluble vitamins ● Effects of local conditions on enzyme activity Control of Enzyme Activity ● Kinetics ○ General (catalysis) ○ Michaelis-­‐Menten ○ Cooperativity ● Feedback regulation ● Inhibition – types ○ Competitive ○ Non-­‐competitive ○ Mixed ○ Uncompetitive ● Regulatory enzymes ○ Allosteric enzymes 59

○ Covalently-­‐modified enzymes ○ Zymogen Nucleic Acid Structure and Function ● Description ● Nucleotides and nucleosides ○ Sugar phosphate backbone ○ Pyrimidine, purine residues ● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure ● Base pairing specificity: A with T, G with C ● Function in transmission of genetic information ● DNA denaturation, reannealing, hybridization DNA Replication ● Mechanism of replication: separation of strands, specific coupling of free nucleic acids ● Semi-­‐conservative nature of replication ● Specific enzymes involved in replication ● Origins of replication, multiple origins in eukaryotes ● Replicating the ends of DNA molecules Repair of DNA ● Repair during replication ● Repair of mutations Genetic Code ● Central Dogma: DNA → RNA → protein ● The triplet code ● Codon-­‐anticodon relationship ● Degenerate code, wobble pairing ● Missense, nonsense codons ● Initiation, termination codons ● Messenger RNA (mRNA) Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA) ● Mechanism of transcription ● mRNA processing in eukaryotes, introns, exons ● Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNA (snRNAs) ● Functional and evolutionary importance of introns Translation ● Roles of mRNA, tRNA, rRNA

60

● Role and structure of ribosomes ● Initiation, termination co-­‐factors ● Post-­‐translational modification of proteins Eukaryotic Chromosome Organization ● Chromosomal proteins ● Single copy vs. repetitive DNA ● Supercoiling ● Heterochromatin vs. euchromatin ● Telomeres, centromeres Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-­‐Monod Model ● Gene repression in bacteria ● Positive control in bacteria Control of Gene Expression in Eukaryotes ● Transcriptional regulation ● DNA binding proteins, transcription factors ● Gene amplification and duplication ● Post-­‐transcriptional control, basic concept of splicing (introns, exons) ● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes ● Regulation of chromatin structure ● DNA methylation ● Role of non-­‐coding RNAs

61

BIO 470

DNA Replication ● Mechanism of replication: separation of strands, specific coupling of free nucleic acids ● Semi-­‐conservative nature of replication ● Specific enzymes involved in replication ● Origins of replication, multiple origins in eukaryotes ● Replicating the ends of DNA molecules

62

BIO 475 & 475L

Reproductive System ● Gametogenesis by meiosis ● Ovum and sperm ○ Differences in formation ○ Differences in morphology ○ Relative contribution to next generation ● Reproductive sequence: fertilization, implantation, development, birth Nervous System: Structure and Function •

• • • •

•

Major Functions o High level control and integration of body systems o Adaptive capability to external influences Organization of vertebrate nervous system Sensor and effector neurons Sympathetic and parasympathetic nervous systems: antagonistic control Reflexes o Feedback loop, reflex arc o Role of spinal cord and supraspinal circuits Integration with endocrine system: feedback control

Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at cell, tissue, and organ level ● Definitions of endocrine gland, hormone ● Major endocrine glands: names, locations, products ● Major types of hormones ● Neuroendrocrinology ― relation between neurons and hormonal systems Respiratory System ● General function ○ Gas exchange, thermoregulation ○ Protection against disease: particulate matter ● Structure of lungs and alveoli ● Breathing mechanisms ○ Diaphragm, rib cage, differential pressure ○ Resiliency and surface tension effects ● Thermoregulation: nasal and tracheal capillary beds; evaporation, panting ● Particulate filtration: nasal hairs, mucus/cilia system in lungs Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of metabolic waste

63

● Four-­‐chambered heart: structure and function ● Pulmonary and systemic circulation ● Arterial and venous systems (arteries, arterioles, venules, veins) ○ Structural and functional differences ○ Pressure and flow characteristics ● Capillary beds ○ Mechanisms of gas and solute exchange ○ Mechanism of heat exchange ○ Source of peripheral resistance Lymphatic System •

Major functions o Equalization of fluid distribution o Transport of proteins and large glycerides o Production of lymphocytes involved in immune reactions o Return of materials to the blood

Digestive System ● Ingestion ○ Saliva as lubrication and source of enzymes ○ Ingestion, esophagus, transport function ● Stomach ○ Storage and churning of food ○ Low pH, gastric juice, mucal protection against self-­‐ destruction ○ Production of digestive enzymes, site of digestion ○ Structure (gross) ● Liver ○ Structural relationship of liver within gastrointestinal system ○ Production of bile ○ Role in blood glucose regulation, detoxification ● Bile ○ Storage in gall bladder ○ Function ● Pancreas ○ Production of enzymes ○ Transport of enzymes to small intestine ● Small Intestine ○ Absorption of food molecules and water ○ Function and structure of villi

64

○ Production of enzymes, site of digestion ○ Neutralization of stomach acid ○ Structure (anatomic subdivisions) ● Large Intestine ○ Absorption of water ○ Bacterial flora ○ Structure (gross) ● Rectum: storage and elimination of waste, feces ● Endocrine control ○ Hormones ○ Target tissues ● Nervous control: the enteric nervous system Excretory System ● Roles in homeostasis ○ Blood pressure ○ Osmoregulation ○ Acid-­‐base balance ○ Removal of soluble nitrogenous waste ● Kidney structure ○ Cortex ○ Medulla ● Nephron structure ○ Glomerulus ○ Bowman’s capsule ○ Proximal tubule ○ Loop of Henle ○ Distal tubule ○ Collecting duct ● Storage and elimination: ureter, bladder, urethra Reproductive System ● Male and female reproductive structures and their functions ○ Gonads ○ Genitalia ○ Differences between male and female structures Muscle System ● Important functions ○ Support: mobility ○ Peripheral circulatory assistance ○ Thermoregulation (shivering reflex)

65

● Structure of three basic muscle types: striated, smooth, cardiac ● Nervous control ○ Motor neurons ○ Neuromuscular junction, motor end plates ○ Sympathetic and parasympathetic innervation ○ Voluntary and involuntary muscles Skeletal System ● Functions ○ Structural rigidity and support ○ Calcium storage ○ Physical protection ● Skeletal structure ○ Specialization of bone types, structures ○ Joint structures ● Cartilage: structure and function ● Ligaments, tendons Skin System ● Structure ○ Layer differentiation, cell types ○ Relative impermeability to water ● Functions in thermoregulation ○ Hair, erectile musculature ○ Fat layer for insulation ○ Sweat glands, location in dermis ○ Vasoconstriction and vasodilation in surface capillaries ● Physical protection ○ Nails, calluses, hair ○ Protection against abrasion, disease organisms Geometrical Optics •

Optical Instruments, including the human eye

Sensory Processing •

Sensory receptors o Sensory pathways o Types of sensory receptors

Vision •

Structure and function of the eye

Hearing •

Auditory processing o Auditory pathways in the brain

66

Other Senses •

•

•

Taste o Taste buds/chemoreceptors that detect specific chemicals Smell o Olfactory cells/chemoreceptors that detect specific chemicals o Pheromones o Olfactory pathways in the brain Vestibular sense

Biological Bases of Behavior •

•

The nervous system o Neurons ! The reflex arc o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior

67

CHEMISTRY CHM 123 & 123L

Work • Derived units, sign conventions • Mechanical advantage • Work Kinetic Energy Theorem Energy • Kinetic Energy: KE = ½ mv2; units • Potential Energy o PE = mgh (gravitational, local) o PE = ½ kx2(spring) • Conservation of energy • Conservative forces • Power, units Gas Phase • Absolute temperature, (K) Kelvin Scale • Pressure, simple mercury barometer • Molar volume at 0°C and 1 atm = 22.4 L/mol • Ideal gas o Definition o Ideal Gas Law: PV = nRT o Boyle’s Law: PV = constant o Charles’ Law: V/T = constant o Avogadro’s Law: V/n = constant • Kinetic Molecular Theory of Gases o Heat capacity at constant volume and at constant pressure o Boltzmann’s Constant • Deviation of real gas behavior from Ideal Gas Law o Qualitative o Quantitative (Van der Waals’ Equation) • Partial pressure, mole fraction • Dalton’s Law relating partial pressure to composition Light, Electromagnetic Radiation • Concept of Interference; Young Double-­‐slit Experiment • Thin films, diffraction grating, single-­‐slit diffraction • Other diffraction phenomena, X-­‐ray diffraction • Polarization of light • Circular polarization • Properties of electromagnetic radiation o Velocity equals constant c, in vacuo o Electromagnetic radiation consists of perpendicularly oscillating electric and magnetic o fields; direction of propagation is perpendicular to both • Classification of electromagnetic spectrum, photon energy E = (hf) • Visual spectrum, color Atomic Nucleus • Atomic number, atomic weight • Neutrons, protons, isotopes • Nuclear forces, binding energy

68

Radioactive decay o α, β, γ decay o Half-­‐life, exponential decay, semi-­‐log plots • Mass spectrometer Electronic Structure • Orbital structure of hydrogen atom, principal quantum number n, number of electrons per orbital • Ground state, excited states • Absorption and emission line spectra • Use of Pauli Exclusion Principle • Paramagnetism and diamagnetism • Conventional notation for electronic structure • Bohr atom • Heisenberg Uncertainty Principle • Effective nuclear charge • Photoelectric effect The Periodic Table -­‐ Classification of Elements into Groups by Electronic Structure • Alkali metals • Alkaline earth metals: their chemical characteristics • Halogens: their chemical characteristics • Noble gases: their physical and chemical characteristics • Transition metals • Representative elements • Metals and non-­‐metals • Oxygen group The Periodic Table -­‐ Variations of Chemical Properties with Group and Row • Valence electrons • First and second ionization energy o Definition o Prediction from electronic structure for elements in different groups or rows • Electron affinity o Definition o Variation with group and row • Electronegativity o Definition o Comparative values for some representative elements and important groups • Electron shells and the sizes of atoms • Electron shells and the sizes of ions Stoichiometry • Molecular weight • Empirical versus molecular formula • Metric units commonly used in the context of chemistry • Description of composition by percent mass • Mole concept, Avogadro’s number NA • Definition of density •

69

Oxidation number o Common oxidizing and reducing agents o Disproportionation reactions • Description of reactions by chemical equations o Conventions for writing chemical equations o Balancing equations, including redox equations o Limiting reactants • Theoretical yields Ions in Solutions • Anion, cation: common names, formulas and charges for familiar ions (e.g., NH4+ ammonium, PO43– phosphate, SO42– sulfate) • Hydration, the hydronium ion Titration • Indicators • Neutralization • Interpretation of the titration curves • Redox titration Covalent Bond • Lewis Electron Dot formulas o Resonance structures o Formal charge o Lewis acids and bases • Partial ionic character o Role of electronegativity in determining charge distribution o Dipole Moment • σ and π bonds o Hybrid orbitals: sp3, sp2, sp and respective geometries o Valence shell electron pair repulsion and the prediction of shapes of molecules (e.g., NH3, H2O, CO2) o Structural formulas for molecules involving H, C, N, O, F, S, P, Si, Cl o Delocalized electrons and resonance in ions and molecules • Multiple bonding o Affect on bond length and bond energies o Rigidity in molecular structure • Stereochemistry of covalently bonded molecules o Isomers ! Structural isomers ! Stereoisomers (e.g., diastereomers, enantiomers, cis/trans isomers) ! Conformational isomers o Polarization of light, specific rotation o Absolute and relative configuration ! Conventions for writing R and S forms o Conventions for writing E and Z forms Energy Changes in Chemical Reactions -­‐ Thermochemistry, Thermodynamics ! Thermodynamic system – state function ! Zeroth Law – concept of temperature ! First Law: ΔE = Q – W (conservation of energy) •

70

! ! ! !

CHM 124 & 124L

! ! ! ! !

•

Second Law – concept of entropy o Entropy as a measure of “disorder” o Relative entropy for gas, liquid, and crystal states Measurement of heat changes (calorimetry), heat capacity, specific heat Heat transfer – conduction, convection, radiation Endothermic/exothermic reactions o Enthalpy, H, and standard heats of reaction and formation o Hess’ Law of Heat Summation Bond dissociation energy as related to heats of formation Free energy: G Spontaneous reactions and ΔG° Coefficient of expansion Heat of fusion, heat of vaporization Phase diagram: pressure and temperature

Plasma Membrane • General function in cell containment • Composition of membranes o Lipid components

71

! Phospholipids (and phosphatids) ! Steroids ! Waxes o Protein components o Fluid mosaic model • Membrane dynamics • Solute transport across membranes o Thermodynamic considerations o Osmosis ! Colligative properties, osmotic pressure o Passive transport o Active transport ! Sodium/potassium pump • Membrane channels • Membrane potential • Membrane receptors • Exocytosis and endocytosis • Intercellular junctions o Gap junctions o Tight junctions o Desmosomes Electrochemistry o Concentration cell: direction of electron flow, Nernst equation Equilibrium • Concept of force, units • Analysis of forces acting on an object • Newton’s First Law of Motion, inertia • Torques, lever arms Electrochemistry • Electrolytic cell o Electrolysis o Anode, cathode o Electrolyte o Faraday’s Law relating amount of elements deposited (or gas liberated) at an electrode to o current o Electron flow, oxidation, and reduction at the electrodes • Galvanic or Voltaic cells o Half-­‐reactions o Reduction potentials, cell potential o Direction of electron flow • Concentration cell • Batteries o Electromotive force, Voltage o Lead-­‐storage batteries o Nickel-­‐cadmium batteries Acid/Base Equilibria • Bronsted-­‐Lowry definition of acid, base • Ionization of water

72

o Kw, its approximate value (Kw = [H+][OH–] = 10-­‐14 at 25°C, 1 atm) o Definition of pH: pH of pure water • Conjugate acids and bases (e.g., NH4+ and NH3) • Strong acids and bases (e.g., nitric, sulfuric) • Weak acids and bases (e.g., acetic, benzoic) o Dissociation of weak acids and bases with or without added salt o Hydrolysis of salts of weak acids or bases o Calculation of pH of solutions of salts of weak acids or bases • Equilibrium constants Ka and Kb: pKa, pKb • Buffers o Definition and concepts (common buffer systems) o Influence on titration curves Solubility • Units of concentration (e.g., molarity) • Solubility product constant; the equilibrium expression Ksp • Common-­‐ion effect, its use in laboratory separations o Complex ion formation o Complex ions and solubility o Solubility and pH Titration • Indicators • Neutralization • Interpretation of the titration curves • Redox titration Liquid Phase -­‐ Intermolecular Forces • Hydrogen bonding • Dipole Interactions • Van der Waals’ Forces (London dispersion forces) Energy Changes in Chemical Reactions -­‐ Thermochemistry, Thermodynamics • Thermodynamic system – state function • Zeroth Law – concept of temperature • First Law: ΔE = Q – W (conservation of energy) • Second Law – concept of entropy o Entropy as a measure of “disorder” o Relative entropy for gas, liquid, and crystal states • Measurement of heat changes (calorimetry), heat capacity, specific heat • Heat transfer – conduction, convection, radiation • Endothermic/exothermic reactions o Enthalpy, H, and standard heats of reaction and formation o Hess’ Law of Heat Summation • Bond dissociation energy as related to heats of formation • Free energy: G • Spontaneous reactions and ΔG° • Coefficient of expansion • Heat of fusion, heat of vaporization • Phase diagram: pressure and temperature Rate Processes in Chemical Reactions -­‐ Kinetics and Equilibrium • Reaction rate

73

•

• •

• • •

CHM 313 & 313L

Dependence of reaction rate upon concentration of reactants o Rate law, rate constant o Reaction order Rate-­‐determining step Dependence of reaction rate upon temperature o Activation energy ! Activated complex or transition state ! Interpretation of energy profiles showing energies of reactants, products, activation energy, and ΔH for the reaction o Use of the Arrhenius Equation Kinetic control versus thermodynamic control of a reaction Catalysts Equilibrium in reversible chemical reactions o Law of Mass Action o Equilibrium Constant o Application of Le Châtelier’s Principle Relationship of the equilibrium constant and ΔG°

•

Molecular Structure and Absorption Spectra • Infrared region o Intramolecular vibrations and rotations o Recognizing common characteristic group absorptions, fingerprint region • Visible region o Absorption in visible region gives complementary color (e.g.,

74

carotene) o Effect of structural changes on absorption (e.g., indicators) • Ultraviolet region o π-­‐electron and non-­‐bonding electron transitions o Conjugated systems • NMR spectroscopy o Protons in a magnetic field; equivalent protons o Spin-­‐spin splitting Covalent Bond • Lewis Electron Dot formulas o Resonance structures o Formal charge o Lewis acids and bases • Partial ionic character o Role of electronegativity in determining charge distribution o Dipole Moment • σ and π bonds o Hybrid orbitals: sp3, sp2, sp and respective geometries o Valence shell electron pair repulsion and the prediction of shapes of molecules (e.g., NH3, H2O, CO2) o Structural formulas for molecules involving H, C, N, O, F, S, P, Si, Cl o Delocalized electrons and resonance in ions and molecules • Multiple bonding o Effect on bond length and bond energies o Rigidity in molecular structure • Stereochemistry of covalently bonded molecules o Isomers ! Structural isomers ! Stereoisomers (e.g., diastereomers, enantiomers, cis/trans isomers) ! Conformational isomers o Polarization of light, specific rotation o Absolute and relative configuration ! Conventions for writing R and S forms o Conventions for writing E and Z forms Separations and Purifications • Extraction: distribution of solute between two immiscible solvents • Distillation • Chromatography o Basic principles involved in separation process ! Column chromatography, gas-­‐liquid chromatography ! High pressure liquid chromatography o Paper chromatography o Thin-­‐layer chromatography • Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography

75

! Size-­‐exclusion ! Ion-­‐exchange ! Affinity Racemic mixtures, separation of enantiomers

o Alcohols • Description o Nomenclature o Physical properties (acidity, hydrogen bonding) • Important reactions o Oxidation o Protection of alcohol o Preparation of mesylates and tosylates

CHM 314 & 314L

Amino Acids • Description o Absolute configuration at the α position o Amino acids as dipolar ions o Classifications ! Acidic or basic ! Hydrophobic or hydrophilic

76

Reactions o Sulfur linkage for cysteine and cysteine o Peptide linkage: polypeptides and proteins o Hydrolysis Nucleic Acid Structure and Function • Description • Nucleotides and nucleosides o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure • Base pairing specificity: A with T, G with C • Function in transmission of genetic information o DNA denaturation, reannealing, hybridization Carbohydrates • Description o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers • Hydrolysis of the glycoside linkage • Monosaccharides • Disaccharides • Polysaccharides Nucleotides and Nucleic Acids • Nucleotides and nucleosides: composition o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid: DNA, double helix • Chemistry • Other functions Amino Acids, Peptides, Proteins • Amino acids: description o Absolute configuration at the α position o Dipolar ions o Classification ! Acidic or basic ! Hydrophilic or hydrophobic o Synthesis of α-­‐amino acids ! Strecker Synthesis ! Gabriel Synthesis • Peptides and proteins: reactions o Sulfur linkage for cysteine and cystine o Peptide linkage: polypeptides and proteins o Hydrolysis • General Principles o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins •

77

o o Isoelectric point Carbohydrates • Description o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers • Hydrolysis of the glycoside linkage • Keto-­‐enol tautomerism of monosaccharides • Disaccharides • Polysaccharides Aldehydes and Ketones • Description o Nomenclature o Physical properties • Important reactions o Nucleophilic addition reactions at C=O bond ! Acetal, hemiacetal ! Imine, enamine ! Hydride reagents ! Cyanohydrin o Oxidation of aldehydes o Reactions at adjacent positions: enolate chemistry ! Keto-­‐enol tautomerism (α-­‐racemization) ! Aldol condensation, retro-­‐aldol ! Kinetic versus thermodynamic enolate • General principles o Effect of substituents on reactivity of C=O; steric hindrance • o Acidity of α-­‐H; carbanions Carboxylic Acids • Description o Nomenclature o Physical properties • Important reactions o Carboxyl group reactions ! Amides (and lactam), esters (and lactone), anhydride formation ! Reduction ! Decarboxylation • Reactions at 2-­‐position, substitution Acid Derivatives (Anhydrides, Amides, Esters) • Description o Nomenclature o Physical properties • Important reactions o Nucleophilic substitution o Transesterification o Hydrolysis of amides • General principles

78

CHM 420

o Relative reactivity of acid derivatives o Steric effects o Electronic effects • Strain (e.g., β-­‐lactams) Phenols • Oxidation and reduction (e.g., hydroquinones), ubiquinones: biological 2e-­‐ redox centers Polycyclic and Heterocyclic Aromatic Compounds • Biological aromatic heterocycles Phosphorus Compounds • Description, structure of phosphoric acids

Amino Acids • Description o Absolute configuration at the α position o Amino acids as dipolar ions o Classifications ! Acidic or basic ! Hydrophobic or hydrophilic • Reactions o Sulfur linkage for cysteine and cysteine o Peptide linkage: polypeptides and proteins o Hydrolysis (mentioned without detail)

79

Protein Structure • Structure o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins; role of proline, cystine, hydrophobic bonding o 4° structure of proteins • Conformational stability o Hydrophobic interactions o Solvation layer (entropy) • Separation techniques o Isoelectric point o Electrophoresis Non-­‐Enzymatic Protein Function • Binding • Immune system • Motors Enzyme Structure and Function • Function of enzymes in catalyzing biological reactions • Reduction of activation energy • Substrates and enzyme specificity • Active Site Model • Induced-­‐fit Model • Mechanism of catalysis o Cofactors o Coenzymes o Water-­‐soluble vitamins Control of Enzyme Activity • Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity • Feedback regulation • Inhibition – types o Competitive o Non-­‐competitive o Mixed o Uncompetitive • Regulatory enzymes o Allosteric enzymes o Covalently-­‐modified enzymes Nucleic Acid Structure and Function • Description • Nucleotides and nucleosides o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure • Base pairing specificity: A with T, G with C

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Principles of Bioenergetics • Bioenergetics/thermodynamics o Free energy/Keq ! Equilibrium constant ! Relationship of the equilibrium constant and ΔG° o Concentration o Endothermic/exothermic reactions o Free energy: G o Spontaneous reactions and ΔG° • Phosphoryl group transfers and ATP o ATP hydrolysis ΔG << 0 o ATP group transfers • Biological oxidation-­‐reduction o Soluble electron carriers o Flavoproteins Carbohydrates • Description o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers • Monosaccharides • Disaccharides • Polysaccharides Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway • Glycolysis (aerobic), substrates and products • Fermentation (anaerobic glycolysis) • Gluconeogenesis • Pentose phosphate pathway • Net molecular and energetic results of respiration processes Principles of Metabolic Regulation • Regulation of metabolic pathways o Maintenance of a dynamic steady state • Regulation of glycolysis and gluconeogenesis • Metabolism of glycogen Citric Acid Cycle • Acetyl-­‐CoA production • Reactions of the cycle, substrates and products • Regulation of the cycle • Net molecular and energetic results of respiration processes Metabolism of Fatty Acids • Description of fatty acids • Digestion, mobilization, and transport of fats • Oxidation of fatty acids o Saturated fats o Unsaturated fats • Ketone bodies • Anabolism of fats

81

• Non-­‐template synthesis: biosynthesis of lipids and polysaccharides • Metabolism of proteins Oxidative Phosphorylation • Electron transport chain and oxidative phosphorylation, substrates and products, general features of the pathway • Electron transfer in mitochondria o NADH, NADPH o Flavoproteins o Cytochromes • ATP synthase o Proton motive force • Net molecular and energetic results of respiration processes Plasma Membrane • General function in cell containment • Composition of membranes o Lipid components ! Phospholipids (and phosphatids) ! Steroids ! Waxes o Protein components o Fluid mosaic model • Membrane dynamics • Solute transport across membranes o Thermodynamic considerations o Osmosis ! Colligative properties o Passive transport o Active transport ! Sodium/potassium pump • Membrane channels • Membrane potential • Membrane receptors Membrane-­‐Bound Organelles and Defining Characteristics of Eukaryotic Cells • Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles, • Nucleus • Mitochondria o Site of ATP production o Inner and outer membrane structure • Lysosomes: membrane-­‐bound vesicles containing hydrolytic enzymes • Endoplasmic reticulum o Rough and smooth components o Rough endoplasmic reticulum site of ribosomes • Golgi apparatus: general structure and role in packaging and secretion • Peroxisomes: organelles that collect peroxides Biosignalling • Gated ion channels o Voltage gated o Ligand gated

82

CHM 451

• Receptor enzymes • G protein-­‐coupled receptors Lipids • Types o Storage ! Triacyl glycerols ! Free fatty acids: saponification o Structural ! Phospholipids and phosphatids ! Sphingolipids ! Waxes o Signals/cofactors ! Fat-­‐soluble vitamins ! Steroids ! Prostaglandins

Amino Acids • Description o Absolute configuration at the α position o Amino acids as dipolar ions o Classifications ! Acidic or basic ! Hydrophobic or hydrophilic • Reactions o Sulfur linkage for cysteine and cysteine o Peptide linkage: polypeptides and proteins o Hydrolysis Protein Structure • Structure o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins; role of proline, cystine, hydrophobic

83

bonding o 4° structure of proteins • Conformational stability o Denaturing and folding o Hydrophobic interactions o Solvation layer (entropy) • Separation techniques o Isoelectric point o Electrophoresis Non-­‐Enzymatic Protein Function • Binding • Immune system • Motors Enzyme Structure and Function • Function of enzymes in catalyzing biological reactions • Enzyme classification by reaction type • Reduction of activation energy • Substrates and enzyme specificity • Active Site Model • Induced-­‐fit Model • Mechanism of catalysis o Cofactors o Coenzymes o Water-­‐soluble vitamins • Effects of local conditions on enzyme activity Control of Enzyme Activity • Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity • Feedback regulation • Inhibition – types o Competitive o Non-­‐competitive o Mixed o Uncompetitive • Regulatory enzymes o Allosteric enzymes o Covalently-­‐modified enzymes • Zymogen Nucleic Acid Structure and Function • Description • Nucleotides and nucleosides o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure • Base pairing specificity: A with T, G with C • Function in transmission of genetic information

84

• DNA denaturation, reannealing, hybridization Evidence that DNA is Genetic Material Principles of Bioenergetics • Bioenergetics/thermodynamics o Free energy/Keq ! Equilibrium constant ! Relationship of the equilibrium constant and ΔG° o Concentration ! Le Châtelier’s Principle o Endothermic/exothermic reactions o Free energy: G o Spontaneous reactions and ΔG° • Phosphoryl group transfers and ATP o ATP hydrolysis ΔG << 0 o ATP group transfers • Biological oxidation-­‐reduction o Half-­‐reactions o Soluble electron carriers o Flavoproteins Carbohydrates • Description o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers • Hydrolysis of the glycoside linkage • Monosaccharides • Disaccharides • Polysaccharides Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway • Glycolysis (aerobic), substrates and products o Feeder pathways: glycogen, starch metabolism • Fermentation (anaerobic glycolysis) • Gluconeogenesis • Pentose phosphate pathway • Net molecular and energetic results of respiration processes Principles of Metabolic Regulation • Regulation of metabolic pathways o Maintenance of a dynamic steady state • Regulation of glycolysis and gluconeogenesis • Metabolism of glycogen • Regulation of glycogen synthesis and breakdown o Allosteric and hormonal control • Analysis of metabolic control Plasma Membrane • General function in cell containment • Composition of membranes o Lipid components ! Phospholipids (and phosphatids)

85

! Steroids ! Waxes o Protein components o Fluid mosaic model • Membrane dynamics • Solute transport across membranes o Thermodynamic considerations o Osmosis ! Colligative properties, osmotic pressure o Passive transport o Active transport ! Sodium/potassium pump • Membrane channels • Membrane potential • Membrane receptors • Exocytosis and endocytosis • Intercellular junctions o Gap junctions o Tight junctions o Desmosomes Membrane-­‐Bound Organelles and Defining Characteristics of Eukaryotic Cells • Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles, • mitotic division • Nucleus o Compartmentalization, storage of genetic information o Nucleolus: location and function o Nuclear envelope, nuclear pores • Mitochondria o Site of ATP production o Inner and outer membrane structure o Self-­‐replication • Lysosomes: membrane-­‐bound vesicles containing hydrolytic enzymes • Endoplasmic reticulum o Rough and smooth components o Rough endoplasmic reticulum site of ribosomes o Double membrane structure o Role in membrane biosynthesis o Role in biosynthesis of secreted proteins • Golgi apparatus: general structure and role in packaging and secretion • Peroxisomes: organelles that collect peroxides Electrochemistry • Concentration cell: direction of electron flow, Nernst equation Biosignalling • Gated ion channels o Voltage gated o Ligand gated • Receptor enzymes • G protein-­‐coupled receptors

86

Lipids • Description; structure o Steroids • Terpenes and terpenoids Equilibrium • Concept of force, units • Analysis of forces acting on an object • Newton’s First Law of Motion, inertia • Torques, lever arms Electrochemistry • Electrolytic cell o Electrolysis o Anode, cathode o Electrolyte o Faraday’s Law relating amount of elements deposited (or gas liberated) at an electrode to o current o Electron flow, oxidation, and reduction at the electrodes • Galvanic or Voltaic cells o Half-­‐reactions o Reduction potentials, cell potential o Direction of electron flow • Concentration cell • Batteries o Electromotive force, Voltage o Lead-­‐storage batteries • Nickel-­‐cadmium batteries Acid/Base Equilibria • Bronsted-­‐Lowry definition of acid, base • Ionization of water o K w, its approximate value (Kw = [H+][OH–] = 10-­‐14 at 25°C, 1 atm) o Definition of pH: pH of pure water • Conjugate acids and bases (e.g., NH4+ and NH3) • Strong acids and bases (e.g., nitric, sulfuric) • Weak acids and bases (e.g., acetic, benzoic) o Dissociation of weak acids and bases with or without added salt o Hydrolysis of salts of weak acids or bases o Calculation of pH of solutions of salts of weak acids or bases • Equilibrium constants Ka and Kb: pKa, pKb • Buffers o Definition and concepts (common buffer systems) o Influence on titration curves Titration • Indicators • Neutralization • Interpretation of the titration curves • Redox titration Separations and Purifications • Extraction: distribution of solute between two immiscible solvents

87

Distillation Chromatography o Basic principles involved in separation process ! Column chromatography, gas-­‐liquid chromatography ! High pressure liquid chromatography o Paper chromatography o Thin-­‐layer chromatography • Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography ! Size-­‐exclusion ! Ion-­‐exchange ! Affinity • Racemic mixtures, separation of enantiomers Nucleotides and Nucleic Acids • Nucleotides and nucleosides: composition o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid: DNA, double helix • Chemistry • Other functions Amino Acids, Peptides, Proteins • Amino acids: description o Absolute configuration at the α position o Dipolar ions o Classification ! Acidic or basic ! Hydrophilic or hydrophobic o Synthesis of α-­‐amino acids ! Strecker Synthesis ! Gabriel Synthesis • Peptides and proteins: reactions o Sulfur linkage for cysteine and cystine o Peptide linkage: polypeptides and proteins o Hydrolysis • General Principles o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins o o Isoelectric point The Three-­‐Dimensional Protein Structure • Conformational stability o Hydrophobic interactions o Solvation layer (entropy) • 4° quaternary structure • Denaturing and Folding Non-­‐Enzymatic Protein Function • Binding • •

88

• Immune system • Motor Lipids • Types o Storage ! Triacyl glycerols ! Free fatty acids: saponification o Structural ! Phospholipids and phosphatids ! Sphingolipids ! Waxes o Signals/cofactors ! Fat-­‐soluble vitamins ! Steroids ! Prostaglandins Carbohydrates • Description o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers • Hydrolysis of the glycoside linkage • Keto-­‐enol tautomerism of monosaccharides • Disaccharides • Polysaccharides Enzymes • Classification by reaction type • Mechanism o Substrates and enzyme specificity o Active site model o Induced-­‐fit model o Cofactors, coenzymes and vitamins • Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity o Effects of local conditions on enzyme activity • Inhibition • Regulatory enzymes o Allosteric o Covalently modified Principles of Bioenergetics • Bioenergetics/thermodynamics o Free energy/Keq o Concentration • § Phosphorylation/ATP o ATP hydrolysis ΔG << 0 o ATP group transfers • Biological oxidation–reduction

89

o o o

CHM 452

Half-­‐reactions Soluble electron carriers Flavoproteins

Non-­‐Enzymatic Protein Function • Binding • Immune system • Motors Enzyme Structure and Function • Function of enzymes in catalyzing biological reactions • Enzyme classification by reaction type • Reduction of activation energy • Substrates and enzyme specificity • Active Site Model • Induced-­‐fit Model • Mechanism of catalysis o Cofactors o Coenzymes o Water-­‐soluble vitamins • Effects of local conditions on enzyme activity Control of Enzyme Activity • Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity • Feedback regulation • Inhibition – types o Competitive

90

o Non-­‐competitive o Mixed o Uncompetitive • Regulatory enzymes o Allosteric enzymes o Covalently-­‐modified enzymes • Zymogen Nucleic Acid Structure and Function • Description • Nucleotides and nucleosides o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure • Base pairing specificity: A with T, G with C • Function in transmission of genetic information • DNA denaturation, reannealing, hybridization DNA Replication • Mechanism of replication: separation of strands, specific coupling of free nucleic acids • Semi-­‐conservative nature of replication • Specific enzymes involved in replication • Origins of replication, multiple origins in eukaryotes • Replicating the ends of DNA molecules Repair of DNA • Repair during replication • Repair of mutations Genetic Code • Central Dogma: DNA → RNA → protein • The triplet code • Codon-­‐anticodon relationship • Degenerate code, wobble pairing • Missense, nonsense codons • Initiation, termination codons • Messenger RNA (mRNA) Transcription • Transfer RNA (tRNA); ribosomal RNA (rRNA) • Mechanism of transcription • mRNA processing in eukaryotes, introns, exons • Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNA (snRNAs)

Translation • Roles of mRNA, tRNA, rRNA • Role and structure of ribosomes • Initiation, termination co-­‐factors • Post-­‐translational modification of proteins

91

Eukaryotic Chromosome Organization • Chromosomal proteins • Single copy vs. repetitive DNA • Supercoiling • Heterochromatin vs. euchromatin • Telomeres, centromeres Evidence that DNA is Genetic Material Principles of Metabolic Regulation • Regulation of metabolic pathways o Maintenance of a dynamic steady state • Regulation of glycolysis and gluconeogenesis • Metabolism of glycogen • Regulation of glycogen synthesis and breakdown o Allosteric and hormonal control • Analysis of metabolic control Citric Acid Cycle • Acetyl-­‐CoA production • Reactions of the cycle, substrates and products • Regulation of the cycle • Net molecular and energetic results of respiration processes Metabolism of Fatty Acids and Proteins • Description of fatty acids • Digestion, mobilization, and transport of fats • Oxidation of fatty acids o Saturated fats o Unsaturated fats • Ketone bodies • Anabolism of fats • Non-­‐template synthesis: biosynthesis of lipids and polysaccharides • Metabolism of proteins Oxidative Phosphorylation • Electron transport chain and oxidative phosphorylation, substrates and products, general features of the pathway • Electron transfer in mitochondria o NADH, NADPH o Flavoproteins o Cytochromes • ATP synthase, chemiosmotic coupling o Proton motive force • Net molecular and energetic results of respiration processes • Regulation of oxidative phosphorylation • Mitochondria, apoptosis, oxidative stress Hormonal Regulation and Integration of Metabolism • Higher level integration of hormone structure and function • Tissue specific metabolism • Hormonal regulation of fuel metabolism • Obesity and regulation of body mass Lipids

92

Description; structure o Steroids • Terpenes and terpenoids Nucleotides and Nucleic Acids • Nucleotides and nucleosides: composition o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid: DNA, double helix • Chemistry • Other functions Lipids • Types o Storage ! Triacyl glycerols ! Free fatty acids: saponification o Structural ! Phospholipids and phosphatids ! Sphingolipids ! Waxes o Signals/cofactors ! Fat-­‐soluble vitamins ! Steroids ! Prostaglandins Phenols • Oxidation and reduction (e.g., hydroquinones), ubiquinones: biological 2e-­‐ redox centers Enzymes • Classification by reaction type • Mechanism o Substrates and enzyme specificity o Active site model o Induced-­‐fit model o Cofactors, coenzymes and vitamins • Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity o Effects of local conditions on enzyme activity • Inhibition • Regulatory enzymes o Allosteric o Covalently modified

•

93

CHM 462L

Protein Structure • Structure o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins; role of proline, cystine, hydrophobic bonding o 4° structure of proteins • Conformational stability o Denaturing and folding o Hydrophobic interactions o Solvation layer (entropy) • Separation techniques o Isoelectric point o Electrophoresis Enzyme Structure and Function • Function of enzymes in catalyzing biological reactions • Enzyme classification by reaction type • Reduction of activation energy • Substrates and enzyme specificity • Active Site Model • Induced-­‐fit Model • Mechanism of catalysis o Cofactors o Coenzymes o Water-­‐soluble vitamins

94

• Effects of local conditions on enzyme activity Genetic Code • Central Dogma: DNA → RNA → protein • The triplet code • Codon-­‐anticodon relationship • Degenerate code, wobble pairing • Missense, nonsense codons • Initiation, termination codons • Messenger RNA (mRNA) Recombinant DNA and Biotechnology • Gene cloning • Restriction enzymes • DNA libraries • Generation of cDNA • Hybridization • Expressing cloned genes • Polymerase Chain Reaction • Gel Electrophoresis and Southern Blotting • DNA sequencing • Analyzing gene expression • Determining gene function • Stem cells • Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture • Safety and ethics of DNA technology Separations and Purifications • Extraction: distribution of solute between two immiscible solvents • Distillation • Chromatography o Basic principles involved in separation process ! Column chromatography, gas-­‐liquid chromatography ! High pressure liquid chromatography o Paper chromatography o Thin-­‐layer chromatography • Separation and purification of peptides and proteins o Electrophoresis o Quantitative analysis o Chromatography ! Size-­‐exclusion ! Ion-­‐exchange ! Affinity • Racemic mixtures, separation of enantiomers • Enzymes • Classification by reaction type • Mechanism o Substrates and enzyme specificity

95

•

• •

•

o Active site model o Induced-­‐fit model o Cofactors, coenzymes and vitamins Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity o Effects of local conditions on enzyme activity Inhibition Regulatory enzymes o Allosteric Covalently modified

96

PHYSICS PHY 201

PHY 202

Translational Motion • Units and dimensions • Vectors, components • Vector addition • Speed, velocity (average and instantaneous) • Acceleration Equilibrium • Concept of force, units • Analysis of forces acting on an object • Newton’s First Law of Motion, inertia • Torques, lever arms Work • Derived units, sign conventions • Mechanical advantage • Work Kinetic Energy Theorem Energy • Kinetic Energy: KE = ½ mv2; units • Potential Energy o PE = mgh (gravitational, local) o PE = ½ kx2(spring) • Conservation of energy • Conservative forces • Power, units Fluids • Density, specific gravity • Buoyancy, Archimedes’ Principle • Hydrostatic pressure o Pascal’s Law o Hydrostatic pressure; P = ρgh (pressure versus depth) • Viscosity: Poiseuille Flow • Continuity equation (A∙v = constant) • Concept of turbulence at high velocities • Surface tension • Bernoulli’s equation • Venturi effect, pitot tube

Electrostatics • Charge, conductors, charge conservation

97

Insulators Electric field E o Field lines o Field due to charge distribution • Potential difference, absolute potential at point in space Circuit Elements • Current I = ΔQ/Δt, sign conventions, units • Electromotive force, voltage • Resistance o Ohm’s Law: I = V/R o Resistors in series o Resistors in parallel o Resistivity: ρ = R•A/L • Capacitance o Parallel plate capacitor o Energy of charged capacitor o Capacitors in series o Capacitors in parallel o Dielectrics • Conductivity o Metallic o Electrolytic • Meters Sound • Production of sound • Relative speed of sound in solids, liquids, and gases • Intensity of sound, decibel units, log scale • Attenuation (Damping) • Doppler Effect: moving sound source or observer, reflection of sound from a moving object • Pitch • Resonance in pipes and strings • Ultrasound • Shock waves Light, Electromagnetic Radiation • Concept of Interference; Young Double-­‐slit Experiment • Thin films, diffraction grating, single-­‐slit diffraction • Other diffraction phenomena, X-­‐ray diffraction • Polarization of light • Circular polarization • Properties of electromagnetic radiation o Velocity equals constant c, in vacuo o Electromagnetic radiation consists of perpendicularly oscillating electric and magnetic o fields; direction of propagation is perpendicular to both • Classification of electromagnetic spectrum, photon energy E = (hf) • Visual spectrum, color Geometrical Optics • •

98

Reflection from plane surface: angle of incidence equals angle of reflection • Refraction, refractive index n, Snell’s law: n1 sin θ1 = n2 sin θ2 • Dispersion, change of index of refraction with wavelength • Conditions for total internal reflection • Spherical mirrors o Center of curvature o Focal length o Real and virtual images • Thin lenses o Converging and diverging lenses o Use of formula 1/p + 1/q = 1/f, with sign conventions o Lens strength, diopters • Combination of lenses • Lens aberration • Optical Instruments, including the human eye Electronic Structure • Orbital structure of hydrogen atom, principal quantum number n, number of electrons per orbital • Ground state, excited states • Absorption and emission line spectra • Use of Pauli Exclusion Principle • Conventional notation for electronic structure • Bohr atom • Effective nuclear charge • Photoelectric effect •

99

PSYCHOLOGY PSY 101

Sensory Processing • Sensation o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation • Sensory receptors o Sensory pathways o Types of sensory receptors Vision • Structure and function of the eye • Visual processing o Visual pathways in the brain o Parallel processing o Feature detection Hearing • Auditory processing o Auditory pathways in the brain • Sensory reception by hair cells Other Senses • Somatosensation o Pain perception • Taste o Taste buds/chemoreceptors that detect specific chemicals • Smell o Olfactory cells/chemoreceptors that detect specific chemicals o Pheromones o Olfactory pathways in the brain • Kinesthetic sense • Vestibular sense Perception • Perception o Bottom-­‐up/Top-­‐down processing o Perceptual organization (e.g., depth, form, motion, constancy) o Gestalt principles Attention • Selective attention • Divided attention Cognition • Information-­‐processing model • Cognitive development o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development

100

o

Influence of heredity and environment on cognitive development • Biological factors that affect cognition • Problem solving and decision making o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion ! Overconfidence and belief perseverance • Intellectual functioning o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability Consciousness • States of consciousness o Alertness o Sleep ! Stages of sleep ! Sleep cycles and changes to sleep cycles ! Sleep and circadian rhythms ! Dreaming ! Sleep disorders o Hypnosis and meditation • Consciousness altering drugs o Types of consciousness altering drugs and their effects on the nervous system and behavior o Drug addiction and the reward pathway in the brain Memory • Encoding o Process of encoding information o Processes that aid in encoding memories • Storage o Types of memory storage (e.g., sensory, working, long-­‐ term) o Semantic networks and spreading activation • Retrieval o Recall, recognition, and relearning o Retrieval cues o The role of emotion in retrieving memories • Forgetting o Aging and memory o Memory dysfunctions (e.g., Alzheimer’s disease, Korsakoff’s syndrome) o Decay o Interference o Memory construction and source monitoring • Changes in synaptic connections underlie memory and learning o Neural plasticity

101

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Memory and learning Long-­‐term potentiation

Language • Theories of language development (e.g., learning, Nativist, Interactionist) • Influence of language on cognition o Different brain areas control language and speech Emotion • Three components of emotion (i.e., cognitive, physiological, behavioral) • Universal emotions (e.g., fear, anger, happiness, surprise, joy, disgust, sadness) • Adaptive role of emotion • Theories of emotion o James-­‐Lange theory o Cannon-­‐Bard theory o Schachter-­‐Singer theory • The role of biological processes in perceiving emotion o Generation and experience of emotions involve many brain regions o The role of the limbic system in emotion o Emotional experiences can be stored as memories that can be recalled by similar o circumstances o Prefrontal cortex is critical for emotional experience, and is also important in o temperament and decision making o Emotion and the autonomic nervous system o Physiological markers of emotion (signatures of emotion) Stress • The nature of stress o Appraisal o Different types of stressors (e.g., cataclysmic events, personal, etc.) o Effects of stress on psychological functions • Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)

Biological Bases of Behavior • The nervous system o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system

102

The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences • Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations • Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence Personality • Theories of personality o Psychoanalytic perspective o Humanistic perspective o Trait perspective o Social cognitive perspective o Biological perspective o Behaviorist perspective o Situational approach to explaining behavior Psychological Disorders • Understanding psychological disorders o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders • Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders !

103

o Schizophrenia o Dissociative disorder o Personality disorders • Biological bases of nervous system disorders o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-­‐based therapy to regenerate neurons in CNS Motivation • Factors that influence motivation o Instinct o Arousal o Drives ! Negative feedback systems o Needs • Theories that explain how motivation affects human behavior o Drive reduction theory o Incentive theory o Other: cognitive and need based theories • Application of theories of motivation to understand behaviors (e.g., eating, sexual, drug and alcohol use, etc.) o Biological factors in regulation of these motivational processes o Socio-­‐cultural factors in regulation of these motivational processes Attitudes • Components of attitudes (i.e., cognitive, affective, and behavioral) • The link between attitudes and behavior o Processes by which behavior influences attitudes (e.g., foot-­‐in-­‐the door phenomenon, o role-­‐playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory How the Presence of Others Affects Individual Behavior • Social facilitation • Deindividuation • Bystander effect • Social loafing • Peer pressure Group Processes • Group polarization • Groupthink Socialization • Definition of socialization • Norms • Agents of socialization (e.g., the family, mass media, peers,

104

workplace) • Stigma and deviance • Conformity and obedience Habituation and Dishabituation Associative Learning • Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous recovery, generalization, discrimination • Operant conditioning o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary, conditional o Reinforcement schedules: fixed-­‐ratio, variable-­‐ratio, fixed-­‐interval, variable-­‐interval o Punishment o Escape and avoidance learning • Cognitive processes that affect associative learning • Biological factors that affect associative learning o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors Observational Learning • Modeling • Biological processes that affect observational learning o Mirror neurons o Role of the brain in experiencing vicarious emotions • Applications of observational learning to explain individual behavior Theories of Attitude and Behavior Change • Elaboration Likelihood Model o Information processing routes to persuasion (e.g., central and peripheral route processing) • Social Cognitive theory • Factors that affect attitude change (e.g., changing behavior, characteristics of the message and target, social factors) Self-­‐Concept and Identity • Definitions of self-­‐concept, identity, and social identity • The role of self-­‐esteem, self-­‐efficacy, and locus of control in self-­‐ concept and self-­‐identity • Different types of identities (e.g., race/ethnicity, gender, age, sexual orientation, class) Formation of Identity • Stages of identity development o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud) • Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-­‐taking)

105

o Influence of group (e.g., reference group) • Influence of culture and socialization on identity formation Attributing Behavior to Persons or Situations • Attribution theory o Fundamental attribution error o How culture affects attributions • How self-­‐perceptions shape our perceptions of others • How perceptions of the environment shape our perceptions of others Prejudice and Bias • Definition of prejudice • Processes that contribute to prejudice o Power, prestige, and class o The role of emotion in prejudice o The role of cognition in prejudice • Stereotypes • Ethnocentrism o In-­‐group and out-­‐group o Ethnocentrism vs. cultural relativism Processes Related to Stereotypes • Self-­‐fulfilling prophecy • Stereotype threat Elements of Social Interaction • Statuses • Roles • Groups • Networks • Organizations Self-­‐presentation and Interacting with Others • Expressing and detecting emotion o Gender shapes expression o Culture shapes expression • Impression management o Front stage vs. back stage self (Dramaturgical approach) • Verbal and nonverbal communication • Animal signals and communication Social Behavior • Attraction • Aggression • Attachment • Social support • Biological explanations of social behavior in animals o Foraging behavior o Mating behavior and mate choice o Applying game theory o Altruism o Inclusive fitness Discrimination

106

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PSY 321

Individual vs. institutional discrimination The relationship between prejudice and discrimination How power, prestige, and class facilitate discrimination

Perception • Perception o Bottom-­‐up/Top-­‐down processing

107

o

Perceptual organization (e.g., depth, form, motion, constancy) Gestalt principles

o Attention • Selective attention • Divided attention Cognition • Information-­‐processing model • Cognitive development o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development o Influence of heredity and environment on cognitive development • Biological factors that affect cognition • Problem solving and decision making o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion ! Overconfidence and belief perseverance • Intellectual functioning o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability o Consciousness • States of consciousness o Alertness o Sleep ! Stages of sleep ! Sleep cycles and changes to sleep cycles ! Sleep and circadian rhythms ! Dreaming ! Sleep disorders o Hypnosis and meditation • Consciousness altering drugs o Types of consciousness altering drugs and their effects on the nervous system and behavior o Drug addiction and the reward pathway in the brain Memory • Encoding o Process of encoding information o Processes that aid in encoding memories • Storage o Types of memory storage (e.g., sensory, working, long-­‐ term) o Semantic networks and spreading activation

108

Retrieval o Recall, recognition, and relearning o Retrieval cues o The role of emotion in retrieving memories • Forgetting o Aging and memory o Memory dysfunctions (e.g., Alzheimer’s disease, Korsakoff’s syndrome) o Decay o Interference o Memory construction and source monitoring • Changes in synaptic connections underlie memory and learning o Neural plasticity o Memory and learning o Long-­‐term potentiation Language • Theories of language development (e.g., learning, Nativist, Interactionist) • Influence of language on cognition o Different brain areas control language and speech

Biological Bases of Behavior • The nervous system o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences •

109

•

•

PSY 322

Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence

Attention • Selective attention • Divided attention Biological Bases of Behavior • The nervous system o Neurons

110

! The reflex arc Neurotransmitters Peripheral nervous system Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences • Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations • Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence Habituation and Dishabituation Associative Learning • Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous recovery, generalization, discrimination • Operant conditioning o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary, conditional o Reinforcement schedules: fixed-­‐ratio, variable-­‐ratio, fixed-­‐interval, variable-­‐interval o Punishment o o o

111

PSY 323

o Escape and avoidance learning • Cognitive processes that affect associative learning • Biological factors that affect associative learning o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors Observational Learning • Modeling • Biological processes that affect observational learning o Mirror neurons o Role of the brain in experiencing vicarious emotions • Applications of observational learning to explain individual behavior

Sensory Processing • Sensation o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation • Sensory receptors o Sensory pathways o Types of sensory receptors

112

Vision • Structure and function of the eye • Visual processing o Visual pathways in the brain o Parallel processing o Feature detection Hearing • Auditory processing o Auditory pathways in the brain • Sensory reception by hair cells Other Senses • Somatosensation o Pain perception • Taste o Taste buds/chemoreceptors that detect specific chemicals • Smell o Olfactory cells/chemoreceptors that detect specific chemicals o Pheromones o Olfactory pathways in the brain • Kinesthetic sense • Vestibular sense Perception • Perception o Bottom-­‐up/Top-­‐down processing o Perceptual organization (e.g., depth, form, motion, constancy) o Gestalt principles Attention • Selective attention • Divided attention Biological Bases of Behavior • The nervous system o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions

113

• • •

•

•

•

PSY 341

• Methods of studying the brain Neurons communicate and influence behavior Influence of neurotransmitters on behavior The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence

Attitudes • Components of attitudes (i.e., cognitive, affective, and behavioral) • The link between attitudes and behavior o Processes by which behavior influences attitudes (e.g., foot-­‐in-­‐the door phenomenon, o role-­‐playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory How the Presence of Others Affects Individual Behavior • Social facilitation • Deindividuation

114

• Bystander effect • Social loafing • Peer pressure Group Processes • Group polarization • Groupthink Culture • Assimilation • Multiculturalism • Subcultures Socialization • Definition of socialization • Norms • Agents of socialization (e.g., the family, mass media, peers, workplace) • Stigma and deviance • Conformity and obedience Theories of Attitude and Behavior Change • Elaboration Likelihood Model o Information processing routes to persuasion (e.g., central and peripheral route processing) • Social Cognitive theory • Factors that affect attitude change (e.g., changing behavior, characteristics of the message and target, social factors) Self Concept and Identity • Definitions of self-­‐concept, identity, and social identity • The role of self-­‐esteem, self-­‐efficacy, and locus of control in self-­‐ concept and self-­‐identity • Different types of identities (e.g., race/ethnicity, gender, age, sexual orientation, class) Formation of Identity • Stages of identity development o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud) • Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-­‐taking) o Influence of group (e.g., reference group) • Influence of culture and socialization on identity formation Attributing Behavior to Persons or Situations • Attribution theory o Fundamental attribution error o How culture affects attributions • How self-­‐perceptions shape our perceptions of others • How perceptions of the environment shape our perceptions of others Prejudice and Bias • Definition of prejudice • Processes that contribute to prejudice

115

PSY 351

o Power, prestige, and class o The role of emotion in prejudice o The role of cognition in prejudice • Stereotypes • Ethnocentrism o In-­‐group and out-­‐group o Ethnocentrism vs. cultural relativism Processes Related to Stereotypes • Self-­‐fulfilling prophecy • Stereotype threat Elements of Social Interaction • Statuses • Roles • Groups • Networks • Organizations Self-­‐presentation and Interacting with Others • Expressing and detecting emotion o Gender shapes expression o Culture shapes expression • Impression management o Front stage vs. back stage self (Dramaturgical approach) • Verbal and nonverbal communication • Animal signals and communication Social Behavior • Attraction • Aggression • Attachment • Social support • Biological explanations of social behavior in animals o Foraging behavior o Mating behavior and mate choice o Applying game theory o Altruism o Inclusive fitness Cognition • Information-­‐processing model • Cognitive development o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development o Influence of heredity and environment on cognitive development • Biological factors that affect cognition • Problem solving and decision making o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving

116

o

Heuristics, biases, intuition, and emotion ! Overconfidence and belief perseverance • Intellectual functioning o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability Language • Theories of language development (e.g., learning, Nativist, Interactionist) • Influence of language on cognition o Different brain areas control language and speech Stress • The nature of stress o Appraisal o Different types of stressors (e.g., cataclysmic events, personal, etc.) o Effects of stress on psychological functions • Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)

Biological Bases of Behavior • The nervous system o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors

117

o

Interaction between heredity and environmental influences • Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations • Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence Habituation and Dishabituation Associative Learning • Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous recovery, generalization, discrimination • Operant conditioning o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary, conditional o Reinforcement schedules: fixed-­‐ratio, variable-­‐ratio, fixed-­‐interval, variable-­‐interval o Punishment o Escape and avoidance learning • Cognitive processes that affect associative learning • Biological factors that affect associative learning o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors Observational Learning • Modeling • Biological processes that affect observational learning o Mirror neurons o Role of the brain in experiencing vicarious emotions • Applications of observational learning to explain individual behavior Self Concept and Identity • Definitions of self-­‐concept, identity, and social identity • The role of self-­‐esteem, self-­‐efficacy, and locus of control in self-­‐ concept and self-­‐identity • Different types of identities (e.g., race/ethnicity, gender, age, sexual orientation, class) Formation of Identity • Stages of identity development o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud)

118

•

PSY 361

Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-­‐taking) o Influence of group (e.g., reference group) Influence of culture and socialization on identity formation

•

Personality • Theories of personality o Psychoanalytic perspective o Humanistic perspective o Trait perspective o Social cognitive perspective o Biological perspective o Behaviorist perspective o Situational approach to explaining behavior Self Concept and Identity • Definitions of self-­‐concept, identity, and social identity • The role of self-­‐esteem, self-­‐efficacy, and locus of control in self-­‐ concept and self-­‐identity • Different types of identities (e.g., race/ethnicity, gender, age, sexual orientation, class) Formation of Identity

119

•

•

PSY 366

Stages of identity development o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud) Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-­‐taking) o Influence of group (e.g., reference group) Influence of culture and socialization on identity formation

•

Emotion • Three components of emotion (i.e., cognitive, physiological, behavioral) • Universal emotions (e.g., fear, anger, happiness, surprise, joy, disgust, sadness) • Adaptive role of emotion • Theories of emotion o James-­‐Lange theory o Cannon-­‐Bard theory o Schachter-­‐Singer theory • The role of biological processes in perceiving emotion o Generation and experience of emotions involve many brain regions o The role of the limbic system in emotion o Emotional experiences can be stored as memories that can be recalled by similar o circumstances o Prefrontal cortex is critical for emotional experience,

120

o o o

and is also important in temperament and decision making Emotion and the autonomic nervous system Physiological markers of emotion (signatures of emotion)

Stress • The nature of stress o Appraisal o Different types of stressors (e.g., cataclysmic events, personal, etc.) o Effects of stress on psychological functions • Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)

Biological Bases of Behavior • The nervous system o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences • Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior

121

o

Genetically based behavioral variation in natural populations • Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence Psychological Disorders • Understanding psychological disorders o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders • Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders o Schizophrenia o Dissociative disorder o Personality disorders • Biological bases of nervous system disorders o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-­‐based therapy to regenerate neurons in CNS Motivation • Factors that influence motivation o Instinct o Arousal o Drives ! Negative feedback systems o Needs • Theories that explain how motivation affects human behavior o Drive reduction theory o Incentive theory o Other: cognitive and need based theories • Application of theories of motivation to understand behaviors (e.g., eating, sexual, drug and alcohol use, etc.) o Biological factors in regulation of these motivational processes o Socio-­‐cultural factors in regulation of these motivational processes Attitudes • Components of attitudes (i.e., cognitive, affective, and behavioral) • The link between attitudes and behavior o Processes by which behavior influences attitudes (e.g., foot-­‐in-­‐the door phenomenon, o role-­‐playing effects)

122

PSY 368

o Processes by which attitudes influence behavior o Cognitive dissonance theory How the Presence of Others Affects Individual Behavior • Social facilitation • Deindividuation • Bystander effect • Social loafing • Peer pressure Attributing Behavior to Persons or Situations • Attribution theory o Fundamental attribution error o How culture affects attributions • How self-­‐perceptions shape our perceptions of others • How perceptions of the environment shape our perceptions of others Health Disparities • Race, gender, and class inequalities in health Healthcare Disparities • Race, gender, and class inequalities in healthcare

Culture • Symbolic culture o Language and symbols o Values and beliefs o Norms and rituals

123

PSY 422

Vision • Structure and function of the eye • Visual processing o Visual pathways in the brain o Parallel processing o Feature detection Hearing • Auditory processing o Auditory pathways in the brain • Sensory reception by hair cells Other Senses • Somatosensation o Pain perception • Taste o Taste buds/chemoreceptors that detect specific chemicals • Smell o Olfactory cells/chemoreceptors that detect specific chemicals o Pheromones o Olfactory pathways in the brain • Kinesthetic sense

124

• Vestibular sense Consciousness • States of consciousness o Alertness o Sleep ! Stages of sleep ! Sleep cycles and changes to sleep cycles ! Sleep and circadian rhythms ! Dreaming ! Sleep disorders o Hypnosis and meditation • Consciousness altering drugs o Types of consciousness altering drugs and their effects on the nervous system and behavior o Drug addiction and the reward pathway in the brain Stress • The nature of stress o Appraisal o Different types of stressors (e.g., cataclysmic events, personal, etc.) o Effects of stress on psychological functions • Stress outcomes/response to stressors o Physiological o Emotional o Behavioral o Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)

Biological Bases of Behavior • The nervous system o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system ! The brain • The brainstem • The cerebellum • The diencephalon • The cerebrum • Control of voluntary movement in the cerebral cortex • Information processing in the cerebral cortex • Lateralization of cortical functions • Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system

125

o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences • Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations • Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence Psychological Disorders • Understanding psychological disorders o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders • Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders o Schizophrenia o Dissociative disorder o Personality disorders • Biological bases of nervous system disorders o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-­‐based therapy to regenerate neurons in CNS

126

PSY 443

Culture • Symbolic culture o Language and symbols o Values and beliefs o Norms and rituals • Evolution and human culture

127

SOCIOLOGY and ANTHROPOLOGY SOC 101

•

•

•

•

•

•

•

•

•

Culture o Assimilation o Multiculturalism o Subcultures Socialization o Definition of socialization o Norms o Agents of socialization (e.g., the family, mass media, peers, workplace) o Stigma and deviance

Formation of Identity o Influence of culture and socialization on identity formation Prejudice and Bias o Definition of prejudice o Stereotypes o Ethnocentrism ! In-­‐group and out-­‐group ! Ethnocentrism vs. cultural relativism Elements of Social Interaction o Statuses o Roles o Groups o Networks o Organizations Discrimination o Individual vs. institutional discrimination o The relationship between prejudice and discrimination o How power, prestige, and class facilitate discrimination Theoretical Approaches o Functionalism o Conflict theory o Symbolic interactionism o Social constructionism Social Institutions o Education o Family o Religion o Government and economy o Health and medicine Culture o Material culture o Symbolic culture ! Values and beliefs

128

•

•

• •

SOC 303

•

! Norms and rituals o Culture and social groups Demographic Structure of Society o Age o Gender o Race and ethnicity Demographic Shifts and Social Change o Demographic transition o Fertility, migration, and mortality o Globalization Spatial Inequality o Global inequalities Social Class o Aspects of social stratification ! Class, status, and power ! Cultural capital and social capital ! Social reproduction ! Privilege and prestige ! Intersections with race, gender and age o Patterns of social mobility ! Intergenerational and intragenerational mobility ! Downward and upward mobility ! Meritocracy o Poverty ! Relative and absolute • Social exclusion (segregation and isolation)

Theoretical Approaches

129

SOC 322

•

SOC 325

•

SOC 328

•

•

• SOC 330

•

SOC 332

•

SOC 333

•

SOC 337

•

SOC 331

•

•

SOC 334

SOC 339

•

•

o o o o

Functionalism Conflict theory Symbolic interactionism Social constructionism

Self-­‐presentation and Interacting with Others o Gender shapes expression Demographic Structure of Society o Sexual orientation Socialization o Stigma and deviance o Conformity and obedience

Prejudice and Bias o Processes that contribute to prejudice ! Power, prestige, and class Demographic Structure of Society o Race and ethnicity Demographic Structure of Society o Age Social Institutions o Family Self-­‐presentation and Interacting with Others o Gender shapes expression Demographic Structure of Society o Gender Demographic Structure of Society o Sexual orientation Social Institutions o Religion Social Institutions o Government and economy

Prejudice and Bias o Processes that contribute to prejudice

130

•

•

SOC 340

•

! Power, prestige, and class Discrimination o Individual vs. institutional discrimination o The relationship between prejudice and discrimination o How power, prestige, and class facilitate discrimination Social Class o Aspects of social stratification ! Class, status, and power ! Cultural capital and social capital ! Social reproduction ! Privilege and prestige ! Intersections with race, gender and age o Patterns of social mobility ! Intergenerational and intragenerational mobility ! Downward and upward mobility ! Meritocracy o Poverty ! Relative and absolute ! Social exclusion (segregation and isolation)

How the Presence of Others Affects Individual Behavior o Social facilitation 131

•

• • •

•

•

•

SOC 341

•

o Deindividuation o Bystander effect o Social loafing o Peer pressure Group Processes o Group polarization o Groupthink Socialization o Conformity and obedience Self-­‐Concept and Identity o Definitions of self-­‐concept, identity, and social identity Formation of Identity o Stages of identity development ! Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud) o Influence of social factors on identity formation ! Influence of individuals (e.g., imitation, role-­‐taking) ! Influence of group (e.g., reference group) o Influence of culture and socialization on identity formation Elements of Social Interaction o Statuses o Roles o Groups o Networks o Organizations Self-­‐presentation and Interacting with Others o Expressing and detecting emotion ! Gender shapes expression ! Culture shapes expression o Impression management ! Front stage vs. back stage self (Dramaturgical approach) o Verbal and nonverbal communication o Animal signals and communication Culture o Symbolic culture ! Language and symbols

Self-­‐Concept and Identity o Definitions of self-­‐concept, identity, and social

132

identity Different types of identities (e.g., race/ethnicity, gender, age, sexual orientation, class) Formation of Identity o Influence of social factors on identity formation ! Influence of individuals (e.g., imitation, role-­‐taking) ! Influence of group (e.g., reference group) Self-­‐presentation and Interacting with Others o Impression management ! Front stage vs. back stage self (Dramaturgical approach) Demographic Shifts and Social Change o Social movements Demographic Shifts and Social Change o Urbanization Spatial Inequality o Racial segregation(neighborhoods) Demographic Structure of Society o Immigration status Demographic Shifts and Social Change o Globalization Spatial Inequality o Global inequalities Spatial Inequality o Environmental justice (location and exposure to health risks) o

•

•

SOC 342

•

SOC 351

•

SOC 368

•

•

SOC 435

•

SWK 335

•

ANT 150

•

•

Culture o Assimilation o Multiculturalism o Subcultures

133

•

• •

ANT 300

•

ANT 315

• •

Prejudice and Bias o Ethnocentrism ! In-­‐group and out-­‐group o Ethnocentrism vs. cultural relativism Self-­‐presentation and Interacting with Others o Culture shapes expression Culture o Material culture o Symbolic culture ! Values and beliefs ! Norms and rituals o Culture and social groups Culture o Evolution and human culture Self-­‐presentation and Interacting with Others o Verbal and nonverbal communication Culture o Symbolic culture ! Language and symbols

134

Topic List with Associated Courses

This document lists the topics that will be found on the MCAT 2015 exam, arranged by content category, along with the University of Dayton course numbers for any course that covers material in that content category.

Specifically, content from the following sections of the MCAT are listed:

• Biological and Biochemical Foundations of Living Systems – p. 137 • Chemical and Physical Foundations of Biological Systems – p. 157 • Psychological, Social, and Biological Foundations of Behavior – p. 168

Note that not every listed course covers every topic in a given content category. Every effort has been made to highlight what topics in a given content category are covered or not covered in each course. However, this document should be used in conjunction with the companion “Course Listing with Associated Topics” to fully discern what content may be found in a given course.

The list in this document follows the order and organization found in the AAMC publications: Preview Guide for the MCAT 2015 Exam and The Official Guide to the MCAT (MCAT 2015) Exam.

The fourth section of the MCAT is titled Critical Analysis and Reasoning Skills.

It includes passages and questions to test the student’s ability to comprehend.

Passages are excerpted from authentic materials found in a variety of books, journals, and magazines, often from disciplines in the social sciences and humanities. This MCAT section is NOT included in this course mapping since it does not test knowledge typically covered in a specific course.

135

Biological and Biochemical Foundations of Living Systems Content Category 1A: Structure and function of proteins and their constituent amino acids Amino Acids ● Description ○ Absolute configuration at the position ○ Amino acids as dipolar ions ○ Classifications ■ Acidic or basic ■ Hydrophobic or hydrophilic ● Reactions ○ Sulfur linkage for cysteine and cysteine ○ Peptide linkage: polypeptides and proteins ○ Hydrolysis

CHM 314, 420, 451 & BIO 151, 151L, 312, 312L, 440

Protein Structure ● Structure ○ 1° structure of proteins ○ 2° structure of proteins ○ 3° structure of proteins; role of proline, cystine, hydrophobic bonding ○ 4° structure of proteins ● Conformational stability ○ Denaturing and folding (Not CHM 420) ○ Hydrophobic interactions ○ Solvation layer (entropy) (Not BIO 151) ● Separation techniques ○ Isoelectric point (Not BIO 151) ○ Electrophoresis

CHM 420, 451, 462L & BIO 151, 151L, 312, 312L, 440, 442L, 462

Enzyme Structure and Function ● Function of enzymes in catalyzing biological reactions (BIO 411) ● Enzyme classification by reaction type (Not BIO 151) (Not CHM 420) ● Reduction of activation energy

BIO 151, 151L, BIO 411, 442L, 462 & CHM 420, 451, 452

Non-­‐Enzymatic Protein Function ● Binding ● Immune system ● Motors

BIO 151, 151L, 312, 312L, 411, 411L, 427,442 & CHM 420, 451, 452

136

● ● ● ●

Substrates and enzyme specificity Active Site Model (Not BIO 151) Induced-­‐fit Model Mechanism of catalysis ○ Cofactors (BIO 411) ○ Coenzymes (BIO 411) ○ Water-­‐soluble vitamins (Not BIO 151) ● Effects of local conditions on enzyme activity

Control of Enzyme Activity ● Kinetics ○ General (catalysis) (BIO 411) ○ Michaelis-­‐Menten(Not BIO 151) ○ Cooperativity ● Feedback regulation (BIO 411) ● Inhibition – types ○ Competitive ○ Non-­‐competitive ○ Mixed (Not BIO 151) ○ Uncompetitive(Not BIO 151) ● Regulatory enzymes ○ Allosteric enzymes ○ Covalently-­‐modified enzymes ○ Zymogen (Not CHM 420)

BIO 151, 151L, 411, 462 & CHM 420, 451, 452

Nucleic Acid Structure and Function ● Description ● Nucleotides and nucleosides ○ Sugar phosphate backbone ○ Pyrimidine, purine residues ● Deoxyribonucleic acid (DNA): double helix, Watson–Crick model of DNA structure ● Base pairing specificity: A with T, G with C ● Function in transmission of genetic information (Not CHM 420) ● DNA denaturation, reannealing, hybridization (Not CHM 420)

CHM 314, 420, 451, 452 & BIO 151, 151L, 312, 312L, 442, 462

Content Category 1B: Transmission of genetic information from the gene to the protein

DNA Replication ● Mechanism of replication: separation of strands, specific

BIO 151, 151L, 312, 312L, 440,

137

● ● ● ●

coupling of free nucleic acids Semi-­‐conservative nature of replication Specific enzymes involved in replication Origins of replication, multiple origins in eukaryotes Replicating the ends of DNA molecules

Repair of DNA ● Repair during replication ● Repair of mutations

Genetic Code ● Central Dogma: DNA → RNA → protein (BIO 411) ● The triplet code ● Codon-­‐anticodon relationship ● Degenerate code, wobble pairing ● Missense, nonsense codons ● Initiation, termination codons ● Messenger RNA (mRNA) (BIO 411)

BIO 151, 151L, 312, 312L, 411, 411L, 440, 462 & CHM 452

BIO 151, 151L, 312, 312L, 411, 442, 462 & CHM 452, 462L

Transcription ● Transfer RNA (tRNA); ribosomal RNA (rRNA) ● Mechanism of transcription ● mRNA processing in eukaryotes, introns, exons ● Ribozymes, spliceosomes, small nuclear ribonucleoproteins (snRNPs), small nuclear RNA (snRNAs) ● Functional and evolutionary importance of introns

BIO 151, 151L, 312, 312L, 442, 462 & CHM 452

Eukaryotic Chromosome Organization ● Chromosomal proteins ● Single copy vs. repetitive DNA ● Supercoiling ● Heterochromatin vs. euchromatin

BIO 151, 151L, 312, 312L, 442, 462 & CHM 452

Translation ● Roles of mRNA, tRNA, rRNA ● Role and structure of ribosomes ● Initiation, termination co-­‐factors ● Post-­‐translational modification of proteins

462, 470 & CHM 452

BIO 151, 151L, 312, 312L, 442, 462 & CHM 452

138

● Telomeres, centromeres

Control of Gene Expression in Prokaryotes ● Operon Concept, Jacob-­‐Monod Model ● Gene repression in bacteria ● Positive control in bacteria

BIO 151, 151L, 312, 312L, 411, 411L, 462

Recombinant DNA and Biotechnology ● Gene cloning (BIO 411) ● Restriction enzymes (BIO 411) ● DNA libraries (BIO 411) ● Generation of cDNA ● Hybridization ● Expressing cloned genes ● Polymerase Chain Reaction(BIO 411) ● Gel Electrophoresis and Southern Blotting ● DNA sequencing (BIO 411) ● Analyzing gene expression (BIO 411) ● Determining gene function (BIO 411) ● Stem cells ● Practical applications of DNA technology: medical applications, human gene therapy, pharmaceuticals, forensic evidence, environmental cleanup, agriculture ● Safety and ethics of DNA technology

BIO 151, 151L, 312, 312L, 411, 442, & CHM 462L

Control of Gene Expression in Eukaryotes BIO 151, 151L, ● Transcriptional regulation(BIO 411) 312, 312L, 411, 442, 462 ● DNA binding proteins, transcription factors ● Gene amplification and duplication ● Post-­‐transcriptional control, basic concept of splicing (introns, exons) ● Cancer as a failure of normal cellular controls, oncogenes, tumor suppressor genes ● Regulation of chromatin structure ● DNA methylation ● Role of non-­‐coding RNAs

139

Content Category 1C: Transmission of heritable information from generation to generation and the processes that increase genetic diversity

Evidence that DNA is Genetic Material

BIO 151, 151L, 312, 312L, & CHM 451, 452

Meiosis and Other Factors Affecting Genetic Variability ● Significance of meiosis ● Important differences between meiosis and mitosis ● Segregation of genes ○ Independent assortment ○ Linkage ○ Recombination ■ Single crossovers ■ Double crossovers ■ Synaptonemal complex ■ Tetrad ○ Sex-­‐linked characteristics ○ Very few genes on Y chromosome ○ Sex determination ○ Cytoplasmic/extranuclear inheritance ● Mutation ○ General concept of mutation — error in DNA sequence ○ Types of mutations: random, translation error,

BIO 151, 151L, 152, 152L, 312, 312L, 442, 442L

Mendelian Concepts ● Phenotype and genotype ● Gene ● Locus ● Allele: single and multiple ● Homozygosity and heterozygosity ● Wild-­‐type ● Recessiveness ● Complete dominance ● Co-­‐dominance ● Incomplete dominance, leakage, penetrance, expressivity (Not BIO 151) ● Hybridization: viability ● Gene pool

BIO 151, 151L, 152, 152L, 301, 312, 312L, 442

140

transcription error, base substitution, inversion, addition, deletion, translocation, mispairing ○ Advantageous vs. deleterious mutation ○ Inborn errors of metabolism ○ Relationship of mutagens to carcinogens ● Genetic drift ● Synapsis or crossing-­‐over mechanism for increasing genetic diversity

Analytic Methods ● Hardy–Weinberg Principle (Not BIO 151) ● Test cross ● Gene mapping: crossover frequencies ● Biometry: statistical methods (Not BIO 151)

BIO 151, 151L, 152, 152L, 312, 312L

Content Category 1D: Principles of bioenergetics and fuel molecule metabolism

Evolution ● Natural selection ○ Fitness concept ○ Selection by differential reproduction ○ Concepts of natural and group selection ○ Evolutionary success as increase in percent representation in the gene pool of the next ○ generation ● Speciation ○ Polymorphism ○ Adaptation and specialization ○ Inbreeding ○ Outbreeding ○ Bottlenecks ● Evolutionary time as measured by gradual random changes in genome

BIO 152, 152L, 312, 312L

Principles of Bioenergetics ● Bioenergetics/thermodynamics ○ Free energy/Keq ■ Equilibrium constant ■ Relationship of the equilibrium constant and ΔG° ○ Concentration

BIO 151, 151L, 411, 411L & CHM 420, 451

141

■ Le Châtelier’s Principle (Not BIO 151) (Not CHM 420) ○ Endothermic/exothermic reactions ○ Free energy: G ○ Spontaneous reactions and ΔG° ● Phosphoryl group transfers and ATP ○ ATP hydrolysis ΔG << 0 ○ ATP group transfers ● Biological oxidation-­‐reduction ○ Half-­‐reactions (Not CHM 420) ○ Soluble electron carriers ○ Flavoproteins

Carbohydrates ● Description ○ Nomenclature and classification, common names ○ Absolute configuration ○ Cyclic structure and conformations of hexoses ○ Epimers and anomers ● Hydrolysis of the glycoside linkage ● Monosaccharides ● Disaccharides ● Polysaccharides

BIO 151, 151L & CHM 314, 420, 451

Principles of Metabolic Regulation ● Regulation of metabolic pathways ○ Maintenance of a dynamic steady state ● Regulation of glycolysis and gluconeogenesis ● Metabolism of glycogen (Not BIO 411) ● Regulation of glycogen synthesis and breakdown (Not BIO 411) (Not CHM 420)

BIO 151, 151L, 411, 411L & CHM 420, 451, 452

Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway BIO 151, 151L, ● Glycolysis (aerobic), substrates and products 411, 411L & ○ Feeder pathways: glycogen, starch metabolism (Not CHM CHM 420, 451 420) ● Fermentation (anaerobic glycolysis) ● Gluconeogenesis ● Pentose phosphate pathway (Not BIO 151) ● Net molecular and energetic results of respiration processes

142

○ Allosteric and hormonal control (Not BIO 411) (Not CHM 420) ● Analysis of metabolic control(Not CHM 420)

Citric Acid Cycle ● Acetyl-­‐CoA production ● Reactions of the cycle, substrates and products ● Regulation of the cycle ● Net molecular and energetic results of respiration processes

BIO 151, 151L, 411, 411L & CHM 420, 452

Oxidative Phosphorylation ● Electron transport chain and oxidative phosphorylation, substrates and products, general features of the pathway ● Electron transfer in mitochondria ○ NADH, NADPH ○ Flavoproteins ○ Cytochromes ● ATP synthase, chemiosmotic coupling (Not CHM 420) ○ Proton motive force ● Net molecular and energetic results of respiration processes ● Regulation of oxidative phosphorylation (Not CHM 420) ● Mitochondria, apoptosis, oxidative stress (Not BIO 411) (Not CHM 420)

BIO 151, 151L, 411, 411L & CHM 420, 452

Metabolism of Fatty Acids and Proteins BIO 151, 151L, ● Description of fatty acids 411, 411L & ● Digestion, mobilization, and transport of fats (Not BIO 151) (Not CHM 420, 452 BIO 411) ● Oxidation of fatty acids ○ Saturated fats ○ Unsaturated fats ● Ketone bodies (Not BIO 411) ● Anabolism of fats (Not BIO 411) ● Non-­‐template synthesis: biosynthesis of lipids and polysaccharides (Not BIO 151) (Not BIO 411) ● Metabolism of proteins (Not BIO 151) (Not CHM 420)

Hormonal Regulation and Integration of Metabolism ● Higher level integration of hormone structure and function ● Tissue specific metabolism ● Hormonal regulation of fuel metabolism

BIO 151, 151L, 403, 403L, & CHM 452 143

● Obesity and regulation of body mass

Content Category 2A: Assemblies of molecules, cells, and groups of cells within single cellular and multicellular organisms Plasma Membrane ● General function in cell containment ● Composition of membranes ○ Lipid components ■ Phospholipids (and phosphatids) ■ Steroids ■ Waxes ○ Protein components ○ Fluid mosaic model ● Membrane dynamics ● Solute transport across membranes ○ Thermodynamic considerations ○ Osmosis ■ Colligative properties, osmotic pressure ○ Passive transport ○ Active transport ■ Sodium/potassium pump ● Membrane channels ● Membrane potential ● Membrane receptors ● Exocytosis and endocytosis(Not BIO 411) (Not CHM 420) ● Intercellular junctions (Not BIO 411) (Not CHM 420) ○ Gap junctions ○ Tight junctions ○ Desmosomes

Membrane-­‐Bound Organelles and Defining Characteristics of Eukaryotic Cells ● Defining characteristics of eukaryotic cells: membrane bound nucleus, presence of organelles, ● Mitotic division (Not CHM 420) ● Nucleus (Not CHM 420) ○ Compartmentalization, storage of genetic information ○ Nucleolus: location and function ○ Nuclear envelope, nuclear pores

BIO 151, 151L, 403, 403L, 411, 411L, 440, 442 & CHM 124, 420, 451

BIO 151, 151L, 403, 403L, 440, 442 & CHM 420, 451

144

● Mitochondria ○ Site of ATP production ○ Inner and outer membrane structure ○ Self-­‐replication (Not CHM 420) ● Lysosomes: membrane-­‐bound vesicles containing hydrolytic enzymes ● Endoplasmic reticulum ○ Rough and smooth components ○ Rough endoplasmic reticulum site of ribosomes ○ Double membrane structure (Not CHM 420) ○ Role in membrane biosynthesis (Not CHM 420) ○ Role in biosynthesis of secreted proteins (Not CHM 420) ● Golgi apparatus: general structure and role in packaging and secretion (Not CHM 420) ● Peroxisomes: organelles that collect peroxides

Cytoskeleton ● General function in cell support and movement ● Microfilaments: composition and role in cleavage and contractility ● Microtubules: composition and role in support and transport ● Intermediate filaments, role in support ● Composition and function of cilia and flagella ● Centrioles, microtubule organizing centers

BIO 151, 151L, 440, 442

Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and viruses

Tissues Formed From Eukaryotic Cells ● Epithelial cells ● Connective tissue cells

BIO 151, 151L, 440, 442

Cell Theory ● History and development ● Impact on biology

BIO 151, 151L, 411, 411L, 440

Classification and Structure of Prokaryotic Cells ● Prokaryotic domains ○ Archaea ○ Bacteria ● Major classifications of bacteria by shape

BIO 151, 151L, 411, 411L

145

● ● ● ●

○ Bacilli (rod-­‐shaped) ○ Spirilli (spiral shaped) ○ Cocci (spherical) Lack of nuclear membrane and mitotic apparatus Lack of typical eukaryotic organelles Presence of cell wall in bacteria Flagellar propulsion, mechanism

Growth and Physiology of Prokaryotic Cells ● Reproduction by fission ● High degree of genetic adaptability, acquisition of antibiotic resistance ● Exponential growth ● Existence of anaerobic and aerobic variants ● Parasitic and symbiotic ● Chemotaxis

BIO 151, 151L, 411, 411L

Virus Structure ● General structural characteristics (nucleic acid and protein, enveloped and nonenveloped) ● Lack organelles and nucleus ● Structural aspects of typical bacteriophage ● Genomic content-­‐-­‐RNA or DNA ● Size relative to bacteria and eukaryotic cells

BIO 151, 151L, 411, 411L

Genetics of Prokaryotic Cells ● Existence of plasmids, extragenomic DNA ● Transformation: incorporation into bacterial genome of DNA fragments from external medium ● Conjugation ● Transposons (also present in eukaryotic cells)

BIO 151, 151L, 312L, 411, 411L

Viral Life Cycle ● Self-­‐replicating biological units that must reproduce within specific host cell ● Generalized phage and animal virus life cycles ○ Attachment to host, penetration of cell membrane or cell wall, and entry of viral genetic ○ material ○ Use of host synthetic mechanism to replicate viral components

BIO 151, 151L, 411, 411L

146

○ Self-­‐assembly and release of new viral particles ● Transduction: transfer of genetic material by viruses ● Retrovirus life cycle: integration into host DNA, reverse transcriptase, HIV ● Prions and viroids: subviral particles

Content Category 2C: Processes of cell division, differentiation, and specialization Mitosis ● Mitotic process: prophase, metaphase, anaphase, telophase, interphase ● Mitotic structures ○ Centrioles, asters, spindles ○ Chromatids, centromeres, kinetochores ○ Nuclear membrane breakdown and reorganization ○ Mechanisms of chromosome movement ● Phases of cell cycle: G0, G1, S, G2, M ● Growth arrest ● Control of cell cycle ● Loss of cell cycle controls in cancer cells

BIO 151, 151L, 312, 312L, 440, 442

Biosignalling ● Oncogenes (Not BIO 151), apoptosis

BIO 151, 151L, 440, 442

Embryogenesis ● Stages of early development (order and general features of each) ○ Fertilization ○ Cleavage ○ Blastula formation ○ Gastrulation

BIO 152, 152L, 442

Reproductive System ● Gametogenesis by meiosis ● Ovum and sperm ○ Differences in formation ○ Differences in morphology ○ Relative contribution to next generation ● Reproductive sequence: fertilization, implantation, development, birth

BIO 152, 152L, 442, 475, 475L

147

■ First cell movements ■ Formation of primary germ layers (endoderm, mesoderm, ectoderm) ○ Neurulation ● Major structures arising out of primary germ layers ● Neural crest ● Environment–gene interaction in development

Mechanisms of Development ● Cell specialization ○ Determination ○ Differentiation ○ Tissue types ● Cell–cell communication in development ● Cell migration ● Pluripotency: stem cells ● Gene regulation in development ● Programmed cell death ● Existence of regenerative capacity in various species ● Senescence and aging

BIO 152, 152L, 442

Content Category 3A: Structure and functions of the nervous and endocrine systems and ways in which these systems coordinate the organ systems

Nervous System: Structure and Function ● Major Functions ○ High level control and integration of body systems ○ Adaptive capability to external influences ● Organization of vertebrate nervous system ● Sensor and effector neurons ● Sympathetic and parasympathetic nervous systems: antagonistic control ● Reflexes ○ Feedback loop, reflex arc ○ Role of spinal cord and supraspinal circuits ● Integration with endocrine system: feedback control

BIO 152, 442, 442L, 475, 475L

Nerve Cell ● Cell body: site of nucleus, organelles ● Dendrites: branched extensions of cell body

BIO 403, 403L, 415, 442 148

● ● ● ● ● ● ●

Axon: structure and function Myelin sheath, Schwann cells, insulation of axon Nodes of Ranvier: propagation of nerve impulse along axon Synapse: site of impulse propagation between cells Synaptic activity: transmitter molecules Resting potential: electrochemical gradient Action potential ○ Threshold, all-­‐or-­‐none ○ Sodium/potassium pump ● Excitatory and inhibitory nerve fibers: summation, frequency of firing ● Glial cells, neuroglia

Electrochemistry ● Concentration cell: direction of electron flow, Nernst equation

BIO 403, 403L & CHM 124, 451

Lipids ● Description; structure ○ Steroids ○ Terpenes and terpenoids (Not BIO 151) (Not BIO 411)

BIO 151, 151L, 411, 411L & CHM 451, 452

Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action ● Transport of hormones: blood supply

BIO 152, 152L, 403, 403L, 442

Biosignalling ● Gated ion channels ○ Voltage gated ○ Ligand gated ● Receptor enzymes ● G protein-­‐coupled receptors

Endocrine System: Hormones and Their Sources ● Function of endocrine system: specific chemical control at cell, tissue, and organ level ● Definitions of endocrine gland, hormone ● Major endocrine glands: names, locations, products ● Major types of hormones ● Neuroendrocrinology ― relation between neurons and hormonal systems

BIO 151, 151L, 312, 312L, 440, 442 & CHM 420, 451

BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L

149

● Specificity of hormones: target tissue ● Integration with nervous system: feedback control regulation by second messengers

Content Category 3B: Structure and integrative functions of the main organ systems

Respiratory System ● General function ○ Gas exchange, thermoregulation ○ Protection against disease: particulate matter ● Structure of lungs and alveoli ● Breathing mechanisms ○ Diaphragm, rib cage, differential pressure ○ Resiliency and surface tension effects ● Thermoregulation: nasal and tracheal capillary beds; evaporation, panting ● Particulate filtration: nasal hairs, mucus/cilia system in lungs ● Alveolar gas exchange ○ Diffusion, differential partial pressure ○ Henry’s Law ● pH control ● Regulation by nervous control ○ CO2 sensitivity

Circulatory System ● Functions: circulation of oxygen, nutrients, hormones, ions and fluids, removal of metabolic waste ● Role in thermoregulation ● Four-­‐chambered heart: structure and function ● Endothelial cells ● Systolic and diastolic pressure ● Pulmonary and systemic circulation ● Arterial and venous systems (arteries, arterioles, venules, veins) ○ Structural and functional differences ○ Pressure and flow characteristics ● Capillary beds ○ Mechanisms of gas and solute exchange ○ Mechanism of heat exchange ○ Source of peripheral resistance

BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L

BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L

150

● Composition of blood ○ Plasma, chemicals, blood cells ○ Erythrocyte production and destruction; spleen, bone marrow ○ Regulation of plasma volume ● Coagulation, clotting mechanisms ● Oxygen transport by blood ○ Hemoglobin, hematocrit ○ Oxygen content ○ Oxygen affinity ○ Oxygen transport by blood; modification of oxygen affinity ● Carbon dioxide transport and level in blood ● Nervous and endocrine control

Lymphatic System BIO 152, 152L ● Structure of lymphatic system 403, 403L, 475, 475L ● Major functions ○ Equalization of fluid distribution ○ Transport of proteins and large glycerides ○ Production of lymphocytes involved in immune reactions ○ Return of materials to the blood Immune System ● Innate (non-­‐specific) vs. adaptive (specific) immunity ● Adaptive immune system cells ○ T-­‐lymphocytes ○ B-­‐lymphocytes ● Innate immune system cells ○ Macrophages ○ Phagocytes ● Concept of antigen and antibody ● Antigen presentation ● Clonal selection ● Antigen-­‐antibody recognition ● Structure of antibody molecule ● Recognition of self vs. non-­‐self, autoimmune diseases ● Major histocompatibility complex Digestive System

BIO 427, 442, 442L

BIO 403, 403L, 151

● Ingestion ○ Saliva as lubrication and source of enzymes ○ Ingestion, esophagus, transport function ● Stomach ○ Storage and churning of food ○ Low pH, gastric juice, mucal protection against self-­‐ destruction ○ Production of digestive enzymes, site of digestion ○ Structure (gross) ● Liver ○ Structural relationship of liver within gastrointestinal system ○ Production of bile ○ Role in blood glucose regulation, detoxification ● Bile ○ Storage in gall bladder ○ Function ● Pancreas ○ Production of enzymes ○ Transport of enzymes to small intestine ● Small Intestine ○ Absorption of food molecules and water ○ Function and structure of villi ○ Production of enzymes, site of digestion ○ Neutralization of stomach acid ○ Structure (anatomic subdivisions) ● Large Intestine ○ Absorption of water ○ Bacterial flora ○ Structure (gross) ● Rectum: storage and elimination of waste, feces ● Muscular control ○ Peristalsis ● Endocrine control ○ Hormones ○ Target tissues ● Nervous control: the enteric nervous system

Excretory System

442, 442L, 475, 475L

BIO 403, 403L, 152

● Roles in homeostasis ○ Blood pressure ○ Osmoregulation ○ Acid-­‐base balance ○ Removal of soluble nitrogenous waste ● Kidney structure ○ Cortex ○ Medulla ● Nephron structure ○ Glomerulus ○ Bowman’s capsule ○ Proximal tubule ○ Loop of Henle ○ Distal tubule ○ Collecting duct ● Formation of urine ○ Glomerular filtration ○ Secretion and reabsorption of solutes ○ Concentration of urine ○ Counter-­‐current multiplier mechanism ● Storage and elimination: ureter, bladder, urethra ● Osmoregulation: capillary reabsorption of H2O, amino acids, glucose, ions ● Muscular control: sphincter muscle

Reproductive System ● Male and female reproductive structures and their functions ○ Gonads ○ Genitalia ○ Differences between male and female structures ● Hormonal control of reproduction ○ Male and female sexual development ○ Female reproductive cycle ○ Pregnancy, parturition, lactation ○ Integration with nervous control Muscle System ● Important functions ○ Support: mobility ○ Peripheral circulatory assistance

442, 442L, 475, 475L

BIO 403, 403L, 442, 442L, 475, 475L

BIO 403, 403L, 475, 475L 153

● ●

● ● ●

○ Thermoregulation (shivering reflex) Structure of three basic muscle types: striated, smooth, cardiac Muscle structure and control of contraction ○ T-­‐tubule system ○ Contractile apparatus ○ Sarcoplasmic reticulum ○ Fiber type ○ Contractile velocity of different muscle types Regulation of cardiac muscle contraction Oxygen debt: fatigue Nervous control ○ Motor neurons ○ Neuromuscular junction, motor end plates ○ Sympathetic and parasympathetic innervation ○ Voluntary and involuntary muscles

Specialized Cell-­‐Muscle Cell ● Structural characteristics of striated, smooth, and cardiac muscle ● Abundant mitochondria in red muscle cells: ATP source ● Organization of contractile elements: actin and myosin filaments, crossbridges, sliding filament model ● Sarcomeres: “I” and “A” bands, “M” and “Z” lines, “H” zone ● Presence of troponin and tropomyosin ● Calcium regulation of contraction Skeletal System ● Functions ○ Structural rigidity and support ○ Calcium storage ○ Physical protection ● Skeletal structure ○ Specialization of bone types, structures ○ Joint structures ○ Endoskeleton vs. exoskeleton ● Bone structure ○ Calcium/protein matrix ○ Cellular composition of bone ● Cartilage: structure and function ● Ligaments, tendons

BIO 403, 403L, 440

BIO 442, 442L, 475, 475L

154

● Endocrine control

Skin System ● Structure ○ Layer differentiation, cell types ○ Relative impermeability to water ● Functions in homeostasis and osmoregulation ● Functions in thermoregulation ○ Hair, erectile musculature ○ Fat layer for insulation ○ Sweat glands, location in dermis ○ Vasoconstriction and vasodilation in surface capillaries ● Physical protection ○ Nails, calluses, hair ○ Protection against abrasion, disease organisms ● Hormonal control: sweating, vasodilation, and vasoconstriction

BIO 403, 403L, 442, 475, 475L

155

Chemical and Physical Foundations of Biological Systems Content Category 4A: Translational motion, forces, work, energy, and equilibrium in living systems Translational Motion • Units and dimensions • Vectors, components • Vector addition • Speed, velocity (average and instantaneous) • Acceleration Equilibrium • Concept of force, units • Analysis of forces acting on an object • Newton’s First Law of Motion, inertia • Torques, lever arms

Work • Derived units, sign conventions • Mechanical advantage • Work Kinetic Energy Theorem

Energy • Kinetic Energy: KE = ½ mv2; units • Potential Energy o PE = mgh (gravitational, local) o PE = ½ kx2(spring) • Conservation of energy • Conservative forces • Power, units Content Category 4B: Importance of fluids for the circulation of blood, gas movement, and gas exchange Fluids • Density, specific gravity • Buoyancy, Archimedes’ Principle • Hydrostatic pressure o Pascal’s Law o Hydrostatic pressure; P = ρgh (pressure versus depth) • Viscosity: Poiseuille Flow • Continuity equation (A∙v = constant) • Concept of turbulence at high velocities • Surface tension • Bernoulli’s equation • Venturi effect, pitot tube Circulatory System • Arterial and venous systems; pressure and flow characteristics Gas Phase • Absolute temperature, (K) Kelvin Scale

PHY 201

PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.

PHY 201 & CHM 124, 420, 451

PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.

PHY 201 & CHM 123

PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.

PHY 201 & CHM 123

PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics.

PHY 201

PHY201 does not cover items in heat, temperature, kinetic theory, and thermodynamics..

BIO 403, 403L CHM 123 156

Pressure, simple mercury barometer Molar volume at 0°C and 1 atm = 22.4 L/mol Ideal gas o Definition o Ideal Gas Law: PV = nRT o Boyle’s Law: PV = constant o Charles’ Law: V/T = constant o Avogadro’s Law: V/n = constant • Kinetic Molecular Theory of Gases o Heat capacity at constant volume and at constant pressure o Boltzmann’s Constant • Deviation of real gas behavior from Ideal Gas Law o Qualitative o Quantitative (Van der Waals’ Equation) • Partial pressure, mole fraction • Dalton’s Law relating partial pressure to composition Content Category 4C: Electrochemistry and electrical circuits and their elements Electrostatics • Charge, conductors, charge conservation • Insulators • Electric field E o Field lines o Field due to charge distribution • Potential difference, absolute potential at point in space Circuit Elements • Current I = ΔQ/Δt, sign conventions, units • Electromotive force, voltage • Resistance o Ohm’s Law: I = V/R o Resistors in series o Resistors in parallel o Resistivity: ρ = R•A/L • Capacitance o Parallel plate capacitor o Energy of charged capacitor o Capacitors in series o Capacitors in parallel o Dielectrics • Conductivity o Metallic o Electrolytic • Meters Electrochemistry • Electrolytic cell o Electrolysis o Anode, cathode o Electrolyte • • •

PHY 202

PHY 202

CHM 124, 451

157

o

Faraday’s Law relating amount of elements deposited (or gas liberated) at an electrode to o current o Electron flow, oxidation, and reduction at the electrodes • Galvanic or Voltaic cells o Half-­‐reactions o Reduction potentials, cell potential o Direction of electron flow • Concentration cell • Batteries o Electromotive force, Voltage o Lead-­‐storage batteries o Nickel-­‐cadmium batteries Specialized Cell -­‐ Nerve Cell • Myelin sheath, Schwann cells, insulation of axon • Nodes of Ranvier: propagation of nerve impulse along axon Content Category 4D: How light and sound interact with matter Sound • Production of sound • Relative speed of sound in solids, liquids, and gases • Intensity of sound, decibel units, log scale • Attenuation (Damping) • Doppler Effect: moving sound source or observer, reflection of sound from a moving object • Pitch • Resonance in pipes and strings • Ultrasound • Shock waves Light, Electromagnetic Radiation • Concept of Interference; Young Double-­‐slit Experiment • Thin films, diffraction grating, single-­‐slit diffraction • Other diffraction phenomena, X-­‐ray diffraction • Polarization of light • Circular polarization • Properties of electromagnetic radiation o Velocity equals constant c, in vacuo o Electromagnetic radiation consists of perpendicularly oscillating electric and magnetic o fields; direction of propagation is perpendicular to both • Classification of electromagnetic spectrum, photon energy E = (hf) • Visual spectrum, color Molecular Structure and Absorption Spectra • Infrared region o Intramolecular vibrations and rotations o Recognizing common characteristic group

BIO 415, 442

PHY 202

PHY 202 & CHM 123

CHM 313

158

absorptions, fingerprint region • Visible region o Absorption in visible region gives complementary color (e.g., carotene) o Effect of structural changes on absorption (e.g., indicators) • Ultraviolet region o π-­‐electron and non-­‐bonding electron transitions o Conjugated systems • NMR spectroscopy o Protons in a magnetic field; equivalent protons o Spin-­‐spin splitting Geometrical Optics • Reflection from plane surface: angle of incidence equals angle of reflection • Refraction, refractive index n, Snell’s law: n1 sin θ1 = n2 sin θ2 • Dispersion, change of index of refraction with wavelength • Conditions for total internal reflection • Spherical mirrors o Center of curvature o Focal length o Real and virtual images • Thin lenses o Converging and diverging lenses o Use of formula 1/p + 1/q = 1/f, with sign conventions o Lens strength, diopters • Combination of lenses • Lens aberration • Optical Instruments, including the human eye Content Category 4E: Atoms, nuclear decay, electronic structure, and atomic chemical behavior Atomic Nucleus • Atomic number, atomic weight • Neutrons, protons, isotopes • Nuclear forces, binding energy • Radioactive decay o α, β, γ decay o Half-­‐life, exponential decay, semi-­‐log plots • Mass spectrometer Electronic Structure • Orbital structure of hydrogen atom, principal quantum number n, number of electrons per orbital • Ground state, excited states • Absorption and emission line spectra • Use of Pauli Exclusion Principle • Conventional notation for electronic structure • Bohr atom

PHY 202 & BIO 442, 442L, 475, 475L

CHM 123

PHY 202 & CHM 123

PHY202 does not cover items in nuclear physics.

159

• Effective nuclear charge • Photoelectric effect The Periodic Table -­‐ Classification of Elements into Groups by Electronic Structure • Alkali metals • Alkaline earth metals: their chemical characteristics • Halogens: their chemical characteristics • Noble gases: their physical and chemical characteristics • Transition metals • Representative elements • Metals and non-­‐metals • Oxygen group The Periodic Table -­‐ Variations of Chemical Properties with Group and Row • Valence electrons • First and second ionization energy o Definition o Prediction from electronic structure for elements in different groups or rows • Electron affinity o Definition o Variation with group and row • Electronegativity o Definition o Comparative values for some representative elements and important groups • Electron shells and the sizes of atoms • Electron shells and the sizes of ions Stoichiometry • Molecular weight • Empirical versus molecular formula • Metric units commonly used in the context of chemistry • Description of composition by percent mass • Mole concept, Avogadro’s number NA • Definition of density • Oxidation number o Common oxidizing and reducing agents o Disproportionation reactions • Description of reactions by chemical equations o Conventions for writing chemical equations o Balancing equations, including redox equations o Limiting reactants o Theoretical yields Content Category 5A: Unique nature of water and its solutions Acid/Base Equilibria • Bronsted-­‐Lowry definition of acid, base • Ionization of water o Kw, its approximate value (Kw = [H+][OH–] = 10-­‐14 at

CHM 123

CHM 123

CHM 123, BIO 442L

CHM 124, 451

160

25°C, 1 atm) o Definition of pH: pH of pure water • Conjugate acids and bases (e.g., NH4+ and NH3) • Strong acids and bases (e.g., nitric, sulfuric) • Weak acids and bases (e.g., acetic, benzoic) o Dissociation of weak acids and bases with or without added salt o Hydrolysis of salts of weak acids or bases o Calculation of pH of solutions of salts of weak acids or bases • Equilibrium constants Ka and Kb: pKa, pKb • Buffers o Definition and concepts (common buffer systems) o Influence on titration curves Ions in Solutions • Anion, cation: common names, formulas and charges for familiar ions (e.g., NH4+ ammonium, PO43– phosphate, SO42– sulfate) • Hydration, the hydronium ion Solubility • Units of concentration (e.g., molarity) • Solubility product constant; the equilibrium expression Ksp • Common-­‐ion effect, its use in laboratory separations o Complex ion formation o Complex ions and solubility o Solubility and pH Titration • Indicators • Neutralization • Interpretation of the titration curves • Redox titration Content Category 5B: Nature of molecules and intermolecular interactions Covalent Bond • Lewis Electron Dot formulas o Resonance structures o Formal charge o Lewis acids and bases • Partial ionic character o Role of electronegativity in determining charge distribution o Dipole Moment • σ and π bonds o Hybrid orbitals: sp3, sp2, sp and respective geometries o Valence shell electron pair repulsion and the prediction of shapes of molecules (e.g., NH3, H2O, CO2) o Structural formulas for molecules involving H, C, N,

CHM 123

CHM 124, BIO 442L

CHM 123, 124, 451

CHM 123, 313

161

O, F, S, P, Si, Cl Delocalized electrons and resonance in ions and molecules • Multiple bonding o Affect on bond length and bond energies o Rigidity in molecular structure • Stereochemistry of covalently bonded molecules o Isomers ! Structural isomers ! Stereoisomers (e.g., diastereomers, enantiomers, cis/trans isomers) ! Conformational isomers o Polarization of light, specific rotation o Absolute and relative configuration ! Conventions for writing R and S forms ! Conventions for writing E and Z forms Liquid Phase -­‐ Intermolecular Forces ! Hydrogen bonding ! Dipole Interactions ! Van der Waals’ Forces (London dispersion forces) Content Category 5C: Separation and purification methods Separations and Purifications • Extraction: distribution of solute between two immiscible solvents • Distillation • Chromatography o Basic principles involved in separation process ! Column chromatography, gas-­‐liquid chromatography ! High pressure liquid chromatography o Paper chromatography o Thin-­‐layer chromatography • Separation and purification of peptides and proteins o Electrophoresis (BIO 442L) o Quantitative analysis o Chromatography ! Size-­‐exclusion ! Ion-­‐exchange ! Affinity • Racemic mixtures, separation of enantiomers Content Category 5D: Structure, function, and reactivity of biologically-­‐relevant molecules Nucleotides and Nucleic Acids • Nucleotides and nucleosides: composition o Sugar phosphate backbone o Pyrimidine, purine residues • Deoxyribonucleic acid: DNA, double helix • Chemistry • Other functions o

CHM 124

CHM 313, 451, 462L

BIO 151, 151L, 312, 312L & CHM 314, 451, 452

162

Amino Acids, Peptides, Proteins • Amino acids: description o Absolute configuration at the α position o Dipolar ions o Classification ! Acidic or basic ! Hydrophilic or hydrophobic o Synthesis of α-­‐amino acids ! Strecker Synthesis ! Gabriel Synthesis • Peptides and proteins: reactions o Sulfur linkage for cysteine and cystine o Peptide linkage: polypeptides and proteins o Hydrolysis • General Principles o 1° structure of proteins o 2° structure of proteins o 3° structure of proteins o o Isoelectric point The Three-­‐Dimensional Protein Structure • Conformational stability o Hydrophobic interactions o Solvation layer (entropy) • 4° quaternary structure • Denaturing and Folding Non-­‐Enzymatic Protein Function • Binding • Immune system • Motor (BIO 442) Lipids • Types o Storage ! Triacyl glycerols ! Free fatty acids: saponification o Structural ! Phospholipids and phosphatids ! Sphingolipids ! Waxes o Signals/cofactors ! Fat-­‐soluble vitamins ! Steroids ! Prostaglandins Carbohydrates • Description o Nomenclature and classification, common names o Absolute configuration o Cyclic structure and conformations of hexoses o Epimers and anomers • Hydrolysis of the glycoside linkage

CHM 314, 451

CHM 451

CHM 451 CHM 420, 451, 452

CHM 314, 451

163

• Keto-­‐enol tautomerism of monosaccharides • Disaccharides • Polysaccharides Aldehydes and Ketones • Description o Nomenclature o Physical properties • Important reactions o Nucleophilic addition reactions at C=O bond ! Acetal, hemiacetal ! Imine, enamine ! Hydride reagents ! Cyanohydrin o Oxidation of aldehydes o Reactions at adjacent positions: enolate chemistry ! Keto-­‐enol tautomerism (α-­‐racemization) ! Aldol condensation, retro-­‐aldol ! Kinetic versus thermodynamic enolate • General principles o Effect of substituents on reactivity of C=O; steric hindrance o o Acidity of α-­‐H; carbanions Alcohols • Description o Nomenclature o Physical properties (acidity, hydrogen bonding) • Important reactions o Oxidation o Protection of alcohol o Preparation of mesylates and tosylates Carboxylic Acids • Description o Nomenclature o Physical properties • Important reactions o Carboxyl group reactions ! Amides (and lactam), esters (and lactone), anhydride formation ! Reduction ! Decarboxylation ! Reactions at 2-­‐position, substitution Acid Derivatives (Anhydrides, Amides, Esters) • Description o Nomenclature o Physical properties • Important reactions o Nucleophilic substitution o Transesterification o Hydrolysis of amides

CHM 314

CHM 313

CHM 314

CHM 314

164

General principles o Relative reactivity of acid derivatives o Steric effects o Electronic effects o Strain (e.g., β-­‐lactams) Phenols • Oxidation and reduction (e.g., hydroquinones), ubiquinones: biological 2e-­‐ redox centers Polycyclic and Heterocyclic Aromatic Compounds • Biological aromatic heterocycles Content Category 5E: Principles of chemical thermodynamics and kinetics Enzymes • Classification by reaction type • Mechanism o Substrates and enzyme specificity o Active site model o Induced-­‐fit model o Cofactors, coenzymes and vitamins • Kinetics o General (catalysis) o Michaelis-­‐Menten o Cooperativity o Effects of local conditions on enzyme activity • Inhibition • Regulatory enzymes (BIO 411) o Allosteric o Covalently modified Principles of Bioenergetics • Bioenergetics/thermodynamics o Free energy/Keq o Concentration • § Phosphorylation/ATP o ATP hydrolysis ΔG << 0 o ATP group transfers • Biological oxidation–reduction o Half-­‐reactions o Soluble electron carriers o Flavoproteins Phosphorus Compounds • Description, structure of phosphoric acids Energy Changes in Chemical Reactions -­‐ Thermochemistry, Thermodynamics ! Thermodynamic system – state function ! Zeroth Law – concept of temperature ! First Law: ΔE = Q – W (conservation of energy) ! Second Law – concept of entropy o Entropy as a measure of “disorder” •

CHM 314, 452 CHM 314

BIO 151, 151L, 312, 312L, 403, 403L & CHM 451, 452, 462L

CHM 451

CHM 314

CHM 123, 124

165

o Relative entropy for gas, liquid, and crystal states Measurement of heat changes (calorimetry), heat capacity, specific heat ! Heat transfer – conduction, convection, radiation ! Endothermic/exothermic reactions o Enthalpy, H, and standard heats of reaction and formation o Hess’ Law of Heat Summation ! Bond dissociation energy as related to heats of formation ! Free energy: G ! Spontaneous reactions and ΔG° ! Coefficient of expansion ! Heat of fusion, heat of vaporization ! Phase diagram: pressure and temperature Rate Processes in Chemical Reactions -­‐ Kinetics and Equilibrium • Reaction rate • Dependence of reaction rate upon concentration of reactants o Rate law, rate constant o Reaction order • Rate-­‐determining step • Dependence of reaction rate upon temperature o Activation energy ! Activated complex or transition state ! Interpretation of energy profiles showing energies of reactants, products, activation energy, and ΔH for the reaction o Use of the Arrhenius Equation • Kinetic control versus thermodynamic control of a reaction • Catalysts • Equilibrium in reversible chemical reactions o Law of Mass Action o Equilibrium Constant o Application of Le Châtelier’s Principle • Relationship of the equilibrium constant and ΔG° !

CHM 124

Psychological, Social, and Biological Foundations of Behavior Content Category 6A: Sensing the environment Sensory Processing • Sensation o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation • Sensory receptors o Sensory pathways o Types of sensory receptors

PSY101, 323 & BIO 415, 475

166

Vision • Structure and function of the eye • Visual processing o Visual pathways in the brain o Parallel processing o Feature detection Hearing • Auditory processing o Auditory pathways in the brain • Sensory reception by hair cells Other Senses • Somatosensation o Pain perception • Taste o Taste buds/chemoreceptors that detect specific chemicals • Smell o Olfactory cells/chemoreceptors that detect specific chemicals o Pheromones o Olfactory pathways in the brain • Kinesthetic sense • Vestibular sense Perception • Perception o Bottom-­‐up/Top-­‐down processing o Perceptual organization (e.g., depth, form, motion, constancy) o Gestalt principles Content Category 6B: Making sense of the environment Attention • Selective attention • Divided attention Cognition • Information-­‐processing model • Cognitive development o Piaget’s stages of cognitive development o Cognitive changes in late adulthood o Role of culture in cognitive development o Influence of heredity and environment on cognitive development • Biological factors that affect cognition • Problem solving and decision making o Types of problem solving o Barriers to effective problem solving o Approaches to problem solving o Heuristics, biases, intuition, and emotion

PSY 101, 323, 422 & BIO 415, 442, 442L, 475, 475L

PSY 101, 323, 422 & BIO 415, 475, 475L PSY 101, 323, 422 & BIO 415, 442, 475, 475L

PSY 101, 321, 323

PSY 101, 321, 322, 323 PSY 101, 321, 351 & BIO 415

167

! Overconfidence and belief perseverance • Intellectual functioning o Multiple definitions of intelligence o Influence of heredity and environment on intelligence o Variations in intellectual ability Consciousness PSY 101, 321, 422 & BIO 415 • States of consciousness o Alertness o Sleep ! Stages of sleep ! Sleep cycles and changes to sleep cycles ! Sleep and circadian rhythms ! Dreaming ! Sleep disorders o Hypnosis and meditation • Consciousness altering drugs o Types of consciousness altering drugs and their effects on the nervous system and behavior o Drug addiction and the reward pathway in the brain Memory PSY 101, 321 & BIO 415 • Encoding o Process of encoding information o Processes that aid in encoding memories • Storage o Types of memory storage (e.g., sensory, working, long-­‐term) o Semantic networks and spreading activation • Retrieval o Recall, recognition, and relearning o Retrieval cues o The role of emotion in retrieving memories • Forgetting o Aging and memory o Memory dysfunctions (e.g., Alzheimer’s disease, Korsakoff’s syndrome) o Decay o Interference o Memory construction and source monitoring • Changes in synaptic connections underlie memory and learning (BIO 403) o Neural plasticity o Memory and learning o Long-­‐term potentiation Language PSY 101, 321, 351 & BIO 415 • Theories of language development (e.g., learning, Nativist, Interactionist) • Influence of language on cognition

168

• Different brain areas control language and speech Content Category 6C: Responding to the world Emotion • Three components of emotion (i.e., cognitive, physiological, behavioral) • Universal emotions (e.g., fear, anger, happiness, surprise, joy, disgust, sadness) • Adaptive role of emotion • Theories of emotion o James-­‐Lange theory o Cannon-­‐Bard theory o Schachter-­‐Singer theory • The role of biological processes in perceiving emotion o Generation and experience of emotions involve many brain regions o The role of the limbic system in emotion (BIO 403) o Emotional experiences can be stored as memories that can be recalled by similar o circumstances o Prefrontal cortex is critical for emotional experience, and is also important in o temperament and decision making o Emotion and the autonomic nervous system (BIO 403) o Physiological markers of emotion (signatures of emotion) Stress • The nature of stress o Appraisal o Different types of stressors (e.g., cataclysmic events, personal, etc.) o Effects of stress on psychological functions • Stress outcomes/response to stressors o Physiological o Emotional o Behavioral • Managing stress (e.g., exercise, relaxation techniques, spirituality, etc.)

Content Category 7A: Individual influences on behavior Biological Bases of Behavior • The nervous system (BIO , 442, 442L, 475, 475L) o Neurons ! The reflex arc o Neurotransmitters o Peripheral nervous system o Central nervous system ! The brain o The brainstem o The cerebellum

PSY 101, 366 & BIO 415

PSY 101, 351, 366, 422 & BIO 415

PSY 101, 321, 322, 323, 351, 366, 422

BIO 312, 415

169

o o o

The diencephalon The cerebrum Control of voluntary movement in the cerebral cortex o Information processing in the cerebral cortex o Lateralization of cortical functions o Methods of studying the brain • Neurons communicate and influence behavior • Influence of neurotransmitters on behavior • The endocrine system (BIO 475, 475L) o Components of the endocrine system o Effects of the endocrine system on behavior • Behavioral genetics o Genes, temperament, and heredity o Adaptive value of traits and behaviors o Interaction between heredity and environmental influences • Genetic and environmental factors contribute to the development of behaviors o Experience and behavior o Regulatory genes and behavior o Genetically based behavioral variation in natural populations • Human physiological development o Prenatal development o Motor development o Developmental changes in adolescence Personality • Theories of personality o Psychoanalytic perspective o Humanistic perspective o Trait perspective o Social cognitive perspective o Biological perspective o Behaviorist perspective • Situational approach to explaining behavior Psychological Disorders • Understanding psychological disorders o Biomedical vs. biopsychosocial approaches o Classifying psychological disorders o Rates of psychological disorders • Types of psychological disorders o Anxiety disorders o Somatoform disorders o Mood disorders o Schizophrenia o Dissociative disorder o Personality disorders

PSY 101, 366

PSY 101, 366, 422

170

Biological bases of nervous system disorders (BIO 442) o Schizophrenia o Depression o Alzheimer’s disease o Parkinson’s disease o Stem cell-­‐based therapy to regenerate neurons in CNS Motivation PSY 101, 366 • Factors that influence motivation o Instinct o Arousal o Drives ! Negative feedback systems o Needs • Theories that explain how motivation affects human behavior o Drive reduction theory o Incentive theory o Other: cognitive and need based theories • Application of theories of motivation to understand behaviors (e.g., eating, sexual, drug and alcohol use, etc.) o Biological factors in regulation of these motivational processes o Socio-­‐cultural factors in regulation of these motivational processes Attitudes PSY 101, 341, 366 • Components of attitudes (i.e., cognitive, affective, and behavioral) • The link between attitudes and behavior o Processes by which behavior influences attitudes (e.g., foot-­‐in-­‐the door phenomenon, o role-­‐playing effects) o Processes by which attitudes influence behavior o Cognitive dissonance theory

•

Content Category 7B: Social processes that influence human behavior How the Presence of Others Affects Individual Behavior • Social facilitation • Deindividuation • Bystander effect • Social loafing • Peer pressure Group Processes • Group polarization • Groupthink Culture

PSY 101, 341, 366 & SOC 340

PSY 101, 341 & SOC 340 PSY 341 & SOC 101

171

• Assimilation • Multiculturalism • Subcultures Socialization • Definition of socialization • Norms • Agents of socialization (e.g., the family, mass media, peers, workplace) • Stigma and deviance • Conformity and obedience Content Category 7C: Attitude and behavior change Habituation and Dishabituation

Associative Learning • Classical conditioning o Neutral, conditioned, and unconditioned stimuli o Conditioned and unconditioned response o Processes: acquisition, extinction, spontaneous recovery, generalization, discrimination • Operant conditioning o Processes of shaping and extinction o Types of reinforcement: positive, negative, primary, conditional o Reinforcement schedules: fixed-­‐ratio, variable-­‐ratio, fixed-­‐interval, variable-­‐interval o Punishment o Escape and avoidance learning • Cognitive processes that affect associative learning • Biological factors that affect associative learning o Innate behaviors are developmentally fixed o Learned behaviors are modified based on experiences o Development of learned behaviors Observational Learning • Modeling • Biological processes that affect observational learning o Mirror neurons o Role of the brain in experiencing vicarious emotions • Applications of observational learning to explain individual behavior Theories

of Attitude and Behavior Change • Elaboration Likelihood Model o Information processing routes to persuasion (e.g., central and peripheral route processing) • Social Cognitive theory • Factors that affect attitude change (e.g., changing behavior, characteristics of the message and target, social factors) Content Category 8A: Self-­‐identity

PSY 101, 341 SOC 101 SOC 101 SOC 101

SOC 101, 325 SOC 325, 340

PSY 101, 322, 351 PSY 101, 322, 351

BIO 415

PSY 101, 322, 351

PSY 101, 341

172

Self-­‐Concept and Identity • Definitions of self-­‐concept, identity, and social identity • The role of self-­‐esteem, self-­‐efficacy, and locus of control in self-­‐concept and self-­‐identity • Different types of identities (e.g., race/ethnicity, gender, age, sexual orientation, class) Formation of Identity • Stages of identity development o Theories of developmental stages (e.g., Erikson, Vygotsky, Kohlberg, Freud) • Influence of social factors on identity formation o Influence of individuals (e.g., imitation, role-­‐taking) o Influence of group (e.g., reference group) • Influence of culture and socialization on identity formation Content Category 8B: Social thinking Attributing Behavior to Persons or Situations • Attribution theory o Fundamental attribution error o How culture affects attributions • How self-­‐perceptions shape our perceptions of others • How perceptions of the environment shape our perceptions of others Prejudice and Bias • Definition of prejudice • Processes that contribute to prejudice o Power, prestige, and class o The role of emotion in prejudice o The role of cognition in prejudice • Stereotypes • Ethnocentrism o In-­‐group and out-­‐group o Ethnocentrism vs. cultural relativism Processes Related to Stereotypes • Self-­‐fulfilling prophecy • Stereotype threat Content Category 8C: Social interactions Elements of Social Interaction • Statuses • Roles • Groups • Networks • Organizations Self-­‐presentation and Interacting with Others • Expressing and detecting emotion o Gender shapes expression (SOC 322,332) o Culture shapes expression (ANT 150) • Impression management o Front stage vs. back stage self (Dramaturgical

PSY 101, 341, 351, 361 & SOC 340, 341

PSY 101, 341, 351, 361 SOC 340 SOC 340

SOC 340 & 341 SOC 340 & 341 SOC 101 & 340

PSY 101, 341, 366

PSY 101, 341 & SOC 101, 328PS PSY 101, 341 SOC 101

SOC 328, 339

SOC 101 & ANT 150 SOC 101 & ANT 150 PSY 101, 341

PSY 101, 341 & SOC 101, 340

PSY 101, 341 & SOC 340, 341

SOC 322, 332 ANT 150

SOC 341

173

approach) • Verbal and nonverbal communication (ANT 315) • Animal signals and communication Social Behavior • Attraction • Aggression • Attachment • Social support • Biological explanations of social behavior in animals o Foraging behavior o Mating behavior and mate choice o Applying game theory o Altruism o Inclusive fitness Discrimination • Individual vs. institutional discrimination • The relationship between prejudice and discrimination • How power, prestige, and class facilitate discrimination Content Category 9A: Understanding social structure Theoretical Approaches • Functionalism • Conflict theory • Symbolic interactionism • Social constructionism Social Institutions • Education • Family • Religion • Government and economy • Health and medicine Culture • Material culture • Symbolic culture

o Language and symbols o Values and beliefs o Norms and rituals • Culture and social groups • Evolution and human culture Content Category 9B: Demographic characteristics and processes Demographic Structure of Society • Age • Gender • Race and ethnicity • Immigration status • Sexual orientation Demographic Shifts and Social Change

ANT 315 PSY 101, 341

PSY 101 & SOC 101, 339

SOC 101, 303

SOC 101 SOC 101, 331 SOC 101, 334 SOC 101, 337 SOC 101

SOC 101 & ANT 150 SOC 101 & ANT 150 & PSY 368, 443 SOC 340 & ANT 315 SOC 101 & ANT 150 SOC 101 & ANT 150 SOC 101 & ANT 150 ANT 300 & PSY 443

SOC 101, 330 SOC 101, 332 SOC 101, 328 SOC 368 SOC 333, 322

174

• Demographic transition • Fertility, migration, and mortality • Social movements • Globalization • Urbanization Content Category 10A: Social inequality Spatial Inequality • Residential segregation (neighborhoods) • Environmental justice (location and exposure to health risks) • Global inequalities Social Class • Aspects of social stratification o Class, status, and power o Cultural capital and social capital o Social reproduction o Privilege and prestige o Intersections with race, gender and age • Patterns of social mobility o Intergenerational and intragenerational mobility o Downward and upward mobility o Meritocracy • Poverty o Relative and absolute o Social exclusion (segregation and isolation) Health Disparities • Race, gender, and class inequalities in health Healthcare Disparities • Race, gender, and class inequalities in healthcare

SOC 101 SOC 101 SOC 342 SOC 101, 435 SOC 351

SOC 351 SWK 335 SOC 101, 435 SOC 101, 339

PSY 366 PSY 366

175