UNIVERSITY OF DAYTON ROADMAP TO THE MCAT: TRACKING MCAT CONTENT IN YOUR NATURAL AND BEHAVIORAL SCIENCE COURSES
UNIVERSITY OF DAYTON OFFICE OF PREMEDICAL PROGRAMS
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 healthcare 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 American Association of Medical Colleges (AAMC) released two documents to help institutions plan for these changes and develop course content, which reflect 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 sub-topics 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 Anthropology, Sociology and Social Work. These faculty were provided the MCAT course-mapping tool and were asked to identify within their courses where specific MCAT content 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 2
disciplines in the social sciences and humanities. The CARS section is NOT included in this course mapping since it tests comprehension and not knowledge typically covered in a specific course. The first document titled “Course List 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 135). 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 sub-topics 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 96 99 128
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BIOLOGY BIO 151 & BIO 151L. Amino Acids ● Description Concepts of Biology I: Cell and Molecular ○ Absolute configuration at the position Biology and ○ Amino acids as dipolar ions Concepts of Biology ○ Classifications Laboratory: Cell and ■ Acidic or basic Molecular Biology ■ 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 5
○ 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) 6
● 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 7
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 10
● 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, 13
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 14
● Regulatory enzymes ○ Allosteric ○ Covalently modified
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BIO152 & BIO 152L. Mendelian Concepts ● Phenotype and genotype Concepts of Biology II: Evolution and ● Gene Ecology & Concepts ● Locus of Biology ● Allele: single and multiple Laboratory II: ● Homozygosity and heterozygosity Evolution and ● Wild-type Ecology ● 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. Evolution
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 General Genetics & Genetics Laboratory ○ 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 22
● 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 23
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 24
● 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 Physiology I & Physiology ● Tissue specific metabolism Laboratory I ● 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 selfdestruction ○ 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
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○ 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 General Microbiology & ● Immune system General ● Motors Microbiology Enzyme Structure and Function Laboratory ● 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
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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. Neurobiology
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)
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● 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 42
○ 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
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BIO 427. Immunology
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
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BIO 440. Cell Biology
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
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BIO 442 & 442L. Developmental Biology & Developmental Biology Laboratory
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 selfdestruction ○ 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
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○ 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
Vision
Motors 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. Molecular Biology
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. Cancer Biology
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. Human Anatomy & Human Anatomy Laboratory
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 selfdestruction ○ 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. General Chemistry & General Chemistry Laboratory
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 68
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 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 69
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 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,
70
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
71
CHM 124 & 124L. General Chemistry & General Chemistry Laboratory
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 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
72
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 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°
73
CHM 313 & 313L. Organic Chemistry & Organic Chemistry Laboratory
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., 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 74
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 o Racemic mixtures, separation of enantiomers
Alcohols
Description o Nomenclature o Physical properties (acidity, hydrogen bonding) Important reactions o Oxidation o Protection of alcohol o Preparation of mesylates and tosylates
75
CHM 314 & 314L. Organic Chemistry & Organic Chemistry Laboratory
Amino Acids
Description o Absolute configuration at the 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
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 76
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
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 77
Acid Derivatives (Anhydrides, Amides, Esters)
Description o Nomenclature o Physical properties Important reactions o Nucleophilic substitution o Transesterification o Hydrolysis of amides General principles 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
78
CHM 420. Biochemistry
Amino Acids
Description o Absolute configuration at the 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)
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 79
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
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
80
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 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, 81
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 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
82
CHM 451. General Biochemistry I
Amino Acids
Description o Absolute configuration at the 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 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 83
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 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 84
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) 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 85
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
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
86
Bronsted-Lowry definition of acid, base Ionization of water 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
Titration
Indicators Neutralization Interpretation of the titration curves Redox titration
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
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 87
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
Lipids
Binding Immune system Motor 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 88
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 P o ATP hydrolysis ΔG << 0 o ATP group transfers Biological oxidation–reduction o Half-reactions o Soluble electron carriers o Flavoproteins
89
CHM 452. General Biochemistry II
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 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 90
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
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 91
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
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 92
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. Biochemistry Laboratory
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 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 94
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 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
95
PHYSICS PHY 201. General Physics
Translational Motion
Units and dimensions Vectors, components Vector addition Speed, velocity (average and instantaneous) Acceleration
Equilibrium
Work
Concept of force, units Analysis of forces acting on an object Newton’s First Law of Motion, inertia Torques, lever arms 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
96
PHY 202. General Physics
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
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) 97
Visual spectrum, color
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
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
98
PSYCHOLOGY PSY 101. Introductory Psychology
Sensory Processing
Vision
Sensation o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation Sensory receptors o Sensory pathways o Types of sensory receptors 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 99
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, longterm) 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 100
o o
Language
Memory and learning Long-term potentiation
Theories of language development (e.g., learning, Nativist, Interactionist) Influence of language on cognition o Different brain areas control language and speech
Emotion
Stress
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) 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 101
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 102
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 103
Agents of socialization (e.g., the family, mass media, peers, 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 selfconcept 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) 104
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 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 105
o o
Altruism Inclusive fitness
Discrimination
Individual vs. institutional discrimination The relationship between prejudice and discrimination How power, prestige, and class facilitate discrimination
106
PSY 321. Cognitive Processes
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 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 107
Types of memory storage (e.g., sensory, working, longterm) 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 o Memory and learning o Long-term potentiation o
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 108
Adaptive value of traits and behaviors 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 o o
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109
PSY 322. Learning
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 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 110
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
111
PSY 323. Psychology of Perception
Sensory Processing
Vision
Sensation o Thresholds o Weber’s Law o Signal detection theory o Sensory adaptation Sensory receptors o Sensory pathways o Types of sensory receptors 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 112
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
113
PSY 341. Social Psychology
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
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 selfconcept 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) 114
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 115
PSY 351. Child Psychology
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
Language
Stress
Theories of language development (e.g., learning, Nativist, Interactionist) Influence of language on cognition o Different brain areas control language and speech 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 116
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 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 117
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 selfconcept 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
118
PSY 361. Personality
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 selfconcept 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
119
PSY 366. Health Psychology
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 The brain The brainstem The cerebellum The diencephalon The cerebrum Control of voluntary movement in the cerebral cortex 120
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
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 121
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
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
122
PSY 368. Community Psychology
Culture ď&#x201A;ˇ
Symbolic culture o Language and symbols o Values and beliefs o Norms and rituals
123
PSY 422. Physiological Psychology
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
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 124
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 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 125
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. Psychology of Women
Culture ď&#x201A;ˇ
ď&#x201A;ˇ
Symbolic culture o Language and symbols o Values and beliefs o Norms and rituals Evolution and human culture
127
SOCIOLOGY and ANTHROPOLOGY SOC 101. Principles of Sociology
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
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)
129
SOC 303. Modern Social Theory
Theoretical Approaches o Functionalism o Conflict theory o Symbolic interactionism o Social constructionism
SOC 322. Sex Roles and Society
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
SOC 325. Deviant Behavior
SOC 328. Racial and Ethnic Relations
SOC 330. Perspectives on Aging SOC 331. Marriage & the Family SOC 332. Sociology of Women
SOC 333. Sociology of Sexualities SOC 334. Religion and Society
SOC 337. Political Sociology
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
130
SOC 339. Social Inequality
Prejudice and Bias o Processes that contribute to prejudice 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)
131
SOC 340. Social Psychology in Society
How the Presence of Others Affects Individual Behavior o Social facilitation 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
132
SOC 341. Self & Society
SOC 342. Collective Behavior
SOC 351. Urban Sociology
SOC 368. Immigration & Immigrants SOC 435. Economy & Society
SWK 335. Social Work & Environmental Justice
Self-Concept and Identity o Definitions of self-concept, identity, and social identity o 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)
133
ANT 150. Cultural Anthropology
ANT 300. Evolution of People & Culture ANT 315. Language & Culture
Culture o Assimilation o Multiculturalism o Subcultures 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. 136 Chemical and Physical Foundations of Biological Systems – p. 156 Psychological, Social, and Biological Foundations of Behavior – p. 167 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
Non-Enzymatic Protein Function ● Binding ● Immune system ● Motors
BIO 151, 151L, 312, 312L, 411, 411L, 427,442 & CHM 420, 451, 452
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
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
Content Category 1B: Transmission of genetic information from the gene to the protein 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
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
462, 470 & CHM 452
Repair of DNA ● Repair during replication ● Repair of mutations
BIO 151, 151L, 312, 312L, 411, 411L, 440, 462 & CHM 452
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, 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
Translation ● Roles of mRNA, tRNA, rRNA ● Role and structure of ribosomes ● Initiation, termination co-factors ● Post-translational modification of proteins
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
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
Control of Gene Expression in Eukaryotes ● Transcriptional regulation(BIO 411) ● 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
BIO 151, 151L, 312, 312L, 411, 442, 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
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
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
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
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
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
Content Category 1D: Principles of bioenergetics and fuel molecule metabolism 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
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway ● Glycolysis (aerobic), substrates and products ○ Feeder pathways: glycogen, starch metabolism (Not CHM 420) ● Fermentation (anaerobic glycolysis) ● Gluconeogenesis ● Pentose phosphate pathway (Not BIO 151) ● Net molecular and energetic results of respiration processes
BIO 151, 151L, 411, 411L & CHM 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
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
Metabolism of Fatty Acids and Proteins ● Description of fatty acids ● Digestion, mobilization, and transport of fats (Not BIO 151) (Not 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)
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
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
BIO 151, 151L, 403, 403L, 411, 411L, 440, 442 & CHM 420, 451
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, 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
Tissues Formed From Eukaryotic Cells ● Epithelial cells ● Connective tissue cells
BIO 151, 151L, 440, 442
Content Category 2B: The structure, growth, physiology, and genetics of prokaryotes and viruses 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
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
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
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
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
Embryogenesis ● Stages of early development (order and general features of each) ○ Fertilization ○ Cleavage ○ Blastula formation ○ Gastrulation
BIO 152, 152L, 442
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
Biosignalling ● Gated ion channels ○ Voltage gated ○ Ligand gated ● Receptor enzymes ● G protein-coupled receptors
BIO 151, 151L, 312, 312L, 440, 442 & CHM 420, 451
Lipids ● Description; structure ○ Steroids ○ Terpenes and terpenoids (Not BIO 151) (Not BIO 411)
BIO 151, 151L, 411, 411L & CHM 451, 452
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 152, 152L, 403, 403L, 442, 442L, 475, 475L
Endocrine System: Mechanisms of Hormone Action ● Cellular mechanisms of hormone action ● Transport of hormones: blood supply
BIO 152, 152L, 403, 403L, 442
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
BIO 152, 152L, 403, 403L, 442, 442L, 475, 475L
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
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 ● 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
BIO 152, 152L 403, 403L, 475, 475L
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
BIO 427, 442, 442L
Digestive System
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 selfdestruction ○ 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
442, 442L, 475, 475L
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
BIO 403, 403L, 442, 442L, 475, 475L
Muscle System ● Important functions ○ Support: mobility ○ Peripheral circulatory assistance
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
BIO 403, 403L, 440
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 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
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 156
Arterial and venous systems; pressure and flow characteristics
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
Content Category 4C: Electrochemistry and electrical circuits and their elements Electrostatics
PHY 202
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
CHM 123
PHY 202
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 157
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
Specialized Cell - Nerve Cell
PHY 202
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
BIO 415, 442
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
CHM 124, 451
PHY 202 & CHM 123
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 158
= (hf) Visual spectrum, color
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., 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
PHY 202 & BIO 442, 442L, 475, 475L
CHM 123
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
CHM 313
PHY 202 & CHM 123
Orbital structure of hydrogen atom, principal quantum 159
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
The Periodic Table - Classification of Elements into Groups by Electronic Structure
CHM 123
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
CHM 123
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
PHY202 does not cover items in nuclear physics.
CHM 123, BIO 442L
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 160
o
Theoretical yields
Content Category 5A: Unique nature of water and its solutions Acid/Base Equilibria
Ions in Solutions
CHM 123, 124, 451
Indicators Neutralization Interpretation of the titration curves Redox titration
Content Category 5B: Nature of molecules and intermolecular interactions Covalent Bond
CHM 124, BIO 442L
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
CHM 123
Anion, cation: common names, formulas and charges for familiar ions (e.g., NH4+ ammonium, PO43– phosphate, SO42– sulfate) Hydration, the hydronium ion
Solubility
CHM 124, 451
Bronsted-Lowry definition of acid, base Ionization of water 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
CHM 123, 313
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 161
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 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
CHM 124
CHM 313, 451, 462L
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 162
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
Amino Acids, Peptides, Proteins
CHM 451
Binding Immune system Motor (BIO 442)
Lipids
CHM 451
Conformational stability o Hydrophobic interactions o Solvation layer (entropy) 4° quaternary structure Denaturing and Folding
Non-Enzymatic Protein Function
CHM 314, 451
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
BIO 151, 151L, 312, 312L & CHM 314, 451, 452
CHM 420, 451, 452 Types o Storage Triacyl glycerols Free fatty acids: saponification o Structural Phospholipids and phosphatids Sphingolipids Waxes o Signals/cofactors 163
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
Aldehydes and Ketones
CHM 313
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
CHM 314
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
CHM 314, 451
CHM 314
Description o Nomenclature o Physical properties Important reactions o Carboxyl group reactions Amides (and lactam), esters (and lactone), anhydride formation Reduction 164
Decarboxylation Reactions at 2-position, substitution
Acid Derivatives (Anhydrides, Amides, Esters)
Phenols
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
CHM 314
Biological aromatic heterocycles
Content Category 5E: Principles of chemical thermodynamics and kinetics Enzymes
CHM 314, 452
Oxidation and reduction (e.g., hydroquinones), ubiquinones: biological 2e- redox centers
Polycyclic and Heterocyclic Aromatic Compounds
CHM 314
Description o Nomenclature o Physical properties Important reactions o Nucleophilic substitution o Transesterification o Hydrolysis of amides General principles o Relative reactivity of acid derivatives o Steric effects o Electronic effects o Strain (e.g., β-lactams)
BIO 151, 151L, 312, 312L, 403, 403L & CHM 451, 452, 462L
CHM 451
Bioenergetics/thermodynamics o Free energy/Keq o Concentration o ATP hydrolysis ΔG << 0 o ATP group transfers Biological oxidation–reduction o Half-reactions o Soluble electron carriers 165
o
Flavoproteins
Phosphorus Compounds
Description, structure of phosphoric acids
Energy Changes in Chemical Reactions - Thermochemistry, Thermodynamics
CHM 123, 124
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
CHM 314
CHM 124
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°
166
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
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
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
Selective attention Divided attention
Cognition
PSY 101, 323, 422 & BIO 415, 442, 442L, 475, 475L
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
PSY101, 323 & BIO 415, 475
Information-processing model
PSY 101, 321, 351 & BIO 415 167
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
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
PSY 101, 321, 422 & BIO 415
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) 168
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
Theories of language development (e.g., learning, Nativist, Interactionist) Influence of language on cognition Different brain areas control language and speech
Content Category 6C: Responding to the world Emotion
PSY 101, 366 & BIO 415
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
PSY 101, 321, 351 & BIO 415
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,
PSY 101, 351, 366, 422 & BIO 415
169
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 o The diencephalon o The cerebrum o 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
PSY 101, 321, 322, 323, 351, 366, 422 BIO 312, 415
PSY 101, 366
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 170
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 (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, 366, 422
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
171
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
PSY 341 & SOC 101
Assimilation Multiculturalism Subcultures
Socialization
PSY 101, 341 & SOC 340
Group polarization Groupthink
Culture
PSY 101, 341, 366 & SOC 340
Definition of socialization Norms Agents of socialization (e.g., the family, mass media, peers, workplace) Stigma and deviance Conformity and obedience
PSY 101, 341 SOC 101 SOC 101 SOC 101 SOC 101, 325 SOC 325, 340
Content Category 7C: Attitude and behavior change Habituation and Dishabituation
PSY 101, 322, 351
Associative Learning
PSY 101, 322, 351
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
BIO 415
PSY 101, 322, 351
Modeling 172
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
PSY 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 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
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
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
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
PSY 101, 341
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
Self-fulfilling prophecy 173
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 approach) Verbal and nonverbal communication (ANT 315) Animal signals and communication
Social Behavior
SOC 322, 332 ANT 150 SOC 341 ANT 315 PSY 101, 341
PSY 101 & SOC 101, 339
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
PSY 101, 341 & SOC 340, 341
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
PSY 101, 341 & SOC 101, 340
SOC 101, 303
Functionalism Conflict theory Symbolic interactionism Social constructionism
Social Institutions
Education Family Religion Government and economy Health and medicine
Culture
Material culture Symbolic culture
SOC 101 SOC 101, 331 SOC 101, 334 SOC 101, 337 SOC 101 SOC 101 & ANT 150 SOC 101 & ANT 150 & PSY 174
o Language and symbols o Values and beliefs o Norms and rituals Culture and social groups Evolution and human culture
368, 443 SOC 340 & ANT 315 SOC 101 & ANT 150 SOC 101 & ANT 150 SOC 101 & ANT 150 ANT 300 & PSY 443
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
Demographic transition Fertility, migration, and mortality Social movements Globalization Urbanization
SOC 101, 330 SOC 101, 332 SOC 101, 328 SOC 368 SOC 333, 322 SOC 101 SOC 101 SOC 342 SOC 101, 435 SOC 351
Content Category 10A: Social inequality Spatial Inequality
Residential segregation (neighborhoods) Environmental justice (location and exposure to health risks) Global inequalities
Social Class
PSY 366
Race, gender, and class inequalities in health
Healthcare Disparities
SOC 101, 339
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
SOC 351 SWK 335 SOC 101, 435
PSY 366
Race, gender, and class inequalities in healthcare
175