Biology_Issuu2

T

O

P

I

C

4

.

1

Chromosomes, Genes, Alleles, and Mutations Eukaryote chromosomes are made of DNA and proteins.

Vocabulary

Issue N° 17 — Fall 2009

Gene

Allele

Genome

Gene mutation

Chromosome

Gene locus

a heritable factor that controls a specific characteristic

one specific form of a gene, differing from other alleles by one or a few bases only and occupying the same gene locus as other alleles of the gene

the whole of the genetic information of an organism

a permanent change in the base sequence of DNA in a base

structural units that are made up of DNA and proteins

The specific position of a gene on a chromosome

Base-Substitution Mutations Examined

Sickle Cell Anemia

anemia. GAG changes to

A base-substitution

valine. This ultimately leads to sickle-cell

GTG causing glutamic acid to be replaced by

mutation is a permanent change in a base

anemia, which can cause major problems for the

sequence when one base is substituted for another.

This new base sequence could code for the production a different amino acid, which could IB Biology HL

circulatory system. Tissues can die because of blood lead to problems. An example of this type of mutation is sickle-cell

clots that will not allow enough blood to flow to them.

Topic 4.1

T

O

P

I

C

4

.

2

MEIOSIS IB BIOLOGY HL

Meiosis is a reduction division of a diploid nucleus to form haploid nuclei.

NONDISJUNCTION Karyotyping In karyotyping, chromosomes are arranged in pairs according to their size and structure.

Karyotyping is performed using cells collected by chorionic villus sampling or amniocentesis, for pre-natal diagnosis of chromosome abnormalities.

Non-disjunction can lead to changes in chromosome number. An example of this is Down syndrome (trisomy 21). A trisomy occurs when there are three copies of a chromosome in a cell.

This is a result of nondisjunction during meiosis, followed by fertilization with another gamete.

HOMOLOGOUS CHROMOSOMES Homologous chromosomes are two identical sets of chromosomes that come from the mother and the father. They are the same size and structure, and they contain the same genes in the same locations.

Process of Meiosis

Karyotype Analysis Since there are two X chromosomes and no Y, the person with whom the karyotype corresponds is female. Because there are two of each chromosome and no extras, non-disjunction has not occurred.

Topic 4.3 Theoretical Genetics It’s all about the genes.

...no, not those.

Topic 4.3

THEORETICAL GENETICS WR ITT TLIN EN BY : F Blo . NOW IB B ck 3B LIN iolo gy H PRE VI L TOP OUS: IC 4 .2 NEX TOP T: IC 4 .4 CAI

March 2013

Definitions

Genotype: the alleles of a gene carried by an organism Phenotype: the expression of a gene (i.e. the characteristic Homozygous: having two copies of the same allele

Heterozygous: having two different alleles

Dominant Allele: expressed whether homozygous or heterozygous (Aa or AA) Recessive Allele: expressed only when in the homozygous state (aa) Codominant Allele: pairs of alleles which are both expressed when present

Carrier: a trait is carried in the genes, but is not expressed

Gene Locus: the specific position of a gene on a chromosome

Chromosomes are very important.

MONOHYBRID CROSSES!

Mono Hybrid Cross single trait

GAME HERE!

PAGE

I am a smug monk and I have scienced more than you ever will puny mortal.

In genetic notation, the same letter is used to denote both alleles of a gene. Generally a capital letter denotes a dominant allele while a lowercase letter denotes a recessive one.

*Genes can have multiple alleles

*This is why things like hair color and eye are so different from person to person.

3

Gregor Mendel

Gregor really liked peas. He liked them so much, he extreme scienced them. He then created the Laws of Segregation (alleles of each gene separate into different gametes when the individual produces gametes).

Then he revolutionized a branch of science for the fun of it.

Yeah, he had a lot of free time. Not much to do when you’re a monk...

BLOOD TYPING AND CODOMINANCE!

PAGE

4

BLOOD Phenotype: O A B AB

Genotype: ii iAi (or iAiA) iBi (or iBiB) iAiB

Type O is the universal

Antigen A and B are codominant

Type AB is the universal

Blood can be either positive or negative. Negative blood is lacking certain proteins, while positive has those proteins. Positive for the protein is dominant over not.

Blood is one of the most common example of codominance and multiple alleles

BLOOD TYPING GAME! Maecenas pulvinar sagittis enim.

SEX-LINKED GENES!

PAGE

The X and Y chromosomes determine your gender. If you have a Y chromosome, you are a boy.

Girls have two X chromosomes.

Women can be either heterozygous or homozygous when in comes to sex-linked genes

5

Sex Linkage: INTERWEB ACTIVITY!

Sex chromosomes are nonhomologous, which means there are many traits found on the Xchromosome not present in the Ychromosome.

Both color

Female carriers are heterozygous for X-linked recessive genes. (because they can have XnXr and not express the gene, while a male would have XrY and therefore have the gene of XnY and not)

blindness and hemophilia are produced by a recessive sexlinked allele on the X chromosome.

Sex linked traits are traits that are carried on the X-chromosome in the non-homologous region (i.e. more common in males) The Ychromosome triggers the production of the SRY gene, which is responsible for developing male organs.

Pedigrees

Pedigrees are useful for following the inheritance of sexlinked traits

Carriers for a trait are usually represented by a half-filled shape. Males are squares, and females are normally curvy circles.

No, not that kind of pedigree.

P E D IG R E E

FO R :

HEMOPH

IL IA

R ed = H as g en e W h it e= H as n o g en e

Pedigree Activity (Hey! That Rhymed!)

Though not a rule, most often the trait being followed in the pedigree is colored, while non-carriers are white.

4.4 Genetic Engineering and Biotechnology Polymerase Chain Reaction: If a small sample of DNA is collected, PCR can be used to amplify it.

By using DNA polymerase, more copies of the target section can be made.

1. DNA is denatured 2. Primers are annealed to the start and end of the required section of DNA 3. DNA polymerase uses complementary base pairing to make more copies of the DNA This cycle is repeated up to 35 times to yield sufficient DNA for lab use. PCR is often used to amplify a small sample found at a crime scene so it can be used as evidence in DNA profiling.

Human Genome Project: An international collaborative effort to record the entire base sequence of the human genome. It was completed in April of 2003. The number and loci of all genes in our genome was found, which has led to targeted research in diagnostics, treatment, and pharmacology. Afterwards, bioinformatics was born.

Many new proteins and their functions were discovered. Also, DNA comparisons can be made with other species and we can find out more about the evolutionary history of humans.

Gel Electrophoresis: 1. DNA sample is taken 2. PCR amplifies DNA to get a useful amount 3. restriction enzymes cut DNA into fragments of various lengths 4. samples are added to the wells at the origin end of the gel 5. smaller fragments move further down

Marker is used to show all of the possible DNA fragments. A tag can be added to bind to fragments at certain base sequences. This will glow under fluorescent light and gives a series of bands that can be compared as results of the DNA profile. DNA is negatively charged, so it travels from the negative electrode to the positive electrode.

The Human Genome Project: It has pushed forwards medical and pharmacological research by helping us to see the real cause. Many more diseases than we first thought are rooted in genetic causes, including lung cancer, obesity, and learning disabilities. By opening up the human genome and locating the genes which are at fault, it can be known which people are more at risk for certain conditions.

Bioinformatics: A way to collect and access information from genetic databases. By scanning a whole set of genetic markers, research and diagnosis can now be completed much more quickly.

Electrophoresis Virtual Lab: http://learn.genetics.utah.edu/ content/labs/gel/ DNA Microarray Virtual Lab: http://learn.genetics.utah.edu/ content/labs/microarray/

Bases: The genetic code is universal, and all living organisms use the same bases. This means that the base sequence can be transferred from one organism to another without changing their function. The bases are Thymine, Adenine, Guanine, and Cytosine. We could take the gene for healthy insulin production from a human and insert it into a bacterial plasmid. The bacteria will then be able to produce human insulin.

Recombinant DNA Technology: In gene transfer techniques, the gene for a favorable trait is identified in one organism and transferred to another. Gene transfer can be used to repair a faulty gene in an organism, to produce large volumes of a desired protein, and to genetically modify organisms for favorable characteristics.

Gene Transfer Steps: 1. Find a gene.

2. Restriction enzyme cleaves the desired DNA fragment.

3. Take out the gene.

4. DNA ligase inserts the gene fragment into the plasmid.

5. The modified plasmid is then inserted into a host cell, which delivers the gene to the target cells.

Go to this link to see gene transfer in insulin production: http://www.abpischools.org.uk/ res/coResourceImport/modules/ hormones/en-flash/ geneticeng.cfm

Gene Therapy and SCID: SCID is Severe Combined Immunodeficiency. The lymphatic system fails to produce T-cells, which are essential for immune system function. It was once fatal to newborns which couldn’t fight infection, but there is early diagnosis and gene therapy to help with that.

1. Bone marrow is taken from the patient.

2. The marrow is cultured with a virus that has been genetically modified to carry the working version of the gene.

3. The virus inserts the gene into the chromosomes of the bone marrow stem cells.

4. In many of these cells, the gene will be inserted in the right position, and these cells are returned to the patient’s bone marrow.

5. These reinserted cells serve as progenitor cells, which are templates for building new, functional killer and helper T-cells.

Genetic Modification: Agriculture • Golden rice is enriched with betacarotene, which can be converted into vitamin A in the body and can prevent blindness.

• Insecticide sweet-corn is resistant to pests so the farmer does not have to spray potentially harmful insecticides.

• Long-lasting, frost-resistant, or saltresistant tomatoes, strawberries, etcetera are able to grow in harsher conditions or remain fresh longer for transportation and consumption.

Medicine and Research • Factor IX producing sheep produce human clotting factor in their milk, which is extracted and used to treat hemophiliacs.

• Glow in the dark pigs have been used in graft or transplant research to find out how far the donor cell DNA propagates in the recipient.

Ethics of Genetic Modification: The idea of genetically modified organisms is very controversial. Although there are great potential benefits of genetic engineering, people must be willing to accept responsibility for the possible risks. There are many benefits of genetic modification. Frost, flood, disease, or pest resistant crops can increase yields in countries with food shortages. This can help to improve both the local and national economy. Genetically modified organisms an be used to produce human proteins, such as insulin and clotting factor, to be used as medical treatments. Added nutrients, such as golden rice, an provide added nutrition n areas where food diversity is low. Human genes an be inserted into other species to allow research into pathology and treatment of genetic illnesses, which can help researchers to find cures.

Cloning: A clone is a group of genetically identical organisms or cells. The most commonly understood meaning of the term is the product of the transfer of a differentiated nucleus.

Cloning by transfer of a differentiated nucleus: 1. Egg cell taken from donor.

2. Nucleus removed.

3. New nucleus fused with donor egg cell.

4. Fused egg cell implanted into uterus of surrogate mother.

5. Surrogate mother carried fetus to term.

6. Clone is born with DNA that is exactly the same as the nuclear donor.

Ethics of Therapeutic Cloning:

Induced Pluripotent Stem Cells:

Possible Benefits • rejection risk reduced in transplants • no need to wait for human donor to die to give organs • some success stories already reported in therapeutic cloning

http://www.nature.com/ nature/journal/v453/n7193/ box/nature07040_BX1.html

Arguments Against • religious objections to “playing God” by creating what many consider to be human life • UN recommendations against reproductive cloning are not ratified by all countries • possible risk of a race to create the first human clone (this is not reproductive cloning, cloning humans is illegal globally)

Therapeutic Cloning: It is the use of embryonic stem cells to produce healthy cells to be transplanted back into a patient.

Therapeutic Cloning Is: • the creation of a new egg cell using the DNA of a desired differentiated cell and a donor egg cell • the creation of a human embryo through scientific means • theoretically, this blastocyst could be implanted as in normal IVF and develop into a baby Therapeutic Cloning Is Not: • it is not creating a minime for use in evil global domination plots or to create armies • it is not creating a copy of a human to use as insurance in case you need a transplant

5.1 Communities and Ecosystems

By Greyson Piesco

Words to Know! Â

Species: a group of organisms that can interbreed and produce fertile offspring.

Habitat: the environment in which a species normally lives or the location of a living organism.

Population: a group of organisms of the same species who live in the same area at the same time.

Community: a group of populations living and interacting with each other in an area.

Ecosystem: a community and its abiotic environment.

Ecology: the study of relationships between living organisms and between organisms and their environment.

Autotroph: an organism that synthesizes its organic molecules from simple inorganic substances.

Heterotroph: an organism that obtains organic molecules from other organisms.

Consumer: an organism that ingests other organic matter that is living or recently killed.

Detritivore: an organism that ingests non-living organic matter.

Saprotroph: an organism that lives on or in non- living organic matter, secreting digestive enzymes into it and absorbing the products of digestion.

Energy Transfer Between Trophic Level: the position of an organism on a food chain or web.

Ex.: Producers, Primary Consumers, Secondary Consumers, Tertiary Consumers A food chain is a tool used to visually map the flow of energy from one organism to another.

Ex.: Cabbage Plant -> Mouse -> Snake -> Hawk  A -> B indicates that A is being eaten by B and therefore transferring its energy to it

A food web is a more complex version of a food chain. It maps the flow of energy within a community. It has arrows, like a food web, showing the transferring of energy and the feeding habits within a community. It has many animals. It also has multiple arrows to and from animals.

A -> B -> C B eats A and gets its energy, however only about 10% of A’s energy is transferred to B (this is true between all trophic levels). This means energy is lost between trophic levels.

Energy flows in the following order: from producers, to primary consumers, to secondary consumers, to tertiary consumers.

Note: Light is the initial energy source for almost all communities.

It all starts here!

Pyramids of Energy

The bottom would be the producer, the middle would be the primary consumer, and the top the secondary consumer. It is clear that only roughly 10% of the energy is transferred to the following tropic level. Â

You Have Made it Through 5.1!

Good Job, as a reward, enjoy this picture:)

YAY! Good job!

Topic 5.2: The Greenhouse Effect by: Josh Doege

Carbon Cycle: Relationship between rising concentrations of Carbon Dioxide, Methane, and Oxides of Nitrogen and the enhanced Greenhouse Effect: The sun emits ultraviolet radiation, which hits the earth. For the most part, the earth’s atmosphere reflects this radiation back as infared radiation, but some of it (the infared) is absorbed by greenhouse gasses and reflected back into the earth. This causes an increase in the earth’s temperature.

Note: the greenhouse effect is a natural phenomenon. Some of the gasses involved are methane and oxides of nitrogen. Additionally the ultraviolet radiation is short waved while the reflected infared is longer waved.

Precautionary Principle: The precautionary principle holds that, if the effects of a human-induced change would be very large, perhaps catastrophic, those responsible for the change must prove that it will not do harm before proceeding. This is the reverse of the normal situation, where those who are concerned about the change would have to prove that it will do harm in order to prevent such changes going ahead.

Pros and Cons of Precautionary Principle used as justification for strong action in response to threats involving the greenhouse effect: Pros: Our future would be green, opportunities for economic growth with green technology, more jobs, new companies and industries, healthier environment, and protecting species.

Cons: unemployment, oil industries hit hard economically, and stock market falling.

Changes in Concentration of Atmospheric Carbon Dioxide:

Consequences of global temperature rise: -There would be a large loss of habitat -Increase in CO2足 concentration and therefore further greenhouse effect -Increase in sea level -As the result of higher CO2, more photosynthesis

Greyson Piesco

Topic 5.3: Populations

Greyson Piesco

Population size is effected by...

Natality: this is an increase in the number of births so the population will increase as a result Immigration: this is people coming into a population so the population will increase as a result Mortality: this is death in a population, so population will decrease as a result

Greyson Piesco

Differences in Growth Phases

Exponential: -There is a rapid increase in the size of a population -This is due to natality exceeding mortality and immigration exceeding emigration -In order to support such a growth, food, water, and shelter have to be readily available Transitional: -Here natality begins to level off and mortality increases -Resources become less plentiful -Disease and predators increase -Immigration slows, but still is higher than emigration -There is still growth, but at a much slower rate Plateau: -Natality and Mortality are relatively even -Immigration and emigration are relatively even -The number of resources and predators keep the population at a constant level -The growth ceases and everything levels off

Greyson Piesco

Limits to Population Increase Fewer resources such The Number of as food, water, and Diseases Increase: shelter: Disease spreads quickly through

The Number of Predators Increase: As predators increase in number, their

When a population gets large enough,

heavily populated areas, killing a

prey, of course, decreases from

competition increases to the point

larger number of a species than can

hunting.

where there are not enough resources

be produced.

to support a population.

The End

5.4 Evolution Evolution is the cumulative change in the heritable characteristics of a population Populations produce more offspring than the environment can support leading to a struggle for survival Struggle for survival includes: Competition for food, predation, parasitism, disease, competition for mates, and competition for space

The consequence of the potential overproduction of offspring is a struggle for survival. With an increase in population, individuals have to struggle for food, water, and shelter. This causes survival of the fittest where only the superior individuals survive.

Fossil Records: -Scientists observed fossils and saw that there were organisms that had similarities. They suggested that the organisms in the fossils evolved over time and that was the reason for there still being some similarities.

Selective breeding of domesticated animals: -This is evidence for evolution because domesticated animals had to start out wild at one point. It has been suggested that wild animals were selected and bread for their desired characteristics that led to very tame and superior domesticated animals. An example of this is with wolves over time into dogs we have as domestic pets today.

Homologous structures: -A number of species have the same structure used for different activities.

This implies divergent evolution (that coming from a common ancestor). An example of this is with the forelimbs of humans, the fins of dolphins, and the wings of bats.

Sexual reproduction promotes variation in a species in a few ways. The first is crossing over in meiosis in prophase I. This produces new combinations of alleles, which leads to a variety of traits expressed. Additionally random assortment of chromosomes occurs in metaphase one. There are 223 combinations of genes on one chromosome so with multiple chromosomes in metaphase I, the random assortment increases the variety. Also random fertilization of the egg by the sperm increases variation in a species.

Peppered moth: prior to the industrial revolution peppered moths blended into trees. Ash and soot fell and the moths were no longer peppered. The black phenotype evolved to become the new dominant trait to blend in.

This was evolution.

In a population that has limited resources, the superior and strongest survive and the weakest die as the result of natural selection. This leads to the superior qualities inherited in the offspring, which is evolution. Â This leads to a stronger, more evolved population.

Antibiotic resistance in bacteria: Bacteria may evolve, which creates various strains. When antibiotics are introduced, some of the bacteria may be killed, while others may not be killed.

The ones that are not killed are resistant. These reproduce creating a large number of antibiotic resistant bacteria.

This is evolution. Ex. MSSA is killed by a certain antibiotic, but MRSA survives and reproduces. This antibiotic is no longer effective.

Classification

Binomial - Nomenclature Binomial - Nomenclature is the scientifically accepted way to officially name organisms by using the Genus and species of the organism.

Remember to Italicize or underline!!

Genus species Remember to capitalize the Genus!!

Example: Homo sapiens Genus species Carl Linnaeus, a Swedish botanist, developed the Binomial - nomenclature. It was originally based on physical traits.

Domain Kingdom Phylum

Eukaryota

Plantae

Magnoliophyta

Chordata

Class

Liliopsida

Order

Asparagales

Perciformes

Family

Orchidacea

Pomacentridae

Genus

Vanilla

Amphiprion

Species

planifolia

As we move from kingdom to species, organisms share more and more characteristics, and are more closely related. This system allows us to accurately group organisms, and to identify and name new species. This system is called TAXONOMY.

Animalia

Actinopterygii

ocellaris

Order of Classification from largest to smallest

Species: A group of Organisms which can breed and produce fertile offspring. It is the smallest taxonomic grouping. Subspecies are also recognized.

Domain is divided into Eubacteria, Achaebacteria, and Protista.

Protista is divided into Kingdoms of Plantae, Animalia, and Fungi.

Taxonomy: Life's Filing System - Crash Course Biology #19 - YouTube