II.+Heredity+and+Evolution

toc =A) Heredity (8%) = (1) What features of meiosis are important in sexual reproduction?
 * i) Meiosis and gametogenesis **

During meiosis, the genome of a diploid germ cell, which is composed of long segments of DNA packaged into chromosomes, undergoes DNA replication followed by two rounds of division, resulting in haploid cells called gametes. Each gamete contains one complete set of chromosomes, or half of the genetic content of the original cell. These resultant haploid cells can fuse with other haploid cells of the opposite sex or mating type during fertilization to create a new diploid cell, or zygote. Thus, the division mechanism of meiosis is a reciprocal process to the joining of two genomes that occurs at fertilization. Because the chromosomes of each parent undergo genetic recombination during meiosis, each gamete, and thus each zygote, will have a unique genetic blueprint encoded in its DNA. In other words, meiosis and sexual reproduction produce genetic variation.

(2) Why is meiosis important in heredity? During meiosis, the genome of a diploid germ cell, which is composed of long segments of DNA packaged into chromosomes, undergoes DNA replication followed by two rounds of division, resulting in haploid cells called gametes. Each gamete contains one complete set of chromosomes, or half of the genetic content of the original cell. These resultant haploid cells can fuse with other haploid cells of the opposite sex or mating type during fertilization to create a new diploid cell, or zygote. Thus, the division mechanism of meiosis is a reciprocal process to the joining of two genomes that occurs at fertilization. Because the chromosomes of each parent undergo genetic recombination during meiosis, each gamete, and thus each zygote, will have a unique genetic blueprint encoded in its DNA. In other words, meiosis and sexual reproduction produce genetic variation.  Also in meiosis crosssing over occurs- this increases genetic variation. Crossover produces recombinant chromosomes that combine genes inherited from both parents. Ensures greater variation among gametes.

(3) How is meiosis related to gametogenesis? Meiosis is the process in which a gamete is created; gametogenesis involves meiosis and is the process in which the haploid cells are converted into functional sperm or ova.

Only one follicle matures each month in a female, with the primary oocyte completing meiosis I. Meiosis II begins but stops at metaphase. The secondary oocyte, which is stopped in meiosis II is released at ovulation when the follicle breaks. Meiosis II resumes if a sperm enters the oocyte in the oviduct. In the meiotic divisions there is unequal cytokinesis. The smaller cells become polar bodies (like in plants! – double fertilization). The fertilization is the fusion of the haploid nuclei of the sperm and the secondary oocyte.  (4) What are the similarities and differences between gametogenesis in animals and gametogenesis in plants? In animals, pregametic cells multiply by mitosis & then divide by meiosis. In plants, pregametic cells divide by meiosis, and then divide by mitosis.

The end result is genetically different haploid cells.

In both the "male" gamete (sperm & the pollen grain - which isn't technically a gamete) are smaller, motile (plants need assistance!) and numerous. The female gamete (eggs & ovule - which isn't strictly a gamete!) are larger, non-motile & less numerous.

(1) How is genetic information organized in the eukaryotic chromosome?
 * ii) Eukaryotic chromosomes **

In Eukaryotic chromosomes, genetic information is organized in a nucleus, within chromosomes. In chromosomes there is a long strand of DNA, which is comprised of a double helix figure of nucleotides.

contrarily: in a prokaryotic organism, the genetic material lies within the nucleoid region HOWEVER there is no concrete nucleus nor nuclear membrane, therefore the communication of the DNA throughout the cell is different. **
 * * A chromosome is a chunk of organized DNA that are bound to proteins (histones). A chromsome is made up of two sister cromatids that around bound together at a centromere. The centromere is where the DNA is wound around the histone. The chromosome and the proteins combined are called cromatin.

(2) How does this organization contribute to both continuity of and variability in the genetic information? the vital genetic information is located at the ends of chromosomes, thus there should be a greater occurrence of genetic variability. This is because during synapsis of the chromosomes, crossing over can occur (this is where an end chunk of the chromosome can switch with and end chunk of its partner chromosome) this happens at the end of the chromosomes. also, information located more near the centromere is less likely to cross over and continuity will occur.

(1) How did Mendel’s work lay the foundation of modern genetics?
 * iii) Inheritance patterns? **

Although Mendel didn't know what genes were (he called them "elements"), he was able to recognize the pattern of inheritance through his experiments with pea plants. He basically disproved the "blending theory" (scientists thought that the offspring was a blend of the two parents) because he noticed that when two heterozygous dominant peas produced a homozygous recessive pea. From these experiments he developed two laws: The Law of Segregation and The Law of Independent Assortment (this one has an exception, though:linked genes), which are described in the next question!

Experimenting with pea plants, Mendel noticed that the plants inherited traits in a predictable way. It was as though the pea plants had a pair of factors responsible for each trait. Even though he never actually saw them, Mendel was convinced that tiny independent units determined how an individual would develop. Until then, traits were thought to be passed on through a mixing of the mother and father's characteristics, much like a blending of two liquids. 

(2) What are the principal patterns of inheritance? The principal patterns of inheritance are Mendel’s Laws of Independent Segregation and Law of Independent Assortment. The **Law of Segregation** is that when an individual produces gametes, the alleles separate so that each gamete only receives one copy of a gene. Pairs of genes reform when gametes fuse during fertilization It’s now known that this segregation of alleles occurs during the process of sex cell formation The **Law of Independent Assortment** states that alleles of different genes assort independently of one another. This is due to the fact that the genes for independently assorted traits are located on different chromosomes For example, Seed shape and seed color are inherited separately from each other or a pea plant's inheritance of the ability to produce purple flowers instead of white ones does not make it more likely that it will also inherit the ability to produce yellow pea seeds in contrast to green ones.

=B) Molecular Genetics (9%) = (1) How do the structure of nucleic acids relate to their functions of information storage and protein synthesis? The bases of the DNA molecule are grouped in threes called codons. These codons are complementary with a amino acid carrying tRNA the oder of the codons determines the order of the amino acids which determines protein function. It is also important to note that not all sections of the DNA are transcribed and translated. Only portions of the DNA, called exons, are actually transcribed, and THESE form the codons that correspond to the twenty various amino acids during translation. AUG is the one and only start codon that calls for translation to begin, and there are three stop codons. Since there are many different types of codons, and there are only twenty different amino acids, there is a little wiggle room with the amino acids. hehehe get it? wiggle room! except it's really called a wobble. Anyway, it means that there are multiple ways to make all of the amino acids, or redundancy. (2) What are the similarities and differences between prokaryotic and eukaryotic genomes? <span style="color: #c81e1e; font-family: arial,helvetica,clean,sans-serif; line-height: 16px;">The genomic similarities are that they are both made of DNA, which is transcribed to RNA with is translated to protein. In eukaryotes the genomic DNA is stored in a separate cellular compartment called the nucleus. The nucleus houses the chromosomes, 46 linear chromosomes in humans, in contrast to the single circular chromosomes seen in prokaryotes. Another significant difference in prokaryotes vs eukaryotes is that the genes (called operons in bacteria) in prokaryotes are constantly actively transcribing unless turned off by repressor proteins. In eukaryotes transcription must be activated, because the default is to keep the genes turned off. (1) What are some mechanisms by which gene expression is regulated in prokaryotes and eukaryotes?
 * <span style="font-family: Arial,Helvetica,sans-serif;">i) RNA and DNA structure and function **
 * <span style="font-family: Arial,Helvetica,sans-serif;">ii) Gene regulation **<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">

<span style="color: #ff00ff; font-family: Arial,Helvetica,sans-serif;">Prokaryotes regulate gene expression through the operon. There are two different models: the inducible (ex: the Lac Operon) and the repressible (ex: The Tryptophan Operon). The lac operon: This only gets turned on when no other sugar is available to the bacteria, so they HAVE to use lactose.Allolactose binds to the repressor and changes its shape. Because its shape is changed, there is no longer anything stopping RNA polyermerase from binding to the promoter, and transcription occurs. The tryptophan operon: If Tryptophan levels are high, then the bacterium doesn't need anymore, so it doesn't need to make anymore. A represser binds to the corepressoer, tryptophan, it changes its shape and binds to the operator, which prevents RNA polymerase from binding to the promoter. And, because of this transcription cannot happen, and no more are made!!

Eukaryotes regualte gene expression through Hormones. There are two different types of hormones: steroids and nonsteroids. Steroids are lipids that just diffuse through the cell membrane and bind to a receptor, causing a cell response. Nonsteroids are proteins that bind to a receptor outside of the cell. This triggers a secondary messenger inside the cell, and triggers the cell response.

Also, hox genes also determine which cells go where (that's why our eye isn't on our foot!).

(1) In what ways can genetic information be altered?
 * <span style="font-family: Arial,Helvetica,sans-serif;">iii) Mutation **<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">

<span style="color: #f51414; font-family: Arial,Helvetica,sans-serif;">mutations during replication <span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">

somatic- altered in a regular body cell germ-line- altered in cells that will become gametes.

Mutations can happen in a nucleotide, multiple nucleotides, and in a whole chromosome. nucleotide mutations- point mutations- results in frameshirt, entire reading frame is altered - substitution, one nucleotide base is changed to another - insertion, one nucleotide is added - deletion, one nucleotide is deleted

multiple nucleotides- includes entire genes - Duplication - Inversion - Rearrangement

multiple nucleotides- (2) What are some of these alterations? Types of Mutations:

Base pair substitution:

Base pair insertion or deletion:
 * ** Missense ** (new amino acid, but is close enough to old one that nothing is really affected)
 * ** Nonsense ** (stop codon)
 * **Silent:** replaces for example a G with an A (doesn't affect amino acid sequence)


 * ** Frame shift **
 * can cause immediate nonsense if 1 base pair is inserted
 * can cause extensive missense if 1 base pair is deleted


 * Point mutations ** (sickle cell anemia) - chemical changes in a single base pair of a gene

**Inversions** (same DNA but in the wrong order)
 * Chromosomal mutations:**
 * Insertions** (Fragile X, Huntington’s, Muscular Dystrophy) - happens with 3 base pairs and adds and extra amino acid
 * Deletions** - happens with 3 base pairs and causes an amino acid to be missing
 * Duplications **
 * Translocations** (DNA is taken from one chromosome and placed on another)

<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">(1) What is the structure of viruses? Viruses are dependent on a host cell for carrying out life-sustaining functions and reproducing. They lack ribosomes, so they can't create proteins to transform their mRNA into without a host. They can't generate or store ATP, but must take energy from their host cell. All viruses have nucleic acid (DNA or RNA) and a protein coat made of capsomeres which surrounds it (a capsid). They can have a lipid envelope derived from the host cell's membrane. Viruses are normally classified by the organisms they infect, and then by their structure (size of nucleic acid, size of the capsid, and whether they have a lipid envelope around the capsid). There are two main shapes of viruses- rods/filaments and spheres.
 * <span style="font-family: Arial,Helvetica,sans-serif;">iv) Viral structure and replication **

(2) What are the major steps in viral reproduction? To reproduce, viruses either undergo the lytic or the lysogenic cycle. In the lytic cycle, the viruses attach onto the bacteria and inject nucleic acid into the cell through their tail. This causes the cell to make more viral piece, put them together, and then the cells lyse and burst, releasing new copies of the viruses. In the lysogenic cycle, the DNA is injected into the bacteria, and instead of taking over the cell, the DNA is integrated into the host DNA. The cell then duplicates like normal, until it is triggered to enter into the lytic cycle. At this point, there are tons of cells which have the viral DNA in them, releasing many more new copies of the viruses.

(3) How do viruses transfer genetic material between cells?

Viruses basically take over a cell by inserting it's own RNA/DNA into it (via reverse transcriptase for RNA), and then depending on which cycle the virus is in, if a) lytic cycle, viruses replicate its own genetic material by taking over the cell and bursting out of the cell to go find more cells to infect, or b) in the lysogenic cycle, viruses incorporates its own genetic material with that of the cells and thereby replicating its genetic material everytime the cell replicates its own genetic material. Then eventually the lysogenic cycle reverts to the lytic cycle stage and the cell blows up.

(1) What are some current recombinant technologies? > People may be tested for the presence of mutated proteins that may be associated with breast cancer, retino-blastoma, and neurofibromatosis. > Tests exist to determine if people are carriers of the cystic fibrosis gene, the Huntington’s disease gene, the Tay-Sachs disease gene, or the Duchenne muscular dystrophy gene. > People suffering from cystic fibrosis, rheumatoid arthritis, vascular disease, and certain cancers may now benefit from the progress made in gene therapy. > Scientists are able to link mutations and disease states to specific sites on chromosomes.
 * <span style="font-family: Arial,Helvetica,sans-serif;">v) Nucleic acid technology and applications **<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">
 * **Isolation of large quantities of protein**
 * **Identification of mutations**
 * **Diagnosis of affected and carrier states for hereditary diseases**
 * **Transferring of genes from one organism to another**
 * **Mapping of human genes on chromosomes**

<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">(2) What are some practical applications of nucleic acid technology? <span style="color: #800080; font-family: Arial,Helvetica,sans-serif;"> (3) What legal and ethical problems may arise from these applications? =<span style="font-family: Arial,Helvetica,sans-serif;">C) Evolutionary Biology (8%) =
 * Diagnosis of diseases
 * Gene therapy
 * Pharmaceutical products
 * Forensics
 * DNA fingerprinting
 * Agricultural use
 * Vaccines for animals
 * Genetically alter cows to grow faster/produce more milk
 * In plants
 * Resistance to herbicides and freezes
 * Environmental use
 * The development of microbes that can degrade toxic compounds into nontoxic forms during the manufacturing process, at waste treatment facilities, at dump sites, and at sites of environmental disasters such as oil spills
 * Might create hazardous new pathogens
 * Safety of genetically modified organisms such as plants and animals
 * Human genome project
 * Who should have the right to examine some else’s genes?
 * How should that information be used?
 * Should that information be used in determining whether a person is suitable for a certain job or insurance?
 * No knows the answers to these questions yet, and it because of these questions that the research and results are slowing down for the applications of DNA technology. The only thing that scientists can do for now is proceed with humility and caution.

(1) What are the current biological models for the origins of biological macromolecules?
 * <span style="font-family: Arial,Helvetica,sans-serif;">i) Early evolution of life **<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">

The theory of endosymbiosis- Larger prokaryotic cells toke up smaller prokaryotic cells through endosymbiosis- these smaller prokaryotic cells were the origins of mitochondria and plastids (ex. choloroplast) in eukaryotic cells.

(2) What are the current models for the origins of prokaryotic and eukaryotic cells?

Eukaryotic cells evolved from prokaryotic cells through the ingestion of a "mitchondria-like" prokaryote by another predatory prokaryote... It couldn't digest another prokaryotic cell that was similar to the mitochondria found in eukaryotic cells and it lacked the enzymes to digest it, so the "mitochondria-like" prokaryote lived inside its captor, ultimately providing a signficant advantage in energy production. The endosymbiosis theory postulates that · The **mitochondria** of eukaryotes evolved from aerobic bacteria (probably related to the [|rickettsias] ) living within their host cell. · The **chloroplasts** of eukaryotes evolved from endosymbiotic ** [|cyanobacteria] **.

<span style="color: #f51414; font-family: Arial,Helvetica,sans-serif;">(1) What types of evidence support an evolutionary point of life? <span style="color: #1481fa; font-family: Arial,Helvetica,sans-serif;"> Homologous structures between species prove the point that certain species evolved from the same ancestor <span style="color: #ff00ff; font-family: Arial,Helvetica,sans-serif;">More evidence: Fossil records- there's a fossil of Archaeopterx, which appears to be a creature that links reptiles and birds evolutionarily. Similar Embryos- all vertebrates go through a stage as an embryo where they have gill pouches (pharyngeal gills!!). Amino Acids- There's only 20!
 * <span style="font-family: Arial,Helvetica,sans-serif;">ii) Evidence for evolution **

<span style="color: #1481fa; font-family: Arial,Helvetica,sans-serif;">Where does this come from? Darwin articulated the theory of evolution in his book On the Origin of Species. Much of the information and observations he gathered were based on the Galapagos finches. He observed that, depending on where the finches lived (trees or ground), they had various unique attributes. Over time, these developments occurred through the process of Natural Selection or Survival of the Fittest (as in, whoever was most ‘fit’ to survive, would live long enough to reproduce and thus their advantageous traits would be passed on).

A more recent example of evolution came from the study done by Peter and Rosemary Grant. Starting in 1973 they studied “Darwin’s” Finches on the Galapagos Islands. After a severe drought the Grants saw natural selection in action. The largest birds with the biggest beaks that could crack the tough seeds survived. Like Darwin’s theory predicted, the difference between life and death was often the slightest variation, like the beak size in this case. When the birds started mating again the new generation of finches was larger birds with deeper beaks: both heritable traits. The Grants saw evolution in action after the natural selection had killed off so many birds.

<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">(1) What is the role of natural selection in the process of evolution? <span style="color: #7a90e1; font-family: Arial,Helvetica,sans-serif;"> Natural selection has made it possible for organisms to change and differ throughout evolutionary history.
 * <span style="font-family: Arial,Helvetica,sans-serif;">iii) Mechanisms of evolution **

Natural selection is the result of genetic differences in a species; a high level of genetic diversity will allow the population to survive in case of an environmental change and continue to reproduce and grow in their environment and their offspring will contain the traits that will allow for survival. An example of this is the Peppered moths that could be found in England during the Industrial Revolution. Originally, the majority of the moths were white so that they blended in with the local tree bark colors and could hide from predators (the darker moths stood out easily and thus were easily preyed upon). As the soot from the coal coated and darkened the tree bark, the proportion of dark moths to white moths continued to increase in the successive generations as the dark moths could now hide from predators more easily than the white moths.

Natural selection gives rise to different alleles with different traits, some traits make the species more fit and live longer and easier. these traits are then, over time, seen more in a species; causing the species to evolve.

<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">(2) How are heredity and natural selection involved in the process of evolution? <span style="color: #ff00ff; font-family: Arial,Helvetica,sans-serif;">In natural selection, nature selects and favors organisms for survival based on their heritable characteristics. These characterisitics allow an organism to survive and reproduce at a higher rate than other members of their species. Withour heredity there could be no evolution.

Heredity, which is the passing on of traits from one generation to the next, is, as said above, the most crucial aspect of evolution. Without heredity, there would be no evolution. Children gain their parents genes, however they do not have the exact genes of either parent, or siblings. In natural selection, which is key in evolution, individuals with certain inherited traits leave more offspring than those with undesirable traits. <span style="color: #00ff00; font-family: Arial,Helvetica,sans-serif;"> BUT it is extremely important to note that organisms do not perform natural selection, because they, themselves, do not evolve. Populations over time are the smallest group of organisms that can evolve.

There are three varying types of natural selection. The first is directional selection. This means that the organisms that are favored are one of the two opposite sides of the spectrum. In other words, natural selection is favoring those of a particular "direction". The second type of natural selection is disruptive selection. This type means that both ends of the spectrum are favored in natural selection, not the average of the two. The third and last form of natural selection is stabilizing selection; this means that the average organisms are favored and that neither end of the spectrum is being favored.

<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;"> (3) What mechanisms account for speciation and macroevolution? Crossing over, Natural selection, and migration There is also allopatric and sympatric speciation. allopatric speciation- caused by geographic isolation- separation by mountain ranges, canyons, rivers, lakes, etc. - a population can be split up and be under different selective pressures causing natural selection to work in different ways- if these two groups come back together and are unable to reproduce succesfully then speciation has occures sympatric- speciation- no geographic speciation- examples: polyploidy, habitat isolation, behavioral isolation, temporal isolation, and reproductive isolation
 * polyploidy- cell has more than two complete sets of chromosomes (occurs through nondisjunction)- cannot breed with other of the same species that are not polyploidy but can with other polyploid plants in their species
 * habitat isolation- live in same area but encounter each other rarely (ex. two species of snake of one genus found in same area but one is terrestrial and the other aquatic)
 * behavioral isolation- mating behavior
 * temporal- time- different times of reproduction
 * reproductive isolation- includes the prezygotic and postzygotic barriers, but these species are closely related, they are just not able to reproduce together.

(4) What are prezygotic/postzygotic barriers? Prezygotic barriers prevent mating- prevent fertilization. These prezygotic barriers consist of habitat isolation (basically when two species of organisms are limited by their habitats), temporal isolation (if they are active at different times during the day, especially during their reproductive periods), behavioral isolation (animals' mating activities vary significantly from species to species, so courting rituals could be completely different), mechanical isolation (morphological differences prevent mating from taking place, and gametic isolation (basically the egg and sperm are just not compatible even if mating is attempted) Postzygotic barriers preen the production of a fertile offspring after mating has occured. These postzygotic barriers consist of reduced hybrid viability (the hybrid of the two species is impaired in development and survival because of the parrents' differing genes), reduced hybrid fertility (hybrids between the two species are sterile, so they cannot possibly succeed in carrying on a new species), and hybrid breakdown (when the first generation of hybrid is both viable and fertile, but when they mate with one of the parent species, the next generation is sterile or not viable)

<span style="color: #800080; font-family: Arial,Helvetica,sans-serif;">(5) What different patterns of evolution have been identified and what mechanisms are responsible for each of these patterns? <span style="color: #fa1414; font-family: Arial,Helvetica,sans-serif;">Divergent Evolution- organisms from the same ancestor evolve in different ways because of the different environments they live in Convergent Evolution- organisms from 2 different ancestors evolve similarly because they both live in similar environments. Coevolution-the joint change of two or more species in close interaction. example- predator and prey