BIOL 3010 Exam 1 Study Questions

What is a gene? What is an allele?

A gene is a segment of DNA found on a chromosome that codes for a particular trait (i.e. pea plant color). Genes are the discrete unit of inheritance that allow for the passing of traits between parents and offspring. Alleles are the alternative forms of genes that are inherited from each parent (i.e yellow vs green). Together, the two alleles inherited determine the visible phenotypes based on dominance and recessive patterns.

Darwin described the process of natural selection. What is needed for this process to occur?

For natural selection to occur, there must be variation, differences in fitness, and inheritance. There must be variation among individuals in a population for some trait. This variation in traits leads to fitness differences. Fitness differences refers to the consistent relationship between the value of a trait and reproductive success. Finally, there must be a consistent relationship for value of a trait between parents and offspring--these variable traits that produce differences in survival must be passed from parent to offspring for natural selection to continue.

What is Mendel's laws of segregation, and what analyses led him to this law?

The law of segregation states that two alleles from each parent separate during gamete formation and then unite at random during fertilization. Essentially, each gamete only receives one allele from each parent, and the allele received from the parent's genotype is random. Mendel's monohybrid crosses with pea plants revealed the law of segregation due to the reappearance of the recessive phenotype in the F2 generation. F2 included two kinds of yellow peas (YY and Yy) and one type of green pea (yy). The 3:1 ratio of yellow to green in F2 is explained by the segregation of dominant and recessive alleles during gamete formation.

What is Mendel's laws of independent assortment, and what analyses led him to this law?

The law of independent assortment states that different pairs of alleles (for different genes) segregate independently from one another during gamete formation. The inheritance of one allele for a trait does not influence the inheritance of a certain allele for a different trait. Mendel's dihybrid crosses (crosses of pea plants differing on two characteristics) revealed the law of independent assortment. In a dihybrid cross of two double heterozygotes (YyRr x YyRr), each dihybrid can make four types of gametes: YR, Yr, yR, and yr. This results in 16 possible zygotes showing four phenotypes that occur in a ratio of 9:3:3:1. This ratio shows that the inheritance of a gene for pea color is unaffected by the inheritance of a gene for pea shape.

Name and explain at least one major technological advance that has facilitated genetic and genomic analysis since the 1970s.

The invention of PCR in 1983 by Kary Mullis and others has led to the ability to amplify gene sequences at a massive level, allowing for advancements in cloning. PCR uses a special, heat-resistant DNA polymerase to rapidly replicate DNA many times, so that gene sequences can be manipulated in different ways.

Define segregation.

Refers to the separation of the parental alleles during gamete formation. Each parent can make four gametes based on his/her own alleles, the alleles inherited by the offspring through the gamete are random because of the random nature of gamete formation.

Define independent assortment.

Refers to the shuffling of gene pairs during gamete formation. The allele for a gene in a gamete has an equal chance of being dominant or recessive when the genotype is heterozygous. The presence of a particular allele of one gene provides no information about the allele of a second gene.

Define gene.

A gene is the discrete unit of inheritance that is passed from parent to offspring. Parents pass on specific alleles to offspring. These alleles are alternative forms of the trait for which the gene codes, and these determine the physical characteristics of the offspring.

Define locus.

Locus refers to the location of a gene on a particular chromosome.

Define allele.

Alleles are alternative forms of a trait (gene). Combinations of alleles determine the visible phenotype.

Define fitness.

Fitness refers to the reproductive success of an organism based on variation in traits that lead to increased survival or fecundity.

Define inheritance/heredity.

Inheritance refers to the pattern of passing of genetic material between parents and offspring.

What is preformationsim?

A pre-mendel theory of inheritance in which it was believed that a fully formed human was encapsulated in the sperm given by the father to the mother. In this theory. only the father contributed to the genetic makeup of the offspring, while the mother was only the incubator.

What is blending inheritance?

Pre-mendel theory that over time, the traits of each parent were combined, or blended, to create a third new phenotype. However, this theory would lead to the loss of genetic diversity, which evidently is not the case.

What is a genetic model organism?

Refers to a nonhuman species that can be studied systematically to gain a better understanding of human inheritance and the passing on of genetic material. Mendel developed the first genetic model organism with his pea plant. By systematically studying the pea plant, Mendel was able to test patterns of inheritance and develop hypotheses that describe inheritance in humans.

Define dominant vs recessive.

The dominant trait is the trait that appeared in all F1 hybrids, while the recessive trait is hidden in hybrids, but appears in later generations when a homozygous genotype is inherited. When one dominant allele is present, the dominant phenotype results regardless of the second allele. For a recessive phenotype to result, two recessive alleles must be present.

Describe the difference between continuous and discrete traits.

Discrete traits are those where the phenotypes that result are qualitatively distinct from one another. For example, yellow vs green seed color. Continuous traits are those where the phenotypes are quantitatively different from each other. For example, height. Rather than inheriting one or the other, the trait inherited reflects a continuous range of phenotypes.

What is the difference between a haploid and diploid?

A haploid is a cell with half of the genetic material of a diploid (n vs 2n). In humans, gametes are haploid cells and after fertilization, the resulting zygote is a diploid cell.

Define phenotype vs genotype.

Genotype refers to the combination of alleles inherited from the parents. Phenotype refers to the resulting physical characteristics from the genotype.

Define heterozygous vs homozygous.

Heterozygous means that the offspring has inherited one dominant allele and one recessive allele for a particular trait. (Yy) and will thus show the dominant phenotype. Homozygous means that the offspring has received either two dominant alleles (YY) or two recessive alleles (yy) and can show either the dominant or recessive phenotype based on which alleles were inherited.

What early evidence showed that genetic material could be transferred between organisms? (Griffith)

Frederick Griffith studied two forms of bacteria that caused pneumonia: smooth (virulent) and rough (nonvirulent). Performed four trials: mice injected with the virulent strain died, mice injected with the nonvirulent strain lived. Mice injected with heat-killed virulent strain lived. Mice injected with mixture of heat-killed virulent and nonvirulent strain died. Griffith observed that the heat killed S bacteria transformed the living R bacteria into virulent S.

What early evidence showed that the transforming material is DNA? (Avery, Hershey and Chase)

Oswald T Avery's lab performed experiments, looking for the transforming principle that changed R bacteria into S bacteria. The living R form was combined with heat-killed S components in medium. After a period of time, the mixture was transformed into the living S form. Enzymes that degraded RNA, protein, or polysaccharide had no effect on the transforming principle, but an enzyme that degrades DNA destroyed its activity completely. When DNAase was introduced to the mixture of R and S strains, the R strain was not transformed into S strain because the DNA was degraded.

Furthermore, Hershey and Chase's experiments showed that DNA contained the transforming material for virus propagation, not protein. Radioactive sulfur and radioactive phosphorus used to tag the protein and DNA components on the bacteriophage. The bacteria cultures were then blended to separate the ghosts from their host cells. Centrifugation caused separation of the heavier host cells from the lighter bacteriophage ghosts. Radioactive phosphorus found in the pellet because the heavier cells containing injected DNA spun down. Radioactive sulfur found in the supernatant because the lighter protein-based phages did not spin down.

What is DNA? Describe the structure of DNA.

DNA (deoxyribonucleic acid) is a polymer composed of nucleotide subunits that contains the genetic material and forms gene sequences. DNA has a double helix structure with two anti-parallel chains (5' to 3' and 3' to 5'). The sugar phosphate backbones form the chains, and the nitrogenous base pairs form the rungs of the ladder. Nucleotides are interconnected by phosphodiester bonds, complementary base pairing occurs between the nitrogenous bases via non-covalent hydrogen bonds. As the double helix spirals around its longitudinal axis, major and minor grooves result based on how close together or far apart the phosphodiester bonds are located.

How is DNA different from RNA?

DNA nucleotides contain the sugar deoxyribose, while RNA nucleotides contain the sugar ribose.

List the needed requirements of genetic material. What must genetic material be able to do?

Any prototypical genetic material must be able to store information, express information, replicate, and accommodate introduction of new variation.

Describe the difference between a nucleoside and a nucleotide.

A nucleoside involves the covalent attachment of a nitrogenous base to the 1' carbon on deoxyribose. The sugar is attached to the nitrogenous base. Nucleosides do not have phosphate groups. Examples include deoxyadenosine (dA in DNA) and adenosine (A in RNA). Nucleotides are nucleosides with the addition of a phosphate group to the 5' carbon. Examples include deoxyadenosine triphosphate (dATP in DNA) and adenosine triphosphate (ATP in RNA).

What is a nitrogenous base?

A nitrogenous base is a nitrogen-containing base that is covalently attached to DNA's alternating sugar-phosphate backbone. Part of the nucleotide that contains DNA's information content. The genetic information of DNA consists of variations in sequences of bases. Complementary base pairing is the result of the hydrogen bonding that occurs between purine and pyrimidines.

What is a phosphate group?

A phosphorus bonded to four oxygens that is covalently bonded to the deoxyribose sugar via phosphodiester bonds in a nucleotide.

What is the difference between ribose and deoxyribose?

Deoxyribose and ribose are both 5-carbon sugars, but deoxyribose has one less oxygen than ribose and is missing a hydroxyl group on the 2' carbon. Deoxyribose is the sugar found in DNA and ribose is the sugar found in RNA

Compare covalent bonds and hydrogen bonds in the structure of DNA.

Strong phosphodiester bonds form a covalent link between the 3' carbon of one nucleotide and the 5' carbon of the following nucleotide. These bonds of the sugar phosphate backbone must be very strong so that when DNA is unwound to perform transcription or replication, only the hydrogen bonds are disrupted. In contrast, hydrogen bonds form between nitrogenous base pairs. H bonds are weak electrostatic bonds that result in the partial sharing of hydrogen atoms between reacting groups. These bonds are much weaker compared to the phosphodiester bonds, allowing for DNA to be opened up without disrupting the sugar/phosphate backbone. A and T form 2 hydrogen bonds, while G and C form 3 hydrogen bonds

Define antiparallel.

DNA consists of two antiparallel chains. Phosphodiester bonds always form between the 3' carbon of one nucleotide and the 5' carbon of the following nucleotide, and as a result, the two ends of the chain are chemically distinct. At the 5' end of DnA, the terminal nucleotide has a free 5' carbon, which may carry a hydroxyl or phosphate. At the 3' end of DNA, the terminal nucleotide has a free 3' carbon. The antiparallel nature of DNA shows that it has polarity/directionality

Compare major and minor grooves.

As DNA spirals around its longitudinal axis, there are regions of more accessibility and regions of less accessibility. Major grooves occur when the phosphodiester bonds are farther apart, while minor grooves occur when the phosphodiester bonds are closer together. The size of the grooves determines whether transcription factors can bind at a particular location.

Define transformation.

Refers to the ability of a substance to change the genetic characteristics of an organism.

What is RNase? What is DNase?

RNase is an enzyme that degrades RNA. DNase is an enzyme that degrades DNA. These two enzymes were used in Oswald Avery's experiments to determine the transforming principle. When RNA was degraded in the mixture of heat killed S strain and living R strain, the nonvirulent R strain was transformed. When DNA was degraded in this mixture, no transformation could occur because the transforming principle had been destroyed.

Describe the difference between purines and pyrimidines? How does this contribute to complementary base pairing?

Purines are double ringed structures, including adenine and guanine. Pyrimidines are single ringed structures that include cytosine and thymine. Purines and pyrmidines form complementary base pairs via hydrogen bonds. A always pairs with T by forming two hydrogen bonds, and C always pairs with G by forming three hydrogen bonds. This base pairing between purines and pyrimidines was discovered through Chargaff ratios, in which Chargaff found that the amount of A always equaled the amount of T, and the amount of C always equalled the amount of G.

What are the phases of interphase and their associated events?

The two main events of mitotic cell division are interphase and mitosis. During interphase, the cel moves through G1, S, and G2 phases. In G1, chromosomes are neither duplicating nor dividing. The cell is growing and using genes to make the materials that it needs to function. During S phase, the cell duplicates its genetic material. Each chromosome doubles to produce identical sister chromatids joined at the centromeres. During G2, the cell grows some and synthesizes the materials it needs for mitosis. The beginnings of spindle formation also occur during interphase when an array of microtubules become visible outside of the nucleus. Centrosomes are replicated during S and G2 phases to allow for spindle formation in mitosis.

What are the phases of mitosis?

Prophase, metaphase, anaphase, telophase, cytokinesis

What cellular events occur in prophase?

During prophase, the chromosomes condense from chromatin into individual chromosomes, marking the start of mitosis. DNA has already been duplicated, so the chromosomes consist of sister chromatids attached at centromeres. The nucleoli break down and ribosome production stops in order to conserve energy for cell division. The interphase scaffolding of long, stable microtubules is replaced by a dynamic set of microtubules that rapidly grow and shrink back to the centrosomes. Centrosomes migrate to opposite poles of the cell.

What cellular events occur in prometaphase?

In prometaphase, the spindle forms. The nuclear envelope breaks down so that the microtubules can invade the nucleus. Chromosomes attach to the microtubules via the kinetochore. During prometaphase, one sister chromatid is attached to a microtubule, while one is unattached. At the end of this phase, the unattached sister chromatid associates with the microtubles on the opposite side, orienting each chromsome so that the sister chromatids face opposite poles.

What cellular events occur in metaphase.

Chromosomes align at the cell equator. Chromosomes remain at the metaphase plate because the microtubule-based forces pulling sister chromatids towards the opposite poles are in a balanced equilibrium. Sister chromatids are being pulled in opposite directions, but are still connected to one another, held together by cohesin proteins.

What cellular events occur in anaphase?

During this phase, the centromeric connections between the sister chromatids are severed and each is pulled towards the spindle pole by kinetochore microtubules as they shorten.

What cellular events occur in telophase?

Spindle fibers disperse, nuclear envelopes form around the groups of chromatids at opposite poles. Nucleoli reappear, and chromosomes decondense into chromatin.

What cellular events occur in cytokinesis?

The cytoplasm divides. In animal cells, a contractile ring pinches the cytoplasm into two cells. Important organelles are distributed to daughter cells.

Distinguish symmetric versus asymmetric cell division.

In symmetric division, the cytoplasm is divided equally between the two daughter cells, resulting in two identical, same sized cells. In asymmetric division, the cytoplasm is divided unequally, resulting in one large daughter cell and one small daughter cell.

What is cohesin? How does cohesin regulate sister chromatid pairing?

Cohesin is a highly conserved, multi-subunit protein complex that forms ring-like structures around the sister chromatids to ensure that they maintain contact. Cohesin regulates sister chromatid pairing because it resists the forces pulling the chromatids apart at their kinetochores and generates tension across the chromosomes. Only when all of the chromosomes are properly attached and under tension does the cell activate separase to cleave the cohesin complexes. As a result, cohesin prevents the missegregation of sister chromatids.

How are changes in cohesin distribution regulated across cell cycle phases (S to M)?

Cohesin degradation by separase is regulated by the anaphase promoting complex (APC). APC is a ubiquitin ligase that targets proteins for degradation. In this case, it targets cohesin to be cleaved by separase. The mad2 protein regulates the APC complex. Mad2 is present on unattached kinetochores. It is active when the kinetochore is not attached to the spindle apparatus and sends out a signal to unhibit the initiation of anaphase. When mad2 is localized to the kinetochore, it inhibits the anaphase promoting complex and prevents the breakdown of the cohesin complex.

Compare cohesin formation and degradation in mitosis vs meiosis.

After chromosomes replicate in the S phase of the cell cycle, cohesin proteins associate with and hold sister chromatids together along the arms and in the centromere region. Cohesin rings scattered along the length of the chromosome, but found in high concentrations in the vicinity of centromeric heterochromatin. In mitosis, the cleavage of cohesin is regulated by the tension of the microtubules attached to the sister chromatids. Only when all sister chromatids are under tension is the proteolytic enzyme separase activated to cleave the cohesin complex and allow for segregation. In meiosis, the protein shugosin protects the centromeric cohesin. During anaphase I, cohesin is cleaved from the arms of the chromosomes so that homologs can segregate, but sister chromatids remain attached due to protection of cohesin complex at the centromere. Then, during anaphase II, cohesin is cleaved by separase at the centromere so sister chromatids can separate.

What is the spindle assembly checkpoint and what does it monitor? What would be the consequence if there was a mutation in a spindle checkpoint protein?

The spindle assembly checkpoint is the metaphase checkpoint that monitors chromosome attachment to the microtubules at their kinetochores and their proper alignment at the metaphase plate. Only when all of the chromosomes are properly aligned and sister chromatids are attached to microtubules of opposite poles is anaphase initiated. if there was a mutation in a spindle checkpoint protein, then anaphase could occur without proper chromosome alignment, leading to mis-segregation and nondisjunction events.

What is the kinetochore and where are kinetochores located?

Kinetochores are specialized structures composed of DNA and protein. Some kinetochore proteins are motor proteins that exert pulling forces on the chromatids towards the spindle pole to which they are attached. Other kinetochore proteins monitor tension of the sister chromatids being pulled in opposite directions as part of the spindle assembly checkpoint. Kinetochore are located and assemble upon centromeric DNA sequences. Centromeric DNA consists of repeated sequences organized into nucleosomes containing CENP-A. Kinetochores organize around these special nucleosomes. In late prophase, kinetochores develop on each sister chromatid. By prometaphase, kinetochores of two sister chromatids attach to the spindle fiber.

What would be the consequence if there was a mutation in a gene that encoded for a kinetochore protein? Would this mutation cause activation of the spindle assembly checkpoint?

A mutation in a gene that encoded for a kinetochore protein would cause the cell to be unable to carry out the spindle assembly checkpoint because kinetochores' normal function includes monitoring tension in the sister chromatids until all are aligned properly at the metaphase plate. A mutation in the kinetochore protein complex would cause a faulty checkpoint and faulty attachment to the sister chromatids at their centromeres, likely causing mistakes in segregation.

How do growth factors promote the G1 to S transition?

DNA replication requires the transition from G1 to S phase. RTK signaling drives the transcription of G1/S cyclin genes. Growth factors are responsible for activation of RTK pathways, in which tyrosine kinase autophosphorylates to activate downstream events. G1/S cyclins phosphorylate the retinoblastoma (Rb) protein. Phosphorylated Rb releases the E2F transcription factor, which unregulates genes required for DNA synthesis.

If a cell has 8 chromosomes total, how many kinetochores would you observe during mitosis?

16

What are cell cycle checkpoints? What happens in the "gap phases" of cell cycle?

Cell cycle checkpoints are additional controls in the cell cycle that check for the integrity of the genome and spindle apparatus before allowing the cell to move on to the next phase. Gap phases in interphase function as decision windows to ensure the cell is prepared to divide.

What are "tumor suppressors" and what kinds of roles do they play during normal development or homeostasis? How would a mutation in RB lead to constitutive DNA synthesis and uncontrolled cell proliferation? What about E2F? How is E2F activity controlled?

A tumor suppressor gene is a gene that produces a protein to help regulate cell growth and division, acting as a brake to prevent uncontrolled cell proliferation. A mutation in RB (a tumor suppressor) results in the inability of the Rb protein to bind to E2F and inactivate it. E2F is a transcription factor that activates the genes necessary for DNA synthesis. When the cell is not dividing, it is bound to and inactivated by Rb. If there is a mutation in Rb, E2F becomes active at all times, causing uncontrolled and continuous cell division because of constant activation of cell cycle genes.

How is the G1 to S phase transition controlled during the eukaryotic cell cycle?

RTK signaling induces the expression of the necessary cyclins for this step (CDK4-cyclin D and CDK2-cyclin E complexes). CDK-cyclin complexes phosphorylate Rb. Phosphorylated Rb no longer inhibits E2F. Because E2F is no longer inhibited, it activates the necessary genes for DNA synthesis, and S phase occurs. Cyclin D is now degraded and cyclin A is synthesized to allow the cell cycle to progress.

What factors control progression through the cell cycle and what do these factors do?

Progression through the cell cycle is controlled by cyclin-CDK complexes. These factors phosphorylate target proteins that have specific functions at specific times in the cell cycle. These complexes enable cell cycle steps as well as other cellular functions such as transcription and splicing. Phosphorylations activate some target proteins and inactivate others to keep the cell cycle progressing.

What are cyclins? What are CDKs? What controls cell cycle progression?

Cyclins are proteins that activate CDK (cyclin dependent kinases) to control cell cycle transitions. Cyclins allow CDKs to function, and their levels rise and fall at specific phases depending on the transition that is occurring. CDKs are a family of protein kinases that guide the transitions from one cell cycle step to another once they are activated by cyclins. Once bound to cyclin, CDK can phosphorylate hundreds of target proteins at serine/threonine/tyrosine residues. The cyclin protion of the complex gives the CDKs specificity and determines which set of proteins are phosphorylated. Different cyclins appear at specific times during the cell cycle for specific transitions: for instance, the G1/S cyclin peaks during the G1/S transition and the S cyclin peaks in S phase.

Define kinetochore.

Structure at the centromeres that are the locations at which chromosomes bind to spindle fibers. A complex of proteins assembles on the centromeric DNA. Some are motor proteins that pull the sister chromatids apart, while others are proteins that monitor the tension in the sister chromatids before the start of anaphase.

Define centromere.

The region of the chromosome where the sister chromatids are tightly bound together. Naturally forming indentation. Site of kinetochore assembly.

Define centrioles.

Organelle that appears during cell division. Once replicated, the two centrioles form a centrosome.

Define centrosome.

Replicated centrioles that form the MTOC. Microtubules radiate out from the centrosomes at each pole of the cell. Centrosomes are replicated during interphase along with the DNA.

What are spindle microtubules? What is the MTOC?

During prophase, the interphase scaffolding of the long stable microtubules is replaced by dynamic microtubules that can shrink back towards the centrosome to allow for segregation of sister chromatids. Spindle microtubules are attached to the centrosomes at either pole of the cell and to the kinetochore complexes on opposite sister chromatids. The MTOC (microtubule organizing complex) refers to the centrosome as it is the origin of all the spindle microtubules.

Define ploidy.

Refers to the number of sets of chromosomes in a cell.

What is cohesin?

Protein complex that forms just after DNA replication in S phase and holds sister chromatids together at the centromeres (and arms) until it is degraded by the enzyme separase. Important in holding sister chromatids together at the metaphase plate until they are properly attached to spindle microtubules.

Define checkpoint. What are cyclins and CDKs?

Checkpoints are times during the cell cycle where the cell evaluates the results of the previous step to make sure that genome integrity is maintained and the cell is ready to progress. Cyclins and CDKs are protein complexes that guide the transition between cell cycle stages. A specific cyclin binds to a CDK, activating it to phosphorylate specific target proteins needed to complete the transition to the next part of the cell cycle.

What are the major differences between meiosis and mitosis?

Mitosis occurs in all types of eukaryotic cells, while meiosis only occurs in sexually reproducing germ cells within reproductive organs that produce haploid gametes. Mitosis is a conservative mechanisms that preserves the genetic status quo, while meiosis is not conservative and introduces genetic variation through independent assortment and recombination. Mitosis also produces growth and regeneration by increasing the number of cells, while meiosis is the source of genetic variation in the human species.

What roles does the synaptonemal complex play?

The synaptonemal complex forms to maintain tight associations of homologs, providing structure for recombination. This complex aligns the homologs, juxtaposing the corresponding genetic regions of the chromosome pair.

How and why does meiosis contribute to genetic diversity?

Meiosis contributes to genetic diversity through independent assortment and crossing over. In independent assortment, chance governs which parental homologs migrate to the two poles during the first meiotic division, so different gametes carry a different mix of maternal and paternal chromosomes. The orientation of maternal and paternal chromosomes is entirely random. Recombination refers to the reshuffling of genetic information through crossing over in prophase I. Recombination is made possible by the process of synapsis and formation of the synaptonemal complex. This process recombines maternally and paternally derived genes so that meiosis results in four genetically identical gametes.

Explain the events and mechanisms of crossing over.

After homologous chromosomes are paired via synapsis and the formation of the synaptonemal complex, the Spo11 protein (an endonuclease expressed in cells undergoing meiosis) induces double stranded breaks in the homologs. Then, an exonuclease degrades the 5' end of each side of the break to produce two 3' tails. Next, in a nucleophilic attack, one of the 3' strands invades the neighboring strand of the non-sister chromatid. Dmc1 and other proteins help one of the 3' tails invade and open up the other chromosome's double helix. A heteroduplex forms between the invading strand and complementary sequence of the nonsister chromatid. the strand displaced forms a D loop, which is stabilized by replication protein A. Next, new DNA added to the heteroduplex enlarges the D loop until the single stranded bases on the displaced strand form complementary base pairs with the 3' tail on the non sister chromatid in a reciprocal second strand invasion. new DNA is added via polymerase and DNA ligase forms phosphodiester bonds to rejoin the strands. The resulting X shaped structures are called Holliday junctions. Branch migration occurs when holliday junctions are stable and move away from each other, expanding the heteroduplex. Recombination is finished when the enzyme resolvase resolves the holliday junctions asymmetrically, resulting in a single cross over event.

Imagine you have two recessive mutations on the same chromosome. What are the expected ratios of progeny if you cross animals heterozygous for both mutations to animals that are homozygous mutant for both? Image now the two mutations are on different chromosomes. What are the expected ratios of progeny? Under which scenario would you observe non-Mendalian ratios? If non-Mendalian ratios, what can you conclude about the two mutations?

If there are two recessive mutations on the same chromosome, then you would expect non-mendelian ratios to occur. Genes on the same chromosome are more likely to be linked, and so a cross between heterozygous for both mutations with homozygous for both mutations would result in a greater proportion of the parental genotypes than recombinant phenotypes. The two largest groups of genotypes would be AaBb and aabb. If the two mutations are on different chromosomes, then you would expect mendelian ratios based on the process of independent assortment.

Using classic genetic techniques of recombination mapping, how would you define location of genes on the same chromosome?

The location of genes on the same chromosome is determined by the recombination frequency. The distance between two genes can be calculated by adding up the total number of recombinants at each loci and dividing by the total number of progeny and multiplying by 100. It is necessary to adjust the recombination frequency by adding double cross overs twice because each individual in the double crossover group is the result of two exchanges.

Define meiosis.

A type of cell division that occurs in the germ cells of an organism. Produces four haploid gametes that are all genetically unique.

Define gamete.

A mature haploid cell that forms a zygote during fertilzation when it unites with a gamete of the opposite sex.

Define mitosis.

Cell division that produces two genetically identical cells.

What is synapsis?

Refers to the lining up of homologous chromosome pairs in a zipper-like formation during prophase I. The synaptonemal complex forms between the two homologs, lining up gene sequences so recombination can occur.

Define chromatid.

One of the two chromosomal strands that are replicated during S phase in interphase and are separated in anaphase of mitosis or anaphase II of meiosis.

Define autosomes

non-sex chromosomes

Define recombination nodule.

Places of recombination between homologous chromosomes during crossing over. During prophase I, recombination nodules assemble on the synaptonemal complex. The exchange of parts between nonsister chromatids occurs here, resulting in the recombination of genetic material

Define linkage.

Genes that travel together after recombination more often than not exhibit genetic linkage. The farther two genes are on a chromosome, the greater the probability of separation through recombination. Gene linkage can be identified by the preponderance of parental classes of gametes.

What is recombination?

The process of shuffling the alleles of genes between homologous chromosomes through physical exchange of genetic material. Promotes genetic diversity and also ensures proper segregation of the homologs in metaphase I.

Define homologous chromosomes.

Two chromosomes (one from each parent) that carry the same genes in the same locations, but may have different alleles.

Define sister and non-sister chromatids.

Sister chromatids are attached to one another at the centromere and are genetically identical because they are the product of DNA replication in S phase. Nonsister chromatids are chromatids from different homologs in the homologous chromosome pair. Carry the same order of genes, but have different genetic material. Crossing over occurs between the non-sister chromatids.

What is Spo11?

Endonuclease that induces double stranded breaks in the DNA in prophase I to initiate recombination.

Define bivalent.

Refers to the pair of synapsed homologous chromosomes.

Define nondisjunction.

Improper segregation of homologous chromosomes or sister chromatids during meiosis or mitosis. Nondisjunction can occur in meiosis I between the homologous chromosomes or in meiosis II (mitosis) between the sister chromatids.

Define trisomy and monosomy.

Trisomy occurs when a cell has three copies of a chromosome. Monosomy occurs when a cell only has one copy of a chromosome.

What are Holliday junctions?

X shaped structures formed during the process of recombination from the first and second invasions and complementary base pairing between the two different strands of DNA of the non-sister chromatids. The resolution of the Holliday junction determines if a crossing over event occurs.

What is a karyotype?

Display of every pair of homologous chromosomes for an individual. Can reveal chromosomal abnormalities including translocations, inversions, intra-chromosomal deletions, and aneuploidy

What is a chiasma?

Regions where crossing over occurs between homologous chromosomes

What experimental observations first supported a semi-conservative mode of DNA replication?

Meselson and Stahl's experiments with heavy nitrogen verified the semiconservative model of replication. They grew one culture E. coli on normal nitrogen-14 media and another on heavy nitrogen-15 media. After several generations of growth on a heavy isotope medium, all of the nitrogen atoms in the DNA of those bacterial cells were labeled with nitrogen-15. Some nitrogen-15 labeled cells were then transferred to the nitrogen-14 medium. Thus, any DNA synthesized after the transfer would contain nitrogen-14 in the newly synthesized strands and nitrogen-15 in the conserved parent strands. Then, equilibrium density gradient centrifugation was used to compare the densities of F1 and F2 generations of the heavy DNA moved to the light medium. F1 cells formed a band between the pure nitrogen-14 and pure nitrogen-15 bands, revealing the F1 DNA contained equal amounts of the two isotopes, invalidating the conservative mode of replication. F2 cells produced two bands--one at the intermediate density and one at the nitrogen-14 density, invalidating the dispersive model because half of the DNA molecules had one nitrogen-15 strand and one nitrogen-14 strand while the other half have two nitrogen-14 strands.

How might Meselson and Stahl's findings have differed were another mode involved?

If conservative replication occurred, F1 cells would have formed two bands at the levels of pure nitrogen-14 and pure nitrogen-15 because one double helix would be completely new and one would be completely old. If dispersive replication occurred, then both F1 and F2 would form different intermediate bands based on the combinations of old and new strands in both double helixes

What proteins function in DNA replication besides DNA polymerase and what are their activities?

Topoisomerase functions to relax supercoils that would otherwise stop the progress of the replication fork. Helicase is an MCM complex that unwinds the double helix. Primase forms the RNA/DNA primer that allows DNA polymerase to add on to the free 3' OH group and begin synthesizing a new strand of DNA. Single stranded DNA binding proteins such as RPA bind to single stranded DNA to stabilize the strands and keep them from reannealing. The sliding clamp holds daughter strands together after new nucleotides are added. The clamp loading protein is a ATPase that allows for the binding of the sliding clamp to the DNA. DNA ligase joins Okazaki fragments together.

What are origins of replication and what does it mean for one to be "licensed"?

Origins of replication are locations on the DNA sequence where replication will begin. Pre-replication complexes assemble at potential origin points, with heterohexamer origin recognition complex, minichromosome maintenance proteins, cell division cycle 6 protein, etc. The origin of recognition complex recognizes the origin points. Once the origin region is specified, protein complexes assemble to activate the structure. The most important protein is MCM2, which is the helicase that opens the double helix. Once MCM2 proteins are localized, the structure is licensed for replication and can attract DNA polymerase to start.

In what direction is the DNA template read and in what direction is a new strand synthesized?

The DNA template is read in the 3' to 5' direction and the new strand is synthesized from 5' to 3'

Distinguish between lagging and leading strand replication and the proteins required for them.

The leading strand runs from 5' to 3', so DNA polymerase can synthesize the new strand continuously. Helicase continues to unwind the double helix and DNA polymerase III moves in the same direction as the replication fork. The clamp proteins hold the strands together after they have been synthesized. Replication of the leading strand is continuous and uses one RNA primer. The lagging strand, in contrast, runs from 3' to 5', so it can not be synthesized continuously. Instead, it is synthesized discontinuously in the 5' to 3' direction via Okazaki fragments. These fragments are initiated by short RNA primers and DNA polymerase III adds nucleotides to the primer. DNA polymerase I then replaces the RNA primer of the Okazaki fragments with DNA nucleotides. DNA ligase then seals the fragments together. Lagging strand replication occurs in the opposite direction of the replication fork, using multiple primers and short fragments.

What would be the sequence of the newly synthesized strand of DNA be if the template strand is

5' GATTCCTCAAGG 3' ? Make sure to write your answer in the 5' to 3' direction.

5' CTAAGGAGTTCC 3'

Define PCR and write out the steps.

PCR (polymerase chain reaction) is a process used to copy and amplify specific DNA sequences. Involves steps of denaturation, annealing, and extension repeated over and over. Using a special form of heat-resistant DNA polymerase, DNA is denatured at 95 degrees to separate the strands and then primers bind to the separated DNA strands at a lower temp. DNA polymerase is active at higher temps and synthesizes new strands.

Define semiconservative replication.

Process of DNA replication in which one strand of each new double helix is conserved from the parent molecule and the other strand is newly synthesized

Define origin of replication.

Short stretch of DNA where replication can begin once the origin is licensed

What is the replication fork?

Y shaped regions formed by the unwinding of DNA by helicase. Replication forks are stabilized by single-strand binding proteins. As helicase unwinds DNA, replication forks move from 5' to 3' and DNA polymerase follows, synthesizing a new strand of DNA.