3.1 Discuss the similarities and differences between MHC's and HLA's. Describe the roles of the three MHC classes.

3.2 Describe antigen processing .How does the process differ from endogenous and exogenous antiges? ( 20 marks)

The sequence of an estrogen-responsive element is given below.

What would you be the most likely consequence of the introduction of this sequence of about 200 bases upstream (-200) of the gene transcirption initiation site encoding the enzyme mucosa?

5' - TGGTCAGGCTGGCT-3

1.      tRNA aminoacylation

a.      What is aminoacylation? Where on the tRNA does it occur?

b.      Why is ATP required for aminoacylation? Why is the hydrolysis of PPi generated during aminoacylation important?

c.       What is the significance of the high-transfer potential of the ester bond created during tRNA aminoacylation?

d.      Why is the specificity of aminoacyl-tRNA synthetases important? How do these enzymes ensure their specificity?

e.      Are you familiar enough with amino acid side chains to answer questions about aminoacyl-tRNA synthetase specificity? (e.g. how might similar amino acids like valine, serine and threonine be distinguished?)

f.        Do you understand why there are differences in amino acid recognition between activation and editing sites? And how those differences dictate the specificity of the two different activities?

What do you envision for the structure of estrogen receptor receptor-bound estradiol?

1. An occurrence of a gene made larger by trinucleotide repeats is:

Allelic expansion

Nucleotide expansion

Translocation mutation

Transformation

2. a chemical that can damage and/or change DNA is called a/an:

Allele

Endonuclease

Vector

Mutagen

3. An occurrence when a section of a chromosome relocates itself to an entirely different (non-homologous) chromosome is called a/an:

Inversion mutation

Translocation mutation

Transformation mutation

Duplication mutation

4. The tandem repeat in the sequence GGGAAGGGAAGGGAAGGGAAGGGAAG is:

GGA

GGGAA

GGAAG

GGAAGGG

A disease characterized by abnormally shaped hemoglobin is called:

Cystic Fibrosis

Sickle Cell Anemia

Marfan Syndrome

Leukemia

5. A point mutation that causes a substitution of a stop codon with an amino acid and leads to the formation of a longer protein is a:

Nonsense mutation

Missense mutation

Sense mutation

Frameshift mutation

6. Addition or deletion of nucleotides in a DNA sequence is known as a:

Nonsense mutation

Missense mutation

Sense mutation

Frameshift mutation

7. The least severe type of chromosomal mutation is:

Point

Frameshift

Inversion

Translocation

8. Chemicals inserting themselves into DNA can cause a:

Missense mutation

Nonsense mutation

Sense mutation

Frameshift mutation

9. A genetic condition caused by allelic expansion is:

Familial hypercholesterolemia

Fragile X syndrome

Alkaptonuria

Galactosemia

10. Which of the following is most likely the original DNA strand if the mutated DNA strand is ATAGUUGATGUA ?

ATAGAAGATGAA

ATAGCCGATGCA

ATAGGGGATGGA

ATAGTTGATGTA

11. An unbalanced chromosomal mutation would include a/an:

duplication (insertion)

inversion

translocation

denaturation

12. Many translocation mutations are found to be involved with:

cancers

sickle cell anemia

Huntington disease

cystic fibrosis

13. A common repeat throughout the human genome that is approximately 300 bases in length is called a/an:

EcoRI repeat

Hind repeat

Exo repeat

Alu repeat

14. A balanced chromosomal mutation includes:

imprintation

denaturation

inversion

deletion

Outline and explain the lytic and lysogenic cycles. please use correct terminology in describing the steps.

3) Proteins are made up of amino acids as the building blocks.

a) The structural integrity of a protein is critical for its functions. Using no more than 300 words, describe TWO (2) examples of mutations or alterations to the native protein sequence which have led to an enhancement or reduction in the biological activity of the mutant proteins. For example, enzyme kinetics, antimicrobial activity, anticancer, drug interaction, and others. (Note: Must only be based on recent (<5 years) research publications). (60%) the research must be based off the above.

Artificial sweeteners, such as NutraSweet and Splenda, have no nutritional value in terms of calories, yet they taste sweet to human subjects.

a) Explain how compounds with no nutritional value can be perceived as ‘sweet’ when ingested.

b) For most of their adult lives, mosquitoes feed on nectar (i.e. sugar water). When you run taste preference tests on lab mosquitoes, you find that though they drink large amounts when presented with sugar water, they avoid drinking water that has been sweetened with Splenda. Describe what might explain this pattern of results, in terms of gustatory receptors in insects.

You have just diagnosed a patient with rheumatoid arthritis in their hands, a chronic, inflammatory disorder that may affect many tissues and organs, but principally attacks the joints producing inflammation and often progresses to destruction of cartilage and joints. Rheumatoid arthritis: extracellular release of lysosomal enzymes. Your patient has a Master of Science in Chemistry, and would like a biochemical explanation of how rheumatoid arthritis is affecting the cells of their hands, so that they can put the disease into perspective. What will you say?

Describe the central role of glutamate synthetase in nitrogen metabolism and the reason why its regulation should be so complex?

Can Western blotting be used as a quantitative technique? How could we use Western analysis to determine the relative change in a protein's expression levels between two treatments? What would we need to be able to determine the absolute level of a protein (i.e. ng/mg of total protein)?

1. Define each of the following terms and give an example.
   1. Simple (complete) dominance =

2. Incomplete dominance =

3. Codominance =

4. Monohybrid cross =

5. Dihybrid cross =

6. Sex-linked trait =

Simple Dominance with one gene:

2. A certain moth species can have either a long (L) or short (l) proboscis.
   1. If you cross a true-breeding long with a true-breeding short proboscis moth in the P generation, what will be the genotypes and phenotypes of the F1 generation?

1. 2. If you cross two of the F1 offspring together, what will be the genotypes and phenotypes of the F2 generation? Give the fraction of the offspring that will have each genotype and phenotype.
2. Roberts’ syndrome causes children to be born with misshapen bones in their faces, skulls, and limbs. Roberts’ syndrome is inherited on a recessive allele, while the dominant allele codes for normal bone shape.
   1. If a carrier for the Roberts’ allele marries someone who is homozygous dominant for the normal allele, what are the chances that their child will be born with Roberts’ syndrome?

2. If both parents were carriers, what would be the likelihood that their child would get Roberts’ syndrome?

4. The polled (meaning hornless) trait in cattle is dominant, the horned trait is recessive. A rancher has a polled bull (male) and mates the same bull to three cows (female). Cow A is horned and produces a polled calf. Cow B is horned and produces a horned calf. Cow C is polled and produces a horned calf. What are the genotypes of the four parents and their calves?

Simple Dominance with 2 genes

4. A gene in cats causes them to be black (dominant) or brown (recessive). A second gene causes cats to be agouti (have stripes on their hairs) or non-agouti (solid colored hairs).
   1. If you did a dihybrid cross between two black haired agouti cats, what fraction of the offspring would be expected to have each phenotype?

2. If a dihybrid black agouti cat mated with a brown cat that was heterozygous for the agouti gene, what fraction of the offspring would be expected to have each phenotype?

Test Cross

5. In mythical dragons, the ability to breath fire (F) is dominant over not being able to breathe fire (f). If you have a fire-breathing dragon and want to know whether it is homozygous or heterozygous, what could you do to find out? Explain how you would do the experiment.

6. In moths, having a long proboscis is dominant over having a short proboscis. You’re trying to figure out whether a particular female moth with a long proboscis is pure or a hybrid, so you cross it with a male moth that has a short proboscis. Half the offspring have long and half have short proboscii. What was the genotype of their mother?

7. In cats, black fur is dominant over brown fur. You have a black cat and you want to know whether it is true breeding for its black fur color, so you mate it with a brown cat. All 10 of their kittens are white. What was the genotype of your parent black cat? Can you be absolutely sure?

Incomplete Dominance

8. In rabbits, alleles for short fur (S) and long fur (L) are incompletely dominant. Hybrids have medium length fur. If you did a monohybrid cross with these rabbits, what ratio of short fur: medium fur: long fur would you see in the offspring?
9. In Andalusian fowl (similar to chickens), if you mate a true breeding white fowl with a true breeding black fowl, all the offspring will be blue. If you were to mate a blue fowl with a white fowl, what fraction of the offspring would be blue?

10. In cats, a particular gene determines whether the cat has white patches on top of its other color(s). Homozygous dominant cats are more than half white. Hybrid cats are less than half white, and homozygous recessive cats have no white patches at all. If a cat with white only on its feet mated with a cat that had no white at all, what fraction of the kittens would have each genotype and phenotype?

Codominance

11. In some horses, hair color is determined by one gene with two alleles. Homozygotes may be either red or white, and heterozygotes are roan (a mixture of red and white hairs). If you crossed two roan horses together, what fraction of the offspring would be roan?

12. Human blood type alleles are codominant. Lucy has type A blood. Her daughter Jenna has type O blood. Jenna’s father Ralph has never had his blood type tested.

1. What is Lucy’s genotype?

2. What are the possible genotypes that Ralph could have?

13. A woman with type 0 blood gives birth to a baby with type 0 blood. In a court case she claims that a man with type A blood is the father of the child. Could he be the father? Show why he can or cannot. Can it be proven on this evidence alone that he is the father?

Sex-linked genes

14. Hemophilia is a rare genetic disorder that results from a deficiency in blood clotting factors. When a person without hemophilia gets a cut, the bleeding lasts for a short time and then the blood clots to form a scab. People with hemophilia have only 1-5% of the blood clotting factors that other people have. Thus, when a hemophiliac gets a cut, it may continue to bleed for days or weeks, sometimes causing dangerous amounts of blood loss.  Hemophiliacs have to do special exercises to prevent their muscles from tearing and producing internal bleeding, and they can take supplemental blood clotting factors, but hemophilia has no known cure. Hemophilia is caused by a recessive allele that is located on the X chromosome.

If X^H is the allele for normal blood clotting, and X^h is the allele for hemophilia, draw a cross between a normal father and a mother who is a carrier for hemophilia. Then list the percentages of offspring that would get each genotype and phenotype.

15. Colorblindness is a sex-linked recessive trait. If a woman who was a carrier married a man who was colorblind, what percentage of their children (males and females) would be colorblind?

16. For a male to be colorblind, does he have to get the colorblindness allele from his mother, from his father, or both? For a female to be colorblind, does she have to get the colorblindness allele from his mother, from his father, or both?

1.(a) How are ecological communities structured? (b) State five reasons why biodiversity is important to an ecosystem?