final exam - practice problems

Question 1

hemophilia inheritance pattern

Answer 1

germline mutations specifically mutations in genes like Factor IX that are present in the egg or sperm cells

• Factor IX mutation outside of the sperm or egg (like in the bone marrow) will not harm the offspring!!
• also women exhibit mosaicism so a mutation in bone marrow cell doesn’t affect all her cells

Question 2

Renegade scientist He Jiankui constructed two babies last year using CRISPR, Lulu has two mutant alleles of CCR5, one with one base inserted in an exon, the other with four bases deleted in an exon. Nana has a wild-type allele and a 15 bp deletion. Describe the CCR5 protein(s) made by Lulu.

Answer 2

both her alleles have frameshift mutations so she will produce 2 distinct, truncated and likely nonfunctional CCR5 proteins

Question 3

Renegade scientist He Jiankui constructed two babies last year using CRISPR, Lulu
has two mutant alleles of CCR5, one with one base inserted in an exon, the other
with four bases deleted in an exon. Nana has a wild-type allele and a 15 bp deletion.
Describe the CCR5 protein(s) made by Nana

Answer 3

she will have 1 normal CCR5 protein from her wild-type allele

her other allele will have 5 amino acids deleted leading to partially functional or nonfunctional protein (but not a frameshift mutation)

Question 4

MHC class 1 molecules are found on:

Answer 4

all nucleated body cells

(all nucleated body cells also present endogenous peptide antigens to CD8+ killer T-cells)

Question 5

Two strains of Drosophila carry recessive alleles that cause the flies to lack wings.

You cross these strains together. All the F1 are normal. What F2 phenotypic ratio do
you expect if you cross the F1 to each other?

Answer 5

• if the 2 different strains that have recessive wingless alleles are crossed and produce normal winged F1, then mutations are in different genes (example of complementation)

3 normal: 1 wingless

• if the alleles were in the same gene, then they would fail to complement and the progeny would all have the mutant phenotype

Question 6

RAG-1 and RAG-2

Answer 6

enzymes that rearrange antibody and T-cell receptor genes

• evolutionary related to transposons
• antibody and T-cell receptor genes are made of multiple V, D, J combinations- these segments are flanked by inverted sequence repeats, which resemble the structure of transposons

Maize activator (Ac) is also a transposon

Question 7

mechanisms that can turn porto-oncogene into oncogene

Answer 7

• point mutations within the gene (Ras is a single amino acid change causing it to be constitutively active)
• point mutation in control element: mutation in promoter or enhancer
• gene amplification

-translocation: moving port-oncogene to new location in the genome

-retroviral insertion

• tumor suppressor mutations

Question 8

balancing selection + example

Answer 8

balancing selection: occurs when natural selection maintains 2 or more alleles in a population b/c heterozygotes have a higher fitness than either homozygote

example: sickle cell anemia and malarial resistance

Question 9

how are organ transplants possible?

Answer 9

because of MHC genes (that are involved in the immune system’s ability to recognize self verses non-self)

MHC restriction: trained to recognize and respond to antigens presented by self-MHC molecules
- immune response triggered when foreign MHC detected on organ transplant

MHC matching: to minimize risk of rejection, doctors try to match the MHC genes of donor & recipient as closely as possible (why siblings are the best candidates for organ transplant)

and also immunosuppressive drugs

Question 10

what is the primary barrier preventing the engineering of enhanced humans?

Answer 10

ethical considerations

Question 11

Figuring out what items to pack in a backpack, making antibodies that bind a virus
tightly, the rise of antibiotic-resistant bacteria, optimizing a bird’s beak for available food sources, tumorigenesis, and creating corn that is larger and more nutritious than what is
naturally available are all examples of what universal process?

Answer 11

Evolution

Question 12

Cas9 and restriction enzymes catalyze what reactions?

Answer 12

cleave DNA at specific sequences

generation of double strand DNA breaks

Question 13

Many articles about the rise of antibiotic-resistant bacteria claim that overuse of antibiotics creates resistant strains. How is this incorrect?

Answer 13

Because the antibiotic doesnt directly induce the mutation, it just selects for the ones that have the antibiotic resistant strain

Question 14

How does natural selection favor different phenotypes at different times?

Answer 14

because environmental conditions and selective pressures are constantly changing

Question 15

How does sexual selection promote traits that seem to decrease survival?

Answer 15

because sexual selection operates on reproductive success which is not always perfectly aligned with survival

• ex. male peacock’s tail which is hard to maintain bc its so extravagant but it attracts the female peacocks

Question 16

Are the lactose-persistence mutations more functionally analogous to lacOc or to the PTC taste receptor gene we genotyped in class?

Answer 16

the LacOc mutation b/c its a regulatory gene unlike the PTC taste receptor gene which is just a structural gene

Question 17

who forms Barr bodies and why?

Answer 17

females, to silence their extra X chromosome

Question 18

what is negative selection in immunology

Answer 18

negative selection: critical process that eliminates immune cells that could potentially attack the body’s own tissues

• occurs in the bone marrow for B cells and in the thymus for T cells

Question 19

fab (fragment antigen-binding) region of a molecule

Answer 19

fab region: key part of an antibody molecule, responsible for antigen recognition and binding

variable region of antibody that binds specifically to a particular antigen

• variability in these regions is caused by V(D) J recombination

Question 20

in what way does Ras contribute to cancers?

Answer 20

Ras proteins: involved in signal transduction pathways that regulate cell growth and division.
- act as molecular switches that relay growth factor signals from cell surface to the nucleus

• constitutive activation (permanently switched on)
• mimicking growth factor stimulation
• resistance to degradation

Question 21

is somatic hypermutation guaranteed to generate better antibodies?

Answer 21

No, its a crucial process for improving the immune response, but it is inherently random and can lead to antibodies with a range of affinities, including some with lower affinity than the original antibody.

Question 22

True or false: 2 identical promoters will produce identical levels of mRNA

Answer 22

false

b/c promoters are only one part of gene regulation; there are other factors that influence rate and level of mRNA production like transcription factors/DNA methylation, etc.

Question 23

An E. coli strain synthesizes beta-galactosidase all the time. Which mutations might this strain carry?

Answer 23

LacI-

inactive lac repressor

Question 24

You decide to clone a mouse by creating iPS cells. You get B-cells from a mouse and re-program them. What do you expect?

Answer 24

De-differentiation: The B-cells, which are differentiated cells, will revert to a pluripotent state, meaning they regain the ability to differentiate into any cell type in the body.

Expression of Pluripotency Genes: reprogrammed iPS cells will express genes associated with pluripotency, such as KLF4, SOX2, c-myc, and Oct-3/4. These genes are crucial for maintaining the pluripotent state and enabling differentiation into various cell types.

Loss of B-cell Specific Characteristics: no longer express genes or proteins specific to B-cells, such as antibodies or B-cell receptors

Potential for Differentiation: potential to differentiate into any cell type in the mouse body, including those not normally derived from B-cells, such as neurons, muscle cells, or liver cells.

Genetic and Immunological Identity: cells will be genetically and immunologically identical to the donor mouse from which the B-cells were originally obtained.
-significant advantage of iPS cell technology as it avoids immune rejection if the cells are used for transplantation back into the same mouse.

Question 25

what is protection against microorganisms or viruses inside cells provided by?

Answer 25

MHC proteins and CD8+ killer T-cells

Question 26

What may play a role in ensuring that only one set of antibody alleles are expressed in a given B-cell?

Answer 26

allelic exclusion

(maybe DNA methyltransferase?)

Question 27

You have an immortal cell line in which one allele of a particular gene are deleted. Which of these could be the deleted gene?

Answer 27

p53

Question 28

Mutations that increase production of the growth factor encoded by Bride-of-sevenless (boss) can suppress sevenless. Which of these could be a sevenless suppressor mutation in boss?

Answer 28

mutation in cis-regulatory region that increases binding of a transcription factor

Question 29

True or false: IgM antibodies have lower affinity than IgG antibodies

Answer 29

true

Question 30

what do T-cell receptors partially recognize?

Answer 30

MHC molecules

• dual specificty: recognize not only the antigen but also the specific MHC molecule presenting it

Question 31

You are working with two true breeding plants in the lab. The two genes controlling flower color and seed spotting are not linked. You cross a plant with red flowers and spotted seeds with a plant that has white flowers and dotted seeds. The F1s have pink flowers and with spotted+dotted seeds. How would you characterize alleles that govern flower color and seed spotting?

Answer 31

alleles for flower color exhibit incomplete dominance, while allele for seed spotting exhibit codominance

Question 32

cancer inheritance of tumor suppressor loss of function alleles

Answer 32

recessive

Question 33

Cycloheximide affects eukaryotic cells in the same manner as streptomycin does to bacterial cells. Eric Kandel received the 2001 Nobel Prize in part for an experiment in which he showed that animals treated with cycloheximide can form short term memories but cannot make long term. From this, surmise which biological process is required for long term memory formation?

Answer 33

translation (answer on doc)

but notebooklm said protein synthesis (Actually theyre the same thing)

Question 34

when are antibodies specific for an antigen readily detectable in serum following primary infection with a pathogen?

Answer 34

during secondary immune response

• around 1 week

Question 35

what are complementarity determining regions?

Answer 35

hypervariable loops within the antibody’s antigen-binding fragment (Fab) that directly interact with the antigen.

Question 36

the most variable part of a MHC molecule is

Answer 36

region that binds peptides

Question 37

You are mapping wingless and epileptic mutants on Drosophila chromosome 3. The wingless and epilepsy alleles are recessive. You create a female fly that is heterozygotic for both genes, and cross her to an inbred wingless and epileptic male. Based on these results, who were your heterozygote female’s parents?

Answer 37

not enough information

Question 38

What type of mutation would be most useful for studying a gene that has no phenotype when mutated on its own?

Answer 38

synthetic mutations

Question 39

The synthesis of purple pigment in flower petals is controlled by two genes, A and B.
The biochemical pathway is shown. They are purple only if both blue and red pigments are
made. What color petals would you expect in a plant missing enzyme B?

Answer 39

blue

Question 40

Via GWAS, you identify a polymorphism that increases the risk of depression. The
polymorphism is a SNP inside an intron. Which of these is the most likely problem?

Answer 40

notebookLM: difficult to determine how SNP functionally contributes to risk of depression b/c introns are non-coding regions therefore SNP in intron doesnt directly alter the protein’s amino acid sequence

document: lariant intermediate cannot form since branch site has been mutated

Question 41

1/400 Vulcans lack an inner eyelid, putting their eyes at risk from the bright light of their star Epsilon Eridani. This trait is recessive. What fraction of the entire population are heterozygotes?

Answer 41

38/400

Question 42

You have an immortal cell line in which one allele of a particular gene has a single amino acid substitution. Which of these could be the mutated gene?

Answer 42

Ras

Question 43

In this family, affected members have a mutated 3’ splice acceptor at the end of the first
intron causing the following exon to be skipped. This mutation causes a BamH1 site.

What is the longest protein that could be generated by this mutant gene assuming stop codon in UTR?

Answer 43

40 amino acids

Question 44

Two strains of mice carry recessive alleles that cause the animals to lack tails. You cross these strings together. All the F1 are normal. What F2 phenotypic ratio do you expect if you cross the F1 to each other?

Answer 44

9 normal: 7 tail-less

this answer came up before too - double check this ratio

Question 45

You would like to transplant a kidney into your patient. What genes should you examine in potential donors and compare to the variants in the recipient to avoid transplant rejection?

Answer 45

MHC

Question 46

You are studying blindness using mice. You find a spontaneous mutant, milton, that is blind. You cross it to wild-type. While none of the F1s were blind, 1⁄4 of the F2’s were. You cross these blind siblings to each other and find all their offspring are blind. You maintain this strain by crossing blind siblings to each other. Other researchers have defined two other mouse stains, homer and braille, that have similar properties, both phenotypically and genotypically. You cross milton and homer, and find that none of their offspring are blind. In contrast, when you cross milton and braille, all of their offspring are blind. What do you expect when you cross homer and braille?

Answer 46

100% wild type

Question 47

MECP2 is required for CpG-methylating LINE elements to give rise to neurons.

Why would cells want to CpG methylate LINE elements?

Answer 47

silence or repress their expression

Line elements = transposons

Question 48

All the individuals in an inbred fly strain have legs in place of the antenna, but the length of the leg varies. How would you express this mutation?

Answer 48

complete penetrance (b/c everyone with the mutation displays the phenotype)

and variable expressivity (b/c variable length of the legs)

Question 49

80% of the individuals in an inbred fly strain have legs in place of the antenna. How would you describe this mutation?

Answer 49

80% penetrant haploinsufficient

Question 50

your muscle and nerve cells have differences in structure and function because they _______

Answer 50

express different genes

Question 51

Improper CpG demethylation of some genes can promote cancer. Which one of these genes may be hyper-methylated in cancers?

Answer 51

Rb

hypo methylated is Ras

b/c CpG methylation silences genes

Question 52

What molecules bind poorly to vaccine-evading variants like beta and omicron?

Answer 52

neutralizing antibodies

• can still neutralize the virus, they do so less effectively than the original virus

Question 53

Select the ingredients in a PCR reaction that specify the DNA that is to be amplified

Answer 53

primers

Question 54

What class of mutagen is more likely to result in a non-functional protein, an alkylating agent that modifies DNA bases or an intercalator that creates single base deletions?

Answer 54

intercalactor

Question 55

chromosome deletion in chromosome 5

Answer 55

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