Genetics Class Exams

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Note these are just sample questions, there are far more questions and answers inside.

1)   Mendel crossed a two yellow, short plants and received the following offspring:
0 yellow, tall   42 yellow, short   0 green, tall   25 green, short
What are the genotypes of the parents assuming Y = yellow allele, y = green allele, T = tall allele, t = short allele?
a)   yytt b)   Yytt
c)   YYTT
d)   YyTT
e)   yyTT

2)   How many sperm cells will form from fifty primary spermatocytes?

Primary spermatocytes are 4n, therefore expect 4*50 = 200

3)   The Purple People Eater has 5 distinct chromosomes (2n = 10) and 40 known genes, each with two alleles.
If an individual is heterozygous at 50% of all known loci, and 50% homozygous recessive at the remainder of the loci, approximately how many different gametes can be produced if all genes independently assort?
a.   1x106
 
b.   1x1012
c.   1x1015
 
20 of the genes do not matter since homozygous,
20   6
 
d.   1x101
e.   1x103
 
other 20 assort independently therefore 2
 
= 1.05x10
 

4)   Assuming a 1:1 sex ratio, what is the probability that 4 children produced by the same parents will be born
 
with the sexes alternating?
 

(1/2)4
 

+ (1/2)4
 

= 0.125

Two possible outcomes, order matters – sum law states: two independent events occurring but the combination can occur in more then one way, therefore add the probability of each event
happening

5)   How many chromatids are present at each stage of the cell cycle in a cell with eight pairs of chromosomes? Stage of Cell Cycle:   G1    G2    G0    G2/M

6)   How many degrees of freedom will there be for a ?2  test of the phenotypes that appear in the F2 generation following a P1 cross of four genes between pea plants that differ for Mendel’s genes assume the following:
1) the initial parents were true breeders, 2) dominance is complete and 3) the traits are not linked?
16 Possible phenotypes (24) Df = n-1 = 16-1 = 15

7)   In the cross above (question #6), what proportion of the offspring are expected to be homozygous dominant for two of the genes and homozygous recessive for the other two?

(1/4)(1/4)(1/4)(1/4) = 1/256

8)   Which of the following diagrams show homologous pairs aligned during mitosis (black = maternal; white =
paternal)?

9)   Which of the following statements about Prophase I of Meiosis is incorrect?
a.   During leptonema, homologous chromosomes align and pair. (Pairing is not yet complete!)
b.   After diplonema, crossing over is complete. c.   During zygonema, synapsis is initiated.
d.   During pachynema, meiotic recombination sites mature.
e.   During the process of synapsis, homologous pairs are held together by cohesion and crossing over.

10) Model organisms are essential to the study of genetic and physiologic mechanisms. Which of the following is not a characteristic of a model organism?
a.   Relatively short life cycles b.   Easy to grow and maintain.
c.   Mechanisms are always the same across species (Mechanisms are the same across most, but not all
species)
d.   Produce many offspring
e.   Discrete variations are available

11) In what stage of meiosis does an error most likely to account for presence of Down’s syndrome (three
copies of chromosome 21) in humans, where homologous pairs fail to separate?
a.   Anaphase I b.   Anaphase II c.   Prophase I
d.   Prophase II
e.   Metaphase I
f.   Metaphase II

12) Which of the following modes of inheritance describes an interaction that occurs between multiple alleles to affect the phenotype?
a.   Epigenesis b.   Pleiotropy
c.   Epistasis
d.   X-linked
e.   Codominance (all other options are interactions between genes, except X-linked which is sex specific)

13) In the ABO blood system in human beings, alleles IA  and IB  are codominant, and both are dominant to the
IO  allele. In a paternity dispute, a type AB woman claimed that one of four men, each with a different blood type, was the father of her child with type B blood. Which of the following could be the blood type of the father of the child on the basis of the evidence given?
a.   Type O
b.   Type AB
c.   Type A
d.   Type B
e.   All of the above
f.   None of the above

14) In the pedigree below, what is (are) the possible mode(s) of inheritance? Select the best answer.
 
a.   X-linked dominant
b.   Autosomal dominant c.   X-linked recessive
d.   Autosomal recessive e.   A or B
f.   C or D
 
X-linked possible because occurs in crisscross pattern, mostly in males

Autosomal recessive possible because it skips generations
 

15) A researcher isolates two types of mutants from pea plants that do not have flowers. Which of the following analysis should the researcher use to determine if the mutations occurred in the same gene?
 
a.   Dihybrid Cross Analysis b.   Testcross Analysis
c.   Pedigree Analysis
d.   2 Analysis
e.   Complementation analysis
 
If cross two mutants together, and offspring are mutant then may be two different mutations in same gene. If offspring are normal,

2)  When DNA is highly G-C rich, which of the following statements is incorrect when compared with A-T rich sequences?
a.  The melting temperature is higher.
b.  The DNA sequence has a UV absorbance at 260 nm.
c.  Genomic imprinting has a higher probability of occurring.
d.  Sequences will migrate more quickly on an electrophoretic gel. – only if DNA
fragments are different sizes
e.  Will have a denser point of neutral buoyancy.

3)   Meselson and Stahl used sedimentation equilibrium centrifugation to determine that DNA replicated in a semiconservative manner. Using this technique, labeled DNA could be isolated and measured. What principles of this technique did not allow isolation of the labeled DNA to occur?
a.   Downward centrifugal force
b.  Velocity of sedimentation – has nothing to do with density dependent centrifugation
c.   Upward frictional force
d.   Density of the solution e.   DNA Density

4)   Which of the following do not have homologous functions in eukaryotes and prokaryotes in the process of replication?
a.  OriC, ORC – OriC is a DNA sequence for origin of replication in prokaryotes, ORC is a protein complex that recognizes the ARS (origin) in eukaryotes, OriC and ARS are homologous OR DnaA and ORC would be homologous
b.   DNA polymerase III, DNA polymerase
c.   DNA primase, DNA polymerase
d.   DnaB/C, Mcm
e.   DNA gyrase, DNA topoisomerase

5)  Which of the following is not true about Telomeres?
a.  Telomeres are highly repetitive sequences at the ends of chromosomes.
b.  Telomeres are maintained through multiple rounds of replication in ALL
cells. . – not true…only in select cells (germ cells, cancer cells, stem cells…)
c.  Telomeres are restored by a ribonucleoprotein, telomerase.
d.  Telomeres are a preventative mechanism for loss of genomic sequence. e.   Telomere repeated sequences are varied from species to species.


6)  Which of the following is not a possible result of single end invasion from a double stranded DNA break?
a.  DNA repair
b.  Crossing over
c.  Gene conversion
d.  Recruitment of RAD51
e.  None of the above

7)  A temperature sensitive mutant of E.coli displays a problem in synthesizing DNA. Which enzyme is likely affected by a mutation which allows accumulation of Okazaki fragments and fails to complete DNA synthesis?
a.  DNA Polymerase III
b.  DNA Polymerase I – need to remove RNA primer
c.  DNA Polymerase
d.  DNA Polymerase
e.  DNA Polymerase II


8)  Goblins contain a diploid genome consisting of at least 105  bp. If this amount of DNA is present in chromatin fibers, how many total histones are present to initiate the first level of chromatin compaction?
a.  2000 b.   2500 c.   3000 d.   4000
e.  4500 -- 105 bp/(200 bp/nucleotide) = 500 nucleosomes * 9 histones with each
nucleosome (including H1 linker histone)= 4500


9)  Which histone tail is methylated at an arginine to allow opening of condensed chromatin by destabilizing interactions with neighboring nucleosomes?
a.  H1
b.  H2A c.   H2B d.   H3
e.  H4 – arginine rich (like H3), but the only one that we discussed which stabilizes interactions with neighboring nucleosomes.


10) Which of the following is not a characteristic of heterochromatin?
a.  Densely coiled with few histone modifications
b.  Darkly staining bands when stained with Giemsa and trypsin digested c.   Can inhibit gene expression through position effects
d.  Replicates earlier in S phase because genes not as important – replicates later in S phase
e.  Present uniquely in eukaryotic genomes


11) Condensin is a holoenzyme involved in which level of chromatin compaction?
a.  Nucleosome wrapping of DNA
b.  Solenoid formation
c.  Looping with the aid of a scaffold d.   Chromatid formation
e.  Both A and B
f.   Both C and D


12) What is the sequence of information that allows chromatin to loop and attach to a scaffold (Note: all are abbreviations we have talked about)?
a.  SAR – scaffold attachment region b.   ORC – origin of replication complex c.   PAR – pseudoautosomal repeat
d.  ARS – autonomously replicated sequence

e.  CDC – cell division control


13) Formation of a solenoid during chromatin compaction results in condensation of chromatin into this sized fiber?
a.   2 nm b.   6 nm
c.   30 nm d.    300 nm e.   700 nm

14) Benzer utilized complementation analysis to map the rII locus of the T4 phage. In a cross of two mutants, he found that one mutant did not rescue the other. Which conclusion(s) could be drawn from the data?
a.  One of the mutations was a deletion
b.  Both of the mutations were in different genes c.   Both of the mutations were in the same gene d.   One of the mutations had an insertion
e.  Both A and C
f.   Both B and D

15) In E. coli, four Hfr strains donate the following markers, shown in the order donated:

strain 1   Q   B   X   T   A
strain 2   G   C   Y   S   A
strain 3   X   B   Q   D   G
strain 4   S   A   T   X   B

All these Hfr strains are derived from the same F+ strain. What is the order of these markers on the circular chromosome of the original F+?
 
a)   QBXTASYCGD b)   SATXBQCYSA c)   GCYSATXBQD d)   XBQDGSATY
e)  None of the Above
 
Typo on my part – will accept either answer
 
16) Which is not a method by which foreign homologous DNA can be integrated in the bacterial genome?
a.  Recombination b.   Transformation
c.  Translocation - chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes.
d.  Transduction
e.  Conjugation

Short Answer/Problem Solving (Points noted for each problem). Organize your thoughts and your work, so that the graders can CLEARLY see what you are doing. Show ALL of your work, if you get a wrong answer but have the right process you may still be awarded partial credit. If there are multiple possibilities, list all possibilities! Answer all questions on these pages. If you need more room, write on the back of the same page, clearly labeling to which question the work belongs. If you come to a question and you do not know how to attack it immediately, do not panic. Skip the question and go on. When you are done with the remainder of the test, return to the question.

7)  Understanding Replication.
a.  List the enzymes required for prokaryotic replication, give a one sentence description of the function of the enzyme and number the enzymes in order of function at a replication fork (16 points).

1)   Which set of experiments contributed to our knowledge that the genetic code consisted of triplets?
a.   Proflavin experiments
b.   Triplet binding assay
c.   Mixed copolymer assays
d.   Polynucleotide Phosphorylase e.   Repeating copolymer assays

2)   Which of the following modes of chromosomal sex determination describes when the female has a pair of heteromorphic chromosomes?
a.   XX/XY b.   XX/XO c.   ZZ/ZW d.   X:A
e.   YY/XY


3)   Which of the following chemical properties of single stranded DNA drives the adhesion of two pieces of DNA together?
a.   Complementarity of bases b.    Stickiness of the ends
c.   Hydrogen bonding capabilities
d.   Ability to form hybrid molecules e.   Hydrophobicity of nucleotides


A short mRNA is depicted below. For each question, circle the correct answer and clearly label the circle with the number of the question.
4)   Which codon encodes a Methionine?
5)   Based on this sequence, which of the remaining codons (not selected in #24) represents an amino acid in proper reading frame?   

6)   On the Y chromosome, genes specific to the male may be found as palindromes. Which of the following statements is NOT true regarding these palindromes?
a.   Palindromes are located in the ampliconic region of the MSY.
b.   Palindromes are sequences of base pairs that read the same but in opposite directions on complementary strands.
c.   Palindromes ONLY occur as inverted repeats on the same DNA strand.
d.   Palindromes are able to undergo recombination if a sister chromatid is present. e.   Palindromes are able to undergo recombination on the same chromatid.

7)   Sanger sequencing is being replaced by next generation sequencing methods. Which of the following is not a limitation of Sanger sequencing?
a.   Isolation DNA to sequence
b.   Polymerization reaction
c.   Individual Reactions
d.   Electrophoresis of reaction products e.   Read and record sequences

8)   Which of the following abnormalities/mutations can lead to a sex reversal phenotype in which a genetic female appears male?
a.   Mutation in SRY
b.   Mutation in AMH
c.   Mutation in androgen receptor
d.   In ability to produce sufficient cortisol
e.   All of the above


9)   Sexual orientation of a human individual can be affected by all of the following except:
a.   Brain development
b.   Maternal hormone environment c.   Genetic Background
d.   Environmental Toxins
e.   Parenting Environment


10) What is the predicted ratio of offspring if non-disjunction of one diad occurs during the second division of meiosis prior to formation of the maternal gamete (assume normal segregation in the paternal gamete)?
a.   2 trisomic:2 monosomic
b.   2 disomic:1 trisomic:1 monosomic
c.   1 disomic:2 trisomic:1 monosomic d.    2 trisomic:2 disomic
e.   1 disomic:1 trisomic:2 monosomic

11) During meiosis of autotetraploid organism, how many chromosomes are present in each cell after telophase of the second meiotic division if the cell started with a chromosome number of 5 (assume normal segregation)?








12) Which model organism(s) has individuals with tissues for both male and female gametes?
a.   Humans
b.   C. elegans
c.   Zebrafish
d.   Chlamydomonas e.   Drosophila

13) EcoRI is a common enzyme used in DNA cloning and recognizes the sequence GAATTC. When that sequence is recognized it is cleaved between the G and the first A. Which of the following is a true statement regarding the result of EcoRI’s actions?
a.   A blunted DNA end will form
b.   Hydrophilic nucleotides will be exposed
c.   Hydrophobic DNA backbone will be cleaved
d.   A 5’ “sticky” DNA end will form
e.   A 3’ single stranded DNA end will form


14) Which of the following regions of the Y chromosome does NOT encode genes?
a.   Heterochromatic region
b.   X-degenerate region c.   Euchromatic region d.    Ampliconic region
e.   Palindromic region


15) Which type of cloning vector is based on the fertility factor plasmid of bacteria?
a.   Lambda Vector b.    Cosmid Vector
c.   Bacterial Artificial Chromosome
d.   Yeast Artificial Chromosome e.   Expression Vector

16) During RNA capping in eukaryotes, 7-methylguanisine is added to the end of the growing mRNA. Which of the following is true regarding this process?
a.   7-methylguanisine is attached 5’ to 3’ at the end of the pre-RNA
b.   7-methylguanisine is attached 5’ to 5’ at the end of the pre-RNA
c.   7-methylguanisine is attached 3’ to 3’ at the end of the pre-RNA
d.   7-methylguanisine is attached at the 3’ end of the pre-RNA
e.   7-methylguanisine is attached after splicing of mRNA


17) In a sample, there is a population of 50 copies of the insulin gene. If I subject this sample to 35 rounds of amplification by PCR, approximately how many copies will have in my final sample?
a.   1.7 x 103
b.   1.7 x 1012 (x*2n  =50*235)
c.   2.9 x 109 d.    3.9 x 1016 e.   3.4 x1010


18) Bread wheat is a hexaploid organism and contains three genomes: A from a diploid wild wheat
(2n = 14); B from a wild goat grass (2n = 14); C from another species of wild goat grass (2n =
14). Chromosomes 1A, 1B, and 1C from the three parental species contain a similar set of genes in spite of their different sizes and banding patterns. Which of the following statements is false regarding the bread wheat organism?
a.   Bread wheat is an allopolyploid organism. b.    Bread wheat is an amphitriploid organism.
c.   Bread wheat is an AUTOpolyploid organism. – REMEMBER AUTO = SAME
d.   Bread wheat is a hybrid organism.
e.   Bread wheat likely forms viable gametes.


19) Which of the following components of a male is the most important to determine maleness?
a.   Y chromosome b.    Amh gene
c.   SRY gene
d.   Testosterone e.   Testes

20) According to genic balance theory, in drosophila, which of the following represents a female individual?
a.   XY:2A b.   X0:2A c.   XY:3A d.   2X:2A
e.   None of the above

21) During Sanger sequencing, dideoxynucleotides are incorporated into the reaction mixture. The purpose of the dideoxynucleotides is:
a.   To provide a means of detection.
b.   To prevent addition of bases by the absence of 5’ triphosphate group. c.   To terminate a chain by incorporating a bulky fluorescent dye.
d.   To terminate a chain by the absence of a 3’ hydroxyl group.
e.   To allow isolation of the chain


22) After the cap is added to the RNA to prevent degradation in eukaryotes, what is the next step required in the transition from pre-RNA to mRNA?
a.   Cleavage of 3’ end of transcript
b.   Addition of Poly-A tail at 3’ end of transcript c.   Recognition of splice sites by proteins
d.   Lariat formation to induce splicing
e.   Recognition of a conserved sequence


23) I have a set of genes related to my favorite disease. I want to study these genes in an isolated but eukaryotic setting. Which cloning vector should I use that can hold 100s of kb?
a.   Lambda Vector
b.   Yeast Artificial Chromosome
c.   Cosmid Vector
d.   Bacterial Artificial Chromosome e.   Expression Vector

24) Which of the following are features of the genetic code was revealed by the studies of Nirenberg after the triplet binding assays were completed?
a.   Degenerate
b.   Ambiguous
c.   Initiation Sequences d.    Non-overlapping
e.   Triplet code


25) In the production of a cDNA library from C. elegans, which of the following is not a step that I
would take in this process?
a.   Use oligo dTs to pull down mRNA
b.   Reverse transcribe the sequence
c.   Digest the mRNA template with RNase H
d.   Use DNA ligase to seal any gaps in copied sequence
e.   Use an RNA polymerase to copy the sequence

28) The chromosome below is originally found in your metaphase spread. Draw this chromosome when the specified mutation occurs (1 point each). Be sure to include the genes on your drawings in the correct order. Beside each drawing, describe in one to two sentences what happened to the chromosome compared to the original (1 point each): NOTE THE ANSWERS BELOW ARE EXAMPLES – IF DRAWN CORRECTLY, ANY OF THE GENES COULD BE REORDERED

29) What are the gametes that are produced if a single cross over event occurs in an inversion loop if
1) the organism is a pericentric inversion heterozygote and 2) the organism is a paracentric inversion heterozygote. Describe the gametes according to centrosome number and define any mutations that might occur. Indicate which are the result of crossing over (8 points total, one for each gamete described correctly).

31) You are attempting to create a plasmid which expresses your gene of interest. You have been provided a vector called MIGR1 (map above). Before you use this vector for cloning you would like to test the vector to ensure it has maintained its integrity by doing a few restriction digests of the plasmid. Based on the map, if you were to cut the plasmid with the following enzymes, predict the size fragments you would expect to see on the gel (1 point each):

1)  Tautomerization can result in all but which of the following mutations?
a.  Transversion mutation – due to normal base pairing, since ring structures are not altered, cannot switch a purine for a pyrimidine and vice versa
b.  Point mutation
c.  Transition mutation d.   Frameshift mutation e.   Nonsense mutation

2)  Prokaryotic gene regulation can occur at which stage below:
a.  Regulation of mRNA processing b.   Regulation of translation
c.  Regulation of mRNA transport d.   Regulation of protein activity
e.  Regulation of gene transcription

3)  You are studying protein translation and come across a cell with rough ER but curiously there are no proteins present at the cell surface.  Of the components in the pathway for secreted and/or membrane bound proteins, which is most likely mutated that allows proper recruitment of the ribosome-mRNA complex to the ER but prevents entrance of the growing peptide chain into the ER?
a.  Signal sequence – arrived at ER ok
b.  Signal recognition particle – arrived at ER ok
c.  SRP receptor – arrived at and binding to ER ok
d.  Sec61 – ribosome binding site could be intact but have a mutation within the channel preventing protein passage into ER
e.  Signal peptidase – do not know, cannot enter ER to be cleaved

4)  Which of the following is a false statement regarding aminoacyl tRNA synthetases?
a.  Facilitates the addition of an amino acid to the proper tRNA
b.  Requires ATP as an energy source to charge a tRNA
c.  Creates a covalent link between the amino acid and the 5’ end of the tRNA (AA added to 3’ end of tRNA)
d.  Creates a covalent link between the 5’ phosphate of ATP and the amino acid e.   None of the above

5)  Which of the following is not a component of the prokaryotic translation initiation complex?
a.  Small ribosomal subunit b.   Protein factors
c.  Shine-Dalgarno sequence (Ribosome initially binds to mRNA through and then slides to start signal, initiation complex will not assemble on this DNA sequence)
d.  tRNA for f-met
e.  mRNA start codon

6)  Which of the following steps during translation does not require GTP as an energy source?
a.  Addition of large ribosomal subunit to initiation complex b.  Shifting of growing chain to P-site
c.  Release of ribosome from the mRNA
d.  Peptide bond formation between two amino acids
e.  None of the above

7)  Which of the following would cause transcription from the lac Operon in the absence of lactose?
a.  Mutation that removes the DNA site bound by CAP-cAMP
b.  Mutation of the lac operator
c.  Mutation of a structural gene in the lac operon d.   Mutation of the CAP gene
e.  A and D

8)  The correct translation from nucleic acid language to amino acid language is primarily driven by:
a.  The base-pairing of the Shine-Dalgarno sequence to the anti-Shine-Dalgarno sequence.
b.  The base-pairing of the start codon sequence to the anti-codon sequence of the proper tRNA. – if do not match f-Met with start codon, protein will not be translated correctly.
c.  The selective introduction of the specific tRNA-f-Met by EF-Tu. – can introduce
but may not recognize anticodon
d.  The correct interaction between a tRNA and its specific aminoacyl tRNA
synthetase.
e.  The identification of the AUG start codon by the translation initiation complex
 
9)  BAD QUESTION – MULTIPLE ANSWERS ACCEPTED
Modified bases, present in the anticodon loop of a tRNA, are recognized by which pocket of the ribosome where tRNAs are matched with the mRNA codon?
a.  A site – only tRNAs in the A site are able to recruit appropriate tRNAs
(modified bases or not)
b.  P site – first tRNA incorporated here
c.  E site – only uncharged tRNAs here (not an accepted answer)
d.  Both A and B
e.  Both B and C

10) Protein functional domains are determined by which level of protein structure?
a.  Primary
b.  Secondary
c.  Tertiary
d.  Quarternary
e.  Exon Sequence

11) When a part of the growing peptide chain in the P pocket, which portion of the amino
acid is involved in peptide bond formation with the amino acid attached to the new tRNA
in the A pocket?
a.  Carboxyl group – if growing peptide chain has an N-terminus (at end of Met) then the chain must be bound to the tRNA in the P pocket through the carboxyl end which then reacts with the N-term of the new AA in the A pocket to form a new peptide bond)
b.  Amino group c.   Radical group d.   Central carbon
e.  Hydrophilic residue

12) Of the components required for a proper Ames test, which is critical for testing substances that by themselves are not harmful but could become harmful in the body?
a.  Bacteria with known mutation
b.  Liver enzymes – need to metabolize chemical
c.  Disc coated with possible mutagen d.   Bacterial culture plates
e.  Control plate

13) Which one of the following mutagenic events does not occur spontaneously?
a.  Deamination
b.  Tautomerizations c.   Depurination
d.  Alkylation – need an agent
e.  Replication slippage
 
14) All of the following statements about mismatch repair are true except:
a.  Mismatch repair depends on the fact that parental strand DNA is more heavily methylated
b.  Mismatch repair requires the action of a methyl transferase
c.  Mismatch repair determines which base in a mismatch is the incorrect one d.   DNA gap is filled in by DNA polymerase
e.  Mismatch repair recognizes methylated cytosine (adenines are methylated)

15) Attenuation regulates expression from the trp operon by which of the following mechanisms?
a.  Blocking initiation of transcription when tryptophan levels are high –
transcription initiated before ribosome hits terminator
b.  Blocking translation of mRNA when tryptophan levels are high – translation
proceed but creates non-functional product
c.  Terminating transcription when tryptophan levels are low - FALSE
d.  Synthesis of a repressor protein when tryptophan levels are high – repressor is made constitutively
e.  Terminating transcription when tryptophan levels are high

16) Which of the following are examples of positive control in operons?
a.  Regulation of the lac operon by the lac repressor.
b.  Action of the catabolite activator protein in the lac operon – all others are negative control
c.  Attenuation of the trp operon
d.  Regulation of the trp operon by the trp repressor e.   Regulation of the trp operon by TRAP

17) Which of the following would result due to a mutation of the trp codons of the attenuator region in the trp operon?
a.  The anti-terminator loop could no longer form – still forms, mutation in loop 1
b.  The terminator loop would no longer form – still forms, mutation in loop 1
c.  The normal function of the attenuator is maintained – not possible…need trp codons
d.  Lack of tryptophan would not promote transcription – ribosome would not stall, terminator loop formed
e.  Lack of tryptophan would promote translation -  cannot translate if not
transcribed

18) In B. subtilis, the trp operon is regulated by TRAP rather than the attenuator. Which of the following is a true statement about the anti-TRAP protein?
a.  Provides a metabolic signal that there is enough tryptophan tRNA
b.  The AT gene is encoded by the trp operon
c.  AT interacts with TRAP when TRAP is not bound to tryptophan
d.  AT prevents TRAP from associating with leader sequence of mRNA
e.  AT prevents the trp operon from being transcribed

19) Which of the following is a gene regulatory mechanism in eukaryotes promotes a reduction in gene activity?
a.  Chromosome location in the center of the nucleus b.   Methylation of histone tails within nucleosome
c.  Methylation of CpG islands on DNA
d.  Acetylation of histone tails within nucleosome
e.  Removal of nucleosomes to allow access to promoter

20) An silencer sequence – just like an enhancer
a.  must be located immediately upstream from the gene it affects.
b.  must be located immediately downstream from the gene it affects. c.   must be located within the gene it affects.
d.  can be inverted without altering its functional ability.
e.  affects the same gene even if its position is altered.

21) Which of the following is not a mechanism by which mRNA can be regulated to affect gene expression?
a.  Alternative splicing of exons
b.  Exon shuffling in mRNA – only happens in DNA
c.  Shortening of the PolyA Tail
d.  Autoregulation by its protein product e.   Response elements in UTRs

22) Which of the following is not true about the regulation of p53 protein stability?
a.  MDM2 binds to the transactivation domain of p53
b.  MDM2 post-transcriptionally modifies p53 – post-translationally modifies!
c.  MDM2 targets p53 for degradation
d.  Phosphorylation of p53 prevents MDM2 binding e.   p53 stimulated MDM2 gene expression
 
1)  Glucose is brought into bacteria as glucose-6-phosphate. Prior to use of glucose-6- phosphate as an energy source, it must be converted to fructose-6-phosphate in order to enter the glycolysis pathway. You are interested in studying how loss of enzymes within this pathway affects the health of your favorite bacteria.  You have identified several bacterial mutants which are unable to produce fructose-6-phosphate when plated on glucose.  Based on the data below, assign the bacterial mutants to the step in the pathway where an enzyme is likely deficient by writing the letter of the mutant in the appropriate
box (5 points).

2)  Dr. Wood studies a protein called Pod1, a bHLH protein. Pod1 is involved in the regulation of the protein SF1. The Sf1 gene has seven exons. SF1 is essential in the transcription of genes which encode steroidogenic enzymes. In proposed stem cells of the adrenal, Pod1 is thought to inhibit Sf1 expression. Sf1 is also regulated by the USF1 and USF2 bHLH proteins which bind to an E-box sequence on the DNA just prior to the transcription start site. SF1 is regulated in a tissue-specific manner. A DNA element within the gene sequence of SF1 between exon 6 and 7 allows expression in the brain. A DNA element 5000 kb upstream of transcription start site allows expression of SF1 in the fetal adrenal. In cells where SF1 is not expressed, the E-box region is methylated.  SF1’s ability to activate expression of steroidogenic enzymes depends on whether it is phosphoylated (required) or SUMOylated (inhibitory).

3)  Luria and Delbruck determined that most mutations are due to spontaneous mutations. Explain how they arose at this conclusion. What were their initial hypotheses and how did they test these hypotheses? Why did their data support this conclusion? (7 points)

5)  RNA Polymerase II transcribes many RNA products that do not result in proteins.
These miRNAs have been found to regulate gene transcription. Describe how these miRNAs are processed to be regulatory factors within the cell and the three possible ways in which gene regulation occurs. In other words, how are the RNAs processed to eventually complex with the RISC and RITS complexes, what do these complexes do, and where do they act? Drawings of this process will be accepted if CLEARLY labeled and functions indicated properly. Drawings are NOT necessary if you prefer to describe it in words (10 points).

6)  There are two types of excision repair mechanisms that we discussed in class: Base excision repair and nucleotide excision repair.
a.  Describe the steps of repair that are shared between the two mechanisms (5 points).