exam 1 (undergrad) practice

Question 1

spontaneous mutations can cause deamination of thymine, resulting in uracil

Answer 1

false

Question 2

okazaki fragments are the result of discontinuous synthesis by DNA polymerase delta

Answer 2

true

Question 3

the enzyme topoisomerase I can create a nick on DNA, relieving torsional stress

Answer 3

true

Question 4

polar side chains of amino acids tend to cluster together in the interior of a protein

Answer 4

false

Question 5

stereoisomers have the same molecular composition but can have different physiological functions in the cell

Answer 5

true

Question 6

Temperature-sensitive mutations are particularly useful for studying the function of essential genes

Answer 6

true

Question 7

DNA ligase is required in the last step of base excision repair, nucleotide excision repair, and mismatch repair

Answer 7

true

Question 8

the secondary structure of a protein is stabilized by hydrogen bonds between the side chains of amino acids and often by disulfide bonds between cysteine residues

Answer 8

false

Question 9

dideoxyribonucleoside triphosphates (ddNTPs) are important in the sanger DNA sequencing technique because they are essential substrates for chain elongation by the DNA polymerase

Answer 9

false

Question 10

inosine is a modified base pair present at the first position of the anticodon in some tRNAs

Answer 10

true

Question 11

which of these is NOT a feature of DNA polymerases?
1. use one strand of DNA as a template for the synthesis of the complementary strand
2. associate with the promoter sequence on DNA
3. require a primer
4. synthesize in 5’-3’ direction
5. use deoxyribonucleotides as substrates

Answer 11

2 - they do NOT associate with the promoter sequences on DNA

Question 12

a nucleoside can vary in…
1. the base
2. the sugar
3. the phosphate group
4. 1 and 2 are correct
5. 1,2,3 are correct

Answer 12

4

Question 12

which type of DNA repair mechanism requires DNA glycosylases

Answer 12

base excision repair

Question 13

which of the following is a covalent interaction
1. protein-protein interaction
2. peptide bond
3. A-G + C-T base pairing
4. TBP associated with the TATA box
5. all the above

Answer 13

2

Question 13

the following enzymes function in DNA replication, DNA recombination, and DNA repair
1. DNA ligase + DNA pol alpha/primase
2. DNA polymerase + DNA ligase
3. RNA polymerase + DNA ligase
4. endonuclease + DNA polymerase
5. endonuclease + DNA ligase

Answer 13

2

Question 13

which statement below explains the uniform width of the DNA molecule along its entire width?
1. a purine nitrogenous base always pairs with another purine base
2. a pyrimidine base always pairs with another pyrimidine base
3. a pyrimidine base always pairs with a purine
4. repulsion between phosphate groups keeps the strands a uniform distance apart
5. attraction between phosphate groups keeps the strands a uniform distance apart

Answer 13

3 - purine always pairs with pyrimidine!!

Question 14

ionizing radiation can cause double-stranded breaks on DNA. the cell repairs this by….
1. homologous recombination
2. nonhomologous end joining
3. mismatch repair

Answer 14

1 and 2

Question 14

all the following statements about molecular chaperons are true except
1. they play a role in the proper folding of proteins
2. the use energy from atp hydrolysis
3. they are only found in mammals
4. they bind a wide range of proteins

Answer 14

3

Question 15

which of the following factors recognizes the UAG, UAA, UGA codons
1. RNA polymerase
2. DNA polymerase
3. termination factors
4. elongation factors
5. tRNAs with anticodons CUA, UUA, UCA

Answer 15

3

Question 16

you are analyzing yeast strains that carry mutations in the large ribosomal subunit. one of the potential phenotypes you could observe is
1. inhibition of aminoacyl-tRNA synthetase activity
2. inhibition of peptidyl transferase activity
3. lack of incorporation of the Met-tRNA to the A site
4. inhibition of the 48S initiation site

Answer 16

2

Question 17

which of the following best describes the defining features of a protein domain
1. a discrete structural and functional unit within a protein
2. a group of proteins that share related functions
3. an evolutionarily conserved sequence of amino acids
4. the region of the cell in which a protein functions
5. the C-terminus of proteins

Answer 17

1

Question 18

eukaryotic DNA replication requires
1. DNA ligase
2. DNA polymerase
3. RNA/DNA primer
4. single-stranded DNA binding proteins
5. all the above

Answer 18

5

Question 19

phosphorylation can affect the structure or function of a protein in which of the following ways
1. charge attraction between the phosphate group and positively charged amino acids cause conformational change in the protein
2. charge repulsion between the phosphate group and negatively charged amino acids cause conformational change in the protein
3. the phosphate group created a binding site for another protein
4. 1 and 2 are right
5. 1,2,3 are right

Answer 19

5

Question 20

during the peptidyl transferase reaction, the polypeptide which is attached to the tRNA in the _____ becomes bound via _______ to an amino acid attached to a tRNA in the ________

Answer 20

p site, peptide bond, a site

Question 21

all the following statements about mismatch repair are true except 1. mismatch repair removes a section of single-stranded DNA that contains the mismatched base 2. mismatch repair determines which base in a mismatch is the incorrect one 3. mismatch repair requires DNA ligase 4. mismatch repair recognizes thymine dimers 5. mutations in genes encoding mismatch repair proteins can lead to human cancers

Answer 21

4

Question 22

the function of helicase (large T antigen) is to

Answer 22

unwind DNA

Question 23

during translation initiation the 5' cap structure on the mRNA is needed for

Answer 23

recognition by the eIF4E

Question 24

bacterial chaperonins function in

Answer 24

protein folding

Question 25

xeroderma pigmentosum is a severe genetic disease caused by mutations in

Answer 25

NER

Question 26

a collapsed replication fork can be repaired via the following mechanism

Answer 26

HR

Question 27

After exonucleases have excised the damaged portion of DNA during mismatch repair, for example, how can DNA polymerase fill in the gap? Is there a primer?

Answer 27

DNA polymerase uses the single-stranded section of DNA as template, using the 3’-OH end left by the nuclease to synthesize the gap (no primer needed), and DNA ligase recreates the phosphodiester bond.

Question 28

How does a protein acquire its tertiary structure?

Answer 28

It is the result of hydrophobic interactions between non-polar side chains of amino acids, along with H bonds between polar side chains and carboxyl groups of the backbone. These stabilize and maintain sections of secondary structure (alpha helices, beta strands, etc). Some proteins contain disulfide bonds between cysteines. Folding is obtained with the help of chaperones.

Question 29

Since there are only 20 amino acids used in protein synthesis, how would you explain the fact that there are more than 20 different tRNAs?

Answer 29

The redundancy of the genetic code implies that there are several triplets encoding the same amino acid (61 codons for 20 amino acids), therefore more that 20 tRNAs are needed. However, there are less than 61 tRNAs because of the Wobble that provides nonstandard base pairing between the 3rd position of the codon and the first of the anticodon (*last sentence is an addition not essential for answering the question).

Question 30

Order the following interactions from the lowest to the highest strength: hydrogen bonds, phosphodiester bonds, van der Waals interactions

Answer 30

van der Waals interactions < hydrogen bonds < phosphodiester bonds

Question 31

Do prokaryotic and eukaryotic cells have the same number of origins of replication per chromosome? In what direction DNA polymerase proceeds from an ori?

Answer 31

No, prokaryotes have one, eukaryotes have multiple origins per chromosome. DNA polymerase proceeds bidirectionally, always synthesizing in the 5’ to 3’ direction.

Question 32

What is the main function of eIF4 during translation? Explain why subunits of eIF4 interact with polyA binding proteins.

Answer 32

eIF4E recognizes the 5’ cap structure (7methyl-G) on the mRNA, essential for the association of the 43S pre-initiation complex. eIF4 interacts with polyA-binding proteins to form the circular structures of mRNA associated with ribosomes observed during translation.

Question 33

pcna

Answer 33

clamp loader

Question 34

covalent interaction

Answer 34

disulfide bond

Question 35

plasmid

Answer 35

circular DNA

Question 36

deamination

Answer 36

base excision repair

Question 37

DNA polymerase alpha

Answer 37

primer

Question 38

double-stranded break

Answer 38

nonhomologous end-joining

Question 39

thymine-thymine dimer

Answer 39

nucleotide excision repair

Question 40

inosine

Answer 40

wobble hypothesis

Question 41

peptidyl transferase

Answer 41

60s ribosomal subunit

Question 42

helicase

Answer 42

unwinding of DNA