exam 1 (undergrad) practice Flashcards
spontaneous mutations can cause deamination of thymine, resulting in uracil
false
okazaki fragments are the result of discontinuous synthesis by DNA polymerase delta
true
the enzyme topoisomerase I can create a nick on DNA, relieving torsional stress
true
polar side chains of amino acids tend to cluster together in the interior of a protein
false
stereoisomers have the same molecular composition but can have different physiological functions in the cell
true
Temperature-sensitive mutations are particularly useful for studying the function of essential genes
true
DNA ligase is required in the last step of base excision repair, nucleotide excision repair, and mismatch repair
true
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
false
dideoxyribonucleoside triphosphates (ddNTPs) are important in the sanger DNA sequencing technique because they are essential substrates for chain elongation by the DNA polymerase
false
inosine is a modified base pair present at the first position of the anticodon in some tRNAs
true
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
2 - they do NOT associate with the promoter sequences on DNA
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
4
which type of DNA repair mechanism requires DNA glycosylases
base excision repair
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
2
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
2
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
3 - purine always pairs with pyrimidine!!
ionizing radiation can cause double-stranded breaks on DNA. the cell repairs this by….
1. homologous recombination
2. nonhomologous end joining
3. mismatch repair
1 and 2
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
3
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
3
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
2
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
1
eukaryotic DNA replication requires
1. DNA ligase
2. DNA polymerase
3. RNA/DNA primer
4. single-stranded DNA binding proteins
5. all the above
5
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
5
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 ________
p site, peptide bond, a site
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
4
the function of helicase (large T antigen) is to
unwind DNA
during translation initiation the 5’ cap structure on the mRNA is needed for
recognition by the eIF4E
bacterial chaperonins function in
protein folding
xeroderma pigmentosum is a severe genetic disease caused by mutations in
NER
a collapsed replication fork can be repaired via the following mechanism
HR
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?
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.
How does a protein acquire its tertiary structure?
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.
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?
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).
Order the following interactions from the lowest to the highest strength: hydrogen bonds,
phosphodiester bonds, van der Waals interactions
van der Waals interactions < hydrogen bonds < phosphodiester bonds
Do prokaryotic and eukaryotic cells have the same number of origins of replication per chromosome?
In what direction DNA polymerase proceeds from an ori?
No, prokaryotes have one, eukaryotes have multiple origins per chromosome. DNA polymerase proceeds
bidirectionally, always synthesizing in the 5’ to 3’ direction.
What is the main function of eIF4 during translation? Explain why subunits of eIF4 interact with polyA binding proteins.
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.
pcna
clamp loader
covalent interaction
disulfide bond
plasmid
circular DNA
deamination
base excision repair
DNA polymerase alpha
primer
double-stranded break
nonhomologous end-joining
thymine-thymine dimer
nucleotide excision repair
inosine
wobble hypothesis
peptidyl transferase
60s ribosomal subunit
helicase
unwinding of DNA
