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Structure-function studies of numerous DNA polymerizing enzymes have shown that the catalytic residues are found within the β sheets of the
_________ domain, whereas other regions form a tunnel through which the DNA passes.
Which of the following descriptions likely explains the finger and thumb domains of a polymerase in terms of their interaction with DNA?
2) Either the finger or the thumb domain interacts with single-stranded DNA.
Which of the following describe the processivity of a DNA polymerase enzyme? DNA polymerases generally....
Have a high binding constant for deoxyribonucleotide triphosphates and have the highest processivity of any enzyme
Eukaryotic chromosomes present a special challenge for replication in terms of nucleotide erosion over time. This is true because eukaryotic chromosomes are
Linear and there are RNA primers that will be removed at each end.
Which of the following occur during the lytic cycle of bacteriophage λ?
Which of the following best describes the relationship between the lytic and the lysogenic cycle of bacteriophage λ?
1) Bacteriophage coat proteins and phage DNA are produced in large quantities.
Infectious bacteriophage particles are released after bacterial cell lysis
2) A lysogenic cycle can revert to the lytic cycle within the same cel
Why is azidothymidine (AZT) an effective medication for HIV patients?
It is a nucleotide analog that cannot participate in nucleotide polymerization
Which of the following best explains why those seeking immunity against retroviruses would need to be constantly injected with vaccine
Because the reverse transcriptase of a retrovirus does not proofread and therefore genomic changes are expected.
Which enzymes are required for the complete process that leads to successful retrotransposon insertion?
What cell is not expected to contain an active telomerase enzyme?
Telomerase contains a ____________ that binds complementary to and extends the length of the
_______________ strand after DNA replication.
1) alveolar epithelial cells within deep lung tissue
2) RNA, template
BRCA1 and BRCA2 genes have been linked to a series of cancers. The gene product of BRCA1 and BRCA2 is involved in which of the following?
Which of the following statements best associates the BRCA genes, protein products, and their involvement in cancer?
1) double-stranded break repair
2) The BRCA proteins are found within the nucleoplasm and are encoded by tumor suppressor genes
Lynch syndrome is caused by inherited autosomal dominant mutation in one of several human mismatch repair genes, such as hMLH1. Which of the following best describes these patients and the condition(s) that they most likely experience?
or patients with Lynch syndrome, why might some cancers, like colon cancer, be more prevalent than others, like brain cancer?
1) higher levels of colon, stomach, uterine and ovarian cancer
2) Cells of the epithelia replicate at a faster rate than neurons and that correlates with these cancers.
Determine what would likely happen first during DNA replication if the temperature were elevated by a few degrees Celsius (normal human temperature is 37°C).
The new polynucleotides of the replicating lagging strand will become denatured from the template strand
Mismatch repair in e.coli is dependent on...
Rank the E.coli mismatch repair proteins in order with regard to their first association with a DNA lesion.
base methylation within the parental DNA strand
Which of the following best relates these three terms: DNA damage, metabolic rate, and antioxidants?
Individuals with a higher metabolic rate who do not consume antioxidants have a greater risk of DNA damage.
A number of different RNAs are required for protein synthesis. Which of the following RNAs are required for the complete process of assembling the protein synthesis machinery as well as translation in eukaryotes?
mRNA, tRNA, rRNA as well as snoRNA and snRNA
The RNA polymerase II C-terminal domain (CTD) consists of multiple repeats of the heptapeptide sequence YSPTSPS, with the number of repeats varying among organisms. Hyperphosphorylation of the CTD is a key step in the transition of the enzyme complex from the initiation to the elongation stage. What does the term "hyperphosphorylation" mean in this context?
Multiple copies of the heptapeptide repeat are phosphorylated on some combination of serine, threonine, and tyrosine residues.
Which of the following is NOT an event that occurs during prokaryotic transcription?
Why is it necessary for σ factor to dissociate from the RNA polymerase in order for elongation to occur efficiently?
The σ factor departs when the closed complex forms at the promoter.
Dissociation of σ factor increases the affinity of RNA polymerase for general DNA.
Which of the following statements is correct concerning eukaryotic mRNA?
Eukaryotic mRNA is monocistronic
Which of the following RNAs is both used during protein synthesis and is NOT recycled?
All three eukaryotic polymerases contain subunits homologous to subunits that make up the bacterial RNA polymerase (α2ββ′ω). However, the eukaryotic polymerases contain additional subunits that are not homologous to these proteins. Which of the following provides one explanation for the role of these subunits in transcription?
Promoter regions and regulatory elements differ for all three eukaryotic RNA polymerases. Additional subunits are required to facilitate the interaction between the polymerase complex and DNA.
What hypothesis might explain why TBP is necessary for transcription from TATA-less promoters?
The DNA-bending function of TBP cannot be performed by another protein in the general transcription factor complex.
Which of the following is not a part of the miRNA pathway for mRNA degradation?
There are several similarities between the miRNA and RNAi pathways. Which of the following are common features of both pathways?
Double-stranded RNA initiates the pathway.
Proteins required for processing of the transcript.
What splicing defect would result if the 3' splice site of the intron between exons 1 and 2 were mutated so that it was no longer recognized by the splicing machinery?
In the wobble position, inosine can bind to adenine, cytosine, and uracil, but not to guanine. Why not?
Inosine and guanine have the wrong arrangement of partial charges to form noncovalent bonds.
How high should the concentration of aminoacyl-tRNA synthetases be, compared to the concentration of tRNAs in a cell?
Low, because a single aminoacyl-tRNA synthetase can catalyze many reactions.
Which of the following nuclear transport steps are directly facilitated by Ran-GTP?
Transport of importins and exportins out of the nucleus.
Of the following proteins that all associate with vesicles, which have membrane-spanning domains?
SNAREs and transporter proteins
Assuming that an ER signal peptide forms an alpha helix, is that helix likely to be amphipathic? Why or why not?
No, hydrophobic amino acids cluster in the sequence
A ribosome waiting to bind the next charged tRNA will not release its elongating polypeptide, no matter how long it waits. However, a ribosome that binds a release factor will quickly release the polypeptide. Why?
Release of the polypeptide requires the breaking of a covalent bond, which is thermodynamically unfavorable.
A newly translated protein that is N-glycosylated could theoretically end up in which of the following locations and orientations?
In plasma membrane with glycan facing extracellular space and in lysosome with glycan facing interior.
The cytoplasm has a reducing environment, while the extracellular space tends to have an oxidizing environment. Based on this information, where would proteins with disulfide bonds most likely be synthesized?
RER b/c more stable in extracellular space
Which of the following statements about aminoacyl-tRNA synthetases are true?
found in cytoplasm and mitochondria
the rxn they catalyze is irreversible
sometimes charge trna with wrong AA
Which of the following statements about tetracycline is true?
Tetracycline binds the ribosome with a lower Kd than a tRNA does.
Why can puromycin block translation in both prokaryotes and eukaryotes, while many other antibiotics only affect prokaryotic translation?
Puromycin is structurally similar to part of a charged tRNA, which has the same structure in prokaryotes and eukaryotes
Which of the following noncovalent interactions occur(s) during translation?
30s ribosome - shine dalgarno sequence
Which steps in eukaryotic translation require the cleavage of a phosphodiester bond from GTP?
all except formation of peptide bond
Ribosomes and other large cellular components are measured in Svedberg units. Which characteristics of a component contribute to its Svedberg value?
Size, shape, and density
Unlike most eukaryotes, prokaryotes make polycistronic mRNAs. These polycistronic mRNAs encode more than one protein. In order to properly synthesize all of the encoded proteins, these prokaryotic polycistronic mRNAs must duplicate which mRNA components?
Shine dalgarno sequence
As stated in the text, Marshall Nirenberg and Heinrich Matthaei discovered that addition of rRNA increased the amount of protein synthesized in vitro by a mixture of lysed bacterial cells, which contained all of the biomolecules needed to synthesize proteins. Given what you know about protein synthesis, what can you conclude from this experiment?
The extract contains ribosomal proteins that are not bound to rRNA, so additional ribosomes form.
Bowen-Conradi syndrome is a developmental disorder, with symptoms including a prominent nose, small head, and curvature of the pinky finger. Babies born with Bowen-Conradi syndrome do not achieve developmental milestones and usually do not survive more than six months. This disease is caused by mutations in the EMG1 gene, which is essential for processing of the 18S rRNA. Why would mutation of EMG1 cause such a severe disease?
The 40S ribosome forms incorrectly in EMG1 mutants, leading to reduced protein synthesis.
During exercise, protein synthesis in muscle cells stops. After exercise, protein synthesis starts again and contributes to the growth of muscle caused by exercise. A study by Dreyer et al found that the protein 4E-BP1 is normally phosphorylated in muscle cells, but becomes dephosphorylated during exercise and phosphorylated again after exercise. The dephosphorylated form of 4E-BP1 can bind to eIF4E to block its normal function. How might 4E-BP1 block protein synthesis during exercise?
4E-BP1 binding to eIF4E prevents loading of the mRNA onto the ribosome.
uvrA encodes a DNA repair protein and is regulated by LexA. Which of the following could be consequences of a mutation that results in an inactive UvrA protein?
uvrB expression remains high and DNA repair cannot be completed
Why might a transcription factor binding site be encoded by an inverted-repeat sequence?
The transcription factor functions as a homodimer, so the DNA binding domains of the two subunits bind the same sequences in reverse
In which of the following types of prokaryotic gene regulation will the affinity of a protein for its operator sequence increase when a ligand is added?
ligand regulated repression and activation
Which of the following statements about DNA methylation are true?
Acts in cis and is heritable
If a protein-coding gene is fused to the lac promoter sequence, then bacteria will produce large amounts of that protein when stimulated with IPTG. As described in the text, this can be accomplished by creating a plasmid that carries the new gene construct. What features other than a promoter must also be present on the plasmid to ensure that the protein is expressed?
shine dalgarno sequence and lac repressor binding site
Which of the following statements is NOT correct about the structure of the nucleosome?
histone tails are rich in negatively charged amino acids
Which of the following is not a mechanism that enables the binding of a pioneer factor to a cis-acting sequence?
Where are pioneer factors least likely to bind?
the pioneer factor binds to the sequence through the help of the mediator complex
linker dna between nucleosomes
Which of the following is not a modification of nucleosome?
Which of the following is not correct about lysine methylation?
Which is an effect of acetylation of lysines in the histone tails?
Methylated lysines bind to bromodomains of proteins.
Interactions between DNA and the histone tail are decreased.
Which of the following are examples of transcriptional activators?
THYROID HORMONE RECEPTOR
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