Question 1

How fast does a bacterial ribosome move on an mRNA?

Accepted Answer

A)  At about 2 nucleotides per second, significantly lower than the speed of the RNA polymerase. 
B)  At about 5 nucleotides per second, comparable to the speed of the RNA polymerase. 
C)  At about 10 nucleotides per second, significantly lower than the speed of the RNA polymerase. 
D)  At about 20 nucleotides per second, comparable to the speed of the RNA polymerase. 
E)  At about 60 nucleotides per second, comparable to the speed of the RNA polymerase. 
A)  At about 2 nucleotides per second, significantly lower than the speed of the RNA polymerase. 
B)  At about 5 nucleotides per second, comparable to the speed of the RNA polymerase. 
C)  At about 10 nucleotides per second, significantly lower than the speed of the RNA polymerase. 
D)  At about 20 nucleotides per second, comparable to the speed of the RNA polymerase. 
E)  At about 60 nucleotides per second, comparable to the speed of the RNA polymerase. E

Question 2

The anticodon sequence of a phenylalanine-specific tRNA is 5'-GAA-3'. Given the wobble base-pairing rules presented in the following table, how many different codons can be "read" by this tRNA? Write down your answer in digits, e.g. 12.

Accepted Answer

2

Question 3

How does a eukaryotic cell deal with the superhelical tension in its genomic DNA resulting from the activity of RNA polymerases?

Accepted Answer

A)  DNA gyrase introduces negative supercoils, keeping the DNA under constant tension. 
B)  The RNA polymerases are allowed to rotate freely around their templates during transcription, leading to the relaxation of the tension. 
C)  DNA topoisomerases rapidly remove the superhelical tension caused by transcription. 
D)  The nucleosomes adjust the tension by binding to positively supercoiled regions behind a moving RNA polymerase. 
E)  All of the above. 
A)  DNA gyrase introduces negative supercoils, keeping the DNA under constant tension. 
B)  The RNA polymerases are allowed to rotate freely around their templates during transcription, leading to the relaxation of the tension. 
C)  DNA topoisomerases rapidly remove the superhelical tension caused by transcription. 
D)  The nucleosomes adjust the tension by binding to positively supercoiled regions behind a moving RNA polymerase. 
E)  All of the above. C

Question 4

This general transcription factor recognizes the TATA box in RNA polymerase II promoters. It is...

Accepted Answer

A)  the only single-subunit general transcription factor. 
B)  able to introduce a rather sharp kink in the double helix upon binding to DNA. 
C)  responsible for the phosphorylation of the RNA polymerase CTD during transcription initiation. 
D)  also responsible for the recognition of the BRE element in the promoter. 
E)  All of the above. 
A)  the only single-subunit general transcription factor. 
B)  able to introduce a rather sharp kink in the double helix upon binding to DNA. 
C)  responsible for the phosphorylation of the RNA polymerase CTD during transcription initiation. 
D)  also responsible for the recognition of the BRE element in the promoter. 
E)  All of the above.

Question 5

Indicate true (T) and false (F) statements below regarding the folding of proteins upon their synthesis. Your answer would be a five-letter string composed of letters T and F only, e.g. TFFFF.
( )	A globular protein can fold to its native form while still within the ribosome.
( )	A protein can begin to fold and to bind to other proteins while still being synthesized on the ribosome.
( )	A protein may undergo several cycles of hsp70 binding and release while still being synthesized on the ribosome.
( )	A molten globule can form only after the synthesis of the protein is complete.
( ) A protein typically undergoes hsp60-assisted folding while still being synthesized.

Accepted Answer

Proteins can start folding as soon as

Question 6

Activation of an amino acid by an aminoacyl-tRNA synthetase involves the covalent linkage of...

Accepted Answer

A)  AMP to the amino acid. 
B)  ADP to the amino acid. 
C)  AMP to the tRNA. 
D)  ADP to the tRNA. 
E)  ADP to the enzyme. 
A)  AMP to the amino acid. 
B)  ADP to the amino acid. 
C)  AMP to the tRNA. 
D)  ADP to the tRNA. 
E)  ADP to the enzyme.

Question 7

Indicate whether each of the following is located (or takes place) in the large (L) or the small (S) ribosomal subunit. Your answer would be a four-letter string composed of letters L and S only, e.g. LLLS.
( )	Peptide bond formation
( )	Codon-anticodon interaction
( )	The path of the mRNA
( )	The polypeptide exit tunnel

Accepted Answer

The RNA components of the ribosome in

Question 8

Fill in the blank. These RNA molecules can catalyze a wide variety of biochemical reactions, including peptide bond formation and RNA splicing. They can be found in nature or selected in vitro for a desired function. Such a molecule is called a(n) ...

Accepted Answer

Ribozymes are RNAs capable of catalyzin

Question 9

What enzyme is depicted in the following schematic drawing?

Accepted Answer

A)  DNA polymerase 
B)  RNA polymerase 
C)  Ribosome 
D)  Reverse transcriptase 
E)  Topoisomerase 
A)  DNA polymerase 
B)  RNA polymerase 
C)  Ribosome 
D)  Reverse transcriptase 
E)  Topoisomerase

Question 10

The enzyme poly-A polymerase is responsible for adding 3' poly-A tails to eukaryotic mRNAs. This enzyme...

Accepted Answer

A)  cuts the mRNA after recognition of the cleavage/polyadenylation signal by CstF and CPSF proteins. 
B)  polymerizes the tail using an RNA template that is part of the enzyme. 
C)  is extremely processive. 
D)  normally adds about 1000 A nucleotides to the mRNA. 
E)  uses ATP as a substrate. 
A)  cuts the mRNA after recognition of the cleavage/polyadenylation signal by CstF and CPSF proteins. 
B)  polymerizes the tail using an RNA template that is part of the enzyme. 
C)  is extremely processive. 
D)  normally adds about 1000 A nucleotides to the mRNA. 
E)  uses ATP as a substrate.

Question 11

Three consecutive nucleotides in RNA (such as AUC or GUA) constitute a triplet called a ..., which can specify an amino acid or a stop signal for translation.

Accepted Answer

Three consecutive nucleotides

Question 12

This complex uses ATP and forms an "isolation chamber" for its misfolded protein substrates, allowing them to fold to their native conformation. It is called...

Accepted Answer

A)  a proteasome. 
B)  a ribosome. 
C)  Mediator. 
D)  a chaperonin. 
E)  an exosome. 
A)  a proteasome. 
B)  a ribosome. 
C)  Mediator. 
D)  a chaperonin. 
E)  an exosome.

Question 13

In humans, nearly 80% of proteins are acetylated on their N-terminal residue, a modification known to be recognized by a specific E3 enzyme, which directs the ubiquitylation of the protein for rapid degradation. Does this mean that all of these proteins are actively degraded at any given time?

Accepted Answer

A)  Yes; this high turnover rate ensures that their activity is under tight control. 
B)  Yes; but they are not fully degraded in this way and can still function as protein fragments. 
C)  No; the destruction signal can be buried in the interior of the protein or bound to other proteins. 
D)  No; the E3 enzyme recognizing this mark is inactive most of the time. 
A)  Yes; this high turnover rate ensures that their activity is under tight control. 
B)  Yes; but they are not fully degraded in this way and can still function as protein fragments. 
C)  No; the destruction signal can be buried in the interior of the protein or bound to other proteins. 
D)  No; the E3 enzyme recognizing this mark is inactive most of the time.

Question 14

Polysomes...

Accepted Answer

A)  are large cytoplasmic assemblies made of several ribosomes each translating their exclusive mRNA. 
B)  are only found in the eukaryotic cytoplasm. 
C)  can take advantage of the circularization of eukaryotic mRNA (by interactions between the 5' and 3' ends of the mRN
A)  to further speed up the rate of protein synthesis. 
D)  are mostly translationally inactive and are normally used by the cell to store the ribosomes and their associated mRNAs for future use. 
E)  All of the above. 
A)  are large cytoplasmic assemblies made of several ribosomes each translating their exclusive mRNA. 
B)  are only found in the eukaryotic cytoplasm. 
C)  can take advantage of the circularization of eukaryotic mRNA (by interactions between the 5' and 3' ends of the mRN
A)  to further speed up the rate of protein synthesis. 
D)  are mostly translationally inactive and are normally used by the cell to store the ribosomes and their associated mRNAs for future use. 
E)  All of the above.

Question 15

In a gene that normally contains three exons, which of the following changes probably will NOT activate the nonsense-mediated mRNA decay pathway? The sizes of exons 1 to 3 are 100, 150, and 200 nucleotide pairs, respectively.

Accepted Answer

A)  A nonsense mutation in exon 1. 
B)  A nonsense mutation in exon 2. 
C)  A mutation in the first intron resulting in the inclusion of a large intronic fragment in the mature mRNA. 
D)  A frameshift mutation in exon 1. 
E)  A mutation in exon 2 leading to its loss through exon skipping. 
A)  A nonsense mutation in exon 1. 
B)  A nonsense mutation in exon 2. 
C)  A mutation in the first intron resulting in the inclusion of a large intronic fragment in the mature mRNA. 
D)  A frameshift mutation in exon 1. 
E)  A mutation in exon 2 leading to its loss through exon skipping.

Question 16

The nucleolus is a dynamic subcompartment within the nucleus and its size varies depending on the circumstances. In which of the following cells would you NOT expect to see the nucleoli?

Accepted Answer

A)  A yeast cell undergoing DNA replication 
B)  A human neuron in a quiescent (G₀) state 
C)  A human macrophage active in phagocytosis 
D)  A fruit fly embryonic nucleus in the G₂ phase of the cell cycle 
E)  A mouse embryonic cell in the metaphase stage of mitosis 
A)  A yeast cell undergoing DNA replication 
B)  A human neuron in a quiescent (G₀) state 
C)  A human macrophage active in phagocytosis 
D)  A fruit fly embryonic nucleus in the G₂ phase of the cell cycle 
E)  A mouse embryonic cell in the metaphase stage of mitosis

Question 17

The modified nucleotide shown below is normally found in mature...

Accepted Answer

A)  tRNAs. 
B)  ribosomes. 
C)  spliceosomes. 
D)  snoRNAs. 
E)  All of the above. 
A)  tRNAs. 
B)  ribosomes. 
C)  spliceosomes. 
D)  snoRNAs. 
E)  All of the above.

Question 18

To ensure the fidelity of splicing, the spliceosome...

Accepted Answer

A)  hydrolyzes ATP to undergo complex rearrangements. 
B)  examines the splicing signals on the pre-mRNA several times. 
C)  assembles on the pre-mRNA co-transcriptionally. 
D)  takes advantage of "exon definition." 
E)  All of the above. 
A)  hydrolyzes ATP to undergo complex rearrangements. 
B)  examines the splicing signals on the pre-mRNA several times. 
C)  assembles on the pre-mRNA co-transcriptionally. 
D)  takes advantage of "exon definition." 
E)  All of the above.

Question 19

Indicate true (T) and false (F) statements below regarding mRNA splicing in human cells. Your answer would be a four-letter string composed of letters T and F only, e.g. TFFF.
( )	Introns must be removed in the order in which they occur along the pre-mRNA.
( )	Nucleosomes tend to be positioned over exons (on average, about one nucleosome per exon).
( )	Exon size tends to be much more variable than intron size.
( )	The exon junction complexes mark the sites on the mRNA where splicing has not been successful.

Accepted Answer

Exon size tends to be much more unifor

Question 20

Comparing mRNA molecules from human and Escherichia coli cells, which of the following is typically NOT true?

Accepted Answer

A)  A human mRNA has a special 5' cap, while a bacterial mRNA does not. 
B)  A human mRNA has a poly-A tail, while a bacterial mRNA does not. 
C)  A human mRNA undergoes alternative splicing, while a bacterial mRNA does not. 
D)  A human mRNA contains noncoding sequences, while a bacterial mRNA does not. 
E)  A typical human mRNA encodes one protein, while many bacterial mRNAs encode several different proteins. 
A)  A human mRNA has a special 5' cap, while a bacterial mRNA does not. 
B)  A human mRNA has a poly-A tail, while a bacterial mRNA does not. 
C)  A human mRNA undergoes alternative splicing, while a bacterial mRNA does not. 
D)  A human mRNA contains noncoding sequences, while a bacterial mRNA does not. 
E)  A typical human mRNA encodes one protein, while many bacterial mRNAs encode several different proteins.

Exam 6: How Cells Read the Genome: From DNA to Protein

How fast does a bacterial ribosome move on an mRNA?

The anticodon sequence of a phenylalanine-specific tRNA is 5'-GAA-3'. Given the wobble base-pairing rules presented in the following table, how many different codons can be "read" by this tRNA? Write down your answer in digits, e.g. 12.

How does a eukaryotic cell deal with the superhelical tension in its genomic DNA resulting from the activity of RNA polymerases?

This general transcription factor recognizes the TATA box in RNA polymerase II promoters. It is...

Activation of an amino acid by an aminoacyl-tRNA synthetase involves the covalent linkage of...

Fill in the blank. These RNA molecules can catalyze a wide variety of biochemical reactions, including peptide bond formation and RNA splicing. They can be found in nature or selected in vitro for a desired function. Such a molecule is called a(n) ...

What enzyme is depicted in the following schematic drawing?

The enzyme poly-A polymerase is responsible for adding 3' poly-A tails to eukaryotic mRNAs. This enzyme...

Three consecutive nucleotides in RNA (such as AUC or GUA) constitute a triplet called a ..., which can specify an amino acid or a stop signal for translation.

This complex uses ATP and forms an "isolation chamber" for its misfolded protein substrates, allowing them to fold to their native conformation. It is called...

In humans, nearly 80% of proteins are acetylated on their N-terminal residue, a modification known to be recognized by a specific E3 enzyme, which directs the ubiquitylation of the protein for rapid degradation. Does this mean that all of these proteins are actively degraded at any given time?

Polysomes...

In a gene that normally contains three exons, which of the following changes probably will NOT activate the nonsense-mediated mRNA decay pathway? The sizes of exons 1 to 3 are 100, 150, and 200 nucleotide pairs, respectively.

The nucleolus is a dynamic subcompartment within the nucleus and its size varies depending on the circumstances. In which of the following cells would you NOT expect to see the nucleoli?

The modified nucleotide shown below is normally found in mature...

To ensure the fidelity of splicing, the spliceosome...

Comparing mRNA molecules from human and Escherichia coli cells, which of the following is typically NOT true?

Cells and Genomes

Cell Chemistry and Bioenergetics

Proteins

DNA, Chromosomes, and Genomes

DNA Replication, Repair, and Recombination

Control of Gene Expression

Analyzing Cells, Molecules, and Systems

Visualizing Cells

Membrane Structure

Membrane Transport of Small Molecules and the Electrical Properties of Membranes

Intracellular Compartments and Protein Sorting

Intracellular Membrane Traffic

Energy Conversion: Mitochondria and Chloroplasts

Cell Signaling

The Cytoskeleton

The Cell Cycle

Cell Death

Cell Junctions and the Extracellular Matrix

Cancer

Development of Multicellular Organisms

Stem Cells and Tissue Renewal

Pathogens and Infection

The Innate and Adaptive Immune Systems

Filters