Final Exam

Question 1

The primary mechanism responsible for variations in the level of constitutive enzymes from different genes is that:

A. all constitutive enzymes are synthesized at the same rate, but are not degraded equally.
B. their promoters have different affinities for RNA polymerase holoenzyme.
C. some constitutively expressed genes are more inducible than others.
D. some constitutively expressed genes are more repressible than others.
E. the same number of mRNA copies are made from each gene, but are translated at different
rates.

Answer 1

B. their promoters have different affinities for RNA polymerase holoenzyme

Question 2

2. The σ (sigma) subunit of E. coli RNA polymerase holoenzyme is an example of a (an)

A. repressor
B. activator
C. specificity factor
D. effector

Answer 2

C. specificity factor

Question 3

Which of the following statements correctly describes promoters in E. coli?

A. A promoter may be present on either side of a gene or in the middle of it.

B. All promoters have the same sequence that is recognized by RNA polymerase holoenzyme.

C. Every promoter has a different sequence, with little or no resemblance to other promoters.

D. Many promoters are similar and resemble a consensus sequence, which has the highest affinity for RNA polymerase holoenzyme.

E. Promoters are not essential for gene transcription, but can increase its rate by two- to three- fold.

Answer 3

D. Many promoters are similar and resemble a consensus sequence, which has the highest affinity for RNA polymerase holoenzyme.

Question 4

Operons consist of

A. a group of clustered genes, a promoter, and regulatory sequences.
B. a group of clustered genes and a promoter.
C. a group of clustered genes.
D. groups of genes controlled by a common regulator.

Answer 4

A. a group of clustered genes, a promoter, and regulatory sequences

Question 5

Beta-galactosidase does not catalyze

A. the cleavage of allolactose.
B. the cleavage of IPTG.
C. the conversion of lactose to allolactose.
D. the cleavage of lactose.

Answer 5

B. the cleavage of IPTG

Question 6

The operator region normally can be bound by:
(Slide.. The negative regulation of lac operon)

A. attenuator.
B. inducer.
C. mRNA.
D. repressor.
E. suppressor tRNA.

Answer 6

D. repressor.

Question 7

Small signal molecules that regulate transcription are not known to:

A. cause activator proteins to bind DNA sites.
B. cause repressor proteins to bind DNA sites.
C. directly bind to DNA sites.
D. prevent activator proteins from binding to DNA sites.
E. release repressor proteins from DNA sites.

Answer 7

C. directly bind to DNA sites.

Question 8

Under what conditions is the E. coli lactose (lac) operon expressed?
(Slide.. Combined effects of glucose and lactose)

A. When glucose and lactose concentrations are low.
B. When galactose concentrations are high and glucose concentrations are low.
C. When lactose concentrations are low and glucose concentrations are high.
D. When glucose concentrations are low and lactose concentrations are high.

Answer 8

D. When glucose concentrations are low and lactose concentrations are high.

Question 9

Transcription of the lactose operon in E. coli is stimulated by:
(Slide.. The trp Operon - dual control)

A. a mutation in the repressor gene that strengthens the affinity of the repressor for the operator.
B. a mutation in the repressor gene that weakens the affinity of the repressor for the operator.
C. a mutation in the repressor gene that weakens the affinity of the repressor for the inducer.
D. binding of the repressor to the operator.
E. the presence of glucose in the growth medium.

Answer 9

B. a mutation in the repressor gene that weakens the affinity of the repressor for the operator.

Question 10

The DNA binding motif for many prokaryotic regulatory proteins, such as the lac repressor, is:
(Slide.. Helix Turn Helix Motif is common in DNA Binding proteins)

A. helix-turn-helix.
B. homeobox.
C. homeodomain.
D. leucine zipper.
E. zinc finger.

Answer 10

A. helix-turn-helix

Question 11

The leucine zipper motif mediates
(Slide.. Leucine zipper - dimerization domains)

A. DNA binding.
B. transcriptional attenuation.
C. protein-protein interactions.
D. RNA binding.

Answer 11

C. protein-protein interactions.

Question 12

Protein structural motifs often have general functions in common. Which one of the following motifs is known to be involved in protein dimer formation, but not in direct protein-DNA interactions?
(Slide.. Leucine zipper - dimerization domains)

A. β-barrel
B. helix-turn-helix
C. homeodomain
D. leucine zipper
E. zinc finger

Answer 12

D. leucine zipper

Question 13

Which of the following statements about regulation of the lac operon is true?
(Slide.. Positive regulation of Lac operon by CRP)

A. Glucose in the growth medium decreases the inducibility by lactose.
B. Glucose in the growth medium does not affect the inducibility by lactose.
C. Glucose in the growth medium increases the inducibility by lactose.
D. Its expression is regulated mainly at the level of translation.
E. The lac operon is fully induced whenever lactose is present.

Answer 13

A. Glucose in the growth medium decreases the inducibility by lactose.

Question 14

The binding of CRP (cAMP receptor protein of E. coli) to DNA in the lac operon:
(Slide.. Positive regulation of Lac operon by CRP)

A. assists RNA polymerase binding to the lac promoter.
B. is inhibited by a high level of cAMP.
C. occurs in the lac repressor region.
D. occurs only when glucose is present in the growth medium.
E. prevents repressor from binding to the lac operator

Answer 14

A. assists RNA polymerase binding to the lac promoter.

Question 15

Consider the lac operon of E. coli. When there is neither glucose nor lactose in the growth medium:
(Slides.. Combined effects of glucose and lactose.. CAP=CRP)

A. CRP protein binds to the lac operator.
B. CRP protein displaces the Lac repressor from the lac promoter.
C. CRP binds to the CRP site near the promoter and repressor is bound to the lac operator.
D. RNA polymerase binds lac promoter and transcribes the lac operon.
E. the operon is fully induced.

Answer 15

C. CRP binds to the CRP site near the promoter and repressor is bound to the lac operator.

Question 16

When the growth medium contains both lactose and glucose, what proteins will bind to the lac operon regulatory region?
(Slides.. Combined effects of glucose and lactose.. CAP=CRP)

A. Neither Lac repressor nor CRP will bind.
B. Lac repressor will bind to the operon regulatory region but not CRP.
C. Lac repressor will not bind, but CRP will.
D. Both Lac repressor and CRP will bind to corresponding regions.
E. From the situation described, we cannot decide.

Answer 16

A. Neither Lac repressor nor CRP will bind.

Question 17

E. coli cells are placed in a growth medium containing lactose. Indicate which of the following circumstances would increase the expression of the lactose operon.
(Slides.. Combined effects of glucose and lactose.. CAP=CRP)

A. Decrease the level of glucose to almost zero.
B. A Lac repressor mutation that prevents dissociation of Lac repressor from the operator
C. A mutation that inactivates β-galactosidase (the enzyme that also converts lactose into
allolactose).
D. A mutation that inactivates galactoside permease (the enzyme that normally allows external
lactose to enter the cell).
E. A mutation that prevents binding of CRP to its binding site near the lac promoter.

Answer 17

A. Decrease the level of glucose to almost zero.

Question 18

A regulon is a(n):
(Slides.. Combined effects of glucose and lactose.. CAP=CRP)

A. group of related triplet codons.
B. network of operons with a common regulator.
C. operon that is subject to regulation.
D. protein that regulates gene expression.
E. ribosomal protein that regulates translation.

Answer 18

B. network of operons with a common regulator.

Question 19

The tryptophan operon of E. coli is repressed by tryptophan added to the growth medium. The tryptophan repressor probably:
(Slide.. The trp Operon - dual control)

A. binds to RNA polymerase when tryptophan is present.
B. binds to the trp operator in the absence of tryptophan.
C. binds to the trp operator in the presence of tryptophan.
D. is a DNA sequence.
E. is an attenuator.

Answer 19

C. binds to the trp operator in the presence of tryptophan.

Question 20

Which one of the following statements about the transcriptional attenuation mechanism is true?

A. In some operons (e.g., the His operon), attenuation may be the only regulatory mechanism.
B. Sequences of the trp operon leader RNA resemble an operator.
C. The leader peptide acts by a mechanism that is similar to that of a repressor protein.
D. The leader peptide gene of the trp operon includes no Trp codons.
E. The leader peptide is an enzyme that catalyzes transcription attenuation.

Answer 20

A. In some operons (e.g., the His operon), attenuation may be the only regulatory mechanism.

Question 21

Which of the following statements is true of the attenuation mechanism used to regulate the tryptophan biosynthetic operon in E. coli?
(Slide.. Transcriptional attenuation in the trp operon)

A. Attenuation is the only mechanism used to regulate the trp operon.
B. One of the enzymes in the Trp biosynthetic pathway binds to the mRNA and blocks
translation when tryptophan levels are high.
C. The leader peptide directly binds to the operator causing RNA polymerase to attenuate transcription.
D. Trp codons in the leader peptide gene allow the system to respond to tryptophan levels in the cell.
E. When tryptophan levels are low, the trp operon transcripts are attenuated (halted before the operon’s structural genes are transcribed).

Answer 21

D. Trp codons in the leader peptide gene allow the system to respond to tryptophan levels in the cell.

Question 22

Transcriptional attenuation in the trp operon of E. coli:

A. can adjust transcription of the structural genes upwards when tryptophan is present.
B. can fine-tune the transcription of the operon in response to small changes in Trp availability.
C. is a mechanism for inhibiting translation of existing complete trp mRNAs.
D. results from the binding of the Trp repressor to the operator.
E. results from the presence of short leader peptides at the 5’ end of each structural gene.

Answer 22

B. can fine-tune the transcription of the operon in response to small changes in Trp availability.

Question 23

An example of coordinate control is the downegulation of ribosomal RNA synthesis in response to amino acid starvation, which will cause synthesis of ribosomal proteins to be limited. What is the correct order of the following events that participate in the signaling process?
(Slide.. Stringent response in E. coli. To amino acid starvation)

1. Binding of stringent factor to the ribosome.
2. Formation of the unusual nucleotide ppGpp (magic spot I).
3. Formation of the unusual nucleotide pppGpp (magic spot II).
4. Uncharged tRNA binds in the ribosomal A-site.

Answer 23

4,1,3,2

Question 24

Which one of the following statements about eukaryotic gene regulation is correct?

A. Large polycistronic transcripts are common.
B. Most regulation is positive, involving activators rather than repressors.
C. Transcription and translation are mechanistically coupled.
D. Transcription does not involve promoters.
E. Transcription occurs without major changes in chromosomal organization.

Answer 24

B. Most regulation is positive, involving activators rather than repressors.

Question 25

Enhancers are DNA sequences that enhance transcription of genes (Slide.. Enhancers can be far away from the promoters in eukaryotes) A. regardless of their orientation in the DNA. B. only if located within a hundred base pairs of a gene's transcription start site. C. in prokaryotes and lower eukaryotes. D. only if located upstream from a gene's transcription start site.

Answer 25

A. regardless of their orientation in the DNA.

Question 26

Which one of the following is NOT involved in steroid hormone action? (Slide.. Typical steroid hormone receptors) ``` A. Cell surface receptors B. Hormone-receptor complexes C. Specific DNA sequences D. Transcription activation and repression E. Zinc fingers ```

Answer 26

A. Cell surface receptors

Question 27

How do steroid hormones alter gene expression? A. They bind to plasma membrane receptors that bring about the activation of the cAMP receptor protein (CRP). B. They act through a hormone-receptor complex that binds specific DNA sequences. C. They bind specific DNA sequences and transactivate transcription. D. They inactivate repressor molecules.

Answer 27

B. They act through a hormone-receptor complex that binds specific DNA sequences.

Question 28

What are the mechanisms of translational repression that are known to exist in eukaryotes? (Slide.. Translation regulation of eukaryotic mRNA) A. inactivation of initiation factors usually by phosphorylation; B. binding of repressor proteins to the mRNA, thereby interfering with initiation factors or the ribosome; C. interference with translation by microRNAs. D. all of above E. none of above

Answer 28

D. all of above

Question 29

In eukaryotes, translational repressor proteins (Slide.. Translation regulation of eukaryotic mRNA) A. bind the initiating AUG codon of mRNAs and block the ribosome from initiating translation. B. bind the 3′ untranslated region of mRNAs and interact with translation initiation factors to prevent translation initiation. C. target mRNAs for degradation by ribonucleases. D. modify particular residues of the mRNA and prevent its translation.

Answer 29

B. bind the 3′ untranslated region of mRNAs and interact with translation initiation factors to prevent translation initiation.

Question 30

Micro-RNAs (miRNAs) and small temporal RNAs (stRNAs) inhibit the expression of specific genes by (Slide.. MicroRNA regulates mRNA stability & transcription) A. methylating the genes to prevent their transcription. B. base pairing with the genes to prevent their transcription. C. activating D Nases to destroy those genes. D. targeting their mRNAs for degradation or by inhibiting their translation.

Answer 30

D. targeting their mRNAs for degradation or by inhibiting their translation

Question 31

Which of the following statements about microRNA is INCORRECT? (Slide.. MicroRNA regulates mRNA stability & transcription) A. Their precursors(pre-miRNAs) are about 70 nucleotides long, withself-complementary internal sequences that can form hairpin structures. B. These precursors are cleaved by endonucleases such as Dicers into 20-25 nucleotide partial miRNA duplexes. C. Partial miRNA duplexes are separated into single strands and go into RISC. D. RISC helps one strand to find the complementary mRNA strand and form hybrids which can then blocks translation or facilitates mRNA degradation. E. Mature miRNA will pair with mRNA targets only if they have a perfect match

Answer 31

E. Mature miRNA will pair with mRNA targets only if they have a perfect match

Question 32

Which one of the following is true about the genetic code? A. All codons recognized by a given tRNA encode different amino acids. B. It is absolutely identical in all living things. C. Several different codons may encode the same amino acid. D. The base in the middle position of the tRNA anticodon sometimes permits “wobble” base pairing with 2 or 3 different codons. E. The first position of the tRNA anticodon is always adenosine.

Answer 32

C. Several different codons may encode the same amino acid.

Question 33

The genetic code has all of the following characteristics except: (Slide.. Every nucleotide sequence has 6 potential reading farmers) A. It is degenerate. B. It is read 3’to5’. C. It is read from a fixed starting point without punctuation. D. It is not overlapping. E. A group of three bases codes for one amino acid.

Answer 33

B. It is read 3’ to 5’.

Question 34

What does it mean when the genetic code is described as "degenerate?" (Slide.. Degeneracy is the redundancy of the genetic code) A. It means that the translation machinery is prone to making errors. B. It means that there are fewer codons than amino acids. C. It means that two or more anticodons can base pair with the same codon. D. It means that more than one codon can specify the same amino acid.

Answer 34

D. It means that more than one codon can specify the same amino acid.

Question 35

Which of the following are features of the wobble hypothesis? (Slide.. Table 27-4) A. A naturally occurring tRNA exists in yeast that can read both arginine and lysine codons. B. A tRNA can recognize only one codon. C. Some tRNAs can recognize codons that specify two different amino acids, if both are nonpolar. D. The “wobble” occurs only in the first base of the anticodon. E. The third base in a codon always forms a normal Watson-Crick base pair.

Answer 35

C. Some tRNAs can recognize codons that specify two different amino acids, if both are nonpolar.

Question 36

Wobble can occur because (Slide.. Inosinate in anticodon in some tRNA is "Wobble") A. aminoacyl-tRNA synthetases can recognize more than one tRNA. B. more than one codon can specify the same amino acid. C. tRNAs contain the nucleotide inosinate. D. more than one tRNA can be dedicated to an amino acid.

Answer 36

C. tRNAs contain the nucleotide inosinate.

Question 37

Which of the following statements about tRNA molecules is false? (Slide.. Inosinate in anticodon in some tRNA is "Wobble") A. A, C, G, and U are the only bases present in the molecule. B. Although composed of a single strand of RNA, each molecule contains several short, double-helical regions. C. Any given tRNA will accept only one specific amino acid. D. The amino acid attachment is always to an A nucleotide at the 3' end of the molecule. E. There is at least one tRNA for each of the 20 amino acids.

Answer 37

A. A, C, G, and U are the only bases present in the molecule.

Question 38

RNA editing can be accomplished by? (Slide.. mRNA are edited before protein synthesis) ``` A. splicing. B. deamination. C. translational frameshifting. D. addition or removal of nucleotides. E. Both B and D. ```

Answer 38

E. Both B and D.

Question 39

Aminoacyl-tRNA synthetases (amino acid activating enzymes): (Slide.. Aminoacyl-tRNA synthetase) A. “recognize” specific tRNA molecules and specific amino acids. B. in conjunction with another enzyme attach the amino acid to the tRNA. C. interact directly with free ribosomes. D. occur in multiple forms for each amino acid. E. require GTP to activate the amino acid.

Answer 39

A. “recognize” specific tRNA molecules and specific amino acids.

Question 40

In E. coli, how many amino-acyl tRNA synthetase enzymes are there? (Slide.. Aminoacyl-tRNA synthetase) ``` A. 5 B. 10 C. 20 D. 32 E. 64 ```

Answer 40

C. 20

Question 41

What happens when Cys-tRNAcys is chemically modified to Ala-tRNAcys? A. ribosome rejects the "wrong" aa-tRNA B. Alanine is used, at Alanine codons only C. Alanine is incorporated at Cysteine codons D. No effect on anything

Answer 41

C. Alanine is incorporated at Cysteine codons

Question 42

Which of the following statements about ribosomes is true? A. There are two major subunits (a big subunit and a small subunit), each with multiple proteins. B. They are relatively small, with molecular weights less than 10,000. C. The large subunit contains rRNA molecules, the small subunit does not. D. There are about 25 of them in an E. coli cell. E. They have specific, different binding sites for each of the 20 tRNAs.

Answer 42

A. There are two major subunits (a big subunit and a small subunit), each with multiple proteins.

Question 43

Proteins are made starting from: A. the amino end and proceeding toward the carboxyl end B. the carboxyl end and proceeding toward the amino end C. the middle and proceeding toward both amino and carboxyl end D. the 3’ end toward the 5’ end E. the 5’ end toward the 3’ end

Answer 43

A. the amino end and proceeding toward the carboxyl end

Question 44

Which of the following is true about the difference between translation in prokaryotes and eukaryotes? A. Only prokaryotes have an initiation factor that binds the 5′ cap structure on mRNAs. B. A Shine-Dalgarno sequence is needed for initiation of only eukaryotic mRNAs. C. Translation and transcription are coupled only in prokaryotes. D. Only eukaryotic mRNAs initiate with a residue of N-formylmethionine.

Answer 44

C. Translation and transcription are coupled only in prokaryotes.

Question 45

What is the role of the Shine-Dalgarno sequence? (Slide.. Translation in bacteria: initiation 1) A. It marks the polypeptide for translocation into the lumen of the endoplasmic reticulum. B. It targets proteins for degradation. C. It guides the 30S ribosome to the initiating (5′) AUG of the mRNA. D. It acts as a signal for the termination of translation.

Answer 45

C. It guides the 30S ribosome to the initiating (5′) AUG of the mRNA.

Question 46

17. The prokaryotic mRNA has a sequence like AGGAG (Shine-Dalgarno sequence) which binds to a sequence near the (Slide.. Consensus (cis-Acting) initiation site in prokaryotic mRNA) ``` A. 3' end of 5S rRNA B. 3' end of 23S rRNA C. 3' end of 16S rRNA D. 3' end of tRNA E. 3' end of mRNA ```

Answer 46

C. 3' end of 16S rRNA

Question 47

18. Which "factor" brings f-Met-tRNAF to the 30S initiation complex? (Slide.. Translation in Bacteria: initiation 1) ``` A. IF-1 B. IF-2 C. IF-3 D. RF-2 E. EF-7 ```

Answer 47

B. IF-2

Question 48

During Initiation of Translation in E. coli, where does f-Met-tRNAF bind? (Slide.. Translation in Bacteria: initiation 1) ``` A. The A site B. EF-Ts C. The P site D. RF-II E. The exit site ```

Answer 48

C. The P site

Question 49

Which of the following is true about the proofreading mechanism on the ribosome? A. Proofreading occurs in the A site of the ribosome. B. The identity of the amino acids attached to tRNAs is checked by the ribosome. C. Proofreading fidelity increases with the rate of protein synthesis. D. Proofreading occurs only after GTP hydrolysis.

Answer 49

D. Proofreading occurs only after GTP hydrolysis.

Question 50

Which one of the following statements about the elongation phase of protein synthesis is true? (Slide.. Second elongation step: peptide bond formation) A. At least five high-energy phosphoryl groups are expended for each peptide bond formed. B. During elongation, incoming aminoacylated tRNAs are first bound in the P site. C. Elongation factor EF-Tu facilitates translocation. D. Peptidyl transferase catalyzes the attack of the carboxyl group of the incoming amino acid on an ester linkage in the nascent polypeptide. E. Peptidyl transferase is a ribozyme.

Answer 50

E. Peptidyl transferase is a ribozyme.

Question 51

In bacteria, the peptidyl transferase activity that catalyzes peptide bond formation is found in (Slide.. Second elongation step: peptide bond formation) A. the 23S ribosomal RNA. B. the EF-G protein. C. tRNAs. D. the 30S ribosomal subunit.

Answer 51

A. the 23S ribosomal RNA.

Question 52

During the ‘elongation’ stage of translation, after the arrival of each new charged tRNA: A. the amino acid is ‘passed’ from the tRNA in the A-site to the tRNA in the P-site. B. newly arriving tRNAs must first bind to the E-site. C. the peptide is ‘passed’ from the tRNA in the P-site to the tRNA in the A-site. D. the new tRNA must first bind to the P-site of the ribosome.

Answer 52

C. the peptide is ‘passed’ from the tRNA in the P-site to the tRNA in the A-site.

Question 53

During translocation, the ribosome moves one codon toward the 3’ of mRNA. The movement requires EF-G (aka translocase). EF-G can bind the A site of the ribosome presumably because A. it can form a complex with tRNA. B. its structure resembles that of EF-Tu. C. its structure resembles that of the EF-Tu/EF-Ts complex. D. its structure resembles an EF-Tu/tRNA complex.

Answer 53

D. its structure resembles an EF-Tu/tRNA complex.

Question 54

Termination of translation in prokaryotic cells requires: (Slide.. Translation termination) A. binding of the terminator tRNA to the termination codon. B. interaction of release factors with the termination codon. C. ternary interaction of the release factor and the termination tRNA with the termination codon. D. release factor interaction with the Shine-Dalgarno sequence and subsequent dissociation of the two ribosomal subunits. E. none of the above.

Answer 54

B. interaction of release factors with the termination codon.

Question 55

In bacteria, which of the following events does not occur during the termination of polypeptide synthesis? A. Termination is initiated in response to a termination codon in the A site. B. A termination factor recognizes its unique cognate termination codon. C. The polypeptide-containing tRNA dissociates from the ribosome. D. The ribosome dissociates into its 30S and 50S subunits.

Answer 55

C. The polypeptide-containing tRNA dissociates from the ribosome.

Question 56

The large structure consisting of a mRNA molecule being translated by multiple copies of the macromolecular complexes that carry out protein synthesis is called a: (Slide.. Eukaryotic Polysomes) ``` A. lysosome. B. polysome. C. proteosome. D. ribosome. E. synthosome. ```

Answer 56

B. polysome.

Question 57

Puromycin resembles__________ which enables puromycin to terminate peptide chain elongation (Slide.. Inhibitor of protein synthesis) ``` A. amyl nitrite B. aminoacyl-tRNA synthetase C. aminopterin D. aminoacyl-tRNA E. aminoglycosides ```

Answer 57

D. aminoacyl-tRNA

Question 58

Erythromycin blocks which step of protein synthesis in bacteria? (Single.. Inhibitors of protein synthesis) ``` A. It blocks the A site. B. It inhibits the activation of amino acids. C. It inhibits the translocation. D. It inhibits the peptidyl transferase. E. It blocks the termination. ```

Answer 58

C. It inhibits the translocation.

Question 59

How does Tetracycline affect translation in procaryotes? (Slide.. Inhibitor of protein synthesis) ``` A. It blocks the A site. B. It inhibits the activation of amino acids. C. It inhibits the translocation. D. It inhibits the peptidyl transferase. E. It blocks the termination. ```

Answer 59

A. It blocks the A site.

Question 60

Which drug inhibits the peptidyl transfer step of translational elongation in bacteria and mitochondria but not in eukaryotes? (Slide.. Inhibitor of protein synthesis) ``` A. erythromycin B. puromycin C. streptomycin D. chloramphenicol E. cycloheximide ```

Answer 60

D. chloramphenicol

Question 61

In comparison to DNA polymerases, RNA polymerases: A. do not need activated precursors (nucleotide triphosphates) B. do not have the 3' → 5' proofreading exonuclease activity C. do not require a primer D. do not need a DNA Template E. both B and C are correct.

Answer 61

E. both B and C are correct.

Question 62

During transcription of DNA to RNA: A. an RNA polymerase moves from the 3’ to the 5’ direction along the template DNA. B. the 3’ end of the RNA molecule is produced first. C. an RNA polymerase must first bind to a promoter sequence. D. transcription is always initiated at a “start codon.” E. Both A and C are correct.

Answer 62

E. Both A and C are correct.

Question 63

During transcription of a particular gene, the RNA polymerase will transcribe: A. both strands, but only one of RNA molecule will be used. B. only one of the DNA strands, moving in a 3’ to 5’ direction along the template. C. both strands, but moving 3’ to 5’ for one and 5’ to 3’ along the other. D. only the exons of the gene while skipping over the introns.

Answer 63

B. only one of the DNA strands, moving in a 3’ to 5’ direction along the template.

Question 64

During transcription RNA polymerase uses one strand of the DNA double helix as a template. Which of the following sentences is true? A. the coding strand is the template strand B. the coding strand is the nontemplate strand C. the noncoding strand is the nontemplate strand D. the coding strand is the antisense strand E. none of the above

Answer 64

B. the coding strand is the nontemplate strand

Question 65

RNA polymerase: A) binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed. B) can synthesize RNA chains de novo (without a primer). C) has a subunit called λ (lambda), which acts as a proofreading ribonuclease. D) separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them. E) synthesizes RNA chains in the 3' → 5' direction.

Answer 65

B) can synthesize RNA chains de novo (without a primer).

Question 66

Which of the following statements about E. coli RNA polymerase is false? A) Core enzyme selectively binds promoter regions, but cannot initiate synthesis without a sigma factor. B) RNA polymerase holoenzyme has several subunits. C) RNA produced by this enzyme will be completely complementary to the DNA template. D) The enzyme adds nucleotides to the 3' end of the growing RNA chain. E) The enzyme cannot synthesize RNA in the absence of DNA.

Answer 66

A) Core enzyme selectively binds promoter regions, but cannot initiate synthesis without a sigma factor.

Question 67

Which of the following statements about E. coli RNA polymerase (core enzyme) is false? (Slide. Alternative (sigma) subunits determine promoter specificity) A) The RNA product is complementary to the DNA template. B) The RNA chain grows in a 5' -> 3' direction. C) The core enzyme has no polymerizing activity until the (sigma) subunit is bound. D) In the absence of the (sigma) subunit, core polymerase has little or no specificity for where initiation begins. E) The core enzyme contains several different subunits.

Answer 67

C) The core enzyme has no polymerizing activity until the (sigma) subunit is bound.

Question 68

Which subunit of prokaryotic RNA Pol possesses the polymerase catalytic activity? (Slide.. Bacterial RNA polymerase has at least six subunits) ``` A. Alpha B. Beta C. Beta+ D. Sigma E. Omega ```

Answer 68

B. Beta

Question 69

The sigma factor of E. coli RNA polymerase: (Slide.. Bacterial RNA polymerase has at least six subunits) A) associates with the promoter before binding core enzyme. B) combines with the core enzyme to confer specific binding to a promoter. C) is inseparable from the core enzyme. D) is required for termination of an RNA chain. E) will catalyze synthesis of RNA from both DNA template strands in the absence of the core enzyme.

Answer 69

B) combines with the core enzyme to confer specific binding to a promoter.

Question 70

The attachment site for RNA polymerase in bacteria is called the: (Slide.. Transcription initiation in E. coli) A. Initiator B. Operator C. Promoter D. Start codon

Answer 70

C. Promoter

Question 71

After binding by E. coli RNA polymerase, the correct order of events for transcription initiation is: (Slide.. Transcription initiation in E. coli) A) closed complex formation, open complex formation, promoter clearance, start of RNA synthesis. B) closed complex formation, open complex formation, start of RNA synthesis, promoter clearance. C) open complex formation, closed complex formation, start of RNA synthesis, promoter clearance. D) start of RNA synthesis, closed complex formation, open complex formation, promoter clearance. E) start of RNA synthesis, open complex formation, closed complex formation, promoter clearance.

Answer 71

B) closed complex formation, open complex formation, start of RNA synthesis, promoter clearance.

Question 72

Approximately how many base pairs form the attachment between the DNA template and RNA transcript during transcription? A. 8 B. 12-14 C. 30 D. The entire RNA molecule remains base-paired to the template until transcription is finished.

Answer 72

A. 8

Question 73

Which of the following is not known to be involved in initiation by eukaryotic RNA polymerase II? ``` A) DNA helicase activity B) DNA polymerase activity C) Formation of an open complex D) Protein binding to specific DNA sequences E) Protein phosphorylation ```

Answer 73

B) DNA polymerase activity

Question 74

The sequences in eukaryotic DNA known as introns are: A) those included in the final sequence of messenger RNA. B) the intervening sequences not expressed in the final sequence of messenger RNA. C) the binding sites for DNA polymerase. D) the binding sites for RNA polymerase to initiate transcription. E) the binding sites for RNA polymerase to terminate transcription

Answer 74

B) the intervening sequences not expressed in the final sequence of messenger RNA.

Question 75

During "RNA processing" A. all of the exons are removed and discarded B. the RNA molecule is made from a DNA template. C. introns are cut from the RNA and the exons are spliced together. D. the RNA molecule is translated into a protein molecule.

Answer 75

C. introns are cut from the RNA and the exons are spliced together.

Question 76

Processing of a primary mRNA transcript in a eukaryotic cell does not normally involve: A) attachment of a long poly(A) sequence at the 3' end. B) conversion of normal bases to modified bases, such as inosine and pseudouridine. C) excision of intervening sequences (introns). D) joining of exons. E) methylation of one or more guanine nucleotides at the 5' end.

Answer 76

B) conversion of normal bases to modified bases, such as inosine and pseudouridine.

Question 77

Which of the following is/are a function that the mRNA cap provides? ``` A. Protection from some ribonucleases B. Enhances transcription C. Enhances splicing of the last intron in some pre-mRNAs D. Promotion of translation E. A and D ```

Answer 77

E. A and D

Question 78

The 5'-terminal cap structure of eukaryotic mRNAs is a(n): A) 7-methylcytosine joined to the mRNA via a 2',3'-cyclic linkage. B) 7-methylguanosine joined to the mRNA via a 5' → 3' diphosphate linkage. C) 7-methylguanosine joined to the mRNA via a 5' → 5' triphosphate linkage. D) N6-methyladenosine joined to the mRNA via a 5' → 5' phosphodiester bond. E) O6-methylguanosine joined to the mRNA via a 5' → 5' triphosphate linkage.

Answer 78

C) 7-methylguanosine joined to the mRNA via a 5' → 5' triphosphate linkage.

Question 79

How does the cell ‘mark’ the positions of introns in an immature RNA? A. There is a special snRNP for each type of intron. B. Codons called ‘cut’ and ‘paste’ are present within the RNA. C. It doesn’t need to, since the boundary between an intron and exon alternates frequently. D. Special sequences are located near the splicing sites which are recognized by ribozymes.

Answer 79

D. Special sequences are located near the splicing sites which are recognized by ribozymes.

Question 80

The excision (splicing) of many group I introns requires, in addition to the primary transcript RNA: A) a cytosine nucleoside or nucleotide and a protein enzyme. B) a guanine nucleoside or nucleotide (only). C) a protein enzyme only. D) a small nuclear RNA and a protein enzyme. E) ATP, NAD, and a protein enzyme

Answer 80

B) a guanine nucleoside or nucleotide (only).

Question 81

In Group I intron splicing, the first step involves which of the following ``` A. the 5' splice site B. the 3' splice site C. GTP (or other guanosine nucleotide) D. ATP (or other adenosine nucleotide) E. both A and C ```

Answer 81

E. both A and C

Question 82

A branched (“lariat”) structure is formed during: ``` A) attachment of a 5' cap to mRNA. B) attachment of poly(A) tails to mRNA. C) processing of preribosomal RNA. D) splicing of all classes of introns. E) splicing of group II introns. ```

Answer 82

E) splicing of group II introns.

Question 83

Splicing of introns in nuclear mRNA primary transcripts requires: ``` A) a guanine nucleoside or nucleotide. B) endoribonucleases. C) polynucleotide phosphorylase. D) RNA polymerase II. E) small nuclear ribonucleoproteins (snurps). ```

Answer 83

E) small nuclear ribonucleoproteins (snurps).

Question 84

The presence of a poly-A tail on a RNA molecule indicates that: A. there are exons present that must be removed. B. this RNA molecule does not contain introns. C. the transcript should be immediately degraded. D. this is a rRNA molecule. E. None of the above answers is correct

Answer 84

B. this RNA molecule does not contain introns.

Question 85

Which of the following is an example of RNA editing? a. Removal of introns from an RNA transcript. b. Degradation of an RNA molecule by nucleases. c. Alteration of the nucleotide sequence of an RNA molecule. d. Capping of the 5’ end of an RNA transcript.

Answer 85

c. Alteration of the nucleotide sequence of an RNA molecule.

Question 86

“Alternative splicing” refers to: A. the use of introns as exons, or vice versa, during RNA processing. B. splicing out of damaged DNA by DNA repair enzymes. C. joining of RNA from two different genes to form a new mRNA. D. the use of alternative reading frames when translating an mRNA. E. a new dance for people with alternative life styles.

Answer 86

A. the use of introns as exons, or vice versa, during RNA processing.

Question 87

Which of the following correctly describes polyadenylation? A. Poly (A) tail probably protects the mRNA from degradation. B. Initial adenylation requires the AAUAAA motif. C. An endonuclease activity cleaves the 3’ terminal of the mRNA 10-30 nucleotides downstream of the AAUAAA cleavage signal. D. PAB (Poly (A) binding protein) binds the tail and helps the initiation of rotein synthesis. E. All of above

Answer 87

E. All of above

Question 88

How does actinomycin D (and Acridine) inhibit RNA transcription? A. terminates RNA chain growth B. blocks the rNTP binding site C. prevents DNA from serving as a good template D. binds the beta subunit of RNA polymerase E. both A and C.

Answer 88

E. both A and C.

Question 89

Which drug specifically inhibits initiation of prokaryotic transcription? ``` A. actinomycin B. alpha -amanitin C. ciprofloxacin D. rifampicin E. streptomycin ```

Answer 89

D. rifampicin

Question 90

A useful inhibitor of RNA Polymerase II is: ``` A. rifampicin B. alpha - aminitin C. actinomycin D D. CIPRO E. none of the above ```

Answer 90

B. alpha - aminitin

Question 91

Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences? A. The lagging strand telomeres are not completely replicated by DNA polymerase. B. Telomeres are made of repeating sequences. C. Additional repeated sequences are added to the template strand. D. The leading strand doubles back on itself to form a primer for the lagging strand.

Answer 91

D. The leading strand doubles back on itself to form a primer for the lagging strand.

Question 92

What are the characteristics of biological N2 cycle?

Answer 92

``` •Nitrogen metabolism –N2 fixation is 4 stage reaction –Nitrogen cycle –Entry of N2 into life (glutamine) –Regulation of glutamate synthase ``` •Fixation: –Reduction of atmosperic nitrogen to ammonia (NH4+) •Nitrification: –Oxidization of NH4+ to nitrite (NO2- )and ultimately to nitrate (NO3-) in soil •Denitrification: –Microbial degradation of amonia from dead animals and plants by bacteria •Anomox: –Ammonia short-circuited by anaerobic bacteria by oxidation directly to N2

Question 93

List the various derivatives of Amino acids

Answer 93

All amino acids are derived from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway

Question 94

Define essential and non-essential amino acids

Answer 94

Nonessential amino acids, not needed in the diet. The remainder, the essential amino acids, must be obtained from food

Question 95

Glutamine and Glutamate significance

Answer 95

Glutamine and glutamate is life's N2 source. Glutamine synthetase is found in all organisms. In addition to its importance for assimilation in bacteria, it has a central role in amino acid metabolism in mammals, converting free , which is toxic, to glutamine for transport in the blood

Question 96

Define Heme oxidation and significance (jaundice)

Answer 96

* High concentration of bilirubin in blood, skin and whites of the eyes * High rate of red cell destruction, liver dysfunction or bile duct obstruction * Premature newborns typically have an insufficient bilirubin UDP- glucuronosyl transferase activity.

Question 97

Define essential fatty acids, eicosanoids, glyceroneogenesis.

Answer 97

Essential fatty acids: FA’s that mammals are unable to produce. Eicosanoids: Signaling molecules Glyceroneogenesis: The pathway is essentially an abbreviated version of gluconeogenesis, from pyruvate to dihydroxyacetone phosphate (DHAP), followed by conversion of DHAP to glycerol 3-phosphate, which is used for the synthesis of triacylglycerol.

Question 98

Classification of lipoproteins and cholesterol transport

Answer 98

* Cellular Membrane and stored energy * Pigments (retinol, carotene) * Cofactors (vitamin K) * Detergents (bile salts) * Transporters (dolicols) * Hormones (sex hormones) * Extracellular and intracellular messengers * Anchors of membrane proteins

Question 99

Disorders of Cholesterol metabolism. Define familial hypercholesterolemia.

Answer 99

Atherosclerosis Obstruction of blood vessels due to pathological accumulation of cholesterol in blood vessels (atherosclerotic plaque) May result in heart failure; leading cause of death in Western world Atherosclerosis is linked to high levels of cholesterol, specifically, high levels of LDLs Familial hypercholesterolemia (genetic) High levels of cholesterol due to defective LDL receptors Cellular uptake of cholesterol affected, resulting in high blood levels Cellular biosynthesis continues unregulated

Question 100

Define peptidoglycan and its significance.

Answer 100

``` –Bacterial envelop –N-GlcNAc and N-Mur2Ac –Linked by B1-4 linkage –Mixture of L and D ammo acids –Detoxification of D amino acids in humans ```

Question 101

Explain the significance of D-amino acid oxidase.

Answer 101

The primary function of D-amino acid oxidase, present at high levels in the kidney, is thought to be the detoxification of ingested D-amino acids derived from bacterial cell walls and from grilled foodstuffs (high heat causes some spontaneous racemization of the L-amino acids in proteins).

Question 102

Define Oxidative phosphorylation, name the universal electron acceptors and membrane bound electron carriers.

Answer 102

Oxidative phosphorylation is the process by which NADH and FADH2 are oxidized and ATP is formed In eukaryotes, oxygen is the ultimate electron acceptor for these electrons

Question 103

Significance of thermogenin, FoF1-ATPase complex, reactive oxygen species (free radicals)

Answer 103

Thermogenin, a protein in brown fat generates heat, not ATP. Protons skip FoF1 complex thus, the energy of oxidation is not conserved by ATP formation but is dissipated as heat, contributing to maintaining the temperature Reactive oxygen species (free radicals) - Produce free radicals - can damage cells; enzymes, membrane lipids, nucleic acids - Superoxide dismutase prevents oxidative damage by producing H2O2 - Glutathione peroxidase converts H2O2 into H2O

Question 104

Define amino acid oxidation, metabolic pathways, urea cycle

Answer 104

Amino Acid Oxidation a) Synthesis of cellular protein b) Synthesis of cellular metabolite - neurotransmitters - hormones - heme - nucleotides c) Oxidative degradation Amino Acid Oxidation Fate of cellular amino acid pool : Oxidative degradation Three metabolic pathways : 1) Normal cellular protein degradation 2) After taking a protein-rich meal when the amino acids exceed the need for protein synthesis 3) During starvation or diabetes mellitus when carbohydrates are not available or not used properly Nitrogen excretion and the urea cycle • Starvation leads to more protein degradation • NH4+ produced as result of protein degradation is channeled to urea cycle • Five enzymatic steps • Takes place in liver cells • Some steps completed in mitochondrial matrix and some in the cytosol Ammonia released in the liver by glutaminase enters a metabolic cycle called urea cycle to produce urea, uric acid and ammonia

Question 105

Explain the fate of ammonia generated via oxidative deamination in extrahepatic tissues (i.e., explain the importance of glutamine synthetase).

Answer 105

* Oxidative deamination in extrahepatic tissue * NH3 can only be excreted via urea cycle in the liver * Transport through blood is toxic * Storage in extrahepatic cells may be lethal * Glutamine synthetase to the rescue

Question 106

Explain Ammonia toxicity.

Answer 106

* High levels of NH4+ lead to increased levels of glutamine, which acts as an osmotically active solute (osmolyte) in brain astrocytes * This triggers an uptake of water into the astrocytes to maintain osmotic balance, leading to swelling of the cells and the brain, leading to coma. * Onset of a comatose state accompanied by cerebral edema (an increase in the brain’s water content) and increased cranial pressure * Potential depletion of ATP in brain cells.

Question 107

Importance of glutamine in metabolic acidosis?

Answer 107

* Increase in glutamine processing by the kidneys. * Not all the excess NH4+ released into the bloodstream or converted to urea * Some is excreted directly into the urine. In the kidney, the NH4+ forms salts with metabolic acids, facilitating their removal in the urine. * Bicarbonate produced by the decarboxylation of α-ketoglutarate in the citric acid cycle can also serve as a buffer in blood plasma. * These effects of glutamine metabolism in the kidney tend to counteract acidosis.

Question 108

Define a chylomicron; describe its components & their functions

Answer 108

Molecular structure: hydrophobic inside, hydrophilic outside. - Composition & densities vary - VLDL to VHDL - Enter blood via lymphatic system - Apo C-II activates capillary lipase - TAGs hydrolyzed into fatty acids and glycerol - Fatty acids enter cells of tissue

Question 109

Describe in detail activation & transport of fatty acids to mitochondria (Significance of carnitine shuttle)

Answer 109

Activation occurs on outer mitochondrial membrane: Different isozymes of Acyl-CoA synthetase specifically activate fatty acids of different carbon lengths. Fatty acid with 12 or less carbon atom can enter mitochondrial membrane Fatty acid with carbon atom 14 and above has to through transporter Therefore it needs modification before transorted into mitochondria Carnitine Shuttle Fatty acids mobilized from intestine to tissue mitochondria for energy production through oxidation

Question 110

Explain the mechanism and ultimate goal of fatty acid oxidation (β-oxidation)

Answer 110

``` Stage 1 • Start at the COOH end • Remove successive 2C units • Form Acetyl-CoA • FADH2, NADH, H+ and e- • Repeat till end of FA molecule Stage 2 • Oxidize Acetyl-CoA via TCA cycle • Produce CO2, and e- Stage 3 • Oxidative phosphorylation • Produce H2O and ATP ```

Question 111

Define ketone bodies, its properties and significance

Answer 111

* Acetone, acetoacetate, D-B-hydroxy butarate formation * Fuel for extrahepatic tissues under starvation and diabetes mellitus * Acidosis/Ketosis

Question 112

What is the significance of TCA cycle?

Answer 112

* Main entry point for cellular respiration and energy production in all aerobes * A hub of CHO, lipid and protein intermediary metabolism * Major source of precursors for synthesis of sterols, purines, pyrimidines, porphyrines, amino acids, glucose * Malfunctions of critical enzymatic reactions lead to serious neurodegenerative diseases and cancer.

Question 113

What is the role of PDH complex in TCA cycle?

Answer 113

•PDH converts pyruvate, the main glycolysis product, to Acetyl CoA, the TCA cycle substrate.

Question 114

What are the major products of TCA cycle?

Answer 114

two CO2, three NADH, one FADH2 and one GTP/ATP molecules.

Question 115

Define glycolysis, gluconeogenesis, pentose phosphate pathway.

Answer 115

Glycolysis: Definition and significance Glycolysis is a metabolic pathway where glucose is oxidized to produce energy in the form of ATP. Gluconeogensis: Definition and significance Gluconeogensis an alternative pathway to produce glucose from other sources Pentose Phosphate Pathway: Definition and significance Pentose Phosphate Pathway n oxidative pathway, generates NADPH and precursor for biosynthesis

Question 116

Explain deregulation of glycolysis in solid tumors.

Answer 116

Glucose uptake ~10 x faster Overproduction of GLUT1 and GLUT3 Glycolysis is also ~10 x faster!

Question 117

Significance of pentose phosphate pathway

Answer 117

Main Functions • Generate Ribose-5-P (RNA and DNA synthesis) • Generate NADPH Generates NADPH required for biosynthesis (fatty acid) and to protect of free radical damage to the cells (RBCs and cells of eye: lens and cornea)

Question 118

Explain homolytic, heterolytic cleavage

Answer 118

In homolytic cleavage, each atom leaves with one-half of the shared electrons (one electron for a single bond, or two for double bonds). A—B --> A* + B* In heterolytic cleavage, one atom leaves with all of the previously shared electrons and the other atom gets none of them. A—B --> A- + B+

Question 119

Define and differentiate between Symport, antiport, active transport, passive transport

Answer 119

Passive transport: Is the diffusion of substances across a membrane. This is a spontaneous process and cellular energy is not expended. Molecules will move from where the substance is more concentrated to where it is less concentrated. Active transport: A kind of transport wherein ions or molecules move against a concentration gradient, which means movement in the direction opposite that of diffusion – or – movement from an area of lower concentration to an area of higher concentration. A symporter: is an integral membrane protein that is involved in movement of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in the same direction, and is, therefore, a type of cotransporter. An antiporter: is an integral membrane protein involved in secondary active transport of two or more different molecules or ions across a phospholipid membrane such as the plasma membrane in opposite directions.

Question 120

Define glycoconjugates

Answer 120

Glycoconjugates is the general classification for carbohydrates covalently linked with other chemical species..

Question 121

Difference between nucleoside and nucleotide

Answer 121

Nucleotide = nitrogen base (purine or pyrimidine) + phosphate group + pentose sugar (ribose or deoxyribose) They are units of DNA. Nucleoside= nitrogen base(purine or pyrimidine) + pentose sugar (ribose or deoxyribose) They are units of RNA.