Question 1

What is required for conversion from the closed-promoter complex to open-promoter complex?

Accepted Answer

A) ATP binding 
B) ATP hydrolysis 
C) GTP binding 
D) GTP hydrolysis 
E) DNA bending 
A) ATP binding 
B) ATP hydrolysis 
C) GTP binding 
D) GTP hydrolysis 
E) DNA bending E

Question 2

What type of RNA is found in the spliceosome?

Accepted Answer

A) snRNA 
B) tRNA 
C) rRNA 
D) triple-stranded RNA 
E) all of the above 
A) snRNA 
B) tRNA 
C) rRNA 
D) triple-stranded RNA 
E) all of the above A

Question 3

Transcription of the 5S rRNA gene occurs by ________ covering the entire gene so that pol III can ____________.

Accepted Answer

A) TFIIB; transcribe the gene several times before dissociating 
B) TFIIIC; transcribe the gene several times before dissociating 
C) TFIIB; transcribe both strands of DNA before dissociating 
D) TFIIIC; transcribe both strands of DNA before dissociating 
E) none of the above 
A) TFIIB; transcribe the gene several times before dissociating 
B) TFIIIC; transcribe the gene several times before dissociating 
C) TFIIB; transcribe both strands of DNA before dissociating 
D) TFIIIC; transcribe both strands of DNA before dissociating 
E) none of the above B

Question 4

Give the mRNA sequence that would result from the following sense strand:
5'-A-T-C-T-C-G-A-T-C-G-T-A-C-G-A-T-G-T-C-A-3'

Accepted Answer

5'-A-U-C-U

Question 5

How does the concentration of ribonucleotide triphosphates play a role in the regulation of initiation?

Accepted Answer

A) a high concentration of ATP is required to form the open-promoter complex 
B) high concentration of both ATP and GTP are required to form the open-promoter complex 
C) the single nucleotide binding site of RNA polymerase undergoes a conformational change after the first nucleotide to allow subsequent nucleotides to bind more readily 
D) binding of the first nucleotide requires a half-saturating concentration of ~100 $\mu$M while the half-saturating concentration for subsequent nucleotides is only ~10 $\mu$M 
E) none of the above 
A) a high concentration of ATP is required to form the open-promoter complex 
B) high concentration of both ATP and GTP are required to form the open-promoter complex 
C) the single nucleotide binding site of RNA polymerase undergoes a conformational change after the first nucleotide to allow subsequent nucleotides to bind more readily 
D) binding of the first nucleotide requires a half-saturating concentration of ~100 $\mu$M while the half-saturating concentration for subsequent nucleotides is only ~10 $\mu$M 
E) none of the above

Question 6

Phosphorylation of the Rpb1 subunit of pol II causes what to occur?

Accepted Answer

A) binding to histone proteins 
B) hydrogen bonding with guanine residues near the start of transcription 
C) dissociation from the promoter 
D) transcription termination 
E) none of the above 
A) binding to histone proteins 
B) hydrogen bonding with guanine residues near the start of transcription 
C) dissociation from the promoter 
D) transcription termination 
E) none of the above

Question 7

Rapid transcription of ribosomal RNA is thought to occur as a result of what unique feature in the DNA that encodes these genes?

Accepted Answer

A) high A-T content 
B) highly repetitive sequence 
C) multiple promoter sites that allow high affinity with RNA polymerase 
D) presence of hairpin structures in the DNA 
E) absence of nucleosomes 
A) high A-T content 
B) highly repetitive sequence 
C) multiple promoter sites that allow high affinity with RNA polymerase 
D) presence of hairpin structures in the DNA 
E) absence of nucleosomes

Question 8

Which of the following is the first event in the post-translational processing of an E. coli tRNA?

Accepted Answer

A) ribonuclease P cleavage to create the proper 5' end of the molecule 
B) methylation of guanine residues 
C) conversion of some uridine residues to pseudouridine 
D) endonuclease cleavage of about 170 bases from the 3' end of the molecule 
E) removal of 9 nucleotides from the 3' end by ribonuclease D 
A) ribonuclease P cleavage to create the proper 5' end of the molecule 
B) methylation of guanine residues 
C) conversion of some uridine residues to pseudouridine 
D) endonuclease cleavage of about 170 bases from the 3' end of the molecule 
E) removal of 9 nucleotides from the 3' end by ribonuclease D

Question 9

Draw a transcription bubble, clearly labeling the proteins and nucleic acids involved in the process.

Accepted Answer

The answer of Draw a transcription bubble, clearly labeling the...

Question 10

As RNA polymerase moves along the DNA, it creates a single stranded region of about 18 base pairs that is called a ________________.

Accepted Answer

A) transcription bubble 
B) transcription single-stranded region 
C) transcription droplet 
D) transcription vesicle 
E) transcription bead 
A) transcription bubble 
B) transcription single-stranded region 
C) transcription droplet 
D) transcription vesicle 
E) transcription bead

Question 11

What is the mechanism by which enhancers, despite the fact that they are often several kilobase pairs away from the promoter, activate transcription?

Accepted Answer

A) DNA unwinding 
B) DNA looping 
C) chromatin remodeling 
D) DNA hairpin formation 
E) none of the above 
A) DNA unwinding 
B) DNA looping 
C) chromatin remodeling 
D) DNA hairpin formation 
E) none of the above

Question 12

The concept of the operon was proposed based on the ability of E. coli to metabolize the disaccharide ________ only when present in large excess over glucose.

Accepted Answer

A) sucrose 
B) cellobiose 
C) galactose 
D) lactose 
E) maltose 
A) sucrose 
B) cellobiose 
C) galactose 
D) lactose 
E) maltose

Question 13

The E. coli core polymerase is missing the ____ subunit and binds to DNA with _______ specificity than the holoenzyme.

Accepted Answer

A)  $\sigma$; less 
B)  $\sigma$; greater 
C) $\alpha$; less 
D) $\alpha$; greater 
E) none of the above 
A)  $\sigma$; less 
B)  $\sigma$; greater 
C) $\alpha$; less 
D) $\alpha$; greater 
E) none of the above

Question 14

In eukaryotic cells, RNA polymerase ____ transcribes most of the ribosomal RNA, RNA polymerase ____ transcribes the major structural genes and RNA polymerase ____ transcribes tRNAs.

Accepted Answer

A) I; II; III 
B) I; III; II 
C) II; I; III 
D) II; III; I 
E) III; II; I 
A) I; II; III 
B) I; III; II 
C) II; I; III 
D) II; III; I 
E) III; II; I

Question 15

During factor-independent termination, RNA polymerase pauses upon encountering a _____________ and is then displaced downstream upon encountering a ___________.

Accepted Answer

A) TATAAT sequence; G-C rich segment 
B) G-C rich segment; TATAAT sequence 
C) G-C rich segment; string of 4-8 A residues 
D) string of 4-8 A residues; TATAAT sequence 
E) string of 4-8 A residues; G-C rich segment 
A) TATAAT sequence; G-C rich segment 
B) G-C rich segment; TATAAT sequence 
C) G-C rich segment; string of 4-8 A residues 
D) string of 4-8 A residues; TATAAT sequence 
E) string of 4-8 A residues; G-C rich segment

Question 16

Which subunit of E. coli RNA polymerase is responsible for the RNA polymerization reaction?

Accepted Answer

A) $\alpha$ 
B) $\beta$ 
C) $\beta$' 
D)  $\sigma$ 
E) $\omega$ 
A) $\alpha$ 
B) $\beta$ 
C) $\beta$' 
D)  $\sigma$ 
E) $\omega$

Question 17

What type of enzyme activity is associated with the termination factor $\rho$?

Accepted Answer

A) topoisomerase 
B) endonuclease 
C) exonuclease 
D) helicase 
E) ligase 
A) topoisomerase 
B) endonuclease 
C) exonuclease 
D) helicase 
E) ligase

Question 18

Rifampicin is known to inhibit RNA synthesis in E. coli. Once the first ten nucleotides have been incorporated, rifampicin does not inhibit RNA synthesis. Which of the following best explains how rifampicin functions?

Accepted Answer

A) rifampicin binds only to the core enzyme when bound to DNA but can bind to the holoenzyme when not bound to DNA 
B) rifampicin can bind to RNA polymerase when the polymerase is not bound to DNA but cannot bind when the polymerase is bound to DNA 
C) rifampicin only inhibits when the $\alpha$ subunit is bound to the core enzyme 
D) rifampicin is able to bind to the nucleotide binding site at any time 
E) none of the above 
A) rifampicin binds only to the core enzyme when bound to DNA but can bind to the holoenzyme when not bound to DNA 
B) rifampicin can bind to RNA polymerase when the polymerase is not bound to DNA but cannot bind when the polymerase is bound to DNA 
C) rifampicin only inhibits when the $\alpha$ subunit is bound to the core enzyme 
D) rifampicin is able to bind to the nucleotide binding site at any time 
E) none of the above

Question 19

Which of the following is the most common promoter element for pol II?

Accepted Answer

A) CAAT box (GGCCAATCT) 
B) GC box (GGGCGG) 
C) TRE (GAGGGACGTACCGC
A)  
D) TATA box (TATAAA
A)  
E) Octamer (ATTTGCAT) 
A) CAAT box (GGCCAATCT) 
B) GC box (GGGCGG) 
C) TRE (GAGGGACGTACCGC
A)  
D) TATA box (TATAAA
A)  
E) Octamer (ATTTGCAT)

Question 20

The E. coli promoter region contains a -10 consensus sequence of _________ on the sense strand.

Accepted Answer

A) GAGAGA 
B) CTCTCT 
C) GAGGAG 
D) GACGTC 
E) TATAAT 
A) GAGAGA 
B) CTCTCT 
C) GAGGAG 
D) GACGTC 
E) TATAAT

Exam 27: Information Readout: Transcription and Post-Transcriptional Processing

What is required for conversion from the closed-promoter complex to open-promoter complex?

What type of RNA is found in the spliceosome?

Transcription of the 5S rRNA gene occurs by ________ covering the entire gene so that pol III can ____________.

Give the mRNA sequence that would result from the following sense strand: 5'-A-T-C-T-C-G-A-T-C-G-T-A-C-G-A-T-G-T-C-A-3'

How does the concentration of ribonucleotide triphosphates play a role in the regulation of initiation?

Phosphorylation of the Rpb1 subunit of pol II causes what to occur?

Rapid transcription of ribosomal RNA is thought to occur as a result of what unique feature in the DNA that encodes these genes?

Which of the following is the first event in the post-translational processing of an E. coli tRNA?

Draw a transcription bubble, clearly labeling the proteins and nucleic acids involved in the process.

As RNA polymerase moves along the DNA, it creates a single stranded region of about 18 base pairs that is called a ________________.

What is the mechanism by which enhancers, despite the fact that they are often several kilobase pairs away from the promoter, activate transcription?

The concept of the operon was proposed based on the ability of E. coli to metabolize the disaccharide ________ only when present in large excess over glucose.

The E. coli core polymerase is missing the ____ subunit and binds to DNA with _______ specificity than the holoenzyme.

In eukaryotic cells, RNA polymerase ____ transcribes most of the ribosomal RNA, RNA polymerase ____ transcribes the major structural genes and RNA polymerase ____ transcribes tRNAs.

During factor-independent termination, RNA polymerase pauses upon encountering a _____________ and is then displaced downstream upon encountering a ___________.

Which subunit of E. coli RNA polymerase is responsible for the RNA polymerization reaction?

What type of enzyme activity is associated with the termination factor ρ\rhoρ ?

Rifampicin is known to inhibit RNA synthesis in E. coli. Once the first ten nucleotides have been incorporated, rifampicin does not inhibit RNA synthesis. Which of the following best explains how rifampicin functions?

Which of the following is the most common promoter element for pol II?

The E. coli promoter region contains a -10 consensus sequence of _________ on the sense strand.

The Scope of Biochemistry

The Matrix of Life: Weak Interactions in an Aqueous Environment

The Energetics of Life

Nucleic Acids

Introduction to Proteins: the Primary Level of Protein Structure

The Three-Dimensional Structure of Proteins

Protein Function and Evolution

Contractile Proteins and Molecular Motors

Carbohydrates: Sugars, Saccharides, Glycans

Lipids, Membranes and Cellular Transport

Enzymes: Biological Catalysts

Chemical Logic of Metabolism

Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Citric Acid Cycle and Glyoxylate Cycle

Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

Photosynthesis

Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

Lipid Metabolism Ii: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

Nucleotide Metabolism

Mechanisms of Signal Transduction

Genes, Genomes and Chromosomes

DNA Replication

DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

Information Decoding: Translation and Post-Translational Protein Processing

Regulation of Gene Expression

Filters

Transcription of the 5S rRNA gene occurs by covering the entire gene so that pol III can ____.

The E. coli core polymerase is missing the subunit and binds to DNA with ___ specificity than the holoenzyme.

In eukaryotic cells, RNA polymerase transcribes most of the ribosomal RNA, RNA polymerase transcribes the major structural genes and RNA polymerase transcribes tRNAs.

During factor-independent termination, RNA polymerase pauses upon encountering a ___ and is then displaced downstream upon encountering a _.

What type of enzyme activity is associated with the termination factor $\rho$ ?