Question 1

The base-pair edges in the ____ groove act as a(n) ____ identifiable through ____ with specific proteins.

Accepted Answer

A)  minor; enhancer; H-bonding 
B)  minor; recognition matrix; H-bonding 
C)  major; recognition matrix; H-bonding 
D)  major; repressor; ionic binding 
E)  major; transcriptional silencer; ionic bonding 
A)  minor; enhancer; H-bonding 
B)  minor; recognition matrix; H-bonding 
C)  major; recognition matrix; H-bonding 
D)  major; repressor; ionic binding 
E)  major; transcriptional silencer; ionic bonding

Question 2

Treatment of the RNA polymerase/DNA complex with DNase in vitro is a DNA footprinting technique used to:

Accepted Answer

A)  identify the termination sequence for transcription. 
B)  locate the start site for transcription. 
C)  locate the promoter site. 
D)  identify the position of enhancer sequences. 
E)  none of the above. 
A)  identify the termination sequence for transcription. 
B)  locate the start site for transcription. 
C)  locate the promoter site. 
D)  identify the position of enhancer sequences. 
E)  none of the above.

Question 3

All are true for transcription activation EXCEPT:

Accepted Answer

A)  takes place when a transcriptional activator protein bound to DNA makes protein : protein contacts with RNA polymerase. 
B)  the degree of transcriptional activation is proportional to the strength of the protein : protein interaction. 
C)  a nucleotide sequence binding site for a DNA-binding protein serves as an activator site if DNA-binding protein can interact with promoter-bound RNA polymerase. 
D)  if the DNA-bound transcriptional activator makes contact with two different components of RNA polymerase, the transcription is markedly elevated. 
E)  all are true. 
A)  takes place when a transcriptional activator protein bound to DNA makes protein : protein contacts with RNA polymerase. 
B)  the degree of transcriptional activation is proportional to the strength of the protein : protein interaction. 
C)  a nucleotide sequence binding site for a DNA-binding protein serves as an activator site if DNA-binding protein can interact with promoter-bound RNA polymerase. 
D)  if the DNA-bound transcriptional activator makes contact with two different components of RNA polymerase, the transcription is markedly elevated. 
E)  all are true.

Question 4

The leucine zipper is a protein motif held together by:

Accepted Answer

A)  H-bonds. 
B)  hydrophobic interactions. 
C)  ionic interactions. 
D)  metal ion binding. 
E)  protein:DNA interactions. 
A)  H-bonds. 
B)  hydrophobic interactions. 
C)  ionic interactions. 
D)  metal ion binding. 
E)  protein:DNA interactions.

Question 5

Most eukaryotic RNA consists of coding regions, called ____, and noncoding regions, called ____.

Accepted Answer

A)  introns; exons 
B)  exons; introns 
C)  spliceons; codons 
D)  codons; spliceons 
E)  introns; codons 
A)  introns; exons 
B)  exons; introns 
C)  spliceons; codons 
D)  codons; spliceons 
E)  introns; codons

Question 6

All are stages in transcription EXCEPT:

Accepted Answer

A)  binding of RNA polymerase holoenzyme at the promoter sites. 
B)  chain elongation. 
C)  DNase I activity on RNA polymerase/DNA complex. 
D)  initiation of polymerization. 
E)  chain termination. 
A)  binding of RNA polymerase holoenzyme at the promoter sites. 
B)  chain elongation. 
C)  DNase I activity on RNA polymerase/DNA complex. 
D)  initiation of polymerization. 
E)  chain termination.

Question 7

All are factors or subunits contained within the E. coli RNA polymerase holoenzyme in prokaryotic organisms EXCEPT:

Accepted Answer

A)  ρ (rho). 
B)  α (alpha). 
C)  β (beta). 
D)  β′ (beta prime). 
E)  σ (sigma). 
A)  ρ (rho). 
B)  α (alpha). 
C)  β (beta). 
D)  β′ (beta prime). 
E)  σ (sigma).

Question 8

Discuss the capping and methylation of eukaryotic heterogeneous nuclear RNA (hnRNA).​

Accepted Answer

Shortly after transcription of hnRNA is

Question 9

The initial event in the conversion of an hnRNA to the mature RNA which leaves the nucleus is:

Accepted Answer

A)  formation of ribonucleoprotein particles (RNPs). 
B)  capping the 5'-end of the transcript with a guanylyl group by guanylyl transferase. 
C)  addition of a poly(
A)  tail to the 3'-end of the transcript by poly(
A)  polymerase. 
D)  splicing together of the exons. 
E)  transesterification reactions in lariat formation. 
A)  formation of ribonucleoprotein particles (RNPs). 
B)  capping the 5'-end of the transcript with a guanylyl group by guanylyl transferase. 
C)  addition of a poly(
A)  tail to the 3'-end of the transcript by poly(
A)  polymerase. 
D)  splicing together of the exons. 
E)  transesterification reactions in lariat formation.

Question 10

Lac repressor is an example of the DNA-binding motif common to many prokaryotic regulatory proteins and is:

Accepted Answer

A)  a homeobox. 
B)  a zinc finger. 
C)  a basic region-leucine finger. 
D)  a helix-turn-helix. 
E)  none of the above. 
A)  a homeobox. 
B)  a zinc finger. 
C)  a basic region-leucine finger. 
D)  a helix-turn-helix. 
E)  none of the above.

Question 11

The initiation site binds a ____ nucleotide base pairing with the ____ base exposed within the ____ promoter complex, and then the second base is added to the ____ of the first base.

Accepted Answer

A)  pyrimidine; −1; closed; 3'-O 
B)  pyrimidine; +1; closed; 5'-O 
C)  purine; +2; closed; 3'-O 
D)  purine; −1; open; 5'-O 
E)  purine; +1; open; 3'-O 
A)  pyrimidine; −1; closed; 3'-O 
B)  pyrimidine; +1; closed; 5'-O 
C)  purine; +2; closed; 3'-O 
D)  purine; −1; open; 5'-O 
E)  purine; +1; open; 3'-O

Question 12

Within the ____ are two consensus sequence elements, the ____ near −10 with a sequence of TATAAT, and the ____ containing the consensus TTGACA.

Accepted Answer

A)  termination sequence; rho subunit; sigma sub 
B)  termination sequence; Pribnow box; sigma subunit unit 
C)  promoter sequence; rho subunit; Pribnow box 
D)  promoter sequence; Pribnow box; −35 region 
E)  promoter sequence; rho subunit; −35 region 
A)  termination sequence; rho subunit; sigma sub 
B)  termination sequence; Pribnow box; sigma subunit unit 
C)  promoter sequence; rho subunit; Pribnow box 
D)  promoter sequence; Pribnow box; −35 region 
E)  promoter sequence; rho subunit; −35 region

Question 13

Explain the transcription termination mechanism that is dependent on the rho termination factor.​

Accepted Answer

​Rho factor is an ATP-dependent hexameri

Question 14

The araBAD operon allows for the use of what metabolite by E. coli?

Accepted Answer

A)  arachidonic acid 
B)  arabinose 
C)  allose 
D)  altrose 
E)  none of the above 
A)  arachidonic acid 
B)  arabinose 
C)  allose 
D)  altrose 
E)  none of the above

Question 15

Intrinsic RNA chain termination is determined by specific sequences in the DNA called ____ sites.

Accepted Answer

A)  termination 
B)  rho binding 
C)  template binding 
D)  supercoil 
E)  all are true 
A)  termination 
B)  rho binding 
C)  template binding 
D)  supercoil 
E)  all are true

Question 16

All are correct about enhancer sequences in eukaryotic cells EXCEPT:

Accepted Answer

A)  they can occur either upstream or downstream of the gene. 
B)  they can be in either orientation (bi-directional). 
C)  enhancer function is dependent on recognition by a specific transcription factor. 
D)  specific transcription factor binding at an enhancer stimulates transcription by interacting with RNA polymerase II. 
E)  all are correct. 
A)  they can occur either upstream or downstream of the gene. 
B)  they can be in either orientation (bi-directional). 
C)  enhancer function is dependent on recognition by a specific transcription factor. 
D)  specific transcription factor binding at an enhancer stimulates transcription by interacting with RNA polymerase II. 
E)  all are correct.

Question 17

The metallothionein gene promoter consists of all EXCEPT:

Accepted Answer

A)  TATA box. 
B)  GC box. 
C)  glucocorticoids response element (GR
E) . 
D)  heat shock element (HS
E) . 
E)  all are true. 
A)  TATA box. 
B)  GC box. 
C)  glucocorticoids response element (GR
E) . 
D)  heat shock element (HS
E) . 
E)  all are true.

Question 18

All are true for translation in eukaryotic cells EXCEPT:

Accepted Answer

A)  transcription and translation are spatially separated. 
B)  mRNAs are monocistronic. 
C)  transcription occurs in the nucleus. 
D)  primary transcripts undergo processing to mature mRNAs. 
E)  all are true. 
A)  transcription and translation are spatially separated. 
B)  mRNAs are monocistronic. 
C)  transcription occurs in the nucleus. 
D)  primary transcripts undergo processing to mature mRNAs. 
E)  all are true.

Question 19

During RNA chain elongation, ____ follows behind the transcription bubble removing _____ supercoils

Accepted Answer

A)  gyrase; negative 
B)  gyrase; positive 
C)  topoisomerase; negative 
D)  topoisomerase; positive 
E)  none of the above 
A)  gyrase; negative 
B)  gyrase; positive 
C)  topoisomerase; negative 
D)  topoisomerase; positive 
E)  none of the above

Question 20

All are components of the basic rule of macromolecular recognition EXCEPT:

Accepted Answer

A)  protein recognizes nucleotide sequences by atomic contacts with bases and sugar-phosphate backbone usually in the major groove. 
B)  protein contacts involve H-bonds and salt bridges with electronegative oxygens of the phosphodiester linkages. 
C)  proteins present a three-dimensional shape or contour structurally and chemically complementary to the surface of the DNA sequence. 
D)  numerous atomic interactions underlie recognition and binding. 
E)  all are components. 
A)  protein recognizes nucleotide sequences by atomic contacts with bases and sugar-phosphate backbone usually in the major groove. 
B)  protein contacts involve H-bonds and salt bridges with electronegative oxygens of the phosphodiester linkages. 
C)  proteins present a three-dimensional shape or contour structurally and chemically complementary to the surface of the DNA sequence. 
D)  numerous atomic interactions underlie recognition and binding. 
E)  all are components.

Exam 29: Transcription and the Regulation of Gene Expression

The base-pair edges in the ____ groove act as a(n) ____ identifiable through ____ with specific proteins.

Treatment of the RNA polymerase/DNA complex with DNase in vitro is a DNA footprinting technique used to:

All are true for transcription activation EXCEPT:

The leucine zipper is a protein motif held together by:

Most eukaryotic RNA consists of coding regions, called ____, and noncoding regions, called ____.

All are stages in transcription EXCEPT:

All are factors or subunits contained within the E. coli RNA polymerase holoenzyme in prokaryotic organisms EXCEPT:

Discuss the capping and methylation of eukaryotic heterogeneous nuclear RNA (hnRNA).​

The initial event in the conversion of an hnRNA to the mature RNA which leaves the nucleus is:

Lac repressor is an example of the DNA-binding motif common to many prokaryotic regulatory proteins and is:

The initiation site binds a ____ nucleotide base pairing with the ____ base exposed within the ____ promoter complex, and then the second base is added to the ____ of the first base.

Within the ____ are two consensus sequence elements, the ____ near −10 with a sequence of TATAAT, and the ____ containing the consensus TTGACA.

Explain the transcription termination mechanism that is dependent on the rho termination factor.​

The araBAD operon allows for the use of what metabolite by E. coli?

Intrinsic RNA chain termination is determined by specific sequences in the DNA called ____ sites.

All are correct about enhancer sequences in eukaryotic cells EXCEPT:

The metallothionein gene promoter consists of all EXCEPT:

All are true for translation in eukaryotic cells EXCEPT:

During RNA chain elongation, ____ follows behind the transcription bubble removing _____ supercoils

All are components of the basic rule of macromolecular recognition EXCEPT:

The Facts of Life: Chemistry Is the Logic of Biological Phenomena

Water: the Medium of Life

Thermodynamics of Biological Systems

Amino Acids and the Peptide Bond

Proteins: Their Primary Structure and Biological Functions

Proteins: Secondary, Tertiary, and Quaternary Structure

Carbohydrates and the Glycoconjugates of Cell Surfaces

Lipids

Membranes and Membrane Transport

Nucleotides and Nucleic Acids

Structure of Nucleic Acids

Recombinant Dna, Cloning, Chimeric Genes, and Synthetic Biology

Enzymeskinetics and Specificity

Mechanisms of Enzyme Action

Enzyme Regulation

Molecular Motors

Metabolism: an Overview

Glycolysis

The Tricarboxylic Acid Cycle

Electron Transport and Oxidative Phosphorylation

Photosynthesis

Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Fatty Acid Catabolism

Lipid Biosynthesis

Nitrogen Acquisition and Amino Acid Metabolism

Synthesis and Degradation of Nucleotides

Metabolic Integration and Organ Specialization

Dna Metabolism: Replication, Recombination, and Repair

Protein Synthesis

Completing the Protein Life Cycle: Folding, Processing, and Degradation

The Reception and Transmission of Extracellular Information

Filters

The base-pair edges in the groove act as a(n) identifiable through with specific proteins.

Most eukaryotic RNA consists of coding regions, called , and noncoding regions, called .

Discuss the capping and methylation of eukaryotic heterogeneous nuclear RNA (hnRNA).

The initiation site binds a nucleotide base pairing with the base exposed within the promoter complex, and then the second base is added to the of the first base.

Within the are two consensus sequence elements, the near −10 with a sequence of TATAAT, and the containing the consensus TTGACA.

Explain the transcription termination mechanism that is dependent on the rho termination factor.

During RNA chain elongation, follows behind the transcription bubble removing _ supercoils