BCHM 4360 - Genes to Proteins Test #2 || with Complete Solution.
What is the information stored in DNA used for? correct answers to make a functional protein or
RNA molecule
Transcription correct answers the copying of one strand of DNA (coding strand) into an RNA
molecule (transcript)
transcript correct answers RNA
translation correct answers reading of the mRNA sequence by the ribosome to produce a protein
from the RNA molecule
RNA polymerase correct answers -large multi-subunit enzyme
-transcribes DNA
-copies the coding strand of DNA by using the complementary strand (the template or non-
coding strand) as a template
-separates the DNA strands and allows nucleoside triphosphate to base-pair with the template
strand
coding vs template strand correct answers coding = identical to mRNA
template = noncoding/complementary to mRNA
transcription can be divided into... correct answers initiation, elongation, termination
initiation of transcription (overview) correct answers -starts when RNA polymerase binds to the
DNA sequence just preceding the gene (the promoter) = promoter recognition
-TSS = +1
,-RNA polymerase separates the DNA strands to make a transcription bubble, and the first few
ribonucleoside triphosphates are added while the RNA polymerase is at the promoter
-when the RNA is a sufficient size, the RNA polymerase moves past the promoter and changes
conformation to be more stably associated with the DNA (allows higher processivity) = promoter
clearance
When does transcription start? correct answers when RNA polymerase binds to the DNA
sequence just preceding the gene (the promoter) = promoter recognition
transcription start site correct answers +1
the first base to be transcribed
direction of transcription correct answers 5' to 3' (template read 3' to 5')
Upstream vs. Downstream correct answers upstream = bases 5' of site on RNA
downstream = bases 3' of site on RNA
promoter clearance correct answers when the RNA is a sufficient size, the RNA polymerase
moves past the promoter and changes conformation to be more stably associated with the DNA
(allows higher processivity)
RNA polymerase undergoes a conformational change that associates it very stably with DNA,
and loosens its grip on initiation factors
-phosphorylated as it converts to the elongating complex (Cdk)
elongation of transcription (overview) correct answers -after promoter clearance, the RNA
polymerase moves along the DNA, adding ribonucleotides and elongating the RNA transcript
-the RNA polymerase unwinds the DNA ahead of it, and the DNA re-pairs behind the enzyme,
maintaining the transcription bubble along the DNA
,-in the bubble, a short region of the transcript is paired with the DNA while the rest of the RNA
is extruded from the polymerase
-elongation continues until the polymerase meets a DNA sequence called a terminator that
signals RNA synthesis to cease (RNA polymerase then dissociates from DNA)
transcription bubble correct answers -much smaller than replication bubble
-contained within RNA polymerase
-maintained along DNA by RNA polymerase unwinding the DNA ahead of it, and the DNA re-
pairing behind the enzyme
-has a short region of the transcript is paired with the DNA while the rest of the RNA is extruded
from the polymerase
How long does elongation continue (transcription)? correct answers until the polymerase meets a
DNA sequence called a terminator that signals RNA synthesis to cease (RNA polymerase then
dissociates from DNA)
heavy regulation of transcription correct answers -so only the required RNA is produced at the
right times
-usually controlled by chromatin packing
chromatin packing and transcription correct answers -chromatin packaged DNA presents a
challenge to transcription
-nucleosomes prevent transcription machinery binding to DNA
three additional types of enzymes required in eukaryotic transcription (due to chromatin packing)
correct answers 1. nucleosome remodeling enzymes that reposition histones away from the DNA
to be transcribed (can also work to block transcription)
-SWI/SNF
2. histone chaperones, which disassemble and reassemble the histone octamer
-Asf1 and Caf1 (H3+H4) and FACT (H2A + H2B)
, 3. enzymes that reversibly modify histone proteins in order to modify chromatin structure or
recruit specific proteins to certain DNA regions
-HAT
Eukaryotic RNA polymerases correct answers Usually 3:
1) RNA pol I -- makes rRNA
2) RNA pol II -- makes mRNA, small regulatory RNAs
3) RNA pol III -- makes tRNA, 5S RNA, sn RNA
plants have a fourth:
4) RNA pol IV -- makes siRNA (regulatory RNA)
RNA polymerases in bacteria and eukaryotes correct answers usually only one
core RNA polymerase correct answers -in all RNA polymerases
-catalyzes RNA synthesis
-cannot act alone - relies on extra proteins
-same basic structure conserved between archaea, bacteria, and eukaryotes ("c-like" architecture
carried throughout)
Bacteria = β + β'
Archaea = A'/A'' + β
Eukarya = 1 + 2
Bacterial RNA polymerase structure correct answers -smallest (40 kDa)
-5 subunits: 2 α, one β, one β', and one ω
-subunits assemble into a complex with jaw-like lobes
-jaws formed by the β and β' subunits, with the 2 α and the ω at the base
What is the information stored in DNA used for? correct answers to make a functional protein or
RNA molecule
Transcription correct answers the copying of one strand of DNA (coding strand) into an RNA
molecule (transcript)
transcript correct answers RNA
translation correct answers reading of the mRNA sequence by the ribosome to produce a protein
from the RNA molecule
RNA polymerase correct answers -large multi-subunit enzyme
-transcribes DNA
-copies the coding strand of DNA by using the complementary strand (the template or non-
coding strand) as a template
-separates the DNA strands and allows nucleoside triphosphate to base-pair with the template
strand
coding vs template strand correct answers coding = identical to mRNA
template = noncoding/complementary to mRNA
transcription can be divided into... correct answers initiation, elongation, termination
initiation of transcription (overview) correct answers -starts when RNA polymerase binds to the
DNA sequence just preceding the gene (the promoter) = promoter recognition
-TSS = +1
,-RNA polymerase separates the DNA strands to make a transcription bubble, and the first few
ribonucleoside triphosphates are added while the RNA polymerase is at the promoter
-when the RNA is a sufficient size, the RNA polymerase moves past the promoter and changes
conformation to be more stably associated with the DNA (allows higher processivity) = promoter
clearance
When does transcription start? correct answers when RNA polymerase binds to the DNA
sequence just preceding the gene (the promoter) = promoter recognition
transcription start site correct answers +1
the first base to be transcribed
direction of transcription correct answers 5' to 3' (template read 3' to 5')
Upstream vs. Downstream correct answers upstream = bases 5' of site on RNA
downstream = bases 3' of site on RNA
promoter clearance correct answers when the RNA is a sufficient size, the RNA polymerase
moves past the promoter and changes conformation to be more stably associated with the DNA
(allows higher processivity)
RNA polymerase undergoes a conformational change that associates it very stably with DNA,
and loosens its grip on initiation factors
-phosphorylated as it converts to the elongating complex (Cdk)
elongation of transcription (overview) correct answers -after promoter clearance, the RNA
polymerase moves along the DNA, adding ribonucleotides and elongating the RNA transcript
-the RNA polymerase unwinds the DNA ahead of it, and the DNA re-pairs behind the enzyme,
maintaining the transcription bubble along the DNA
,-in the bubble, a short region of the transcript is paired with the DNA while the rest of the RNA
is extruded from the polymerase
-elongation continues until the polymerase meets a DNA sequence called a terminator that
signals RNA synthesis to cease (RNA polymerase then dissociates from DNA)
transcription bubble correct answers -much smaller than replication bubble
-contained within RNA polymerase
-maintained along DNA by RNA polymerase unwinding the DNA ahead of it, and the DNA re-
pairing behind the enzyme
-has a short region of the transcript is paired with the DNA while the rest of the RNA is extruded
from the polymerase
How long does elongation continue (transcription)? correct answers until the polymerase meets a
DNA sequence called a terminator that signals RNA synthesis to cease (RNA polymerase then
dissociates from DNA)
heavy regulation of transcription correct answers -so only the required RNA is produced at the
right times
-usually controlled by chromatin packing
chromatin packing and transcription correct answers -chromatin packaged DNA presents a
challenge to transcription
-nucleosomes prevent transcription machinery binding to DNA
three additional types of enzymes required in eukaryotic transcription (due to chromatin packing)
correct answers 1. nucleosome remodeling enzymes that reposition histones away from the DNA
to be transcribed (can also work to block transcription)
-SWI/SNF
2. histone chaperones, which disassemble and reassemble the histone octamer
-Asf1 and Caf1 (H3+H4) and FACT (H2A + H2B)
, 3. enzymes that reversibly modify histone proteins in order to modify chromatin structure or
recruit specific proteins to certain DNA regions
-HAT
Eukaryotic RNA polymerases correct answers Usually 3:
1) RNA pol I -- makes rRNA
2) RNA pol II -- makes mRNA, small regulatory RNAs
3) RNA pol III -- makes tRNA, 5S RNA, sn RNA
plants have a fourth:
4) RNA pol IV -- makes siRNA (regulatory RNA)
RNA polymerases in bacteria and eukaryotes correct answers usually only one
core RNA polymerase correct answers -in all RNA polymerases
-catalyzes RNA synthesis
-cannot act alone - relies on extra proteins
-same basic structure conserved between archaea, bacteria, and eukaryotes ("c-like" architecture
carried throughout)
Bacteria = β + β'
Archaea = A'/A'' + β
Eukarya = 1 + 2
Bacterial RNA polymerase structure correct answers -smallest (40 kDa)
-5 subunits: 2 α, one β, one β', and one ω
-subunits assemble into a complex with jaw-like lobes
-jaws formed by the β and β' subunits, with the 2 α and the ω at the base
