Molecular Biology Exam questions
and answers graded A+
Central Dogma of Molecular Biology - ANS✅✅DNA-transcription-RNA-translation-protein
DNA replication - ANS✅✅the process of making a copy of DNA using DNA Polymerase
Transcription - ANS✅✅synthesis of an RNA molecule from a DNA template by RNA polymerase
Which step is most important for regulation in the cell? (especially in multicellular organisms) -
ANS✅✅Transcription
*What are the general features of Transcription? - ANS✅✅-uses RNA polymerase
-RNA product is displaced nearly immediately from template
-less accurate compared to DNA replication
-not interested in the whole genome (only sections)
-novel (no primer is needed)
*What are the RNA polymerases in eukaryotes? - ANS✅✅RNA polymerase I: rRNA precursors
RNA polymerase II: mRNAs, some small RNAs
RNA polymerase III: tRNAs, 5s rRNA, some small RNAs
*RNA polymerases consist of - ANS✅✅multiple subunits, pincher shaped, 2-metal ion catalysis
similar to DNA polymerase
Transcription is a 3 phase progression - ANS✅✅1. initiation
2. elongation
3. termination
*What is initiation? - ANS✅✅-promoter recognition and binding by RNA poly (closed complex)
-DNA melting (open complex)
,-initial transcribing complex
Which process produces mRNA - ANS✅✅elongation during transcription
Which phase of transcription releases polymerase and RNA? - ANS✅✅termination
*Bacterial Transcription - ANS✅✅-promoters decide where to start transcription
-contain core enzyme (a2BB'w) which will begin transcription almost anywhere
-the σ provides specificity
-σ + core = holoenzyme
*E. coli contains ____ promoter - ANS✅✅σ70 (has 2 conserved sequences of 6 base pair each at -
35 and -10)
*Bacterial Consensus Sequences - ANS✅✅-35 = TTGACA
-10 = TATAAT
*Other types of bacterial transcription promoter sequences include - ANS✅✅-UP-element (found
in some strong promoters esp. rRNA genes)
-extended -10 elements (lack of -35 sequence)
-discriminator (GC rich seq. that increases σ specificity-binding stability)
UP element - ANS✅✅- A promoter element characteristic of certain strong promoter regions.
- Consists of an AT rich region.
- it increases polymerase binding by providing an additional specific interaction between the enzyme
and the DNA.
*Explain σ promotor structure - ANS✅✅-4 σ regions corresponding to promoter sequences
-alpha helices in regions 2, 3, & 4 bind to -10 seq, extended seq, and -35 promoter elements
-alpha-subunit, alphaNTD and alpha CTD bind to UP element
,What makes up helix-turn-helix? - ANS✅✅- Two helices within region 4 form a common DNA-
binding motif
- One of these helices inserts into the major groove and interacts with bases in the - 35 region
- the other lies across the top of the groove, making contacts with the DNA backbone
*Alpha helices in regions 2,3, & 4 bind to what elements? - ANS✅✅- -10 seq (σ2)
- extended seq (σ3)
- -35 promoter elements (σ4)
*What subunits bind to UP element? - ANS✅✅- alpha-subunit
- alphaNTD
- alpha CTD
*What is the transition from closed to open complex bearing σ70? - ANS✅✅Isomerization
Which subunit forms pinchers in bacterial transcription of RNA polymerase? - ANS✅✅β and β'
*What subunit initially blocks entrance between the pinchers? - ANS✅✅σ
What positions is dsDNA meted between? - ANS✅✅-11 and +3
*Is ATP required for bacterial transcription? - ANS✅✅No; energetically favorable!
In σ2 when the -10 promoter is not melting - ANS✅✅no transcription occurs because no
isomerization occurs therefor it does not bind properly due to dsDNA
In σ2 when the -10 promoter is melting - ANS✅✅transcription occurs because ssDNA binds
properly to σ2
reverse transcriptase - ANS✅✅An enzyme encoded by certain viruses (retroviruses) that uses RNA
as a template for DNA synthesis. (RNA guided DNA repair)
, *During Bacterial Transcription, how many channels are in the open complex? - ANS✅✅5
- NTP uptake back side of +1
- RNA exit channel (by -35)
- Downstream DNA entrance (by +1)
- Non-Template exit [NT] (behind +1)
- Template [T] exit (behind -10 region)
*Bacterial Transcription begins ______. - ANS✅✅de novo (without primer)
*RNA poly remains _____ and pulls DNA into itself during ________ transcription. -
ANS✅✅stationary; initial
*What is the role of the σ 3/4 linker? - ANS✅✅interacts with template strand by organizing it into
correct conformation and location to allow initiation by allowing interactions with the nucleotides
(think isomerization); (initiating NTP and incoming NTP)
NTP stands for - ANS✅✅nucleotide triphosphates
What are the 3 modes of bacterial transcription? - ANS✅✅Transient excursion
inchworming
scrunching
experiments on modes of transcription initiation show - ANS✅✅- pol remains stationary on
promoter
- pol subunits remain stationary relative to one another
What mode provides energy to break polymerase-promoter interactino and dislodge σ? -
ANS✅✅scrunched DNA
initial transcribing complex - ANS✅✅the polymerase-promoter complex Incorporates the first 10
or so ribonucleotides (a rather inefficient process) and at that stage, the enzyme often releases short
transcripts (each of less than 10 or so nucleotides) and then begins synthesis again
and answers graded A+
Central Dogma of Molecular Biology - ANS✅✅DNA-transcription-RNA-translation-protein
DNA replication - ANS✅✅the process of making a copy of DNA using DNA Polymerase
Transcription - ANS✅✅synthesis of an RNA molecule from a DNA template by RNA polymerase
Which step is most important for regulation in the cell? (especially in multicellular organisms) -
ANS✅✅Transcription
*What are the general features of Transcription? - ANS✅✅-uses RNA polymerase
-RNA product is displaced nearly immediately from template
-less accurate compared to DNA replication
-not interested in the whole genome (only sections)
-novel (no primer is needed)
*What are the RNA polymerases in eukaryotes? - ANS✅✅RNA polymerase I: rRNA precursors
RNA polymerase II: mRNAs, some small RNAs
RNA polymerase III: tRNAs, 5s rRNA, some small RNAs
*RNA polymerases consist of - ANS✅✅multiple subunits, pincher shaped, 2-metal ion catalysis
similar to DNA polymerase
Transcription is a 3 phase progression - ANS✅✅1. initiation
2. elongation
3. termination
*What is initiation? - ANS✅✅-promoter recognition and binding by RNA poly (closed complex)
-DNA melting (open complex)
,-initial transcribing complex
Which process produces mRNA - ANS✅✅elongation during transcription
Which phase of transcription releases polymerase and RNA? - ANS✅✅termination
*Bacterial Transcription - ANS✅✅-promoters decide where to start transcription
-contain core enzyme (a2BB'w) which will begin transcription almost anywhere
-the σ provides specificity
-σ + core = holoenzyme
*E. coli contains ____ promoter - ANS✅✅σ70 (has 2 conserved sequences of 6 base pair each at -
35 and -10)
*Bacterial Consensus Sequences - ANS✅✅-35 = TTGACA
-10 = TATAAT
*Other types of bacterial transcription promoter sequences include - ANS✅✅-UP-element (found
in some strong promoters esp. rRNA genes)
-extended -10 elements (lack of -35 sequence)
-discriminator (GC rich seq. that increases σ specificity-binding stability)
UP element - ANS✅✅- A promoter element characteristic of certain strong promoter regions.
- Consists of an AT rich region.
- it increases polymerase binding by providing an additional specific interaction between the enzyme
and the DNA.
*Explain σ promotor structure - ANS✅✅-4 σ regions corresponding to promoter sequences
-alpha helices in regions 2, 3, & 4 bind to -10 seq, extended seq, and -35 promoter elements
-alpha-subunit, alphaNTD and alpha CTD bind to UP element
,What makes up helix-turn-helix? - ANS✅✅- Two helices within region 4 form a common DNA-
binding motif
- One of these helices inserts into the major groove and interacts with bases in the - 35 region
- the other lies across the top of the groove, making contacts with the DNA backbone
*Alpha helices in regions 2,3, & 4 bind to what elements? - ANS✅✅- -10 seq (σ2)
- extended seq (σ3)
- -35 promoter elements (σ4)
*What subunits bind to UP element? - ANS✅✅- alpha-subunit
- alphaNTD
- alpha CTD
*What is the transition from closed to open complex bearing σ70? - ANS✅✅Isomerization
Which subunit forms pinchers in bacterial transcription of RNA polymerase? - ANS✅✅β and β'
*What subunit initially blocks entrance between the pinchers? - ANS✅✅σ
What positions is dsDNA meted between? - ANS✅✅-11 and +3
*Is ATP required for bacterial transcription? - ANS✅✅No; energetically favorable!
In σ2 when the -10 promoter is not melting - ANS✅✅no transcription occurs because no
isomerization occurs therefor it does not bind properly due to dsDNA
In σ2 when the -10 promoter is melting - ANS✅✅transcription occurs because ssDNA binds
properly to σ2
reverse transcriptase - ANS✅✅An enzyme encoded by certain viruses (retroviruses) that uses RNA
as a template for DNA synthesis. (RNA guided DNA repair)
, *During Bacterial Transcription, how many channels are in the open complex? - ANS✅✅5
- NTP uptake back side of +1
- RNA exit channel (by -35)
- Downstream DNA entrance (by +1)
- Non-Template exit [NT] (behind +1)
- Template [T] exit (behind -10 region)
*Bacterial Transcription begins ______. - ANS✅✅de novo (without primer)
*RNA poly remains _____ and pulls DNA into itself during ________ transcription. -
ANS✅✅stationary; initial
*What is the role of the σ 3/4 linker? - ANS✅✅interacts with template strand by organizing it into
correct conformation and location to allow initiation by allowing interactions with the nucleotides
(think isomerization); (initiating NTP and incoming NTP)
NTP stands for - ANS✅✅nucleotide triphosphates
What are the 3 modes of bacterial transcription? - ANS✅✅Transient excursion
inchworming
scrunching
experiments on modes of transcription initiation show - ANS✅✅- pol remains stationary on
promoter
- pol subunits remain stationary relative to one another
What mode provides energy to break polymerase-promoter interactino and dislodge σ? -
ANS✅✅scrunched DNA
initial transcribing complex - ANS✅✅the polymerase-promoter complex Incorporates the first 10
or so ribonucleotides (a rather inefficient process) and at that stage, the enzyme often releases short
transcripts (each of less than 10 or so nucleotides) and then begins synthesis again
