BCH5413 3 Exam A+ Questions and
Answers Verified Solutions Latest Update
2026/2027
Answer:
Technique that separates DNA, RNA, or proteins based on size by migration through a gel matrix
in an electric field.
■Transcription and gene regulation- prokaryote v eukaryote.
Answer:
Prokaryote- no nucleosome - regulatory sequences immediately available for transcription without
having to regulate accessibility and chromatin structure- no nucleus - transcription tightly coupled
with translation
■Southern blot.
Answer:
Detects specific DNA sequences by hybridization of a labeled probe to DNA transferred from a gel
to a membrane.
■Northern blot.
Answer:
Detects RNA size and abundance by hybridization of a labeled probe to RNA on a membrane.
■RNA synthesis- direction- type of bond (between what two things)- incoming nucleotide
determined by....
Answer:
5' -> 3' synthesis- formation of phosphodiester bond btwn/ incoming ribonucleotide and 3' hydroxyl
of nascent RNA- incoming ribonucleotide determined by DNA sequence of template strand
■Western blot.
Answer:
,Detects specific proteins using antibodies after separation by gel electrophoresis.
■What happens after phosphodiester bond formation?.
Answer:
Release of PPi- synthesis 5' -> 3'
■In situ hybridization.
Answer:
Uses labeled nucleic acid probes to detect specific DNA or RNA sequences within intact cells or
tissues.
■PCR.
Answer:
Amplifies a specific DNA sequence using primers, DNA polymerase, and thermal cycling.
■Does RNA synthesis require a primer?.
Answer:
RNA synthesis and transcription does not require primer- can initiate de novo
■TaqMan vs SYBR.
Answer:
TaqMan uses a sequence-specific fluorescent probe; SYBR Green binds any double-stranded DNA
and is less specific.
■RNA transcription- carried out by..- what does it do- separation of two DNA strands?.
Answer:
transcription carried out by RNA Pol- Pol catalyzes synthesis of nascent RNA - separation of two
DNA strands creates transcription bubble
■Microarray.
Answer:
High-throughput technique that measures gene expression by hybridization of labeled cDNA to
immobilized DNA probes.
■Rate of transcription.
,Answer:
eukaryotes: 15-30 nt/secBacteria: 50-100 nt/sec
■RNA-Seq.
Answer:
High-throughput sequencing method that quantifies RNA abundance by sequencing cDNA
fragments.
■Hi-C chromatin steps.
Answer:
Crosslink chromatin, digest DNA, fill ends with biotin, ligate interacting fragments, shear DNA,
and sequence to identify 3D chromatin
interactions.
■Mechanisms of bacterial transcription initiation: RNA Pol- synthesizes what from what- in E. coli
how many Pol synthesize most of the DNA.
Answer:
- synthesizes RNA from one strand of dsDNA template- in E. coli a
single RNA Pol synthesizes most mRNA, tRNA, rRNA
■Holoenzyme subunits.
Answer:
4 subunits: alpha, beta, beta', sigma- Core enzyme: alpha, beta, beta' (synthesizes RNA randomly
on dsDNA templates)- sigma factor: confers promoter binding and specificty
■Sigma factor(s) with Pol- most E. coli promoters bound by...- allows for...- sigma is released
upon.... what continues transcription elongation?- alternative sigma factors recognize....
Answer:
- most E. coli promoters bound by sigma 70 associated RNA Pol-
allows correct binding and transcription initiation at specific promoters- sigma is released upon
transcription initiation; core enzyme continues transcription elongation- alternative sigma factors
recognize different promoters
■Corresponding gene to holoenzyme subunit- subunit functions.
, Answer:
rpoA: 2 alpha subunits (enzyme assembly, promoter recognition, binds some activators)rpoB: beta
subunit (catalytic center)rpoC: Beta' subunit (catalytic center)rpoD: sigma subunit (promoter
specificity)
■What is the use of the following factors:- sigma70- sigma 32- sigmaE- sigma54- sigmaF.
Answer:
- sigma70: general- sigma 32: heat shock- sigmaE: heat shock-
sigma54: nitrogen- sigmaF: flagellar
■X-ray picture of chromosome.
Answer:
Reveals overall chromosome structure and density but does not provide DNA sequence
information.
■Sticky end ligation.
Answer:
Ligation of DNA fragments with complementary single-stranded overhangs created by restriction
enzymes.
■Shuttle vector ( E. coli / yeast).
Answer:
A plasmid designed to replicate in both bacterial and eukaryotic hosts.
■Transfection of mammalian cells.
Answer:
Introduction of foreign DNA into eukaryotic cells.
■Prokaryotic transcription: overall steps- transcription unit is..- during transcription..- transcription
takes place in....
Answer:
- transcription unit is a sequence of DNA transcribed into a single
RNA, starting at the promoter and ending at the terminator- during transcription, the bubble is
maintained within bacterial RNA Pol, which unwinds and rewinds DNA, maintains the conditions
of the partner and template DNA strands, and synthesizes RNA- transcription takes place in a
Answers Verified Solutions Latest Update
2026/2027
Answer:
Technique that separates DNA, RNA, or proteins based on size by migration through a gel matrix
in an electric field.
■Transcription and gene regulation- prokaryote v eukaryote.
Answer:
Prokaryote- no nucleosome - regulatory sequences immediately available for transcription without
having to regulate accessibility and chromatin structure- no nucleus - transcription tightly coupled
with translation
■Southern blot.
Answer:
Detects specific DNA sequences by hybridization of a labeled probe to DNA transferred from a gel
to a membrane.
■Northern blot.
Answer:
Detects RNA size and abundance by hybridization of a labeled probe to RNA on a membrane.
■RNA synthesis- direction- type of bond (between what two things)- incoming nucleotide
determined by....
Answer:
5' -> 3' synthesis- formation of phosphodiester bond btwn/ incoming ribonucleotide and 3' hydroxyl
of nascent RNA- incoming ribonucleotide determined by DNA sequence of template strand
■Western blot.
Answer:
,Detects specific proteins using antibodies after separation by gel electrophoresis.
■What happens after phosphodiester bond formation?.
Answer:
Release of PPi- synthesis 5' -> 3'
■In situ hybridization.
Answer:
Uses labeled nucleic acid probes to detect specific DNA or RNA sequences within intact cells or
tissues.
■PCR.
Answer:
Amplifies a specific DNA sequence using primers, DNA polymerase, and thermal cycling.
■Does RNA synthesis require a primer?.
Answer:
RNA synthesis and transcription does not require primer- can initiate de novo
■TaqMan vs SYBR.
Answer:
TaqMan uses a sequence-specific fluorescent probe; SYBR Green binds any double-stranded DNA
and is less specific.
■RNA transcription- carried out by..- what does it do- separation of two DNA strands?.
Answer:
transcription carried out by RNA Pol- Pol catalyzes synthesis of nascent RNA - separation of two
DNA strands creates transcription bubble
■Microarray.
Answer:
High-throughput technique that measures gene expression by hybridization of labeled cDNA to
immobilized DNA probes.
■Rate of transcription.
,Answer:
eukaryotes: 15-30 nt/secBacteria: 50-100 nt/sec
■RNA-Seq.
Answer:
High-throughput sequencing method that quantifies RNA abundance by sequencing cDNA
fragments.
■Hi-C chromatin steps.
Answer:
Crosslink chromatin, digest DNA, fill ends with biotin, ligate interacting fragments, shear DNA,
and sequence to identify 3D chromatin
interactions.
■Mechanisms of bacterial transcription initiation: RNA Pol- synthesizes what from what- in E. coli
how many Pol synthesize most of the DNA.
Answer:
- synthesizes RNA from one strand of dsDNA template- in E. coli a
single RNA Pol synthesizes most mRNA, tRNA, rRNA
■Holoenzyme subunits.
Answer:
4 subunits: alpha, beta, beta', sigma- Core enzyme: alpha, beta, beta' (synthesizes RNA randomly
on dsDNA templates)- sigma factor: confers promoter binding and specificty
■Sigma factor(s) with Pol- most E. coli promoters bound by...- allows for...- sigma is released
upon.... what continues transcription elongation?- alternative sigma factors recognize....
Answer:
- most E. coli promoters bound by sigma 70 associated RNA Pol-
allows correct binding and transcription initiation at specific promoters- sigma is released upon
transcription initiation; core enzyme continues transcription elongation- alternative sigma factors
recognize different promoters
■Corresponding gene to holoenzyme subunit- subunit functions.
, Answer:
rpoA: 2 alpha subunits (enzyme assembly, promoter recognition, binds some activators)rpoB: beta
subunit (catalytic center)rpoC: Beta' subunit (catalytic center)rpoD: sigma subunit (promoter
specificity)
■What is the use of the following factors:- sigma70- sigma 32- sigmaE- sigma54- sigmaF.
Answer:
- sigma70: general- sigma 32: heat shock- sigmaE: heat shock-
sigma54: nitrogen- sigmaF: flagellar
■X-ray picture of chromosome.
Answer:
Reveals overall chromosome structure and density but does not provide DNA sequence
information.
■Sticky end ligation.
Answer:
Ligation of DNA fragments with complementary single-stranded overhangs created by restriction
enzymes.
■Shuttle vector ( E. coli / yeast).
Answer:
A plasmid designed to replicate in both bacterial and eukaryotic hosts.
■Transfection of mammalian cells.
Answer:
Introduction of foreign DNA into eukaryotic cells.
■Prokaryotic transcription: overall steps- transcription unit is..- during transcription..- transcription
takes place in....
Answer:
- transcription unit is a sequence of DNA transcribed into a single
RNA, starting at the promoter and ending at the terminator- during transcription, the bubble is
maintained within bacterial RNA Pol, which unwinds and rewinds DNA, maintains the conditions
of the partner and template DNA strands, and synthesizes RNA- transcription takes place in a
