1|Page
BCHM 4360 Exam 2 Study Guide 2025 –
Biochemistry Metabolism, Enzyme Regulation &
Practice Questions with Answers
Ace your BCHM 4360 Exam 2 with this complete 2025 biochemistry review guide. Covers
metabolic pathways, enzyme regulation, glycolysis, TCA cycle, and practice exam questions
with detailed explanations. Perfect for college biochemistry and pre-med students.
BCHM 4360 Exam 2,
BCHM 4360 biochemistry exam,
BCHM 4360 study guide,
BCHM 4360 Exam 2 answers,
Changes in supercoiling caused by the transcription bubble could cause stalling of RNA Polymerase, and
the tension must be relieved by ______________. - ANSWER-topoisomerases
In bacteria, DNA _______ removes the ________ supercoils and DNA ____________ I removes the
________ supercoils. - ANSWER-gyrase, positive, topoisomerase, negative
What are the two main classes of bacterial terminators? - ANSWER-Intrinsic and Rho-dependent
Intrinsic, or ______, terminators end transcription in the _______ of any other factors - ANSWER-simple,
absence
,2|Page
What are the two main features of bacterial intrinsic terminators? - ANSWER-1. An inverted repeat
sequence that, when transcribed, forms a step-loop in the RNA.
2. A string of 8-10 angstrom residues. This pairs with the transcribed poly-U in the transcription bubble
(a weak, unstable structure)
The weak base pairing in the transcription bubble is thought to _______ transcription and the RNA
hairpin is thought to interact with the RNA Polymerase and help ____ the RNA ___ of the active site. -
ANSWER-arrest, pull, out
When entering into transcription termination, a lot of ___ residues must be present to have the
temperature high enough. - ANSWER-G-C
What is the main function of phosphorylation with regards to RNA processing? - ANSWER-
phosphorylation recruits the RNA-processing enzymes, such as those that add a guanosine cap to the 5'
end of the mRNA
Capping leads to phosphorylation of the ______ ______ in the CTD heptad repeat, which casues the
polymerase to ______ elongation. - ANSWER-second serine, resume
What happens if there is an error in transcription? - ANSWER-The DNA-RNA duplex could be distorted,
causing stalling of the RNA Polymerase. The elongaton complex can backtrack and transcription cleavage
factors can then chop off the 3' protruding RNA by enhancing the endonuclease activity of RNA
Polymerase, and transcription can resume
What are two transcript cleavage factors in bacteria and what is the transcript cleavage factor in
eukaryotes? - ANSWER-GreA and GreB, TFIIS
Within which region of RNA Polymerase do transcript cleavage factors bind within? - ANSWER-funnel
region
What is a proposed mechanism for how transcript cleavage factors work? - ANSWER-Transcript cleavage
factors are thought to position a metal ion at the active site, which activates a water molecule for
hydrolysis of the phosphodiester bond
, 3|Page
How doe eukaryotes solve the problem of nucleosomes hindering RNA Polymerase? - ANSWER-use
histone chaperones to remove nucleosomes ahead of RNA Polymerase, and reassemble them behind
the polymerase
What are the three main histone chaperones in eukaryotes? - ANSWER-FACT (Facilitates Chromatin
Transcription), Asf1, and Spt6
In bacteria, certain genes need the ___ protein to terminate transcription. - ANSWER-Rho
True or False: Rho-dependent genes have the hairpin and poly-A structures that are found in intrinsic
terminators. - ANSWER-False, rho-dependent genes do not have these structures
Rho is a _________ ATP-ase with a ____ structure. It binds to ______ areas of RNA - ANSWER-
hexameric, ring, C-rich
In eukaryotes, intrinsic terminator sites are recognized by which RNA Polymerase? - ANSWER-Pol III
Eukaryotic intrinsic terminators have a stretch of which nucleotide? Also what is the function of this? -
ANSWER-As, which is thought to destabilize the DNA-RNA hybrid the same way as bacterial intrinsic
terminators
Termination for which RNA Polymerase requires additional proteins? What are these proteins in yeast
and mice? - ANSWER-Pol I, DNA binding proteins such as Reb1p in yeast and TTF1 in mice
True or False: RNA Pol II continues to transcribe after the polyadenylation signal, but the mRNA is
cleaved at the poly(A) signal and the 3' end of the mRNA is processed. - ANSWER-True
What are the two main models of transcription termination by RNA Pol II? - ANSWER-allosteric and
torpedo
Describe the allosteric model of transcription termination by RNA Pol II. - ANSWER-1. RNA Pol II
transcribes through the polyA and 3' processing signals
BCHM 4360 Exam 2 Study Guide 2025 –
Biochemistry Metabolism, Enzyme Regulation &
Practice Questions with Answers
Ace your BCHM 4360 Exam 2 with this complete 2025 biochemistry review guide. Covers
metabolic pathways, enzyme regulation, glycolysis, TCA cycle, and practice exam questions
with detailed explanations. Perfect for college biochemistry and pre-med students.
BCHM 4360 Exam 2,
BCHM 4360 biochemistry exam,
BCHM 4360 study guide,
BCHM 4360 Exam 2 answers,
Changes in supercoiling caused by the transcription bubble could cause stalling of RNA Polymerase, and
the tension must be relieved by ______________. - ANSWER-topoisomerases
In bacteria, DNA _______ removes the ________ supercoils and DNA ____________ I removes the
________ supercoils. - ANSWER-gyrase, positive, topoisomerase, negative
What are the two main classes of bacterial terminators? - ANSWER-Intrinsic and Rho-dependent
Intrinsic, or ______, terminators end transcription in the _______ of any other factors - ANSWER-simple,
absence
,2|Page
What are the two main features of bacterial intrinsic terminators? - ANSWER-1. An inverted repeat
sequence that, when transcribed, forms a step-loop in the RNA.
2. A string of 8-10 angstrom residues. This pairs with the transcribed poly-U in the transcription bubble
(a weak, unstable structure)
The weak base pairing in the transcription bubble is thought to _______ transcription and the RNA
hairpin is thought to interact with the RNA Polymerase and help ____ the RNA ___ of the active site. -
ANSWER-arrest, pull, out
When entering into transcription termination, a lot of ___ residues must be present to have the
temperature high enough. - ANSWER-G-C
What is the main function of phosphorylation with regards to RNA processing? - ANSWER-
phosphorylation recruits the RNA-processing enzymes, such as those that add a guanosine cap to the 5'
end of the mRNA
Capping leads to phosphorylation of the ______ ______ in the CTD heptad repeat, which casues the
polymerase to ______ elongation. - ANSWER-second serine, resume
What happens if there is an error in transcription? - ANSWER-The DNA-RNA duplex could be distorted,
causing stalling of the RNA Polymerase. The elongaton complex can backtrack and transcription cleavage
factors can then chop off the 3' protruding RNA by enhancing the endonuclease activity of RNA
Polymerase, and transcription can resume
What are two transcript cleavage factors in bacteria and what is the transcript cleavage factor in
eukaryotes? - ANSWER-GreA and GreB, TFIIS
Within which region of RNA Polymerase do transcript cleavage factors bind within? - ANSWER-funnel
region
What is a proposed mechanism for how transcript cleavage factors work? - ANSWER-Transcript cleavage
factors are thought to position a metal ion at the active site, which activates a water molecule for
hydrolysis of the phosphodiester bond
, 3|Page
How doe eukaryotes solve the problem of nucleosomes hindering RNA Polymerase? - ANSWER-use
histone chaperones to remove nucleosomes ahead of RNA Polymerase, and reassemble them behind
the polymerase
What are the three main histone chaperones in eukaryotes? - ANSWER-FACT (Facilitates Chromatin
Transcription), Asf1, and Spt6
In bacteria, certain genes need the ___ protein to terminate transcription. - ANSWER-Rho
True or False: Rho-dependent genes have the hairpin and poly-A structures that are found in intrinsic
terminators. - ANSWER-False, rho-dependent genes do not have these structures
Rho is a _________ ATP-ase with a ____ structure. It binds to ______ areas of RNA - ANSWER-
hexameric, ring, C-rich
In eukaryotes, intrinsic terminator sites are recognized by which RNA Polymerase? - ANSWER-Pol III
Eukaryotic intrinsic terminators have a stretch of which nucleotide? Also what is the function of this? -
ANSWER-As, which is thought to destabilize the DNA-RNA hybrid the same way as bacterial intrinsic
terminators
Termination for which RNA Polymerase requires additional proteins? What are these proteins in yeast
and mice? - ANSWER-Pol I, DNA binding proteins such as Reb1p in yeast and TTF1 in mice
True or False: RNA Pol II continues to transcribe after the polyadenylation signal, but the mRNA is
cleaved at the poly(A) signal and the 3' end of the mRNA is processed. - ANSWER-True
What are the two main models of transcription termination by RNA Pol II? - ANSWER-allosteric and
torpedo
Describe the allosteric model of transcription termination by RNA Pol II. - ANSWER-1. RNA Pol II
transcribes through the polyA and 3' processing signals
