1|Page
BCHM 4360 Exam 1 Study Guide 2025 – Biochemistry
Foundations, Enzyme Structure, and Metabolism Practice
Questions with Answers
Get ready for BCHM 4360 Exam 1 with this complete 2025 biochemistry study guide. Covers
amino acids, enzyme structure and function, protein folding, and metabolic foundations,
plus practice questions and answer explanations to help you ace your first biochemistry exam.
BCHM 4360 Exam 1,
BCHM 4360 study guide,
BCHM 4360 biochemistry exam 1,
BCHM 4360 practice test,
What were the main results of the Kornberg experiment? - ANSWER-Two different sized bands were
produced. One was about 170bp and the other was about 205bp. The shorter fragments resulted from
"nibbling" up to the histone octamer by the nuclease. The longer fragments results from "multiples" -
where the nuclease did not cut between one or more histone octamers
What were the steps and the conclusion of the Mavrich experiment? - ANSWER-Modern sequencing
allowed identification of the DNA sequences wrapped around histones. Histones were chemically linked
to DNA. DNA was digested and histone-linked DNA was isolated using histone antibodies. Histones were
removed and the DNA sequenced. The DNA was mapped onto chromosomes. Showed that promoter
and terminator regions of yeast genes are relatively free of histones.
What did the Brownell and Allis paper do and find? - ANSWER-The enzyme that acetylates histones was
discovered using an assay with a histone-impregnated gel. Proteins were separated on the gel, then SDS
removed to allow proteins to re-fold and regain activity. Labeled acetyl-CoA was added to the gel, and
,2|Page
peptide sequences identified from a protein that could add the label to the histones. Peptide sequences
allowed the gene to be identified and cloned by PCR methods.
How were histone modifications mapped to the human genome? - ANSWER-Using a nuclease technique
with antibodies that are highly specific for different histone modifications
How did Clarke and Carbon determine the molecular structure for centromeres? - ANSWER-Regions of
DNA from chromosome III were transferred into the ARS plasmid and examined for segregation into
daughter cells after division. Chromosome walking was used to isolate overlapping regions of the
centromeric region for insertion into the plasmid. Regions were narrowed down to a 1.6kb region that
conferred segregation. The identified centromeric piece of DNA also conferred meiotic stability. Yeast
cells containing the plasmid were able to survive without histidine due to the presence of a histidine
gene on the plasmid.
The position of chromosome territories may be related to the position of chromosomes just after what
event? - ANSWER-mitosis
True or False: When transcription on a certain chromosome increases, its territory size decreases. -
ANSWER-False: increases
True or False: Genes are only transcribed during interphase because mitosis is focused on division. -
ANSWER-False: genes are transcribed whenever the cell needs them to be
Chromosomes can ______, replicate, and then ______ back together in pretty much the same structure.
- ANSWER-unfold, refold
Are heterochromatic regions often found near the nuclear envelope or the middle of the nucleus? -
ANSWER-nuclear envelope
Human chromosomes 18 and 19 are similar in size. Gene-rich 19 is found near the ______ of the nucleus
whereas gene-poor 18 is at the _________ of the nucleus. - ANSWER-center, periphery
,3|Page
True or False: A gene can be silenced if brought into the proximity of heterochromatin, even on another
chromosome. - ANSWER-True
If a small region of heterochromatin is inserted into a certain locus of one copy, what happens to the
other copy? - ANSWER-It is also silenced, probably due to the relocation of the region containing the
locus to a heterochromatic region of the nucleus
True or False: The nucleolus is a membrane-bound organelle that sits in the middle of the nucleus. -
ANSWER-False: the nucleolus is not separated by a membrane
What was Kornberg attempting to solve? - ANSWER-The arrangement of histones and DNA
Describe the steps of Kornberg experiment. - ANSWER-Micrococal nuclease digestion was used to test a
model of the way DNA is packaged into chromatin. Exposed ds-DNA is digested by the nuclease but
regions wrapped around the histones are protected. After digestion, the remaining intact DNA can be
visualized by gel electrophoresis.
Define DNA replication. - ANSWER-The complete, faithful copying of the DNA comprising the cell's
chromosomes.
What does semi-conservative mean? - ANSWER-Each strand of the parental double helix acts as a
template for synthesis of a new daughter strand, resulting in two copies each comprised of one parent
and one daughter strand.
True or False: Replication moves away from the origin in both directions, forming a replication bubble. -
ANSWER-True
Which direction does DNA synthesis on each strand occur during replication? - ANSWER-5' - 3'
Replication is continuous on the _______ strand but discontinuous on the _______ strand. - ANSWER-
leading, lagging
What are the three phases of DNA replication? - ANSWER-initiation, elongation, termination
, 4|Page
How does DNA replication begin? What is first step? - ANSWER-The origin of replication is recognized by
an intiator protein that opens up the double helix and recruits helicases.
What do DNA helicases do? - ANSWER-unwind the helix to expose ssDNA
What do ssDNA-binding proteins do? - ANSWER-coat the ssDNA that is opened up via helicase to
prevent anything besides replication from occurring
True or False: Initiation is controlled to occur only once per cell cycle. Multiple initiations typically result
in problems. - ANSWER-True
DNA synthesis needs a ______. It can only add nucleotides to the existing __ ________ group. -
ANSWER-primer, 3' hydroxyl
The primer required for DNA synthesis is a short ___ strand synthesized by _______. - ANSWER-RNA,
primase
What must happen to the nucleosomes before DNA replication can even be initiated? - ANSWER-
Nucleosome remodeling enzymes must be used to move the nucleosomes out of the way
Why is the sliding clamp required for DNA replication? - ANSWER-Without the clamp, the DNA
Polymerase could fall off before it finishes transcribing (every 10,000 bases or so)
When is the sliding clamp recruited for DNA replication? - ANSWER-directly after the RNA primer is
synthesized
What two components are necessary for DNA Polymerase to be associated with DNA? - ANSWER-the
clamp loader and the sliding clamp
The clamp loader uses ___ hydrolysis to _______ clamp, ____ DNA, and then _____ the clamp again. -
ANSWER-ATP, reshape, bind, close
BCHM 4360 Exam 1 Study Guide 2025 – Biochemistry
Foundations, Enzyme Structure, and Metabolism Practice
Questions with Answers
Get ready for BCHM 4360 Exam 1 with this complete 2025 biochemistry study guide. Covers
amino acids, enzyme structure and function, protein folding, and metabolic foundations,
plus practice questions and answer explanations to help you ace your first biochemistry exam.
BCHM 4360 Exam 1,
BCHM 4360 study guide,
BCHM 4360 biochemistry exam 1,
BCHM 4360 practice test,
What were the main results of the Kornberg experiment? - ANSWER-Two different sized bands were
produced. One was about 170bp and the other was about 205bp. The shorter fragments resulted from
"nibbling" up to the histone octamer by the nuclease. The longer fragments results from "multiples" -
where the nuclease did not cut between one or more histone octamers
What were the steps and the conclusion of the Mavrich experiment? - ANSWER-Modern sequencing
allowed identification of the DNA sequences wrapped around histones. Histones were chemically linked
to DNA. DNA was digested and histone-linked DNA was isolated using histone antibodies. Histones were
removed and the DNA sequenced. The DNA was mapped onto chromosomes. Showed that promoter
and terminator regions of yeast genes are relatively free of histones.
What did the Brownell and Allis paper do and find? - ANSWER-The enzyme that acetylates histones was
discovered using an assay with a histone-impregnated gel. Proteins were separated on the gel, then SDS
removed to allow proteins to re-fold and regain activity. Labeled acetyl-CoA was added to the gel, and
,2|Page
peptide sequences identified from a protein that could add the label to the histones. Peptide sequences
allowed the gene to be identified and cloned by PCR methods.
How were histone modifications mapped to the human genome? - ANSWER-Using a nuclease technique
with antibodies that are highly specific for different histone modifications
How did Clarke and Carbon determine the molecular structure for centromeres? - ANSWER-Regions of
DNA from chromosome III were transferred into the ARS plasmid and examined for segregation into
daughter cells after division. Chromosome walking was used to isolate overlapping regions of the
centromeric region for insertion into the plasmid. Regions were narrowed down to a 1.6kb region that
conferred segregation. The identified centromeric piece of DNA also conferred meiotic stability. Yeast
cells containing the plasmid were able to survive without histidine due to the presence of a histidine
gene on the plasmid.
The position of chromosome territories may be related to the position of chromosomes just after what
event? - ANSWER-mitosis
True or False: When transcription on a certain chromosome increases, its territory size decreases. -
ANSWER-False: increases
True or False: Genes are only transcribed during interphase because mitosis is focused on division. -
ANSWER-False: genes are transcribed whenever the cell needs them to be
Chromosomes can ______, replicate, and then ______ back together in pretty much the same structure.
- ANSWER-unfold, refold
Are heterochromatic regions often found near the nuclear envelope or the middle of the nucleus? -
ANSWER-nuclear envelope
Human chromosomes 18 and 19 are similar in size. Gene-rich 19 is found near the ______ of the nucleus
whereas gene-poor 18 is at the _________ of the nucleus. - ANSWER-center, periphery
,3|Page
True or False: A gene can be silenced if brought into the proximity of heterochromatin, even on another
chromosome. - ANSWER-True
If a small region of heterochromatin is inserted into a certain locus of one copy, what happens to the
other copy? - ANSWER-It is also silenced, probably due to the relocation of the region containing the
locus to a heterochromatic region of the nucleus
True or False: The nucleolus is a membrane-bound organelle that sits in the middle of the nucleus. -
ANSWER-False: the nucleolus is not separated by a membrane
What was Kornberg attempting to solve? - ANSWER-The arrangement of histones and DNA
Describe the steps of Kornberg experiment. - ANSWER-Micrococal nuclease digestion was used to test a
model of the way DNA is packaged into chromatin. Exposed ds-DNA is digested by the nuclease but
regions wrapped around the histones are protected. After digestion, the remaining intact DNA can be
visualized by gel electrophoresis.
Define DNA replication. - ANSWER-The complete, faithful copying of the DNA comprising the cell's
chromosomes.
What does semi-conservative mean? - ANSWER-Each strand of the parental double helix acts as a
template for synthesis of a new daughter strand, resulting in two copies each comprised of one parent
and one daughter strand.
True or False: Replication moves away from the origin in both directions, forming a replication bubble. -
ANSWER-True
Which direction does DNA synthesis on each strand occur during replication? - ANSWER-5' - 3'
Replication is continuous on the _______ strand but discontinuous on the _______ strand. - ANSWER-
leading, lagging
What are the three phases of DNA replication? - ANSWER-initiation, elongation, termination
, 4|Page
How does DNA replication begin? What is first step? - ANSWER-The origin of replication is recognized by
an intiator protein that opens up the double helix and recruits helicases.
What do DNA helicases do? - ANSWER-unwind the helix to expose ssDNA
What do ssDNA-binding proteins do? - ANSWER-coat the ssDNA that is opened up via helicase to
prevent anything besides replication from occurring
True or False: Initiation is controlled to occur only once per cell cycle. Multiple initiations typically result
in problems. - ANSWER-True
DNA synthesis needs a ______. It can only add nucleotides to the existing __ ________ group. -
ANSWER-primer, 3' hydroxyl
The primer required for DNA synthesis is a short ___ strand synthesized by _______. - ANSWER-RNA,
primase
What must happen to the nucleosomes before DNA replication can even be initiated? - ANSWER-
Nucleosome remodeling enzymes must be used to move the nucleosomes out of the way
Why is the sliding clamp required for DNA replication? - ANSWER-Without the clamp, the DNA
Polymerase could fall off before it finishes transcribing (every 10,000 bases or so)
When is the sliding clamp recruited for DNA replication? - ANSWER-directly after the RNA primer is
synthesized
What two components are necessary for DNA Polymerase to be associated with DNA? - ANSWER-the
clamp loader and the sliding clamp
The clamp loader uses ___ hydrolysis to _______ clamp, ____ DNA, and then _____ the clamp again. -
ANSWER-ATP, reshape, bind, close
