MOLECULAR BIOLOGY FINAL EXAM
(ALL RIGHT ANSWERS FOR HW 1-5,
SELF-CHECK EXAM, AND EXAM MC
QUESTIONS) WITH CORRECT
SOLUTIONS
Which of the following is NOT a stabilizing force for the structure and stability of double-
stranded nucleic acids? - ANSWER-disulfide bonds
A reaction can only occur spontaneously when the free-energy change is - ANSWER-
negative
Which of the following statements regarding protein domains is NOT true? - ANSWER-
Proteins are only comprised of one protein domain
Which of the following statements about DNA and RNA is TRUE? - ANSWER-All
portions of the genome are replicated but only discrete genes are transcribed
Which of the following is NOT a hydrophobic amino acid - ANSWER-lysine
How did Brownell and Allis detect the activity of histone acetyl transferase? - ANSWER-
HAT was detected by the transfer of [3H]acetyl group to histones in specific region of
activity gel
Which of the follwoing statements best describes the basic mechanism by which
boundary elements carry out their function? - ANSWER-Specific proteins bind the
boundary element sequence and physically block the formation of heterochromatin
Prokaryotes use DNA methylation to __________ while many eukaryotes use DNA
methylation to ______. - ANSWER-distinguish newly synthesized DNA and protect their
DNA; silence genes
Which of the following statements regarding the use of catalysts is FALSE? - ANSWER-
Catalysts increase the number of reactions that can happen spontaneously
The HP1 protein plays a key role in formation of heterochromatin in mammals by: -
ANSWER-binding to methylated histone H3.
The association of DNA with histones - ANSWER-can lead to higher order packing of
the DNA
,Histone modification has the biggest impact on - ANSWER-the accessibility of DNA to
cellular enzymes
The major secondary structures of proteins are - ANSWER-alpha helix and beta sheet
Although all protein structures are unique, there are common structural building blocks
that are referred to as regular secondary structures. Some have alpha helices, some
have beta sheets, and still others have a combination of both. What makes it possible
for proteins to have these common structural elements? - ANSWER-hydrogen bonds
along the protein backbone
Hydrogen bonds in proteins - ANSWER-are individually weak but collectively strong and
contribute to the formation of higher order structure
Which histone protein attaches to DNA strands between nucleosomes - ANSWER-H1
Each nucleotide in DNA and RNA has an aromatic base. What is the principal force that
keeps the bases in a nucleic polymer from interacting with water? - ANSWER-
hydrophobic interactions
Methylation and acetylation are common changes made to histone H3, and the specific
combination of these changes is sometimes referred to as the histone code. Which of
the following patterns will probably lead to gene silencing? - ANSWER-lysine 9
methylation
Intergenic DNA is best decribed as - ANSWER-DNA between genes that does not code
for a protein but may have regulatory function
Which of the following statements is FALSE regarding chromatin immunoprecipitation
(ChIP) - ANSWER-ChIP-seq data enables the detection of sequence of the protein
domain that is bound to DNA
Base pairing depends on - ANSWER-hydrogen bonds; there are 2 bonds between A
and T and 3 bonds between C and G
Which amino acid side chain may be modified by the addition of a sugar molecule? -
ANSWER-asparagine
Which type of covalent bond is important for linking cysteine residues located at various
places in a polypeptide? - ANSWER-disulfide bond
Which type of amino acid would be most likely found on the interior of a DNA binding
protein - ANSWER-hydrophobic
,Chromatin refers to the form of genomic DNA found in the nucleus of interphase cells.
Actively transcribed genes are likely to be found in which kind of chromatin? -
ANSWER-euchromatin
What is the defining feature of all centromeres? - ANSWER-All centromeres contain
nucleosomes with a characteristic H3 histone variant.
what is the function of the nucleolus? - ANSWER-it is the site for synthesis and
processing of rRNA molecules
Which of the following is NOT a type of non-covalent interaction? - ANSWER-
Phosphate bond
Which of the following amino acids causes kinks in the protein backbone and may
disrupt secondary structure? - ANSWER-proline
The N-terminal tail of histone H3 can be extensively modified, and depending on the
number, location, and combination of these modifications, these changes may promote
the formation of heterochromatin. What is the result of heterochromatin formation? -
ANSWER-gene silencing
Which of the following statements about amino acids is TRUE? - ANSWER-All amino
acids contain an NH3+ and a COO- group
What is the effect of the repressor complex - ANSWER-N terminal tails of histones are
deacetylated resulting in repression of gene expression
Which statement is true regarding negative supercoiled DNA? - ANSWER-Since
negative supecoiled DNA is under-rotated, it allows for easier strand separation durng
replication and transcription
Why are lysine and arginine amino acids present in all four common core histone
proteins? - ANSWER-They have positively charged side chain residues and allow the
histone to interract with DNA's negatively charged backbone
What are the complementary base pairs to the following nucleotides. 5'GTCCATATTGC
3' - ANSWER-3'CAGGTATAACG5'
The active site of an enzyme differs from an antibody-antigen binding site in that the
enzyme active site - ANSWER-catalyzes a chemical reaction
All of the following are considered "weak" interactions in proteins, except: - ANSWER-
peptide bonds
The process by which enzymes accelerate the rate of a biochemical reaction is called
____. - ANSWER-catalysis
, How are telomeric repeats added to the ends of chromosomes without a template for
DNA synthesis? - ANSWER-the enzyme telomerase has an RNA subunit containing the
template for synthesizing the repeats
The difference between RNA and DNA is the presence of a: - ANSWER-2' hydroxyl
group on the ribose sugar in RNA
Model organisms are important in the study of biological processes. Which statement is
FALSE regarding model organisms? - ANSWER-Two well studied genetically tractable
model organisms are Danio rario and Xenopus laevis
How is DNA packaged in the bacterial cell (E. coli, for example)? - ANSWER-It is
package by small basic proteins to bend DNA, then supercoiled by DNA gyrase and
DNA topoisomerase.
Bromodomains bind - ANSWER-acetylated lysine
Cholesterol is an essential component of biological membranes. Although it is much
smaller than the typical phospholipids and glycoplipids in the membrane, it is a(n)
_________________ molecule, having both hydrophilic and hydrophobic regions. -
ANSWER-amphipathic
Primary structure of a protein is determined by - ANSWER-the sequence of the amino
acids.
Which amino acid side chain is subject to modification by the addition of phosphate? -
ANSWER-tyrosine
Which level of protein structure describes the folded conformation of a multisubunit
protein? - ANSWER-quaternary structure
Which of the following is an example of tertiary structure in a protein? - ANSWER-a
helix-turn-helix domain.
Which type of bonds link the individual nucleotides together in DNA? - ANSWER-
phosphodiester
Which statement about nucleic acids is TRUE? - ANSWER-The polarity of a DNA
strand results from the polarity of the nucleotide subunits.
Although the chromatin structure of interphase and mitotic chromosomes is very
compact, DNA-binding proteins and protein complexes must be able to gain access to
the DNA molecule. Chromatin-remodeling complexes provide this access by
__________________. - ANSWER-using the energy of ATP hydrolysis to move
nucleosomes
(ALL RIGHT ANSWERS FOR HW 1-5,
SELF-CHECK EXAM, AND EXAM MC
QUESTIONS) WITH CORRECT
SOLUTIONS
Which of the following is NOT a stabilizing force for the structure and stability of double-
stranded nucleic acids? - ANSWER-disulfide bonds
A reaction can only occur spontaneously when the free-energy change is - ANSWER-
negative
Which of the following statements regarding protein domains is NOT true? - ANSWER-
Proteins are only comprised of one protein domain
Which of the following statements about DNA and RNA is TRUE? - ANSWER-All
portions of the genome are replicated but only discrete genes are transcribed
Which of the following is NOT a hydrophobic amino acid - ANSWER-lysine
How did Brownell and Allis detect the activity of histone acetyl transferase? - ANSWER-
HAT was detected by the transfer of [3H]acetyl group to histones in specific region of
activity gel
Which of the follwoing statements best describes the basic mechanism by which
boundary elements carry out their function? - ANSWER-Specific proteins bind the
boundary element sequence and physically block the formation of heterochromatin
Prokaryotes use DNA methylation to __________ while many eukaryotes use DNA
methylation to ______. - ANSWER-distinguish newly synthesized DNA and protect their
DNA; silence genes
Which of the following statements regarding the use of catalysts is FALSE? - ANSWER-
Catalysts increase the number of reactions that can happen spontaneously
The HP1 protein plays a key role in formation of heterochromatin in mammals by: -
ANSWER-binding to methylated histone H3.
The association of DNA with histones - ANSWER-can lead to higher order packing of
the DNA
,Histone modification has the biggest impact on - ANSWER-the accessibility of DNA to
cellular enzymes
The major secondary structures of proteins are - ANSWER-alpha helix and beta sheet
Although all protein structures are unique, there are common structural building blocks
that are referred to as regular secondary structures. Some have alpha helices, some
have beta sheets, and still others have a combination of both. What makes it possible
for proteins to have these common structural elements? - ANSWER-hydrogen bonds
along the protein backbone
Hydrogen bonds in proteins - ANSWER-are individually weak but collectively strong and
contribute to the formation of higher order structure
Which histone protein attaches to DNA strands between nucleosomes - ANSWER-H1
Each nucleotide in DNA and RNA has an aromatic base. What is the principal force that
keeps the bases in a nucleic polymer from interacting with water? - ANSWER-
hydrophobic interactions
Methylation and acetylation are common changes made to histone H3, and the specific
combination of these changes is sometimes referred to as the histone code. Which of
the following patterns will probably lead to gene silencing? - ANSWER-lysine 9
methylation
Intergenic DNA is best decribed as - ANSWER-DNA between genes that does not code
for a protein but may have regulatory function
Which of the following statements is FALSE regarding chromatin immunoprecipitation
(ChIP) - ANSWER-ChIP-seq data enables the detection of sequence of the protein
domain that is bound to DNA
Base pairing depends on - ANSWER-hydrogen bonds; there are 2 bonds between A
and T and 3 bonds between C and G
Which amino acid side chain may be modified by the addition of a sugar molecule? -
ANSWER-asparagine
Which type of covalent bond is important for linking cysteine residues located at various
places in a polypeptide? - ANSWER-disulfide bond
Which type of amino acid would be most likely found on the interior of a DNA binding
protein - ANSWER-hydrophobic
,Chromatin refers to the form of genomic DNA found in the nucleus of interphase cells.
Actively transcribed genes are likely to be found in which kind of chromatin? -
ANSWER-euchromatin
What is the defining feature of all centromeres? - ANSWER-All centromeres contain
nucleosomes with a characteristic H3 histone variant.
what is the function of the nucleolus? - ANSWER-it is the site for synthesis and
processing of rRNA molecules
Which of the following is NOT a type of non-covalent interaction? - ANSWER-
Phosphate bond
Which of the following amino acids causes kinks in the protein backbone and may
disrupt secondary structure? - ANSWER-proline
The N-terminal tail of histone H3 can be extensively modified, and depending on the
number, location, and combination of these modifications, these changes may promote
the formation of heterochromatin. What is the result of heterochromatin formation? -
ANSWER-gene silencing
Which of the following statements about amino acids is TRUE? - ANSWER-All amino
acids contain an NH3+ and a COO- group
What is the effect of the repressor complex - ANSWER-N terminal tails of histones are
deacetylated resulting in repression of gene expression
Which statement is true regarding negative supercoiled DNA? - ANSWER-Since
negative supecoiled DNA is under-rotated, it allows for easier strand separation durng
replication and transcription
Why are lysine and arginine amino acids present in all four common core histone
proteins? - ANSWER-They have positively charged side chain residues and allow the
histone to interract with DNA's negatively charged backbone
What are the complementary base pairs to the following nucleotides. 5'GTCCATATTGC
3' - ANSWER-3'CAGGTATAACG5'
The active site of an enzyme differs from an antibody-antigen binding site in that the
enzyme active site - ANSWER-catalyzes a chemical reaction
All of the following are considered "weak" interactions in proteins, except: - ANSWER-
peptide bonds
The process by which enzymes accelerate the rate of a biochemical reaction is called
____. - ANSWER-catalysis
, How are telomeric repeats added to the ends of chromosomes without a template for
DNA synthesis? - ANSWER-the enzyme telomerase has an RNA subunit containing the
template for synthesizing the repeats
The difference between RNA and DNA is the presence of a: - ANSWER-2' hydroxyl
group on the ribose sugar in RNA
Model organisms are important in the study of biological processes. Which statement is
FALSE regarding model organisms? - ANSWER-Two well studied genetically tractable
model organisms are Danio rario and Xenopus laevis
How is DNA packaged in the bacterial cell (E. coli, for example)? - ANSWER-It is
package by small basic proteins to bend DNA, then supercoiled by DNA gyrase and
DNA topoisomerase.
Bromodomains bind - ANSWER-acetylated lysine
Cholesterol is an essential component of biological membranes. Although it is much
smaller than the typical phospholipids and glycoplipids in the membrane, it is a(n)
_________________ molecule, having both hydrophilic and hydrophobic regions. -
ANSWER-amphipathic
Primary structure of a protein is determined by - ANSWER-the sequence of the amino
acids.
Which amino acid side chain is subject to modification by the addition of phosphate? -
ANSWER-tyrosine
Which level of protein structure describes the folded conformation of a multisubunit
protein? - ANSWER-quaternary structure
Which of the following is an example of tertiary structure in a protein? - ANSWER-a
helix-turn-helix domain.
Which type of bonds link the individual nucleotides together in DNA? - ANSWER-
phosphodiester
Which statement about nucleic acids is TRUE? - ANSWER-The polarity of a DNA
strand results from the polarity of the nucleotide subunits.
Although the chromatin structure of interphase and mitotic chromosomes is very
compact, DNA-binding proteins and protein complexes must be able to gain access to
the DNA molecule. Chromatin-remodeling complexes provide this access by
__________________. - ANSWER-using the energy of ATP hydrolysis to move
nucleosomes
