BCH5413 Exam 3 Final Exam A+ Changes IN
GENE Expression Patterns OR Phenotype THAT
ARE NOT Questions and Answers Verified
Solutions Latest Update 2026/2027
Answer:
Epigenetics
●● What are some examples of epigenetic modifications?.
Answer:
• histone modifications and variants
• chromatin remodeling
• DNA methylation
• non-coding RNAs
• 3D genome architecture
●● In general, describe how the ChIP-Seq assay can be used to map histone marks throughout the
genome..
Answer:
You need a DNA+protein with a stable histone DNA interaction, chromatin is fragmented into
small pieces, and antibodies are added to be bound to specific histone modifications that you are
interested in. Then the isolated fragments are reversed crosslinked so they can release the genomic
DNA, then is purified for creating a sequencing library. Finally, the DNA is aligned with a
reference genome and the histone modifications can be mapped in the reference genome.
●● Core histones are made up of 2 copies of each of these subunits per nucleosome:.
Answer:
histone H2A - slightly lys rich
histone H2B - slightly lys rich
histone H3 - arg rich
histone H4 - arg rich
●● What are the three players and their functions in histone modification?.
,Answer:
Writers: These are histone modify enzymes that add a variety of covalent modifications to histone
tails. (histone acetyltransferases, histone methyltransferases)
Erasers: They perform the opposite functions to writers, they remove histone modifications.
(histone deacetylaces, lysine demethylaces)
Readers: These are proteins that contain specific domains that can recognize specific histone
modifications. (bromodomains, chromodomains, PHD Fingers, malignant brain tumor domains,
tudor domains, PWWP domains)
●● How does lysine acetylation affect histone interaction with DNA?.
Answer:
Lysine acetylation changes the charge from positively charged to neutralized, affecting the
interaction with negatively charged DNA.
Reduces electrostatic interaction between the histone tails and the negatively charged phosphate
backbone of DNA, resulting in loosening of chromatin.
●● What enzyme is responsible for acetylation?.
Answer:
Acetyl CoA
●● How is the acetylation removed from a lysine?.
Answer:
By a deacetylation process
●● How is the action of p300/CBP (HATs) different in vitro and in vivo?.
Answer:
Both of them have a catalytic domain. But when analyzed in vitro, it does not have a strong
substrate specificity. P300 and CBP can acetylate a lot of lysine residues, in all histone tails, but in
vivo, not many histone tails can be acetylated.
●● Describe both similarities and differences between histone acetylation and histone
methylation..
Answer:
Both are writers. One transfers an acetyl group, and the other transfers a methyl group.
Acetylation activates, methylation either suppresses or elevates gene expression. Acetylation
neutralizes the positive charge of lysine.
, Methylation does not change net charge.Depending on the position and extent, methylated residues
act as specific histone marks and lead to different outcomes. Methyltransferases are also highly
specific.
●● In mammalian methyltransferases, what is the difference between the MLL1/2 and MLL3/4
methytransferase complexes?.
Answer:
MLL1/2 are responsible for H3K4 tri-methylation and are associated with active promotors.
MLL3/4 are responsible for H3K4 mono-methylation and are associated with enhancers.
●● In the polycomb repressor complexes, what is the difference between PRC1 and PRC2?.
Answer:
PRC1 = Recognizes H3K27me3. Also can catalyze mono- ubiquitination of lysine (H2AK119)
PRC2 = Contains catalytic subunit for H3K27 trimethylation.
Together they condense chromatin.
●● What is the difference between constitutive and facultative heterochromatin in terms of
transcription and histone methylation?.
Answer:
In terms of transcription, constitutive heterochromatin is always condensed/transcriptionally
inactive while facultative heterochromatin may be converted into euchromatin. This means that
facultative
heterochromatin has the potential to be transcribed or not. In terms of histone methylation
constitutive heterochromatin exhibits H3K9me3 and facultative heterochromatin exhibits
H3K27me3.
●● Describe the differences in histone methylation found at active vs. inactive gene promoters.
What is an enhancer element and what differences are found at enhancer elements that are inactive,
poised for activation, and those that are active?.
Answer:
Generally, methylation of H3K4, H3K36 and H3K79 is associated with actively transcribed genes,
whereas methylation of H3K27, H3K9 and H4K20 is associated with inactive genes.Within
actively transcribed genes, H3K4me3 is mainly found at the promoter area or around TSS, whereas
H3K36me3 is found in the gene bodies. On repressed genes, the H3K9 and H4K20 methylation
marks are relatively homogeneously distributed, whereas H3K27me3 is enriched at the promoters.
●● How are the histone marks on H4K16 and R19 related to the ability of chromatin to condense?.
GENE Expression Patterns OR Phenotype THAT
ARE NOT Questions and Answers Verified
Solutions Latest Update 2026/2027
Answer:
Epigenetics
●● What are some examples of epigenetic modifications?.
Answer:
• histone modifications and variants
• chromatin remodeling
• DNA methylation
• non-coding RNAs
• 3D genome architecture
●● In general, describe how the ChIP-Seq assay can be used to map histone marks throughout the
genome..
Answer:
You need a DNA+protein with a stable histone DNA interaction, chromatin is fragmented into
small pieces, and antibodies are added to be bound to specific histone modifications that you are
interested in. Then the isolated fragments are reversed crosslinked so they can release the genomic
DNA, then is purified for creating a sequencing library. Finally, the DNA is aligned with a
reference genome and the histone modifications can be mapped in the reference genome.
●● Core histones are made up of 2 copies of each of these subunits per nucleosome:.
Answer:
histone H2A - slightly lys rich
histone H2B - slightly lys rich
histone H3 - arg rich
histone H4 - arg rich
●● What are the three players and their functions in histone modification?.
,Answer:
Writers: These are histone modify enzymes that add a variety of covalent modifications to histone
tails. (histone acetyltransferases, histone methyltransferases)
Erasers: They perform the opposite functions to writers, they remove histone modifications.
(histone deacetylaces, lysine demethylaces)
Readers: These are proteins that contain specific domains that can recognize specific histone
modifications. (bromodomains, chromodomains, PHD Fingers, malignant brain tumor domains,
tudor domains, PWWP domains)
●● How does lysine acetylation affect histone interaction with DNA?.
Answer:
Lysine acetylation changes the charge from positively charged to neutralized, affecting the
interaction with negatively charged DNA.
Reduces electrostatic interaction between the histone tails and the negatively charged phosphate
backbone of DNA, resulting in loosening of chromatin.
●● What enzyme is responsible for acetylation?.
Answer:
Acetyl CoA
●● How is the acetylation removed from a lysine?.
Answer:
By a deacetylation process
●● How is the action of p300/CBP (HATs) different in vitro and in vivo?.
Answer:
Both of them have a catalytic domain. But when analyzed in vitro, it does not have a strong
substrate specificity. P300 and CBP can acetylate a lot of lysine residues, in all histone tails, but in
vivo, not many histone tails can be acetylated.
●● Describe both similarities and differences between histone acetylation and histone
methylation..
Answer:
Both are writers. One transfers an acetyl group, and the other transfers a methyl group.
Acetylation activates, methylation either suppresses or elevates gene expression. Acetylation
neutralizes the positive charge of lysine.
, Methylation does not change net charge.Depending on the position and extent, methylated residues
act as specific histone marks and lead to different outcomes. Methyltransferases are also highly
specific.
●● In mammalian methyltransferases, what is the difference between the MLL1/2 and MLL3/4
methytransferase complexes?.
Answer:
MLL1/2 are responsible for H3K4 tri-methylation and are associated with active promotors.
MLL3/4 are responsible for H3K4 mono-methylation and are associated with enhancers.
●● In the polycomb repressor complexes, what is the difference between PRC1 and PRC2?.
Answer:
PRC1 = Recognizes H3K27me3. Also can catalyze mono- ubiquitination of lysine (H2AK119)
PRC2 = Contains catalytic subunit for H3K27 trimethylation.
Together they condense chromatin.
●● What is the difference between constitutive and facultative heterochromatin in terms of
transcription and histone methylation?.
Answer:
In terms of transcription, constitutive heterochromatin is always condensed/transcriptionally
inactive while facultative heterochromatin may be converted into euchromatin. This means that
facultative
heterochromatin has the potential to be transcribed or not. In terms of histone methylation
constitutive heterochromatin exhibits H3K9me3 and facultative heterochromatin exhibits
H3K27me3.
●● Describe the differences in histone methylation found at active vs. inactive gene promoters.
What is an enhancer element and what differences are found at enhancer elements that are inactive,
poised for activation, and those that are active?.
Answer:
Generally, methylation of H3K4, H3K36 and H3K79 is associated with actively transcribed genes,
whereas methylation of H3K27, H3K9 and H4K20 is associated with inactive genes.Within
actively transcribed genes, H3K4me3 is mainly found at the promoter area or around TSS, whereas
H3K36me3 is found in the gene bodies. On repressed genes, the H3K9 and H4K20 methylation
marks are relatively homogeneously distributed, whereas H3K27me3 is enriched at the promoters.
●● How are the histone marks on H4K16 and R19 related to the ability of chromatin to condense?.
