BCHM 4360 Exam Review Detailed
Questions and Answers Verified Solutions
Latest Update 2026/2027
Question:
What is sumo and why is it important?.
Answer:
Small ubiquitin- like modifier that also plays roles in transcription regulation and DNA repair
Question:
True or False: Chromatin packing is good for efficient transcription. Explain the correct answer..
Answer:
False: It presents a barrier to proteins that need to access the DNA
Question:
What are three ways by which ATP-dependent remodeling complexes increase the accessibility of
DNA on histones?.
Answer:
1) Sliding the histone octamer along the DNA
2) Removing the histone octamer or transferring it elsewhere
3) Introducing loops into the DNA wrapped around a histone core
Question:
Which method of nucleosome remodeling is least favored and why?.
Answer:
Removing the histone completely is the least favored because the nucleosome must be reassembled
after destruction
,Question:
What are the two main classes of nucleosome remodeling complexes and what are their main
functions?.
Answer:
SWI/SNF disrupts nucleosome positioning, ACF (ISWI) positions nucleosomes during chromatin
assembly
Question:
What are the four main nucleosome remodeling complex subunits?.
Answer:
ATPase domain (two parts Dexx and HELICc), bromodomain, chromodomain, and SANT-SLIDE
Question:
If SWI/SNF fails, what usually happens to the cells?.
Answer:
Substitute with INO80 family, which is very similar. The cells will continue to live but will operate
poorly
Question:
What are the two possible models that explain how nucleosome remodeling complexes might
work?.
Answer:
Pushing and sliding the DNA (propagation), twisting the DNA (global distortion)
Question:
How do cells recruit remodeling complexes?.
Answer:
Via proteins that bind in a sequence-specific manner
,Question:
What two ways do cells recruit nucleosome remodeling complexes?.
Answer:
Transcriptional regulators and histone modifications
Question:
Why doesn't the brain cool down as efficiently as the rest of the body?.
Answer:
There isn't an overexpression of heat-shock proteins like there is elsewhere in the body so it takes
longer to activate heat- shock system
Question:
True or False: Like histones, DNA can also be directly chemically modified..
Answer:
True
Question:
Give an example of a direct DNA methylation and its possible effects..
Answer:
Methylation of cytosine can make 5-methyl cytosine which can then be turned into thymine via an
easy deamination
Question:
True or false: DNA methylation is generally safe and DNA alteration isn't permanent..
Answer:
False: DNA methylation is very risky and typically gives rise to mutations, even in normal
processes
Question:
, What is the method that DNA methyltransferases use to access cytosines and what are the three
steps?.
Answer:
base-flipping
1) A cytosine is flipped out of the DNA double helix
2) An amino acid is temporarily inserted to stack in the double helix
3) The cytosine is methylated and reinserted into the double helix
Question:
Explain how DNA methylation distinguishes newly synthesized DNA in repair processes in
bacteria..
Answer:
Just after replication, only the parental strand of DNA is methylated (called hemi-
methylated). When mismatch repair enzymes detect a mismatch, the methylation status is read,
allowing the repair machinery to identify the parental strand and correclty repair the mismatch
Question:
Explain how DNA methylation allows bacteria to distinguish genomic DNA from invading
bacteriophage DNA..
Answer:
Restriction enzymes cut DNA at specific recognition sites so bacteria defend their own DNA from
being cut by methylating the recognition sites. The bacteriophage DNA is not methylated and will
therefore be cut by the restriction enzymes and destroyed.
Question:
True or False: Methylation in eukaryotes is only used to silence transcription, not activate it..
Answer:
False
Question:
Eukaryotic methylation is usually at which two sites?.
Questions and Answers Verified Solutions
Latest Update 2026/2027
Question:
What is sumo and why is it important?.
Answer:
Small ubiquitin- like modifier that also plays roles in transcription regulation and DNA repair
Question:
True or False: Chromatin packing is good for efficient transcription. Explain the correct answer..
Answer:
False: It presents a barrier to proteins that need to access the DNA
Question:
What are three ways by which ATP-dependent remodeling complexes increase the accessibility of
DNA on histones?.
Answer:
1) Sliding the histone octamer along the DNA
2) Removing the histone octamer or transferring it elsewhere
3) Introducing loops into the DNA wrapped around a histone core
Question:
Which method of nucleosome remodeling is least favored and why?.
Answer:
Removing the histone completely is the least favored because the nucleosome must be reassembled
after destruction
,Question:
What are the two main classes of nucleosome remodeling complexes and what are their main
functions?.
Answer:
SWI/SNF disrupts nucleosome positioning, ACF (ISWI) positions nucleosomes during chromatin
assembly
Question:
What are the four main nucleosome remodeling complex subunits?.
Answer:
ATPase domain (two parts Dexx and HELICc), bromodomain, chromodomain, and SANT-SLIDE
Question:
If SWI/SNF fails, what usually happens to the cells?.
Answer:
Substitute with INO80 family, which is very similar. The cells will continue to live but will operate
poorly
Question:
What are the two possible models that explain how nucleosome remodeling complexes might
work?.
Answer:
Pushing and sliding the DNA (propagation), twisting the DNA (global distortion)
Question:
How do cells recruit remodeling complexes?.
Answer:
Via proteins that bind in a sequence-specific manner
,Question:
What two ways do cells recruit nucleosome remodeling complexes?.
Answer:
Transcriptional regulators and histone modifications
Question:
Why doesn't the brain cool down as efficiently as the rest of the body?.
Answer:
There isn't an overexpression of heat-shock proteins like there is elsewhere in the body so it takes
longer to activate heat- shock system
Question:
True or False: Like histones, DNA can also be directly chemically modified..
Answer:
True
Question:
Give an example of a direct DNA methylation and its possible effects..
Answer:
Methylation of cytosine can make 5-methyl cytosine which can then be turned into thymine via an
easy deamination
Question:
True or false: DNA methylation is generally safe and DNA alteration isn't permanent..
Answer:
False: DNA methylation is very risky and typically gives rise to mutations, even in normal
processes
Question:
, What is the method that DNA methyltransferases use to access cytosines and what are the three
steps?.
Answer:
base-flipping
1) A cytosine is flipped out of the DNA double helix
2) An amino acid is temporarily inserted to stack in the double helix
3) The cytosine is methylated and reinserted into the double helix
Question:
Explain how DNA methylation distinguishes newly synthesized DNA in repair processes in
bacteria..
Answer:
Just after replication, only the parental strand of DNA is methylated (called hemi-
methylated). When mismatch repair enzymes detect a mismatch, the methylation status is read,
allowing the repair machinery to identify the parental strand and correclty repair the mismatch
Question:
Explain how DNA methylation allows bacteria to distinguish genomic DNA from invading
bacteriophage DNA..
Answer:
Restriction enzymes cut DNA at specific recognition sites so bacteria defend their own DNA from
being cut by methylating the recognition sites. The bacteriophage DNA is not methylated and will
therefore be cut by the restriction enzymes and destroyed.
Question:
True or False: Methylation in eukaryotes is only used to silence transcription, not activate it..
Answer:
False
Question:
Eukaryotic methylation is usually at which two sites?.
