BCHM 4360 EXAM REVIEW 2026 DETAILED
QUESTIONS AND SOLVED SOLUTIONS
◉What is sumo and why is it important?. Answer: Small ubiquitin-
like modifier that also plays roles in transcription regulation and
DNA repair
◉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
◉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
◉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
,◉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
◉What are the four main nucleosome remodeling complex
subunits?. Answer: ATPase domain (two parts Dexx and HELICc),
bromodomain, chromodomain, and SANT-SLIDE
◉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
◉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)
◉How do cells recruit remodeling complexes?. Answer: Via proteins
that bind in a sequence-specific manner
◉What two ways do cells recruit nucleosome remodeling
complexes?. Answer: Transcriptional regulators and histone
modifications
,◉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
◉True or False: Like histones, DNA can also be directly chemically
modified.. Answer: True
◉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
◉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
◉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
◉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
◉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.
◉True or False: Methylation in eukaryotes is only used to silence
transcription, not activate it.. Answer: False
◉Eukaryotic methylation is usually at which two sites?. Answer: CpG
or CpXpG
◉Up to __% of human CpGs are methylated, and methylation state
can be _________.. Answer: inherited
◉What is an example of epigenetic silencing in mammals and how
does it work?. Answer: X-chromosome inactivation, one X
chromosome in each cell is inactivated in females so they have the
same amount of gene product as in males
QUESTIONS AND SOLVED SOLUTIONS
◉What is sumo and why is it important?. Answer: Small ubiquitin-
like modifier that also plays roles in transcription regulation and
DNA repair
◉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
◉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
◉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
,◉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
◉What are the four main nucleosome remodeling complex
subunits?. Answer: ATPase domain (two parts Dexx and HELICc),
bromodomain, chromodomain, and SANT-SLIDE
◉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
◉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)
◉How do cells recruit remodeling complexes?. Answer: Via proteins
that bind in a sequence-specific manner
◉What two ways do cells recruit nucleosome remodeling
complexes?. Answer: Transcriptional regulators and histone
modifications
,◉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
◉True or False: Like histones, DNA can also be directly chemically
modified.. Answer: True
◉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
◉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
◉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
◉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
◉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.
◉True or False: Methylation in eukaryotes is only used to silence
transcription, not activate it.. Answer: False
◉Eukaryotic methylation is usually at which two sites?. Answer: CpG
or CpXpG
◉Up to __% of human CpGs are methylated, and methylation state
can be _________.. Answer: inherited
◉What is an example of epigenetic silencing in mammals and how
does it work?. Answer: X-chromosome inactivation, one X
chromosome in each cell is inactivated in females so they have the
same amount of gene product as in males
