BCH5413 Comprehensive Exam Questions
and Answers Verified Solutions Latest
Update 2026/2027
Question:
Core Histones
Answer:
H3, H4, H2A, H2B
Question:
Linker Histone
Answer:
H1
Question:
Explain the role of each of the histones in the formation of chromatin
Answer:
DNA is wrapped around a nucleosome, which is composed of eight core histones (histone
octamer). Each histone octamer is composed of a H3-H4 tetramer and two H2A-H2B dimers.
Linker histone H1 interacts with the core histones to bring them closer together in an up-down
structure to form a tighter and more organized chromatin that is compacted 7-fold.
Question:
What is the significance of the fact that histones have an overall basic pH?
Answer:
The basic pH (positive charge) of the histones attracts the more negative charge of DNA. The
interactions between histones and DNA are non-sequence specific. Instead, the interactions
between histones and DNA are due to the positive charge of histones and the negative charge of
,DNA attracting each other.
Question:
What is the difference between a two start supercoiled model and a two start twisted or helical
model for the 30nm fiber? Which is more supported by x-ray crystallography data?
Answer:
Two-start supercoiled model: two nucleosomes at the top that wrap around in a helical form.
Two-start twisted/helical model: two nucleosomes at the top but they go one opposite to the other,
one nucleosome is opposite to the next.
Most predominant structure found in cells: two-start twisted model.
Question:
What is the difference between euchromatin and heterochromatin?
Answer:
Euchromatin:
Found more towards the center of the nucleus.
Lightly stained, more accessible DNA (not compacted), transcriptionally active.
Heterochromatin:
Found closest to the nuclear membrane.
Darkly stained, closed inaccessible DNA (very compacted), transcriptionally inactive, higher levels
of chromatin organization.
DNA can be arranged differently within the same nucleus.
All cells have different levels of organization of their DNA but what's in them is different from
each other depending upon the function of that cell.
Question:
Initially investigators believed that the nucleolus was an organelle within the nucleus of some cells.
Explain why that is no longer considered to be accurate.
Answer:
The nucleolus is a region found within the nucleus that stains dark, like heterochromatin, but
caused by the highly active transcription occurring in this area.
This is also where ribosomal RNA is produced.
The nucleolus has a unique density that separates it from its surrounding nucleoplasma, making it a
separate compartment without the need of a membrane.
,Question:
Explain what happens to the 30nm fiber in order to create a metaphase chromosome.
Answer:
When a cell is ready to divide during mitosis or meiosis, DNA needs to be very compacted so that
it can be efficiently transferred.
The 30nm fiber is further looped onto a protein scaffold. Scaffolding proteins in the center give the
metaphase chromosome its unique shape.
Question:
How is DNA organized in an interphase nucleus?
Answer:
DNA in an interphase nucleus is not as compacted as in a metaphase nucleus.
In interphase nucleus, DNA needs to be more accessible for transcription. DNA is loose and not
condensed.
Question:
In gel electrophoresis, why does DNA move towards the positive pole?
Answer:
DNA has a negative charge and is attracted towards the positive pole of the gel electrophoresis.
Question:
In gel electrophoresis, why does DNA move according to size?
Answer:
Smaller DNA fragments will move faster towards the positive pole when compared to larger DNA
fragments. Hence, smaller DNA fragments will travel a longer distance than larger fragments and
these will be separated according to size.
Question:
What is the basic difference between a Southern, a northern, and a western blot? (ie. What does
each detect?)
, Answer:
Southern blot detects DNA, agarose gel to nylon membrane.
Northern blot detects RNA, agarose gel (containing formaldehyde) to nylon or nitrocellulose
membrane.
Western blot detects proteins, polyacrylamide gel (containing SDS and b-ME) to membrane.
Question:
What is the importance of blocking in a Southern Blot?
Answer:
Blocking with nonspecific DNA or protein decreases non-specific binding of the labeled probe to
the DNA that is fixed on the nylon membrane.
Bovine serum albumin (BSA) will coat the membrane and will help in making sure that will only
get specific interaction with probe and DNA of interest.
Question:
Why does denaturing DNA on a blot allow for the detection of fragments based upon sequence?
Answer:
DNA is first denatured dsDNA to ssDNA in the gel to increase affinity of transfer from gel to
membrane.
Having ssDNA in the membrane allows for probes to anneal to the ssDNA.
Question:
Lower stringency
Answer:
greater mismatch and higher background noise.
Question:
In Southern blot analysis:
What is the meaning of the term stringency?
Answer:
and Answers Verified Solutions Latest
Update 2026/2027
Question:
Core Histones
Answer:
H3, H4, H2A, H2B
Question:
Linker Histone
Answer:
H1
Question:
Explain the role of each of the histones in the formation of chromatin
Answer:
DNA is wrapped around a nucleosome, which is composed of eight core histones (histone
octamer). Each histone octamer is composed of a H3-H4 tetramer and two H2A-H2B dimers.
Linker histone H1 interacts with the core histones to bring them closer together in an up-down
structure to form a tighter and more organized chromatin that is compacted 7-fold.
Question:
What is the significance of the fact that histones have an overall basic pH?
Answer:
The basic pH (positive charge) of the histones attracts the more negative charge of DNA. The
interactions between histones and DNA are non-sequence specific. Instead, the interactions
between histones and DNA are due to the positive charge of histones and the negative charge of
,DNA attracting each other.
Question:
What is the difference between a two start supercoiled model and a two start twisted or helical
model for the 30nm fiber? Which is more supported by x-ray crystallography data?
Answer:
Two-start supercoiled model: two nucleosomes at the top that wrap around in a helical form.
Two-start twisted/helical model: two nucleosomes at the top but they go one opposite to the other,
one nucleosome is opposite to the next.
Most predominant structure found in cells: two-start twisted model.
Question:
What is the difference between euchromatin and heterochromatin?
Answer:
Euchromatin:
Found more towards the center of the nucleus.
Lightly stained, more accessible DNA (not compacted), transcriptionally active.
Heterochromatin:
Found closest to the nuclear membrane.
Darkly stained, closed inaccessible DNA (very compacted), transcriptionally inactive, higher levels
of chromatin organization.
DNA can be arranged differently within the same nucleus.
All cells have different levels of organization of their DNA but what's in them is different from
each other depending upon the function of that cell.
Question:
Initially investigators believed that the nucleolus was an organelle within the nucleus of some cells.
Explain why that is no longer considered to be accurate.
Answer:
The nucleolus is a region found within the nucleus that stains dark, like heterochromatin, but
caused by the highly active transcription occurring in this area.
This is also where ribosomal RNA is produced.
The nucleolus has a unique density that separates it from its surrounding nucleoplasma, making it a
separate compartment without the need of a membrane.
,Question:
Explain what happens to the 30nm fiber in order to create a metaphase chromosome.
Answer:
When a cell is ready to divide during mitosis or meiosis, DNA needs to be very compacted so that
it can be efficiently transferred.
The 30nm fiber is further looped onto a protein scaffold. Scaffolding proteins in the center give the
metaphase chromosome its unique shape.
Question:
How is DNA organized in an interphase nucleus?
Answer:
DNA in an interphase nucleus is not as compacted as in a metaphase nucleus.
In interphase nucleus, DNA needs to be more accessible for transcription. DNA is loose and not
condensed.
Question:
In gel electrophoresis, why does DNA move towards the positive pole?
Answer:
DNA has a negative charge and is attracted towards the positive pole of the gel electrophoresis.
Question:
In gel electrophoresis, why does DNA move according to size?
Answer:
Smaller DNA fragments will move faster towards the positive pole when compared to larger DNA
fragments. Hence, smaller DNA fragments will travel a longer distance than larger fragments and
these will be separated according to size.
Question:
What is the basic difference between a Southern, a northern, and a western blot? (ie. What does
each detect?)
, Answer:
Southern blot detects DNA, agarose gel to nylon membrane.
Northern blot detects RNA, agarose gel (containing formaldehyde) to nylon or nitrocellulose
membrane.
Western blot detects proteins, polyacrylamide gel (containing SDS and b-ME) to membrane.
Question:
What is the importance of blocking in a Southern Blot?
Answer:
Blocking with nonspecific DNA or protein decreases non-specific binding of the labeled probe to
the DNA that is fixed on the nylon membrane.
Bovine serum albumin (BSA) will coat the membrane and will help in making sure that will only
get specific interaction with probe and DNA of interest.
Question:
Why does denaturing DNA on a blot allow for the detection of fragments based upon sequence?
Answer:
DNA is first denatured dsDNA to ssDNA in the gel to increase affinity of transfer from gel to
membrane.
Having ssDNA in the membrane allows for probes to anneal to the ssDNA.
Question:
Lower stringency
Answer:
greater mismatch and higher background noise.
Question:
In Southern blot analysis:
What is the meaning of the term stringency?
Answer:
