BCH5413 COMPREHENSIVE EXAM SCRIPT
2026 FULL QUESTIONS AND CORRECT
ANSWERS
◉Core Histones Answer: H3, H4, H2A, H2B
◉Linker Histone Answer: H1
◉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.
◉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.
,◉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.
◉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.
,◉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.
◉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.
◉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.
, ◉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.
◉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.
◉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.
◉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.
2026 FULL QUESTIONS AND CORRECT
ANSWERS
◉Core Histones Answer: H3, H4, H2A, H2B
◉Linker Histone Answer: H1
◉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.
◉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.
,◉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.
◉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.
,◉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.
◉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.
◉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.
, ◉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.
◉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.
◉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.
◉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.
