Molecular Cell Biology Exam Questions with Verified Solutions (Graded A+)
-How large is our genome? How many base pairs does it contain? How long is it when fully extended? -
Answers Our genome consists of 6.4 billion base pairs, 200bp, 20,000 genes and when fully extended it
can reach 6ft or 2m.
-What is Chromatin? - Answers Chromatin is the fibrous complex of eukaryotic DNA and histone
proteins.
-What are Histones? - Answers The main histones are H1, H2A, H2B, H3, and H4.
What's their charge (polarity)? What amino acid residues are responsible for their net charge? Why is
the charge of Histones important? - Answers The charge of histones is positive. The amino acid residues
that are responsible for that net charge are lysine and arginine. It's important because lysine and
arginine are positively charged amino acids that can bind to the negatively charged DNA molecule.
-What does Micrococcal Nuclease do to chromatin? What type of a nuclease is Micrococcal Nuclease?
Is it specific for DNA or can it cut RNA as well?
Can it cut inside DNA or can it cut only at the ends? - Answers Micrococcal Nuclease partially digests the
chromatin to obtain gel electrophoresis of DNA fragments.
-By the way, what are exonucleases? And how about endonuclease? What's the difference? If you have
a "nick" in the DNA (a break in one of the strands of the DNA), and you want to "chew up" the DNA
starting at that point, what kind of nuclease activity would be needed, an endonuclease or an
exonuclease? Why? - Answers Exonucleases "chew" the ends of a DNA strand . Endonucleases "chew"
within the strand of DNA. An endonuclease would be needed because since one of the DNA strands
broke within itself, endonucleases can "chew" within the DNA.
-What's a Nucleosome? How many base pairs (bp) of DNA are contained in a typical mammalian
nucleosome? - Answers A nucleosome is the basic structural unit of chromatin consisting of DNA
wrapped around a histone core. It has 200 base pairs.
-What types of proteins are usually associated to "linker" DNA? - Answers
-What's a Nucleosome Core Particle? How long is it (in bp)? - Answers A nucleosome core particle is a
particle containing 146 base pairs of DNA wrapped around an octamer consisting of two molecules each
of histones H2A, H2B, H3 and H4.
-What's a Chromatosome? How long is it (in bp)? - Answers A chromatosome is a chromatin subunit
consisting of 166 base pairs of DNA wrapped around a histone core and held in place by linker histone.
-What happens to chromatin if you allow its digestion with Micrococcal Nuclease for extended amounts
of time? What would happen if you allow the digestion to go on for several hours? How may bands
would you get? - Answers
, -How many copies of each histone are there in each of the above structures? - Answers There are two
copies of each histone in each of the above structure.
-Different levels of chromatin structure: (Hierarchical model of DNA packaging) - Answers 1st order -
"Beads on a String" or 10 nm fiber
2nd order - Chromatin fiber or 30 nm fiber - can be in the solenoid or zigzag form
3rd order - Looped form
4th order - Minibands (in Heterochromatin and in condensed chromosomes during Metaphase)
-Is this hierarchical model considered correct nowadays? If not, what's the current model for large scale
chromatin organization? - Answers
-What are TADs? - Answers
-What protein(s) play a role in each of the above structures? - Answers The proteins are histones.
-What's heterochromatin? What's euchromatin? - Answers Heterochromatin is condensed,
transcriptionally inactive chromatin. Euchromatin is decondensed, transcriptionally active interphase
chromatin.
-During what stage of the cell cycle is chromatin fully packed? Is there any transcription at that time?
Why? - Answers Metaphase is the stage of the cell cycle the chromatin is fully packed. There is no
transcription at that time because the DNA is not accessible and inactive.
-What's a Centromere? What's the Kinetochore? - Answers A centromere is a specialized chromosomal
region that connects sister chromatids and attaches them to the mitotic spindle. A kinetochore is a
specialized structure consisting of proteins attached to a centromere that mediates the attachment and
movements of chromosomes along the mitotic spindle.
-What's a Telomere? - Answers A telomere is a repeat of simple sequence DNA that maintains the ends
of linear chromosomes.
-What's the main role of Centromeres? - Answers The main role is ensuring the correct distribution of
duplicated chromosomes to daughter cells during mitosis.
-Why are Telomeres important? What type of sequence is found at the Telomere? Why is that relevant?
- Answers Telomeres are important because they play critical roles in chromosome replication and
maintenance. Telomeres consist of repeats of a simple sequence DNA containing clusters of G residues
on one strand. Its relevant because it forms loops at the ends of chromosomes and bind a protein
complex that protects the chromosome termini from degradation.
-What's the only shared feature of all eukaryotic Centromeres? - Answers The only shared feature is
CENP-A.
-How large is our genome? How many base pairs does it contain? How long is it when fully extended? -
Answers Our genome consists of 6.4 billion base pairs, 200bp, 20,000 genes and when fully extended it
can reach 6ft or 2m.
-What is Chromatin? - Answers Chromatin is the fibrous complex of eukaryotic DNA and histone
proteins.
-What are Histones? - Answers The main histones are H1, H2A, H2B, H3, and H4.
What's their charge (polarity)? What amino acid residues are responsible for their net charge? Why is
the charge of Histones important? - Answers The charge of histones is positive. The amino acid residues
that are responsible for that net charge are lysine and arginine. It's important because lysine and
arginine are positively charged amino acids that can bind to the negatively charged DNA molecule.
-What does Micrococcal Nuclease do to chromatin? What type of a nuclease is Micrococcal Nuclease?
Is it specific for DNA or can it cut RNA as well?
Can it cut inside DNA or can it cut only at the ends? - Answers Micrococcal Nuclease partially digests the
chromatin to obtain gel electrophoresis of DNA fragments.
-By the way, what are exonucleases? And how about endonuclease? What's the difference? If you have
a "nick" in the DNA (a break in one of the strands of the DNA), and you want to "chew up" the DNA
starting at that point, what kind of nuclease activity would be needed, an endonuclease or an
exonuclease? Why? - Answers Exonucleases "chew" the ends of a DNA strand . Endonucleases "chew"
within the strand of DNA. An endonuclease would be needed because since one of the DNA strands
broke within itself, endonucleases can "chew" within the DNA.
-What's a Nucleosome? How many base pairs (bp) of DNA are contained in a typical mammalian
nucleosome? - Answers A nucleosome is the basic structural unit of chromatin consisting of DNA
wrapped around a histone core. It has 200 base pairs.
-What types of proteins are usually associated to "linker" DNA? - Answers
-What's a Nucleosome Core Particle? How long is it (in bp)? - Answers A nucleosome core particle is a
particle containing 146 base pairs of DNA wrapped around an octamer consisting of two molecules each
of histones H2A, H2B, H3 and H4.
-What's a Chromatosome? How long is it (in bp)? - Answers A chromatosome is a chromatin subunit
consisting of 166 base pairs of DNA wrapped around a histone core and held in place by linker histone.
-What happens to chromatin if you allow its digestion with Micrococcal Nuclease for extended amounts
of time? What would happen if you allow the digestion to go on for several hours? How may bands
would you get? - Answers
, -How many copies of each histone are there in each of the above structures? - Answers There are two
copies of each histone in each of the above structure.
-Different levels of chromatin structure: (Hierarchical model of DNA packaging) - Answers 1st order -
"Beads on a String" or 10 nm fiber
2nd order - Chromatin fiber or 30 nm fiber - can be in the solenoid or zigzag form
3rd order - Looped form
4th order - Minibands (in Heterochromatin and in condensed chromosomes during Metaphase)
-Is this hierarchical model considered correct nowadays? If not, what's the current model for large scale
chromatin organization? - Answers
-What are TADs? - Answers
-What protein(s) play a role in each of the above structures? - Answers The proteins are histones.
-What's heterochromatin? What's euchromatin? - Answers Heterochromatin is condensed,
transcriptionally inactive chromatin. Euchromatin is decondensed, transcriptionally active interphase
chromatin.
-During what stage of the cell cycle is chromatin fully packed? Is there any transcription at that time?
Why? - Answers Metaphase is the stage of the cell cycle the chromatin is fully packed. There is no
transcription at that time because the DNA is not accessible and inactive.
-What's a Centromere? What's the Kinetochore? - Answers A centromere is a specialized chromosomal
region that connects sister chromatids and attaches them to the mitotic spindle. A kinetochore is a
specialized structure consisting of proteins attached to a centromere that mediates the attachment and
movements of chromosomes along the mitotic spindle.
-What's a Telomere? - Answers A telomere is a repeat of simple sequence DNA that maintains the ends
of linear chromosomes.
-What's the main role of Centromeres? - Answers The main role is ensuring the correct distribution of
duplicated chromosomes to daughter cells during mitosis.
-Why are Telomeres important? What type of sequence is found at the Telomere? Why is that relevant?
- Answers Telomeres are important because they play critical roles in chromosome replication and
maintenance. Telomeres consist of repeats of a simple sequence DNA containing clusters of G residues
on one strand. Its relevant because it forms loops at the ends of chromosomes and bind a protein
complex that protects the chromosome termini from degradation.
-What's the only shared feature of all eukaryotic Centromeres? - Answers The only shared feature is
CENP-A.
