BIO210 EXAMS QUESTIONS AND ANSWERS
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GC-content
The fraction of nucleotides in a gene, chromosome, or genome that are G or C rather
than A or T. DNA with a lower GC-content is generally less stable.
DNA major groove
Strucutral grove in the DNA helix. A major groove occurs when the backbones are far
apart.
DNA minor groove
Strucutral grove in the DNA helix. A minor groove occurs when the backbones are close
together.
Semiconservative DNA replication
Semiconservative replication means that the two DNA strands separate, and form
templates for free nucleotides to bind to, creating two daughter strands.
Template DNA
A single strand of DNA used as template to synthesize a new strand of DNA.
Base stacking
The bases in the DNA helix stack at a contact distance, excluding water and maximizing
Van der Waals interactions. Stabilizing hydrophobic interactions between bases in the
same strand of DNA.
One helical turn in DNA double helix
Includes around 10,5 base pairs.
Base flipping
When a nucleotide base in the DNA helix is rotated outside the double helix. Occurs
when the hydrogen bond between the bases break, catalyzed by a nucleic acid enzyme,
which needs to work on the base (such as replacement with another base).
Melting temperature of DNA
Temperature at which DNA has reached half total maximum denaturation. Varies from
50 to 100 degrees Celcius, based on length, base composition, and salt concentration.
Supercoiling in DNA (negative and positive)
The amount of twist in a DNA strand. Positive supercoiling (overwound) leads to a less
amount of bp per turn. Negative supercoiling (underwound) leads to more bp per turn.
Affects biological processes, such as compacting DNA and regulating access to the
genetic code.
Topoisomerases
Enzymes that catalyze changes in the topological state of DNA
A chromosome
A package of DNA, which consists of DNA coiled around proteins
A genome
The entire genetic material of an organism
Histone octamer
An eight-protein complex, which DNA is coiled around in the nucleosome
Nucleosome
, Bead-like structure in eukaryotic chromatin, composed of a short length of DNA
wrapped around a core of histone proteins
Euchromatin
Lightly packed form of chromatin (DNA, RNA and protein) that is enriched in genes, and
is often (but not always) under active transcription
Heterochromatin
DNA that is densely packed around histones. The genes in heterochromatin are
generally inaccessible to enzymes and are turned off.
A pseudogene
A DNA segment very similar to a real gene but which does not yield a functional
product; a gene that has become inactivated in a particular species because of
mutation. Does not contain promoter or regulatory elements.
Introns versus exons
Introns are part of the gene that is not included during transcription, while exons are.
Introns -> non-coding, exons -> coding.
Primase
An enzyme which catalyses the creation of a short RNA sequence complementary to
the DNA called a primer. This is used as an initiator for DNA synthesis, and is later
removed.
Helicase
An enzyme that untwists the double helix of DNA at the replication forks.
DNA ligase
A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3'
end of a new DNA fragment to the 5' end of a growing chain.
Clamp loader
Uses the energy of ATP hydrolysis to lock the sliding clamp onto DNA
Endonucleases
Enzymes that cut RNA or DNA at specific sites
Exonucleases
Enzymes that cut RNA or DNA at the end of the chain
DNA polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA
molecule
DNA polymerase holoenzyme
Large enzyme complex involved in prokaryotic DNA replication.
Proofreading in DNA synthesis
When DNA polymerase recognizes that an incorrect nucleotide has been added and
resynthesizes the region following the targeted action of an associated exonuclease
function.
Processivity in DNA synthesis
The typical number of nucleotides that a DNA polymerase adds throughout a single
binding event
Replication fork
A Y-shaped region on a replicating DNA molecule where new strands are growing.
Leading vs lagging strand during DNA synthesis
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GC-content
The fraction of nucleotides in a gene, chromosome, or genome that are G or C rather
than A or T. DNA with a lower GC-content is generally less stable.
DNA major groove
Strucutral grove in the DNA helix. A major groove occurs when the backbones are far
apart.
DNA minor groove
Strucutral grove in the DNA helix. A minor groove occurs when the backbones are close
together.
Semiconservative DNA replication
Semiconservative replication means that the two DNA strands separate, and form
templates for free nucleotides to bind to, creating two daughter strands.
Template DNA
A single strand of DNA used as template to synthesize a new strand of DNA.
Base stacking
The bases in the DNA helix stack at a contact distance, excluding water and maximizing
Van der Waals interactions. Stabilizing hydrophobic interactions between bases in the
same strand of DNA.
One helical turn in DNA double helix
Includes around 10,5 base pairs.
Base flipping
When a nucleotide base in the DNA helix is rotated outside the double helix. Occurs
when the hydrogen bond between the bases break, catalyzed by a nucleic acid enzyme,
which needs to work on the base (such as replacement with another base).
Melting temperature of DNA
Temperature at which DNA has reached half total maximum denaturation. Varies from
50 to 100 degrees Celcius, based on length, base composition, and salt concentration.
Supercoiling in DNA (negative and positive)
The amount of twist in a DNA strand. Positive supercoiling (overwound) leads to a less
amount of bp per turn. Negative supercoiling (underwound) leads to more bp per turn.
Affects biological processes, such as compacting DNA and regulating access to the
genetic code.
Topoisomerases
Enzymes that catalyze changes in the topological state of DNA
A chromosome
A package of DNA, which consists of DNA coiled around proteins
A genome
The entire genetic material of an organism
Histone octamer
An eight-protein complex, which DNA is coiled around in the nucleosome
Nucleosome
, Bead-like structure in eukaryotic chromatin, composed of a short length of DNA
wrapped around a core of histone proteins
Euchromatin
Lightly packed form of chromatin (DNA, RNA and protein) that is enriched in genes, and
is often (but not always) under active transcription
Heterochromatin
DNA that is densely packed around histones. The genes in heterochromatin are
generally inaccessible to enzymes and are turned off.
A pseudogene
A DNA segment very similar to a real gene but which does not yield a functional
product; a gene that has become inactivated in a particular species because of
mutation. Does not contain promoter or regulatory elements.
Introns versus exons
Introns are part of the gene that is not included during transcription, while exons are.
Introns -> non-coding, exons -> coding.
Primase
An enzyme which catalyses the creation of a short RNA sequence complementary to
the DNA called a primer. This is used as an initiator for DNA synthesis, and is later
removed.
Helicase
An enzyme that untwists the double helix of DNA at the replication forks.
DNA ligase
A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3'
end of a new DNA fragment to the 5' end of a growing chain.
Clamp loader
Uses the energy of ATP hydrolysis to lock the sliding clamp onto DNA
Endonucleases
Enzymes that cut RNA or DNA at specific sites
Exonucleases
Enzymes that cut RNA or DNA at the end of the chain
DNA polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA
molecule
DNA polymerase holoenzyme
Large enzyme complex involved in prokaryotic DNA replication.
Proofreading in DNA synthesis
When DNA polymerase recognizes that an incorrect nucleotide has been added and
resynthesizes the region following the targeted action of an associated exonuclease
function.
Processivity in DNA synthesis
The typical number of nucleotides that a DNA polymerase adds throughout a single
binding event
Replication fork
A Y-shaped region on a replicating DNA molecule where new strands are growing.
Leading vs lagging strand during DNA synthesis
