CMMB 411 Quiz 1
What is the optimal number of base pairs per turn in B-Form DNA? - *answers *10.5
bp/turn
Why does DNA naturally form a helix? - *answers *Because the base pairs are
hydrophobic and don't want to interact with water. Therefore, forming a helix will
maximize these hydrophobic interactions and limit the amount of interaction with water.
What is the length between bases? - *answers *2.7 Angstroms
What is the average twist angle? - *answers *34 degrees
Why do bases in DNA twist? - *answers *To optimize electrostatic interactions.
Minimizing repulsion.
Name the 3 reasons for DNA twisting. - *answers *1. Optimize electrostatics
2. H2O can fit inbetween the bases if there is no twist
3. When the DNA twists, it stacks on top of one another and this stacking adds up the
interactions like VDW's.
What are the different types of DNA and some of their characteristics? - *answers *1.
A-Form: Right-Handed, dehydrated. Found in bacteria, usually dsRNA. DNA binidng
proteins can't bind to this type of DNA.
2. B-Form: naturally occuring in humans and most living organisms. ALWAYS double-
stranded and right-handed.
3. Z-Form: Left-Handed and the broadest of all.
What is the STEM region? - *answers *mRNA that has complementarity and is/ends up
double stranded.
Why is A-form DNA found in bacteria? - *answers *Because there is no metabolism in
spores and that means that there is no gene expression
What happens if RNAPol can't bind to the promoter? - *answers *Gene expression is
shut off.
What is the function of a positional helix? - *answers *it helps position the recognition
sequence in the major groove.
What is the angle of the major groove? - *answers *240 degrees.
What happens if the glycosidic bond is 180 degrees? - *answers *Then there is no
major groove.
What does it mean when dsDNA is "constrained"? - *answers *The ends are anchored
and can't twist freely.
, CMMB 411 Quiz 1
When inserting at the major groove, what does this tell you/give you? - *answers *1. H-
bonding (acceptors and donors)
2. Sterics
What is meant by "linking number"? - *answers *It is the number of times that one
strand of DNA crosses over the other when the DNA is laid down flat on a plane
When does the linking number stay the same? - *answers *When there ISN'T any
breakage or formation
What is the formula for linking number? - *answers *L = T + W
T= Twist
W= Writhe or Supertwist
What does "twist" mean? - *answers *The number of helical turns
Are there any twists or supertwists when DNA is in the single-stranded form? -
*answers *No.
List the Rules of DNA topology - *answers *1. Topology is only meant to describe
dsDNA
2. If W=0 then L=T and the DNA is in the relaxed state
3. R.H. Twist = +
4. R.H. SuperCoil/SuperTwist = -
What form of DNA/RNA do you need in order for replication, translation or transcription
to occur? - *answers *The single-stranded form.
How many Hydrogen bonds do the C-G base pairs contain? What about the A-T base
pairs? - *answers *3 and 2
What kind of supercoil is negative and what are the properties of these types of coils? -
*answers *These are right-handed supercoils and this energy contained within them
causes strand seperation and once seperation the replication/transcription/translation
processes can potentially occur.
What does L-L0 tell you? - *answers *The degree of the supercoiling
What 2 factors can affect supercoiling? - *answers *1. EtBr
2. Topoisomerases
Explain EtBr's affect on a piece of helical DNA. - *answers *With its planar, 3-ring
structure, EtBr can slide in between base pairs and the negative Br balances the +
charge. It intercalates by unwinding the DNA slightly.
What is the optimal number of base pairs per turn in B-Form DNA? - *answers *10.5
bp/turn
Why does DNA naturally form a helix? - *answers *Because the base pairs are
hydrophobic and don't want to interact with water. Therefore, forming a helix will
maximize these hydrophobic interactions and limit the amount of interaction with water.
What is the length between bases? - *answers *2.7 Angstroms
What is the average twist angle? - *answers *34 degrees
Why do bases in DNA twist? - *answers *To optimize electrostatic interactions.
Minimizing repulsion.
Name the 3 reasons for DNA twisting. - *answers *1. Optimize electrostatics
2. H2O can fit inbetween the bases if there is no twist
3. When the DNA twists, it stacks on top of one another and this stacking adds up the
interactions like VDW's.
What are the different types of DNA and some of their characteristics? - *answers *1.
A-Form: Right-Handed, dehydrated. Found in bacteria, usually dsRNA. DNA binidng
proteins can't bind to this type of DNA.
2. B-Form: naturally occuring in humans and most living organisms. ALWAYS double-
stranded and right-handed.
3. Z-Form: Left-Handed and the broadest of all.
What is the STEM region? - *answers *mRNA that has complementarity and is/ends up
double stranded.
Why is A-form DNA found in bacteria? - *answers *Because there is no metabolism in
spores and that means that there is no gene expression
What happens if RNAPol can't bind to the promoter? - *answers *Gene expression is
shut off.
What is the function of a positional helix? - *answers *it helps position the recognition
sequence in the major groove.
What is the angle of the major groove? - *answers *240 degrees.
What happens if the glycosidic bond is 180 degrees? - *answers *Then there is no
major groove.
What does it mean when dsDNA is "constrained"? - *answers *The ends are anchored
and can't twist freely.
, CMMB 411 Quiz 1
When inserting at the major groove, what does this tell you/give you? - *answers *1. H-
bonding (acceptors and donors)
2. Sterics
What is meant by "linking number"? - *answers *It is the number of times that one
strand of DNA crosses over the other when the DNA is laid down flat on a plane
When does the linking number stay the same? - *answers *When there ISN'T any
breakage or formation
What is the formula for linking number? - *answers *L = T + W
T= Twist
W= Writhe or Supertwist
What does "twist" mean? - *answers *The number of helical turns
Are there any twists or supertwists when DNA is in the single-stranded form? -
*answers *No.
List the Rules of DNA topology - *answers *1. Topology is only meant to describe
dsDNA
2. If W=0 then L=T and the DNA is in the relaxed state
3. R.H. Twist = +
4. R.H. SuperCoil/SuperTwist = -
What form of DNA/RNA do you need in order for replication, translation or transcription
to occur? - *answers *The single-stranded form.
How many Hydrogen bonds do the C-G base pairs contain? What about the A-T base
pairs? - *answers *3 and 2
What kind of supercoil is negative and what are the properties of these types of coils? -
*answers *These are right-handed supercoils and this energy contained within them
causes strand seperation and once seperation the replication/transcription/translation
processes can potentially occur.
What does L-L0 tell you? - *answers *The degree of the supercoiling
What 2 factors can affect supercoiling? - *answers *1. EtBr
2. Topoisomerases
Explain EtBr's affect on a piece of helical DNA. - *answers *With its planar, 3-ring
structure, EtBr can slide in between base pairs and the negative Br balances the +
charge. It intercalates by unwinding the DNA slightly.
