"When the glycosidic bonds of two joined bases point down, the top edges of the bases point into the ________ groove; the bottom edges point into the __________ groove."
1.) Major
2.) Minor
True or false?
The double stranded forms of DNA and RNA always run anti-parallel.
True.
In RNA guanine is paired with _________, and adenine is paired with __________.
1.) Cytosine
2.) Uracil
What base is the unmethylated form of thymine?
Uracil.
Why can't RNA form a B-type helix?
Ribonucleic acid has a hydroxyl group on the 2' carbon of the ribose. This group sits almost directly in the center of the helix and causes steric hindrance that is not present in DNA.
The A-type helix has a large hole going down the center, this allows room for the 2' hydroxyl on the ribose.
Why is the B-type helix the more stable of the two types?
It allows for good stacking of the base pairs to minimize its hydrophobic interactions with water.
The B-type helix has a 0-10 degree tilt on the base pairs.
Describe why the helix is a stable form for double stranded DNA.
1.) The hydrophobic bases can pack tightly to limit contact with H2O
2.) The negatively charged phosphates of the backbone repel each other. The helical formation allows them to be as far apart as possible without separating.
In A-type DNA, the base pairs are towards the (center/side) of the helix.
Side.
True or False?
RNA's most complex form is its secondary structure.
False.
RNA can fold into complex tertiary structures, similar to proteins.
Define RNA motif.
"A recurrent portion of RNA with a specific structure. The sequence may vary, but fuction is generally conserved."
Give some examples of RNA motifs.
1.) Pentaloop
2.) Quartet link
3.) 3-purine asymmetric bulge
4.) 7-nucleotide bubble
5.) A-form helices
What structures on a DNA-binding-protein serve the function of docking the protein on the major groove?
1.) specific domains of Alpha-helices
2.) specific domains of Beta-strands
What structures on a DNA-binding-protein serve the function of docking the protein on the minor groove?
Specific domains of Beta-strands.
Aplha-helices are not the right shape to penetrate the minor groove.
What two ways does a DNA-binding-protein recognize target sequences on DNA?
1.) Direct readout
2.) Indirect readout
In regards to DNA super-coiling, what is a twist?
A complete 360 degree turn of a double strand of DNA.
How many base pairs of DNA are in a single twist?
10.4
In regards to DNA super-coiling, what is a writhe?
When a DNA helix axis crosses itself.
True or False?
Writhes and twists in DNA can be inter-converted.
True.
True or False?
Topoisomers have the the same linking number.
False.
How do you calculate linking number?
LK = twists + writhesl
How do you calculate LK in a relaxed circle, given only the number of base pairs?
LK = # base pairs / 10.4
In a negatively super-coiled circle, the LK will be (greater than, less than) the LK of the corresponding relaxed circle?
Less than.
LK < # base pairs / 10.4
True or False?
Biological sources of DNA usually consist of positive super-coils.
False.
They usually consist of negative super-coils.
What is the significance of having biological DNA with negative super-coils?
*Rubber tube example:
Negative super-coiling allows for DNA to be unwound into two single strands of a relaxed circle for easy transcription.
If you start with a relaxed circle of DNA and begin to unwind the two strands, you will form 2 (positive, negative) writes.
Positive.
This is undesirable when transcribing DNA to RNA.
A DNA super-coil with 25 twists and 2 negative writhes has a LK of ________.
23.
Which type of topoisomerase changes a DNA's LK by breaking one of the strands, twisting it around the strand that is still in tact, and reattaching it? By how much will the LK change?
1.) Topoisomerase Type 1
2.) +/- 1
True or False?
Type 1 topoisomerase expends ATP, and adds twists to a double strand of DNA.
False.
Type 1 topoisomerase expends no energy, and always works towards a relaxed circle.
Which type of topoisomerase breaks DNA at both strands, passes a piece through the break, and reattaches the two strands? By how much does the LK change?
1.) Type 2
2.) +/- 2
What is the result to the double strand of DNA if a Type 2 topoisomerase is used?
Two twists will be added to the DNA.
Therefore, type 2 topoisomerase is able add strain.
