Test 1: Nucleic acid structure and structures

Question 1

Draw all five nucleic acids, number them, label major and minor groove

Answer 1

Check online

Question 2

Draw ribose.

Answer 2

Check online

Question 3

Define Nucleoside:

Answer 3

Purine or pyrimidine bound to a sugar

Remember (side), it is just the side, not the whole thing

Question 4

Define Nucleotide:

Answer 4

a phosphate ester of the nucleoside (phosphate added to the 5’ or 3’ position)

Question 5

Where does the phosphate attach in a nucleotide?

Answer 5

5’ carbon

Question 6

in dATP the d means what?

How does this differ from ATP?

Answer 6

Deoxy. The whole thing is deoxyadenosine triphosphate. Precursor to DNA

ATP is not deoxy, it is the precursor to RNA.

Question 7

Prime number aka 5’, dictates a location in what?

A non-primed number, aka 5, dictates a location in what?

Answer 7

In the ribose (the sugar)

In the base (purine or pyrimidine)

Question 8

DNA is synthesized in what direction?

Why?

Answer 8

5’ to 3’

Because the 3’ end has OH that a new nucleotide can attack. The free OH group is required

Question 9

What is necessary for DNA polymerase 1 to synthesize DNA.

Answer 9

dATP, dGTP, dCTP, dTTP
A 3’ free OH group
A template.

Question 10

What suffix indicates a a monophosphate nucleotide? Name the 4 monophosphate nucleotides used to synthesize DNA?

Answer 10

ylate

Deoxyadenylate, deoxyguanylate, deoxycytodylate, deoxythymadylate

Question 11

What is pApCpCpGpT?
Which end is 3’?
This can also be abbreviated further to what?

Answer 11

It is an abbreviation saying phosphate adenine phosphate etc…
The T/right side, it has no phosphate.
ACCGT (note, 3’ is still the right side)

Question 12

How to recognize a right handed verses left handed helix.

Answer 12

Point thumb down. If fingers follow the curvature of helix as it follows the thumb on right hand, it is right handed, and visa versa.

Question 13

Which helices are right handed? Which are left handed?

Answer 13

A, B dna (right) Z dna (left)

Question 14

Define pitch of a helix.
Which type of DNA has the smallest pitch?
Middle?
Which has the largest?

Answer 14

The distance covered
A DNA (2.8 nm)
B DNA (3.5 nm)
Z DNA (4.5 nm)

Question 15

Define number of residues per turn of a helix.
Which type of DNA has the least?
Middle?
Which has the most?

Answer 15

How many nucleotides make up a turn
B DNA (10)
A DNA (11)
Z DNA (12)

Question 16

Which type of DNA is most compact?
Middle?
Least?
Why?

Answer 16

A DNA ((10 / 2.8) * 11 = 39.2 residues in 10 nm)
B DNA ((10 / 3.5) * 10 = 28.6 residues in 10 nm)
Z DNA ((10 / 4.5) * 12 = 26.6 residues in 10 nm)
The lack of an ox

Question 17

Is A or B form DNA better for macromolecular interactions? Why?

Answer 17

B form. The A form’s deep groove is too deep for macromolecular binding.

Question 18

What DNA form is RNA in?

Why?

Answer 18

A form.
C2’ OH found in ribose causes an C3’ pucker, which makes B-form less doable. A form has less residues per turn because of this.

Question 19

Can DNA be A form and B form? Which is it normally?

Answer 19

Yes it can be.

B form.

Question 20

What is endo pucker?

Answer 20

Movement of carbon out of the plane of a sugar ring towards the methyl carbon in the ring.

Question 21

Do the higher or lower labelled atom numbers face the major groove?
The minor?
Which side is the phosphate backbone on?

Answer 21

Higher
Lower
The minor groove side (check this online to confirm)

Question 22

Unusual U base pairings occur almost exclusively in RNA or DNA in vivo?

Answer 22

RNA

Question 23

Triple helix formation:

Answer 23

When helix consists of a long strand of purines bound to a long strand of pyrimidines a third strand of nucleic acids can fill the major groove, binding with the purines.

Question 24

Draw, and note which require protonation:
C+ -G:C
T-A:T
A-A:T
G-G:C
T-A:T

Answer 24

C+ -G:C, the guanine requires protonation

Question 25

In ATP (or any other nucleotide), the phosphate closest to carbon is called what? Middle is called what? Far phosphate is called what?

Answer 25

alpha
beta
gamma

Question 26

What does polymerase do?

Answer 26

It activates 3’ hydroxyl to make a nucleophilic attack on the alpha phosphate

Question 27

Base stacking occurs even in the absence of base ______

Why does this occur?

Answer 27

Pairing
(ssDNA will stack into a single stranded DNA)
Allows london dispersion forces

Question 28

What range does dispersion forces work in?

Answer 28

2.5 - 3 angstrom. Which is why 2.5 - 3 angstroms is the distance between bases

Question 29

Is the enzymatic specificity for right handed and left handed helices?

Answer 29

Yes.

There is enzymatic specificity for right and left handed helices

Question 30

DMS (dimethyl sulfate):

Answer 30

methylates N3-adenine in minor groove

Question 31

DMS N7-guanine:
Dam methylase:
SSS methylase:

Answer 31

Note: (likely wouldn’t work in a triple helix)
Major (N7 guanine)
Major (N6 adenine of GATCs)
Major (C5 cytodine of CpGs

Question 32

How are A-T and G-C connected?

Answer 32

New A-T and G-C where the same length. Backbone positions determine where the helices will be (which is why U-G binding and reverse hoogsteen is so unusual)
(which is why single stranded RNA can bind in more unusual conformations)

Question 33

How much will free nucleotides absorb?

Answer 33

The most light!
ds absorbs the least,
So if DNA or RNA is broken down we will see an increase in UV in the 260 wavelength spectrum.

Question 34

What can you use the ratio of the 260 to 280 uv absorbance of nucleic acids for?

Answer 34

260 should be much larger than 280. If 280 is high it means you are having aromatic protein absorption of UV, which is contamination

Question 35

Compounds which intercalate in DNA are mutagens

Answer 35

So where freakin gloves

Question 36

Ligase will use what as its energy source?

Answer 36

ATP

Question 37

ATP is what by convention?

Answer 37

rATP

Question 38

He may ask what other high energy molecules could be used in a ligase reaction:

Answer 38

Look up some others which can be used

Question 39

Opposite of a phosphatase?

Answer 39

A kinase!

Question 40

How can you check to see if DNA is circular?

Answer 40

Endonucleases will cut it, but exonuclease will not

Question 41

S1 nuclease will cut _____ but not _____

Answer 41

Look it up

Question 42

RNAse A can be boiled and it will refold

Answer 42

This is unique can be used for purification

Question 43

Restriction enzymes

Answer 43

Enzymes that were discovered genetically to restrict

Question 44

Methylation is typically the system used to modify DNA so that it is not destroyed by restriction enzymes

Answer 44

Restriction enzymes will have a recognition site to test whether

Question 45

If a segment of DNA is palindromic it is likely to be a restriction enzyme. Why?

Answer 45

Because restriction enzymes are dimers and will often have mirror recognition sites

Question 46

How high of pH is necessary for RNA scission?

Answer 46

10 is worrisome. 12 is very bad.

Question 47

Can ethidium bromide and other mechanisms which fluoresce while intercalated bind to ssDNA?

Answer 47

Yes, ssDNA and RNA still stack

However, light produced will be weaker

Question 48

The amount of UV light absorbed is inversely proportional to what?

Answer 48

Stability of the nucleotides. (ssDNA and ssRNA less stable then dsDNA and dsRNA, free nucleotides are the least stable and absorb the most)

Question 49

Is ethidium bromide specific for RNA or DNA?

Answer 49

It is not specific, but it does far prefer DNA. (might be preference for double stranded nucleotides, and RNA has less dsRNA)