2. Nucleic Acids

Question 1

What are the components of a nucleotide

Answer 1

• sugar
• phosphate
• nitrogen bases

Question 2

Draw and label the donor and accpetor in the nitrogen bases

Question 3

Draw Uracil and compare it to thymine

Question 4

where are the nitrogenbases attached to the sugar?

Answer 4

• N1 in pyrimidines
• N9 in purines

Question 5

How to differinatiate DNA and RNA by the sugar base

Answer 5

• OH group on C2

Question 6

Draw a sugar and label the carbons

label chirality

Question 7

How to name nucelosides (base + sugar)

Answer 7

1. pruines uses osine as a suffix
2. pyrimidines become idine as a suffix

Question 8

label the differnces of phosphodiester, phosphoester and phosphanhyride bonds within a dinucleotide structure

Question 9

What is the overall net charge of the nucleotide, is the back bone polar or non-polar? and compare the backbone of RNA and DNA, which is more polar?

Answer 9

• net charger = more negative largely consistent within the strucutre (cause of phosphate groups)
• sugar is polar and the phosphate is more polar
• backbone in RNA vs DNA = RNA is more polar

Question 10

explain spontanous, alkaline hydrolysis of phosphodiester bonds in RNA

Answer 10

• 2 products are fromed:
• a free nucleotide
• and a nucleotide with phosphate group attachment
• in DNA the absense of the OH group prevents this reaction, making it more stable than RNA in alkaline conditions

Question 11

Explain the deamination of cytosine to uracil

Answer 11

• spontaneous (uncatalyzed) reaction
• uncorrected in DNA can cause a mutation
• DNA repair mechanisma will reocgnize U and remove it

Question 12

what is a dideoxynucleotide

Question 13

Explain the properties of the bases

Answer 13

• heterocyclic
• aromatic with elctron delocalization
• basically planar
• poorly soluble
• largely hydrophobic with some polar groups (abilit to form H-bonds)

Question 14

Explain absorbance

how to measure pure DNA, what is used to measure concentration

Answer 14

• A260nm/280nm = 1.95 for pure DNA
• contamination lowers the ratio
• protein abs maxi at 280nm
• DNA abs is about 50% at 280 nm
• A260nm is used to meaure the concentration of nucleic acids in solution

Question 15

Draw the hydrogen bonding between the nucleotides in DNA

Question 16

What is DNA (B-form) and describe the characteristics

Answer 16

• stablized by base stacking interactions and H-bond but base stacking is the primary force
• base stacking: primarily van der wasl forces and hydrophobic forces
• has an overall right handed twist
• ~10bp per turn

Question 17

Explain the denaturation of DNA

Answer 17

• separation of the two paried stranded ds -> ss
• disruption of non-covalent forces (H-bonds and base stacking)
• essential for some cellular processes
• changes in absorption properties; increase at 260nm as the strands separate

Question 18

What does DNA melting (denaturating) look like on a graph

Label Tm

Answer 18

• Absorbance increases as temp increases
• Tm = midpoint of melting with comprise of dsDNA and ssDNA 50;50

Question 19

Define hyperchromicity and hypochromicity

Answer 19

• hyper = is a relatively high abosrbance
• hypo = is a low absorbance

Question 20

Explain DNA zippering

Answer 20

• theres a fast zippering
• slow rate depends on the complexity of the necleic acid = nucleatio; eg. its like the slow step of alinging the zipper before it zips properly

Question 21

Explain the relationship b/w Tm and the GC content of a DNA

Answer 21

• as GC content increases so does Tm
• GC bairs have stronger base stackng interactions than AT pairs

Question 22

What can affect Tm?

Answer 22

• changing PH: affects protonation state of DNA; but a bell curve
• changing slat concentrations; increase causes more stabilization as there are less repulsions on the phosphate backbone; increase salt -> increase Tm; decrease salth -> decrease in Tm
• Tm of hybridization; more identical = an increase in Tm

Question 23

What is the differnce in DNA and RNA structures

define : inter and intrastrand base pairing

Answer 23

• RNA has intrastrand base pairing; DNA has interstrand
• strucutre of RNA is much more dependent on nucleotide sequecence thn double-stranded DNA