Module 03 - Section 01

Question 1

What is an oligonucleotide?

Answer 1

Short nucleic acid of 50 or fewer nucleotides

Question 2

What is a polynucleotide?

Answer 2

Longer nucleic acid of 50 or more nucleotides

Question 3

How is the self-assembly of of Nucleic Acids coordinated?

Answer 3

(1) Weak forces; Watson-Crick base-pairing and base stacking

(2) based on how the atoms are arranged in space

Question 4

What is the 3D helical structure of DNA the result of?

Answer 4

Base-pairing and the most energetically favorable conformation

Question 5

What is a heterocyclic base?

Answer 5

A cyclic compound with one or more ring structures that contain atoms of at least two different elements

Question 6

What are the 3 components of nucleotide?

Answer 6

(1) Nitrogenous base aka heterocyclic base
(2) Pentose (5-carbon sugar)
(3) Phosphate groupe (at least one)

Question 7

What are the 4 heterocyclic bases of DNA? (and their category)

Answer 7

Purine: Adenosine (A), Guanine (G)
Pyrimidine: Cytosine (C), Thymine (T)

Question 8

Why are the heterocyclic compounds called bases?

Answer 8

Free purines and pyrimidines are weakly basic compounds.

Question 9

What is Chargaff’s Rule?

Answer 9

A+G=T+C

Question 10

True or false: A=T

Answer 10

true

Question 11

True or false: G=C

Answer 11

true

Question 12

How many hydrogen bonds do G and C share?

Answer 12

3

Question 13

How many hydrogen bonds do A & T share?

Answer 13

2

Question 14

Which one is stronger A-T or G-C? Why?

Answer 14

G-C because it has 3 hydrogen bonds vs 2 for A-T

Question 15

Is the sugar phosphate backbone; 
A- Highly positively charged
B- positively charged
C- Negatively charged
D- Highly negatively charged

Answer 15

D

Question 16

Why is the DNA helix antiparallel?

Answer 16

antiparallel orientation is more energetically favorable due to the geometry of the component bases

Question 17

What are the two periodicities of the DNA double-helix?

Answer 17

(1) Primary: vertically started bases inside the double helix are 3.4 A apart
(2) Secondary: repeat distance of about 34A is accounted for by the presence of about 10.5 base pairs in each complete turn fo the double helix

Question 18

What are the 2 key interactions in the stabilization of the duplex?

Answer 18

Hydrophobic Stacking

Base pairing

Question 19

What is hydrophobic stacking?

Answer 19

Arises because the bases are hydrophobic (insoluble in water) - Bases align such that two or more are poisition with the planes of their rings in parallel, like a stack of coins - van der waals forces also play a role - energetically favorable because it minimizes contact of the bases with water

Question 20

What is Base pairing?

Answer 20

Extensive network of weak bonds within the DNA and between base pairs. Include; van der Waals interactions, hydrogen bonds, electrostatic interactions - arranged so that one cannot break without also breaking many others. - 10 bps or more are quite stable

Question 21

What are the 3 main functions of DNA?

Answer 21

(1) Long-term storage of genetic information
(2) Acting as a template for DNA replication
(3) Coding for proteins

Question 22

What are the 2 main properties of DNA that makes is a good long-term storage of genetic information

Answer 22

(1) Strand complementarity, hydrogen bonding between bases on opposing strands is the most significant property of the double helix - specific base-pairing allows for exact copies to be made
(2) Replication Fidelity, structure of the double helix allows for the 2 strands to be separated and then each original strand could be used to synthesize a complementary strand

Question 23

What are the 4 internal forces affecting DNA stability?

Answer 23

(1) Hydrophobic interaction
(2) Hydrogen bonds
(3) Van der Waals forces
(4) ionic interactions

Question 24

How do hydrophobic interactions affect DNA stability?

Answer 24

(1) stabilizes base pairing
(2) hydrophobic bases face the interior of the helix, away from water
(3) sugar-phosphate backbone is hydrophilic and faces exterior to interact with water

Question 25

How do Van der Waals forces affect DNA stability?

Answer 25

Stacked bases interact through ring structures

Question 26

How do hydrogen bonds affect DNA stability?

Answer 26

(1) occurs between paired bases

2) GC bonds are more stable than AT (3 HB vs 2

Question 27

How do ionic interactions affect DNA stability?

Answer 27

(1) Negative charge of backbone phosphates are neutralized by interactions with cations
(2) Na+ and Mg+ commonly interact with the backbone to neutralize electrostatic repulsion between strands

Question 28

What are the 4 external factors affecting DNA stability?

Answer 28

(1) Temperature
(2) Salt
(3) Proteins
(4) Organic solvents

Question 29

How does Temperature affect DNA stability?

Answer 29

Heating DNA above its melting temperature causes it to unwind into single-stranded form, destabilizing DNA

Question 30

How does salt affect DNA stability?

Answer 30

Increase in salt concentration causes an increase in duplex stability, bc sodium ions interact with the negatively charged DNA backbone and stabilize it

Question 31

How do proteins affect DNA stability

Answer 31

DNA binding proteins are involved in the compaction of genomes and contribute to both the global and local structure of DNA

Question 32

How do organic solvents affect DNA stability?

Answer 32

Carbon based solvents destabilize DNA Helix by disrupting hydrogen bonds and solvating bases

Question 33

What kind of interactions can the sugar-phosphate backbone have?

Answer 33

(1) Hydrophilic, therefore hydroxyl groups of the sugar residues form hydrogen bonds with water
(2) Phosphate groups (pKa = 2) are completely ionized and negatively charge at pH=7. Charges are neutralized by ionic interaction with positive charges on proteins, metal ions, or short linear organic molecules called polyamines