Chapter 8 Definitions/Concepts

Question 1

Nucleotide

Answer 1

Nitrogenous Base
Pentose Sugar
Phosphate Group

Question 2

Nucleoside

Answer 2

Nitrogenous Base
Pentose Sugar
NO Phosphate

Question 3

Nitrogenous Bases

Answer 3

Purines

Pyrimidines

Question 4

Purines

Answer 4

Adenine and Guanine

Question 5

Pyrimidines

Answer 5

Cytosine, Thymine and Uracil.

Question 6

Minor Nitrogenous Bases

Answer 6

Ribose, found in DNA subjected to oxidative damage.

Question 7

Pentose Sugars

Answer 7

Found in beta Furanose form.

Question 8

Ribose Conformation

Answer 8

Place C1’ and C4’ in the same plane with the nitrogen up. Up is endo, down is exo.

Question 9

Phosphodiester Bond

Answer 9

Forms 3’-5’ bond between nucleotides.

Question 10

RNA Alkaline Hydrolysis

Answer 10

RNA is susceptible to non-enzymatic hydrolysis in alkaline conditions because of the 2’-hydroxyl group.

Question 11

Nucleotide Base Properties (6)

Answer 11

1. Weakly basic.
2. Highly Conjugated/ Planar
3. Absorb UV light around 260nm.
4. Free bases are very hydrophobic and insoluble at physiological pH.
5. Bases stack antiparallel to minimized hydrophobic surfaces due to pi interactions.
6. Ring nitrogens, carbonyl groups, and exocyclic amino groups form hydrogen bonds with other bases.

Question 12

Watson and Crick Basepairs

Answer 12

G-C has 3 hydrogen bonds

A-T has 2 hydrogen bonds

Question 13

Miescher

Answer 13

First isolated DNA in 1868. He originally called it nuclein. It consisted of an acidic portion (DNA) and basic portion (protein).

Question 14

Avery, McLeod and McCarthy

Answer 14

1944 extracted DNA from a virulent strain of strep pneumonia and transformed a non-virulent strain into a virulent strain.

Question 15

Hershey and Chase

Answer 15

1952 radioactively labeled P viral DNA that enters a host cell and provides genetic information for viral replication whereas S viral protein doesn’t enter the cell.

Question 16

Erwin Chargaff

Answer 16

1940’s established the base composition rules.

• varies across species
• constant across tissues
• constant through age
• shows amounts of A=T and C=G

Question 17

Furberg

Answer 17

1951 first crystal structure of cytidine nucleoside. Used this info to start building structure because it gave bond angles.

Question 18

Dekker, Michelson and Todd

Answer 18

Early 1950’s established the 3’-5’ phosphodiester linkage

Question 19

Gulland

Answer 19

Electromagnetic titration found hydrogen bond linkage in 1947.

Question 20

Astbury

Answer 20

Fiber x-ray diffraction hinted at base stacking in 1947.

Question 21

Rosalind Franklin and Maurice Wilkins

Answer 21

Analyzed DNA fibers with x-ray diffraction and were able to interpret results in 1953.

• Franklin found 2 strands
• Phosphate groups on the outside
• 2 forms of DNA
• 3.4A and 34A

Question 22

Watson and Crick

Answer 22

Put the pieces from Franklin and Wilkins together in 1953. They found base pairing with the correct tautomer, 2 anti-parallel strands, base paired and helical with 10 nucleotides per turn.

Question 23

1962 Nobel Prize

Answer 23

Wilkins, Perutz, Crick, Steinbeck, Watson and Kendrew.

Question 24

Characteristics Causing Conformational Variability

Answer 24

1. Ribose Conformation
2. Backbone Bond Rotations (5 bonds)
3. Glycosidic Bond Rotation (between sugar and anything else)

Question 25

DNA Conformational Variability

Answer 25

A-Form B-Form Z-Form

Question 26

A-Form

Answer 26

Function of binding protein - right handed - shorter and fatter turns - high bp tilt - C3' endo

Question 27

B-Form

Answer 27

Most common - right handed - tall and thin turns - low bp tilt - C2' endo

Question 28

Z-Form

Answer 28

- left handed - smallest diameter - C2' endo and C3' endo

Question 29

Complementarity

Answer 29

T-A and C-G are found opposite each other on the helix.

Question 30

Palindrome Sequence

Answer 30

Inverted repeat over both strands.

Question 31

Mirror Repeat

Answer 31

Inverted repeat in one strand.

Question 32

Unusual Patterns

Answer 32

Hairpin and Cruciform | Can be caused by supercoiling and can regulate gene transcription.

Question 33

RNA

Answer 33

The product of transcription of DNA into a single strand. Forms right handed helix with base stacking. Has self-complementary sequence to form complex structures. G=U.

Question 34

RNA Interactions

Answer 34

Complementary sequences can form RNA in A-Form, breaks in this form can make mismatched bases to form bulges and loops. Hairpins are the most common structure. Non-Watson and Crick hydrogen bonding is common with the 2' hydroxyl group of ribose.

Question 35

Denaturing double-helical DNA/RNA

Answer 35

Heat and pH can denature globular proteins. Hydrogen bonds between basepairs are disrupted causing unwinding.

Question 36

Renaturation

Answer 36

Annealing. Structure is reformed when conditions are restored. Dependent on GC vs AT content.

Question 37

Hypochromic Effect

Answer 37

When DNA/RNA stack within the double-helical conformation, a decrease in the absorption of UV light compared to free nucleotides, called a hypochromic effect.

Question 38

Hyperchromic Effect

Answer 38

Occurs when DNA/RNA is denatured, exposing more of the free nucleotides, increasing UV absorption.

Question 39

Deamination

Answer 39

Nucleotides with exocyclic amino groups under go this. Producing mutations in structure of the nucleotide and potentially the nucleic acid. This happens everyday, DNA falls apart.

Question 40

Sanger Method

Answer 40

Method used to sequence DNA by polymerization.

Question 41

Energy in Nucleotides

Answer 41

Can give off a lot of energy. Coupled with positive free energy reactions to shift product formation to favor. Energy comes from anhydride bonds.

Question 42

Roles of Nucleotides

Answer 42

Coenzymes used in transfer of acyl groups, hydride groups or electrons. Can also serves as regulatory or messenger molecules.