DNA and RNA Structure

Question 1

Nucleotides

Answer 1

Monomers of nucleic acid polymers

Question 2

dNTP

Answer 2

Deoxynucleoside triphosphate

Question 3

Difference between purines and pyrimidines

Answer 3

Purines have 2 rings, whereas pyridimines only have 1

Question 4

Turning uracil into thymine

Answer 4

Methyltransferase adds methyl group to uracil to make it into thymine

Question 5

Standard form and rare form of pyrimidines

Answer 5

Standard: amino
Rare: imino

Question 6

Standard form and rare form of purines

Answer 6

Standard: keto
Rare: enol

Question 7

Tautomers

Answer 7

Molecules with same molecular formulas, but different bonding/arrangement of atoms
Caused by spontaneous proton shift

Question 8

Base pairing in standard vs. rare forms

Answer 8

Standard forms properly base pair, but rare forms don’t

Base pairing between rare forms can cause mutations

Question 9

Nucleoside

Answer 9

Nitrogenous base and ribose sugar (no phosphate)

Question 10

Chargraff’s rule

Answer 10

1:1 ratio of A:T and G:C

Question 11

Periodicity of DNA double helix

Answer 11

10 bp/ 360 degree turn

Question 12

Space between base pairs in double helix

Answer 12

0.34 nm

Question 13

Charge of double helix

Answer 13

Negatively charged: phosphate groups on outside

Question 14

Structure of double helix

Answer 14

Phosphate groups on outside (covalently bound to each other)
Nitrogenous bases on inside (H-bonded to each other)
Bases are usually on parallel planes
2 strands run antiparallel to one another

Question 15

Things that cover DNA

Answer 15

Water and proteins

Question 16

Major and minor grooves

Answer 16

Result of glycosidic bonds
Major groove: larger gap than minor groove
Proteins usually bind to major groove: more stuff to recognize

Question 17

Propellor twist

Answer 17

Slight twist in base pair ladder (bases aren’t exactly 180 degrees apart)
Results from stress on DNA from protein binding

Question 18

3 forms of DNA

Answer 18

B-DNA
Z-DNA
A-DNA

Question 19

B-DNA

Answer 19

Form of DNA most frequently found in cells

Watson and Crick’s model

Question 20

Z-DNA

Answer 20

Left-handed form of DNA

Question 21

A-DNA

Answer 21

More compact form of DNA
11 bp/turn
Results from reduced humidity

Question 22

Melting point of DNA depends on…

Answer 22

G:C content

Length of dsDNA

Question 23

Using a spectrophotometer to measure denaturation of DNA

Answer 23

dsDNA has a lower absorbance than ssDNA

Question 24

Hyperchromicity

Answer 24

Increase in absorbance of a material

Occurs when dsDNA is denatured

Question 25

cccDNA

Answer 25

Covalently closed, circular DNA

Found in prokaryotes

Question 26

Positive supercoiling

Answer 26

Adding more twists to DNA

Question 27

Negative supercoiling

Answer 27

Untwisting DNA, which actually adds twists downfield of untwisted area

Question 28

Form of supercoiling that cccDNA undergoes

Answer 28

Negative supercoiling (easier to break apart)

Question 29

Linking number

Answer 29

Made up of twist and writhe

Lk=Tw+Wr

Question 30

Supercoiling formula

Answer 30

delta Lk= Lk- Lk0
Lk0=relaxed form
delta Lk > 0: positive supercoiling
delta Lk <0: negative supercoiling

Question 31

Twist

Answer 31

of times 1 strand passes over the other; # of helical turns

Question 32

Writhe

Answer 32

Double helix crossing over itself

Question 33

Gel electrophoresis of different forms of DNA

Answer 33

Top of gel -> bottom of gel: catenated, relaxed, linear, supercoiled, even more supercoiled

Question 34

Topoisomerases

Answer 34

Relax DNA
Decatenate 2 linked DNA molecules
Can be used to untie knotted DNA

Question 35

General properties of RNA

Answer 35

Rotational freedom
Not linear- has secondary and tertiary structures
Uracil rather than thymine
Can have both complementary and non-complementary base pairing

Question 36

Examples of RNA secondary structure

Answer 36

Bulge (extra nucleotide that isn’t base paired)
Internal loop (large bulge with several nucleotides on both sides that aren’t base paired)
Hairpin (Area with base pairing followed by area without base pairing; looks like light bulb)
Loop (bulges on both sides of base paired area)
Pseudoknot (partial helical structure)

Question 37

RNA structure is important for…

Answer 37

Function

Recognition by proteins

Question 38

Base triples

Answer 38

3 nucleotides bound to each other

Can occur in RNA

Question 39

Ribozyme

Answer 39

Catalytically active RNA