nucleic acid structure and function

Question 1

parts of a nucleotide

Answer 1

phosphate group

sugar

nitrogenous base

Question 2

nucleotides

nucleosides

Answer 2

have phosphates

do not have phosphates

Question 3

pKa of phosphate group

Answer 3

0-2 → explains why DNA and RNA are negatively charged

pH > pKa = deprotonated at phosphate

Question 4

base attaches to sugar through

Answer 4

a glycosidic bond

Question 5

OH at C-2’ =

H at C-2’ =

Answer 5

ribose

deoxyribose

Question 6

bonds through OH on C-3’ =

Answer 6

phosphodiester bond

Question 7

OH on C-5’ =

Answer 7

where phosphate group attaches

Question 8

what is responsble for the antiparallel double helix of consistent width

Answer 8

purines always base-pairing with pyrimidines

Question 9

direction of growth of RNA and DNA is always

Answer 9

5’ to 3’

Question 10

which helix structure is right handed

Answer 10

B and A

Question 11

which helix structure is left handed

Answer 11

Z

Question 12

which helix structure has the closest stacking of base-pairs

which has the furthest stacking of base-pairs

Answer 12

A

Z

Question 13

which helix structure has the tightest turns

which has the loosest turns

Answer 13

B

Z

Question 14

which helix stucture has the largest diameter

which has the smallest diameter

Answer 14

A

Z

Question 15

Describe the major groove of B form

Describe the minor groove of B form

Answer 15

wide, deep

narrow shallow

Question 16

describe the major groove of A form

describe the minor groove of A form

Answer 16

narrow, deep

wide, shallow

Question 17

describe the major groove of Z form

describe the minor groove of Z form

Answer 17

flat

narrow, deep

Question 18

which helix structure is perpendicular to helix axis

Answer 18

B

Question 19

sugar pucker of B form

Answer 19

C-2’ endo

Question 20

sugar pucker of A form

Answer 20

C3’ endo

Question 21

nitrogenous base orientation of B and A form helix

Answer 21

anti

Question 22

nitrogenous base orientation of Z form

Answer 22

syn (pur)

anti (pyr)

Question 23

constitutional isomers are

Answer 23

tautomers

Question 24

conformational isomers are

Answer 24

reversible rotations (e.g. sugar pucker, anti/syn)

Question 25

rotation around the glycosidic bond results in ____ vs ____ conformational isomers

Answer 25

syn vs anti

Question 26

____ DNA is the physiologically-relevant conformation

Answer 26

B

Question 27

____ helix structure is seen primarilly in RNA

Answer 27

A

Question 28

A, C, and Z DNA conformations can be

Answer 28

artificially induced

Question 29

DNA:

1. function
2. structure
3. sugar
4. sugar pucker
5. helix type
6. pyrimidines
7. purines

Answer 29

1. storage
2. 2 strands
3. deoxyribose
4. C2’ -endo
5. B
6. C, T
7. A, G

Question 30

RNA:

1. function
2. structure
3. sugar
4. sugar pucker
5. helix type
6. pyrimidines
7. purines

Answer 30

1. transport, catalysis, regulaiton
2. 1 strand
3. ribose
4. C3’ -endo
5. A
6. C, U
7. A, G

Question 31

non-traditional structures:

• hairpins and cruciforms
  
  • requires:
  • extruded from DNA due to:
  • ____ bind site (in RNA)
  • example: ____

Answer 31

• • a palindromic sequence (inverted repeat)
    
    • superhelical strain
    • ricin
    • tRNA

Question 32

non-traditional structure:

• triplexes
  
  • may or may not occur in ____
  • requries a ____ duplex
  • uses ____ hydrogen bonds
  • 3rd strand binds in ____ groove
  • stable in ____ pH

Answer 32

• • nature
    
    • homopurine-homopyrimidine
    • Hoogsteen
    • major
    • acidic

Question 33

non-traditional structures:

• quadruplexes
  
  • ____ only
  • occurs at ____ and some ____

Answer 33

• • guanines
    
    • telemeres and some promotors

Question 34

induced mutations (mutagens) can be caused by

Answer 34

• base analogs
• alkylating agents
• intercalating agents
• adduct-forming agents
• UV light
• ionizing radiation

Question 35

base analogs

Answer 35

molecules that have a very simliar structure to one of the 4 nitrogenous bases used in DNA

e.g. bromouracil (similiar to thymine and cytosine) can base pair with either A or G, depending on which tautomer is present

subsequent DNA replication has the potential to introduce mutations

Question 36

5-bromouracil (keto form) looks like ____ and pairs with ____

Answer 36

thymine adenine

Question 37

5-bromouracil (enol form) looks like ____ and pairs with ____

Answer 37

cytosine guanine

Question 38

alkylating agents

Answer 38

add alkyl group to guanine impacting its ability to hydrogen bond (now binds with thymine instead of cytosine)

e.g. mustard gasses add butyl (C2H5) groups

Question 39

intercalating agents

Answer 39

chemicals that can slide in between the rungs of the ladder (vanderwaals interactions)

Question 40

adducting-forming agents

Answer 40

intercalating agents that form covalent bonds with rungs of ladder

form covalent bonds upon activation with UV light

Question 41

UV light

Answer 41

forms T-T dimers

Question 42

ionizing radiation

Answer 42

beta, gamma, and x-rays causes electrons to be ejected from an atom, leaving behind a free radical

e.g. OH radical can attack guanine, forming 8-oxoG (syn isomer of 8-oxoG base pairs with A, subsequent DNA replication has the potetial to introduce mutations)