nucleic acid structure and function Flashcards
parts of a nucleotide
phosphate group
sugar
nitrogenous base
nucleotides
nucleosides
have phosphates
do not have phosphates
pKa of phosphate group
0-2 → explains why DNA and RNA are negatively charged
pH > pKa = deprotonated at phosphate
base attaches to sugar through
a glycosidic bond
OH at C-2’ =
H at C-2’ =
ribose
deoxyribose
bonds through OH on C-3’ =
phosphodiester bond
OH on C-5’ =
where phosphate group attaches
what is responsble for the antiparallel double helix of consistent width
purines always base-pairing with pyrimidines
direction of growth of RNA and DNA is always
5’ to 3’
which helix structure is right handed
B and A
which helix structure is left handed
Z
which helix structure has the closest stacking of base-pairs
which has the furthest stacking of base-pairs
A
Z
which helix structure has the tightest turns
which has the loosest turns
B
Z
which helix stucture has the largest diameter
which has the smallest diameter
A
Z
Describe the major groove of B form
Describe the minor groove of B form
wide, deep
narrow shallow
describe the major groove of A form
describe the minor groove of A form
narrow, deep
wide, shallow
describe the major groove of Z form
describe the minor groove of Z form
flat
narrow, deep
which helix structure is perpendicular to helix axis
B
sugar pucker of B form
C-2’ endo
sugar pucker of A form
C3’ endo
nitrogenous base orientation of B and A form helix
anti
nitrogenous base orientation of Z form
syn (pur)
anti (pyr)
constitutional isomers are
tautomers
conformational isomers are
reversible rotations (e.g. sugar pucker, anti/syn)
rotation around the glycosidic bond results in ____ vs ____ conformational isomers
syn vs anti
____ DNA is the physiologically-relevant conformation
B
____ helix structure is seen primarilly in RNA
A
A, C, and Z DNA conformations can be
artificially induced
DNA:
- function
- structure
- sugar
- sugar pucker
- helix type
- pyrimidines
- purines
- storage
- 2 strands
- deoxyribose
- C2’ -endo
- B
- C, T
- A, G
RNA:
- function
- structure
- sugar
- sugar pucker
- helix type
- pyrimidines
- purines
- transport, catalysis, regulaiton
- 1 strand
- ribose
- C3’ -endo
- A
- C, U
- A, G
non-traditional structures:
- hairpins and cruciforms
- requires:
- extruded from DNA due to:
- ____ bind site (in RNA)
- example: ____
- a palindromic sequence (inverted repeat)
- superhelical strain
- ricin
- tRNA
- a palindromic sequence (inverted repeat)
non-traditional structure:
- triplexes
- may or may not occur in ____
- requries a ____ duplex
- uses ____ hydrogen bonds
- 3rd strand binds in ____ groove
- stable in ____ pH
- nature
- homopurine-homopyrimidine
- Hoogsteen
- major
- acidic
- nature
non-traditional structures:
- quadruplexes
- ____ only
- occurs at ____ and some ____
- guanines
- telemeres and some promotors
- guanines
induced mutations (mutagens) can be caused by
- base analogs
- alkylating agents
- intercalating agents
- adduct-forming agents
- UV light
- ionizing radiation
base analogs
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
5-bromouracil (keto form) looks like ____ and pairs with ____
thymine adenine
5-bromouracil (enol form) looks like ____ and pairs with ____
cytosine guanine
alkylating agents
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
intercalating agents
chemicals that can slide in between the rungs of the ladder (vanderwaals interactions)
adducting-forming agents
intercalating agents that form covalent bonds with rungs of ladder
form covalent bonds upon activation with UV light
UV light
forms T-T dimers
ionizing radiation
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)
