Biochem Exam 2

DNA is the

genetic molecule

nucleotides are comprised of

a base, (deoxy)ribose (sugar) and PO4 (phosphate)

in nucleotides, sugar-phosphodiester forms a polynucleotide ______

backbone

nucleotides can be _____ stranded or _____ stranded

single, multi

base stacking in nucleotides

stabilizes polynucleotide structures

purine and pyrimidine bases pair via

hydrogen bonding

base conformation affects ________ between bases

hydrogen bonding

________ affects nucleic acid tertiary structure

sugar pucker

DNA structure

double stranded in cells

2 stands form an anti-parallel, right handed helix

RNA structure

single stranded in cells

widely variable secondary structures

multi-functional molecule

nucleotide structure is essential to

DNA based activities

ex: genome replication, gene expression

phosphodiester bonds link nucleotides in

the polynucleotide backbone

glycosidic bonds link the base to the

ribose ring

hydrogen bonds form between

bases

5'=

the 5' carbon of a nucleotide

3'=

the 3' hydroxyl of a nucleotide

sugar pucker determines

the distances between phosphates in the phosphodiester backbone

the conformation of the base (syn vs anti) determines

how nucleotide bases interact

nucleotides are added in a

5' to 3' manner

hydroxyl initiates

nucleophilic attack

nucleic acids are polymers built from

nucleotides

two base types

purine and pyrimidine

Purine structure

shorter word=bigger structure

pyrimidine structure

longer word=shorter structure

The purine bases are

Adenine and Guanine

The pyrimidine bases are

cytosine, thymine, uracil

Adenine

Guanine

Cytosine

Thymine (DNA)

Uracil (RNA)

The presence or absence of the _______ is the defining difference between RNA and DNA

2' OH

N-glycosidic linkage

the connection between the base and the sugar occurs between the 1' position on the sugar and a nitrogen on the base

nucleoside

base + sugar

DNA uses

A, T, C, G

RNA uses

A, U, C, G

nucleotides are joined together through

phosphodiester bonds

the nucleic acid polymer grows in the

5' to 3' direction

-nucleic acids will always be added on the 3' end

Core mechanism of joining nucleotides together

1: base activation of 3' OH

2: nucleophilic attack of 3' OH on the alpha phosphate of a nucleoside triphosphate

3: pyrophosphate acts as a leaving group to drive the rxn forward

nucleotides can interact through

complementary base pairing

Watson-Crick-Franklin Base Pairs

In watson-crick-franklin, adenine forms ______ with thymine

2 H bonds

In watson-crick-franklin, guanine forms ______ with cytosine

3 H bonds

A/T and C/G base pairing interactions are completely

orthogonal

-they will not pair with something that isnt their match

B-form dna double helix

right handed dna helix, 2 antiparallel strands, held together via hydrogen bonding in A-T and C-G base pairs

*****asymmetrical

Major groove (in b-form DNA) is __________

wide and deep

minor groove (in b-form DNA)

shallow and narrow

proteins can bind to dsDNA through the ________ in a sequence specific manner

major groove

C3'-endo

position 3 is up

-RNA

-tighter

C2'-endo

position 2 is up

-DNA

-looser

the ____ conformation of a nucleotide is more energetically favorable

anti

Only _________ nucleotides can adopt the syn conformation.

purine

(A and G)

traditional watson-crick-franklin base pairs are

anti/anti

Hoogsteen base pairs

less common than watson-crick

occurs when one base is in the syn conformation

allows 3-4 strands to be present

found in damaged DNA

single stranded nucleic acid can

fold to form a secondary strcuture

genome

all of an organism's genetic material

double stranded dna=

2 stands annealed together

separation of 2 dna strands requires

hydrogen bonds to break

A/T base pairs are ____ to break than C/G base pairs

easier

2 H bonds vs 3 H bonds

Topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

In eukaryotes, DNA is further packaged by wrapping the DNA around proteins called ______ to form _______

histones, nucleosomes

nucleosomes are further compacted into _______ in _______ chromosomes

chromatin, linear

chromatin is good for

storage

acetylation of histones makes DNA

more accesible (euchromatin)

methylation of histones makes DNA

less accessible (heterochromatin)

3' OH attacks

5' triphosphate

why is the genome (the principal storage) DNA and not RNA?

RNA is more susceptible for destruction

The 2' OH can lead to breakdown of the chain

What sets the relative stability of the two strands being annealed together versus separated as free strands?

the annealed form is good for long term storage but also need to separate the strands to be able to make use of base-pairing for replication, transcription etc

which base pairs form stronger interactions?

C/G

3 hydrogen bonds

closer together in the alphabet, so stronger bond

Tm=

temperature at which the helix is half double stranded and half single stranded

-50% denatured

stable helix=

high Tm

unstable helix

low Tm

more _____ base pairs makes it harder to separate bonds

C/G

-bc they have more hydrogen bonds per pair

melting

process of unwinding strands of DNA

topology

number of cross-overs in the material

topology of a DNA fragment is described by the

Linking number (Lk)

Lk=Tw+Wr

Linking number=twist+writhe

DNA in the B-form configuration has an ______ to it

intrinsic twist

DNA being in a B-form geometry is a very

energetically favorable state

if the change in Lk=0, then

the DNA is relaxed

if the change in Lk

underwound, negative-supercoiling

if the change in Lk>0, the DNA is _________ and _________ will result

overwound, positive-supercoiling

supercoiled DNA is more ______ than relaxed DNA

compact

if you were to cut the dna structure, add or remove some twist you could change the

linking number

what can change the structure and add/remove some twist?

topoisomerase

as a general rule, most DNA inside the cell is

negatively supercoiled

topoisomerases are also needed to resolve _______ that develops when the genome is locally unwound for DNA replication or transcription

supercoiling

the linking number cannot be changed by

deformation alone

topoisomerases play important roles in DNA _______, and dealing with disruptive structures that form during _______ and ________

compaction, replication, transcription

dna wraps around _____ proteins to form nucleosomes

histone

histone modification impacts

chromatin compaction

euchromatin vs heterochromatin

Euchromatin - available for transcription;

Heterochromatin - not available for transcription

packaging DNA into chromatin makes it

inaccessible

histone acetylation makes DNA

more accessible

histone methylation makes DNA

less accessible

topological constraints on dna cause it to ______ if you try to unwind or overwind it

supercoil

base activation of the 3' OH leads to

nucleophilic attack on a nucleoside triphosphate

DNA polymerases are the enzymes that catalyze

DNA synthesis

DNA polymerases require a

primer to extend off

DNA synthesis requires 3' OH in order to add the next

dNTP