How do nucleotides incorporate into nucleic acids?

DNA and RNA

What are some high-energy molecules?

- NTP's - Electron Carriers

What is a nucleotide comprised of?

- Phosphate - Nitrogen containing aromatic base - Sugar

What are the pyrimidines?

- Cytosine - Thymine

What are the purines?

- Guanine - Adenine

LP's in resonance (can/cannot) accept h bonds?

Cannot

Thymine is in _____, Uracil is in _______

DNA, RNA

What is the structural difference between thymine and uracil?

Thymine has a methyl group at C5

What is a nucleoside comprised of?

Sugar and a base

Where do pyrimidines link to sugars from? Purines?

N1 for pyr N9 for pur

Which C's in ribonucleotides are chiral? Achiral?

C1-C4 are chiral C2 in deoxyribonucleotides are achiral

Describe purine naming

-ine becomes -osine

Describe pyrimidine naming

ends in -idine

Nucleic acids ar epolymers of nucleotides linked by ______ bonds

3`->5` phosphodiester bonds

What do phosphoesters link?

Carbons to phosphate groups

What do phosphodiesters link?

Link two different C atoms to one P group

What do phosphoanhydrides link?

Link 2 phosphates to eachother

How is a "sense of direction" created?

Phosphodiester bonds in nucleic acids create asymmetric structures

Nucleotide sequences are written from ______

5` to 3`

What is the primary structure for a nucleic acid?

Sequence of nucleotide residues

Phosphates attached to single C/OH groups are named _____ prefixes

Mono, di, tri

Phosphates attached to multiple C/OH groups are _______ prefixes

Bis, Tris

What prevents the hydrolysis of phosphodiester bonds in DNA?

Absence of a 2` OH makes it more stable than RNA

What happens to RNA in the hydrolysis of phosphodiester bonds in RNA?

Product mixture w/ OH on 2` or 3`

Cytosine __________ to form uracil

Deaminates

Is deamination spontaneous?

- Spontaneous (uncatalyzed)

Are bases soluble in water? What interactions do they experience?

- Poorly soluble - Hydrophobic w/ some polar groups

T/F: The sugar phosphate backbone is nonpolar

Why do bases absorb light?

Because of e- delocalization

What is the 260/280 absorbance ratio for pure DNA

1.95 2:1

What does A260 tell you?

Concentration of nucleic acids (DNA) in a solution

Each DNA chain is connected to the other through ____________ bonds between bases

Hydrogen - Noncovalent

What does the erwin chargaff rules say about bases?

A = T G = C Purines = Pyrimidines

Are H bonds a polar interaction?

Yes

Are H bonds weaker or stronger than covalent bonds?

Weaker

What allows for H bonding in DNA between bases?

Amino and Carbonyl group

What is B form DNA stabilized by? 2

Base stacking (primary force) and H bonds

What is base stacking?

- Van der waals - Hydrophobic forces

Describe the B form DNA configuration

Antiparallel Right-handed twist

What are features of B form DNA? 4

- Hydrophobic core - Bases excluded from H2O - Ribose/deoxyribose exposed to H2O - HBonds in pairing

What do other H bonding groups do when not bonding to one another?

Open to major and minor grooves to interact w/ solvent

What is DNA melting?

Separation of 2 paired strands DS -> SS - Disrupting noncovalent forces (base stacking and HBonding)

What happens to absorption during DNA melting?

Increase abs at 260nm as strands separate

What is hyperchromicity? What DNA is associated w/ it?

High abs - SS DNA

What is Tm?

Midpoint of melting

What it hyperchromicity? What DNA is associated w/ it?

Low abs - DS DNA

When must denaturation happen?

Replication or transcription

What is renaturation?

Reforming dsDNA - Base pairing - Nucleation (slow) and zippering (fast)

Which pairs are stronger, GC or AT? What would the Tm look like?

GC - Elevated Tm

Regions of DNA rich in ____ base pairs denature most readily

AT

What affects Tm?

-pH (protonation state) - Salt conc

What is salt concentration effect on Tm?

Low salt: decrease Tm (destabilize double helix) High salt: Increase Tm (stabilize dbl helix)

Does RNA have inter or intrastrand bonding?

Intrastrand bonding

The structure of RNA is much more dependent on _______ than double stranded DNA

Nucleotide sequence

What forces is RNA stabilized by?

Hbonds Base stacking

DNA and ___________ can form a dbl stranded helix

Complementary RNA