Nucleic Acids and Nucleotides: Structure, Function, and DNA/RNA Chemistry

Nucleic Acids are _________ :

polymers of nucleotides

What are Nucleic Acids used for?

-storage of genetic info (DNA)

- transmission of genetic info (mRNA)

- protein synthesis (tRNA and rRNA

Nucleotide are used in the ____ form for cellular functions such as?

-Monomer

-energy for metabolism (ATP)

- enzyme cofactors (NAD+)

- signal transduction (cAMP)

Nucleic Acids are long, linear polymers constructed from how many types of monomers?

four types

What does each nucleotide monomer consist of?

a sugar, a phosphate and a nitrogenous base

What does a nucleoside consist of?

base and a pentose(sugar)

What position is the phosphate group in a nucleotide?

phosphate group is attached 5' position

Nucleic acids are built using the ___ version of the nucleotide

5'-triphosphates

ATP, GTP, TTP, CTP

___of the three phosphates used for building nucleic acids form a _______, and

completed nucleic acids contain _______ moiety per _________.

-Two

-leaving group

-one phosphate

-nucleotide

Ribonucleic acid (RNA) contains what sugar

ribose

Deoxyribonucleic acid (DNA) Contains what sugar

-deoxyribose

a ribose in which the 2'-hydroxyl is replaced with a hydrogen.

Name all the nitrogenous bases in DNA vs RNA

DNA

adenine

guanine

cytosine

thymine

RNA

adenine

guanine

cytosine

uracil

Which bases are purines and which are pyrimidines?

Purines: adenine and guanine

Pyrimidines: cytosine, thymine, uracil

what are the characteristics for nitrogenous bases?

-Planar structures

• Absorb UV light around 250-270 nm

• All are good H-bond donors and acceptors

In nucleotides the pentose ring is attached to the nucleobase via __________

N-glycosidic bond

The N-glycosidic bond is formed to the anomeric carbon of the sugar in _______

Beta-configuration

anomeric carbon

the new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form

Relatively ______ can occur around the________bond in free

nucleotides

-free rotation

-N-glycosidic bond

In polynucleotides covalent bonds formed via _________ where the _________

phosphodiester linkages

-5'-phosphate group of one nucleotide

is joined to the 3'-hydroxyl group of

the next nucleotide

Direction of polynucleotides

Directionality

- 5' end is different from 3' end

- We read the sequence from 5' to 3'

The backbones of both DNA and RNA are

hydrophilic

-negatively charged backbone!

______polymers

- No branching or cross-links

Linear

Describe primary structure of nucleic acids

Sequence of nucleotides

- Covalently attached

- A strand has a 5'-to-3' direction

- Conventional representation is 5' end to the left

Describe secondary structure of nucleic acids

3D arrangements of nucleotide residues with respect to one

another.

- Double helix

- H-bonds and hydrophobic interactions involved

Describe tertiary structure of nucleic acids

Longer range 3D interactions.

- The elaborate folding of large tRNA or rRNA

- The complex folding of DNA into large chromosomes

How did Watson and Crick: propose the 3D model of DNA?

-2 helical DNA chains wound around the same

axis to form a right handed double helix

- Helix held together by hydrogen bonds

between bases

Secondary Structure Depends on _______

Interactions

hydrogen-bonding

Two bases can form______ to form a base pair

-hydrogen bonds

What are the Watson-Crick base pairs predominate in double-stranded DNA?

- A pairs with T (two H-bonds)

- C pairs with G (three H-bonds)

- Purine pairs with pyrimidine (involve ring N, carbonyls, amino groups)

What is Chargaff's Rule?

(DNA base composition):

mole % A = mole % T

mole % G = mole % C

Two DNA chains of opposite directionality - intertwined to

form a ___________

right-hand double helix

Two DNA chains are

complementary to each other

The hydrophilic _______ backbones are on the

_______of the DNA helix

-sugar-phosphate backbones

-outside

The hydrophobic _____are _______the DNA helix.

-bases

-inside

The bases are ________to the axis of the helix with

adjacent bases separated by 3.4 Å. (DNA)

-perpendicular

How is the DNA double helix stabilized?

The helix is stabilized by:

- hydrogen bonds between base pairs

- hydrophobic interactions (stacking forces) between

adjacent bases

Most RNA molecules are ________

single stranded

How are RNA molecules stabilized

- right handed helix

stabilized by base stacking (no H-bonding).

Any complementary sequences can ____________

to form ________structures

-fold back on themselves

-complex

The paired regions have an ______double helical structure.

A form

What happens to DNA in DNA denaturation?

-Covalent bonds remain intact

:Genetic code remains intact

-Hydrogen bonds are broken

:Two strands separate

- Base stacking is lost

:UV absorbance increases

Denaturation can be induced by ________, or _______

-high temperature

-change in pH

Denaturation reversal: Two strands ______when temperature is lowered

re-anneal

The midpoint of melting (Tm) depends on ________

base composition

________ increases Tm (because more _______

bonds)

-High CG

-hydrogen

Tm depends on DNA length. Longer DNA has ______Tm

-higher

Tm depends on pH and ionic strength. High salt ______Tm

-increases

Hydrolysis of an anhydride bond yields

______energy than hydrolysis of the _______

-more

-ester