nucleotides

compare ribonucleotides to deoxyribonucleotides

• carbon 2 of ribonucleotides has OH, deoxy has just H

• ribonucleotide has phosphate attached on C5, deoxy on C3

compare purines to pyrimidines

PURAG- purine is A and G, pyrimidines are C and T

purines have 2 ring shapes, pyrimidines have 1.

difference between the two purines

guanine is longer than adenine

difference between three pyrimidines

cytosine has only one C=O, uracil and thymine have 2, thymine has methyl group which uracil and cytosine lack

describe the methylation of cytosine

• often occurs at cytosine, carbon 5

• use enzyme with a cysteine residue, so that S- can attack carbon 6, making a C-S bond that makes C5 enolate-like and nucleophilic

• C5 takes a methyl group from S-adenosylmethionine

• base group from enzyme then deprotonates C5, breaking enzyme off cytosine and returning aromaticity to cytosine, making m⁵C

what number linkages are formed between DNA or RNA?

5’-3’

why is DNA said to have conformational freedom?

there is rotatable single bond character around sugar-phosphate linkages

what are syn and anti?

which conformations more common for the linkage between a purine base and a (deoxy)ribose?

syn and anti are rotational isomers, syn= same side, anti= facing away from each other

anti. this is because there are significantly more VDW clashes for syn than anti.

this means syn is higher in energy

is syn or anti more common for a pyrimidine?

anti is more common

less steric hindrance for pyrimidine syn conformation than for purine, since pyrimidines are smaller

why is it better that sugar rings in DNA are puckered rather than planar?

puckering avoids VDW repulsion between substituents

describe the puckering of ribose sugars in RNA

C3-endo’:

• C3 of the ribose sugar is most distant from the ribose plane

• 5.9A between each of the two phosphatex that connects the nucleotide to others

describe the puckering of deoxyribose sugars in B-DNA

C2-endo’:

• C2 most distant from deoxyribose plane

• 7A between connecting phosphates

explain why deoxyribose and ribose are well-suited for their function

ribose has OH at C2, making it prone to cleavage. this means it’s not good for long-term storage, but can be used as a messenger molecule

deoxyribose doesnt have this OH at C2, making it more stable and useful for long-term storage

nucleotide reductases are one of the few examples of radical reactions. describe generally the 3 stages of radical reactions

initiation- homolytic fission. not heterolytic when it comes to nucleotide recutases

propagation- chain reactions where more radicals are being made from radicals

termination- radicals react to make normal product

describe the mechanism for the generation of deoxyribose from ribose via ribonucleotide reductases

• enzyme has a stable radical, and propagation occurs, remove H from C3 of ribose and making ribose into a radical

• enzyme then reduces a sulfur from one of its residues by giving the ribose C2 OH another hydrogen

• presence of radical on C3 and protonation of C2 alcohol make C2 carbocation possible, done by removal of the H2O+

• formation of a disulfide in the enzyme via reduction provides a hydrogen to give to the carbocation

• radical propagation occurs, restoring the stable enzyme radical by giving a proton from the enzyme to the radical deoxyribose

image showing the final step, formation of deoxyribose

describe how RNAases work

acid/base catalysis

base deprotonates 2’ OH, while the oxygen bonds with the phosphate attached on the C3, and the phosphate then loses an oxygen to an acid

for this to occur, RNA must be unstructured, so that the C2 OH is close enough to the phosphate. trna and rrna is not as susceptible to RNAses/ hydrolysis

true or false: nucleotides’ only function is to store genetic material

false, they can also play catalytic roles, some RNAses are ribozymes, can cleave self

describe nucleotides’ propensity to perform acid-base chemistry

at pH7 they are all neutral and will not perform this chemistry

briefly describe how ribozyme catalysis works

faulty base pairs like A-G can be cleaved once proton transfer occurs.

proton transfer is between deprotonated guanine which takes proton from OH of ribose, which is recovered by taking a proton off protonated adenine

describe the catalytic site of a ribosome

the active site is made entirely of RNA, not protein. thus the ribosome is a ribozyme

describe how adenine is proposed to allow the formation of a peptide bond in ribosome

adenine can act as a base first and deprotonate the amine group of one amino acid, allowing it to form a bond with the carbonyl group of another amino acid (attached to tRNA)

then the carbonyl group is reformed (from negative O), and the O binding tRNA to the amino acid breaks away from tRNA as it regains its H from protonated adenine, making carboxyl group