MBB lecture 19

what is a gene

the part of DNA that encodes the information for producing a functional product

primary structure of DNA

the nucleotide sequence

secondary structure of DNA

any regular, stable structure adopted by a segment of DNA, typically a base-paired double helix

tertiary structure of DNA

the 3D fold- complex folding into

• DNA into bacterial nucleoids (supercoiled) or eukaryotic chromatin

• or RNA into tRNA and other molecules

main difference between DNA and RNA

the sugar deoxyribose vs. ribose (2’ on RNA has a OH group while on DNA the 2’ has a hydrogen)

where is everything attach on the sugar in DNA and RNA

• base is attached at 1’

• phosphate is attached at 5’

• the nest phosphate attaches to the OH at 3’

which bases are purines

• (2 rings)

• adenine

• guanine

which bases are pyrimidines

• (one ring)

• cytosine

• uracil (RNA)

• thymine

what type of linkage is between the sugar and the base

beta-glycosidic

adenine+sugar

adenosine

Guanine+sugar

guanosine

cytosine+sugar

cytidine

thymine+sugar

thymidine

how do ribonucleotides differ from deoxyribonucleotides

• have a hydroxyl at ribose 2’ carbon

• have a uracil base instread of thymine

uracil+ribose

uridine

what is a nucleotide residue with only a few nucleotides called

oligonucleotide

bonds between nucleotides

phosphodiester bonds

what carbon is the phosphate bond on

5’

is a phosphate bond an acid or base

• its an acid

• at physiological pH phosphate group is an anionic polymer with a net negative charge

what mainly hold DNA strands together

base stacking

what angle is the perfect hydrogen bond

180 degrees (why the strands are antiparallel)

what complementary base pairs have better stacking interactions

g and c (slightly)

distance between C-1’ atoms in DNA

about 11A

what does base stacking do

• between hydrophobic bases, minimizes contact with water and stabilizes double helix

• form of van der Waals

• slightly offset so they are not directly on top of each other

how many base pairs per turn (usually)

10.5

how many A per turn

about 34-36A

major groove and minor groove

• the base pairs are exposed to more solvent on the major groove side than on the minor groove side

• most molecules that recognize DNA bind in the major groove

A form DNA

• dsDNA

• DNA:RNA hybrid

• right-handed

• 10.7bp/turn

B form DNA

• dsDNA

• right handed

• 10.5 bp/turn

Z form DNA

• dsDNA

• alternating pur/pyrim

• left handed

• 12 bp/turn