nucleic acid structure

What does each monomeric unit consist of

Sugar, base, and phosphate

What sugar is in a nucleic acid

Ribose

RNA

Ribonucleic acid with an OH on the 2’ carbon

DNA

Deoxyribonucleic acid with an H on the 2’ carbon

What carbons are involved in the formation of the nucleic acid backbone

3’-OH and 5’-OH

How are sugars linked in the backbone

By phosphodiester bonds between the 3’ OH of one sugar and the 5’ OH of the next sugar

What is the charge of the backbone

Negatively charged

Why is DNA more stable than RNA

DNA has an H on the 2’ carbon instead of an OH which is a good nucleophile and can attach the phosphate of the phosphodiester bond and hydrolyze it. Therefore DNA is more stable

Purines

Adenine and guanine

Pyrimidines

Cytosine, uracil, thymine

What atoms from the bases form the glycosidic bonds to the sugar

N9 for purines and N1 for pyrimidines

Nucleotide

Consists of a base, pentose sugar, one or more phosphates (nucleoside joined to phosphoryl group by ester linkage)

Nucleoside

Consists of base and pentose sugar

How many bases per turn of a double helix

10.4 bases

Are bases parallel or perpendicular to the axis

Perpendicular

How is the double helix structured

Negatively charged Sugars and phosphates are on the outside and bases are on the inside. The strands run antiparallel

What is the width of the double helix

20 A

How many degrees of the rotation per base in the double helix

36

How much are adjacent bases separated by

3.4 A

What kind of double helix is formed in DNA

Two DNA chains of opposite directionality intertwine to form a right handed double helix (B-form)

Watson crick base pairs

G-C with 3 H bonds and A-T with 2 H bonds

Why do base pairs have weak non covalent bonds instead of covalent bonds

Because they need to separate for replication and non covalent bonds are easier to break and reform

Regions with what kind of base pairs would be easier to separate

AT

Hydrophobic effect

Hydrophobic interactions drive bases inside of the helix and more polar residues outside

Base stacking

Stacked bases attract each other through van der waals forces (energy of the VDW is small but it sums across the length of the DNA)

Major groove

210 degrees

Minor groove

150 degrees

Major groove of AT

N-NH2-O

Minor groove of AT

N-O

Major groove of GC

N-O-NH2

Minor grove of GC

N-NH2-O

Why does DNA have major and minor grooves

Because glycosidic bonds of each base pair are not diametrically opposite each other

Would relaxes circle DNA or supercoiled DNA migrate faster on agarose gel

Supercoiled bc it’s smaller and more compact

RNA folds

Fold onto itself allowing bases that are far away to interact.