Nucleic acid structure and function

Nucleobase

Just the base part, ATCG

Nucleoside

The nucleobase and the pentose

Nucleotide

A phsophate ester of a nucleotide

Purines

Adenine and Guanine

Pyridines

Cytosine, Thymine, Uracil

Phosphodiester linkage

The linkages between nucleotides

3 Hydrogen bonds

Adenine bonds to thymine or uracil with:

2 hydrogen bonds

cytosine bonds to guanine with:

B form

the common form of DNA

A form

wider and shorter, found in DNA/RNA hybrids, plays a role in RNA function and information processing

z form

Left-handed double helix, found in host-pathogen interactions

mRNA

encodes proteins

rRNA

forms the ribosomes

tRNA

matches mRNA with amino acids

snRNA

part of various nuclear processes, notably splicing

DNA polymerase I

Primer removal and DNA repair. exonuclease activity in both directions in both directions. Removed primers from the lagging strand and connects the Okazaki fragments with DNA

DNA polymerase III

Replication, exonuclease only in 3’→5’ direction to fix it’s own errors

Palm

where the DNA sits in the polymerase

Thumb and fingers

wrap around the DNA molecule to hold it in place

Induced fit mechanism

How DNA poly recognizes DNA. Hand closes when it comes in contact with the DNA strand

Helicase

separates the DNA strands using ATP

SSB

Prevent the separated parent strands from reannealing, and from being identified as viral DNA and destroyed

Primase

RNA polymerase, synthesizes a short RNA strand de novo to give a starting point to DNA synthesis

Trombone slide

coordinates synthesis of both DNA strands

DNA ligase

joins DNA fragments after primer removal

Topoisomerase I

Breaks one strand of DNA, can remove supercoils only. Does not require ATP

Topoisomerase II

Can break both strands of DNA. Can remove and introduce supercoils. Requires ATP

Balanced levels of dNTPs

mechanism of ensuring fidelity. equal proportion of nucleotides

5’ → 3’

direction of synthesis

Mismatch repair

Recognises mismatched nucleases and digests a segment of nucleotides, then recruits DNA pol I to fill them in