2: Nucleic acid fundamentals Flashcards
What is the central dogma of molecular biology?
DNA makes RNA makes protein
Building blocks of DNA
sugar, phosphate, bases
Characteristics of nucleobases
- nitrogenous heterocycle
- planar
- endocyclic nitrogens are basic and can function as hydrogen acceptors
nuceloside vs nucleotide
nucleoside - two groups (sugar and base)
nucleotide - sugar, base, and phosphate
Difference between DNA and RNA sugars
2’ carbon of DNA has a hydrogen attached and RNA has a hydroxyl group attached
Phosphodiester bonds hold together…
nucleotides in single stranded DNA (ssDNA)
true or false: Directionality of genetic information in DNA is carried from 5’ to 3’
True!
How do base pairs bind?
They bind through H-bonding which forms dimers between A:T and G:C
Cell cycle of typical mammalian cell
- DNA synthesis (46 pairs of chromosomes)
- G2 - post dna synthesis (46 pairs of chromosomes)
- mitosis - splits into two cells (23 pairs of chromosomes)
- pre-dna synthesis (23 pairs of chromosomes)
What are the steps to adding nucleotides to the 3rd-H terminus of a growing strand?
- based on the base pairs of the template strand, the next nucleotide is added
- the 3’ hydroxyl group at the 3’ end of the growing strand attacks the inner most phosphate group from the incoming trinucleotide
- A bond is formed between the O and P of the new nucleotide
- The other two phosphates are released (pyrophosphate)
Role of gyrase (topoisomerase II)
Holds the twisted section of DNA so that the stress of the twisting is relieved and it doesn’t unravel.
Role of helicase
unbinds the base pairs and opens the double stranded DNA (like a zipper)
Role of single-strand binding proteins
prevent the unwound DNA strand from pre-maturely twisting itself.
Role of DNA polymerase complex (contains Pol III)
responsible for adding new base pairs
Role of RNA primase complex (primosome)
Synthesizes primers (start template DNA) in order for polymerase to add onto the 3’ end of the primer.
Role of ligase
“glue of the DNA strand”
seals any gaps in the lagging strand
How are primers removed in lagging strand synthesis?
DNA polymerase I
1. primer nucleotide is cleaved and rejected
2. next DNA nucleotide is added
3. done until all RNA nucleotides are ejected
(similar concept to ripping up train tracks to lay down new ones)
How is DNA packed in the body as chromosomes?
- the dna double helix wraps around histones (that make nucleosomes) “beads on a string”
- the “beads on a string” chromatin coils and forms a chromatin fibre of tightly packed nucleosomes
- a chromosome is a densely packed thing of chromatin
Why are grooves in DNA important for ligand interactions?
major grooves and minor grooves allow for interactions with proteins (e.g. transcription factors)
What is a DNA motif?
an amino acid sequence pattern with a high affinity for binding DNA
helix-turn-helix motif
two alpha-helixes held together by a strand of amino acids (AKA the turn)
- first helix stabilizes interaction with DNA
- second helix interacts with base pairs in the major groove
Zinc finger motif
contain finger-like projections and bind to zinc
- Arg 46 and His 49 form sequence-specific contacts
- nonspecific contacts between PO4 groups and side chains
3 steps of transcription
- initiation - RNA polymerase recognizes the promoter then de-basepairs the DNA (unzips helix)
- elongation - creates a copy of DNA strand (RNA)
- termination - there is a signal that releases the RNA
Role of mRNA
- single stranded with some self-interactions
- serves as a template and for protein biosynthesis
