Block A Flashcards
DNA Replication and Gene Expression
Purine bases
Adenine, Guanine
Pyrimidine Bases
Cytosine, Thymine (DNA), Uracil (RNA)
What is a nucleoside?
a base conjugated to a sugar via a Beta-Glycosidic linkage (eg. deoxyadenosine)
what is a nucleotide?
a base conjugated to one or more phosphoryl groups (eg. dATP, deoxyadenosine triphosphate)
“ideal” DNA helix conditions
10 base pairs per turn
each aromatic base 3.4Å thickness
helix pitch of 34Å (rise per turn)
Hydrolysis of PPi to 2Pi
PPi broken down to two molecules of inorganic Pi with addition of water
(DNA synthesis reaction 1)
Strongly negative ΔG⁰’
Gibbs free energy change (ΔG⁰’) of reaction is very negative, indicates reaction is EXERGONIC
-releases energy, spontaneous under standard conditions
(DNA synthesis reaction 2)
Messenger RNA
-Template for protein synthesis
-Transcribed by RNA polymerase II
Ribosomal RNA
-major component of ribosomes
-synthesised by RNA polymerase I
Transfer RNA
-carries activated amino acids to ribosomes
-synthesised by RNA polymerase III
Steps of mRNA synthesis
- Initiation
- Elongation
- Termination
mRNA synthesis:
1. Initiation
Promoters contain CAAT, TATA, or GC boxes
CAAT and TATA boxes recruit RNA Pol II and initiate transcription
mRNA synthesis:
2. Elongation
RNA Pol moves along DNA template to synthesise mRNA (3’-5’ direction)
Sequence of growing mRNA driven by base pairing to DNA strand - copy of DNA template produced
mRNA synthesis;
3. Termination
Occurs at defined sites
mRNA very unstable, so processed by 1. a modified 5’ cap, 2. Poly A tail at 3’
Transcription Factors
-turn gene expression on/off
-recognise specific DNA sequences near promoters
-characteristic DNA binding structures
-targets for signaling pathways
-activated by phosphorylation + movement to nucleus
what is epigenetics?
Modifications to the genome that affect gene expression, but DONT alter DNA sequence
Can be reversible, therefore can be modulated
DNA Methylation
-addition of methyl groups to nitrogen bases of nucleotides - mostly to CYTOSINE, sometimes adenine
-regulates gene expression (gene silencing) by recruitment of gene expression proteins or hindering binding of TFs to DNA
-modulates DNA structure
CpG Islands
-G/C content of genome 42%, CpG should occur at 4.4% freq., observed at 1%
-5’-CpG-3’
(“p” represents phosphate residue)
-Methylation: gene silencing
-Methyl groups protrude into major grooves of DNA, prevents binding of TFs
-High density of CpGs = CpG islands
-Highest in promoter regions
CpG methylation
-cytosine methylated by DNA methyltransferase (DNMT)
-DNMT1 actively maintains DNA methylation during cell replication
Eurochromatin
-loosely packed form of Chromatin
-enriched in genes
-under active transcript
Heterochromatin
-tightly packed form of Chromatin
-genetically active
-inaccessible to RNA Polymerase
Histone Acetylation
-acetylated by histone acetyltransferases (HATs)
-reduce +ve charge of histones, neutralise +ve lysines, decrease attraction between histones(+) and DNA(-)
-deacetylated by histone deacetylases (HDACs)
-NOT AN EPIGENETIC MODIFICATION
Histone Methylation
-can correlate to both transcriptional activity and inactivity
Epigenetics in Worker Bees
-all methylation removed in Queen Bee, all genes active
-when new Queen needed, egg is fed royal jelly
-compound in jelly inhibits methyl transferase
-demethylation in egg -> egg becomes Queen
