RNA

• Acts as a direct template for protein synthesis
• Has a ribose sugar instead of deoxyribose
• Uracil instead of thymine
• Single stranded though it can folded into secondary strucutres
• Not as stable - short half life

• mRNA - template for protein synthesis
• rRNA (ribosomal RNA) - major component of ribosomes, part of protein translation
• tRNA (transfer RNA) - carries amino acids in activated form to ribosome (specific)
• snRNA (small nuclear RNA) - used in RNA splicing (removes introns)
• miRNA (micro RNA) - ~21 bases long, binds to mRNA and inhibits translation (specific)
• siRNA (small interfereing RNA) - experimentally to control gene expression, binds to mRNA and promotes degredation

• Copying one strand using base pairing rules
• Catalyses by RNA polymerase using rNTPs, releasing pyrophosphate 
• No primer required
• Synthesised in 5'---->3' direction (antiparrallel)
• 17 base pairs unwound at one time
• RNA-DNA hybrid duplex about 8 base pairs long at any time
• RNA polymerase is a holoenzyme - made up of enzyme/coenzyme combination
  • 6 subunits (core)
  • Sigma initiation factor - directs enzymes by finding promoter regions (removed after bond)
• Promoters determin transcription start:
  • Pribnow box - AT-rich region at -10 bases 
  • Consensus sequence - most common binding sequence at -35 bases (vary per gene). Strong promoters match more closely
• Transcription faster in eukaryotes
• Termination signals in synthesised RNA and can be palindromic (forms hairpin structure that interferes with RNA polymerase's binding affinity)

Transcription and translation occurs togehter meaning a fast response to the environment. 

Modified RNAs:

• tRNAs - sugars/bases modified and CCA added to 3' end
• rRNAs - spliced into component parts

Factors influencing gene expression:

• Nuclear membrane - sperates 2 things
• RNA processing
• Complex transcriptional regulation

Different types of RNA polymerase:

• RNA polymerase I - rRNA
• RNA polymerase II - mRNA
• RNA polymerase III - tRNA/rRNA

Trasncription in the nucleus while translation is in the cytoplasm

pre-mRNA processed by:

• Addition of polyA tail to 3' end - increases stability and specifices export to cytoplasm
• Addition of cap to 5' end

Introns - non-coding section of DNA/RNA

Exons - coding section of DNA/RNA (expressed in RNA)

Splicing is performed by a splicosome and recognises splicable areas by splice acceptor sites. It allows the synthesis of several proteins from a single gene e.g. in different tissues. 

Incorrect splicing = mutations (cause of genetic disease)

Interaction of RNA polymerase with promoters can be enhanced by activators or blocked by repressors. 

Operon - a common pathway controlled together as a single unit from one promoter

e.g. lac operon - positive feedback regulation:

• When no lactose is present there is no need to make lactase so repressor protein binds to operator sequence and prevents transcription
• Wnen lactose is present it binds to the repressor protein so it cannot bind to operator = gene switched on

• Similiar but more complicated
• Our mRNA is monosictroic - can only code for one type of polypeptide
  • Need tissue specificity, cell type specificity and developmental regulation
• Chromatin remodeling may need to occur - histones modified to open DNA parts that are condensed in chromatin
• Basal transcription factors - bind to promotors and allow for RNA polymerase to bind
• Regulatory transcription factors - bind to promotor-proximal elements and enhancers 
  • Specific for particular genes
  • Upstream of start site

• Small non-coding RNA (around 21-25 bases long)
• Synthesised as a precursor from nuclear DNA and then processed into mRNA 
• Functions by base-pairing complementary sequencing within mRNA
• Results in silencing and repression of protein translation