DNA to protein

Central dogma

→ describes the genetic flow of information from DNA to RNA to proteins

• how genetic instructions stored in DNA are used to build proteins

• Ensures preservation and accuracy of info transferred

• Protein production = costly in energy, and the 3D structure is unsuitable template

Transcription

→ transfer of genetic information from DNA to mRNA

3 key steps: initiation, elongation and termination

• catalysed by RNA polymerase

• eukaryotes have 3 different RNA polymerases

• Prokaryotes = only 1 RNA polymerase

Location of points along a gene for transcription

Promoter = upstream of sequence

• transcription initiation site

Terminator = downstream of gene

• termination site for transcription

RNA polymerase types

• RNA polymerase 1 = rRNA

• 2 = mRNA and some reg.ncRNA

• 3 = tRNA, rRNA and some reg.ncRNA

Transcription initiation eukaryotes

• enhancers can be far from transcription start - DNA bends round)

• TFIID (TATA binding protein and factors) binds first at the TATA box

• Complex of enzymes assembles including RNA polymerases Prokaryotes 2, and TFIIH (unravels DNA)

Transcription initiation prokaryotes

• sigma (o) factor binds at the -35 and -10 promoter regions

• Allows RNA polymerase to bind, then change conformation (opens)

• DNA strand is opened, DNA-RNA hybrid forms and (o) factors dissociates

Elongation of RNA strand

• Growth from 5’ to 3’ end

• hydrogen bonds form between bases

• Bases joined by phosphodiester bonds

• RNA has U instead of T, so Adenine binds to U

MRNA processing in eukaryotes

• eukaryotic termination is not fully understood

• Conserved sequence that recruits cleavage factors, dissociates on its own

(Pre-)mRNA transcript is altered before leaving the nucleus

• introns spliced out

• 5’ cap added

• Poly-A tail

Transcription termination prokaryotes

2 mechanisms of termination:

1. Formation of hair pin, Rho independent

2. Rho factor

• both prise open the transcription complex, terminating the process

How many codons are stop/start etc.

• 3 bases per codon

• 20 amino acids

• 3 stop codons

• 1 start codon (methionine AUG)

TRNA molecule

• each has an anticodon which is complementary to the codon on mRNA

• Has an amino acid attached when it binds

• Some flexibility in 3rd nucleotide in a codon = base wobble (allows cell not to have all the tRNAs available)

• Cross shape

What so the reading frame

• polypeptide only reads between the start and stop codons

• In groups of 3 = corresponding AA

• Mutations can shift the reading frame

Ribosome structure

• large and small subunit

• E, P and A sites (in that order)

• E = exit

• P = peptidyl

• A = aminoacyl

• Small subunit contains the mRNA binding site/area

Ribosome measurements in pro/eukaryotes

Ribosomes are made of proteins and rRNA

• subunit differences can be utilised in drug design.

Translation: initiation

1. Initiation factor (protein) and a tRNA with the start codon and an AA (methionine) arrives, the small subunit binds the tRNA to the P site.

2. Initiation complex binds to 5’ cap (eukaryotes)

3. Large subunit recruited, initiation complex finds start codon

4. Large subunit binds to small, and another tRNA recruited with the next anticodon

5. Second tRNA binds to A site and peptidyl bond forms between the AAs

Translation: elongation

1. A new tRNA joins the A site, peptidyl bonds keep forming

2. Peptidyl bond forms between AA 3 and 4

3. Large subunit moves along, so 3 is in E site and 4 is in P site

4. Small subunit follows, tRNA in E site is ejected

Translation: termination

1. Another tRNA binds, forms a bond etc

2. Release factor recruited as STOP codon is read

3. Ribosome dissociates ad both mRNA and peptide chain released