Central Dogma: DNA to Proteins Process:
- DNA
- Transcription: make pre-mRNA
- 5’ Capping, PolyA Tail, Splicing
- Mature mRNA
- Translation
- Protein
Amino Acid Structure:
- Amino group (NH2)
- Central Carbon
- Carboxyl group (CHO2)
- R Side group. Different for each amino acid.
Amino Acid Classifications based on side group properties: Nonpolar
Hydrophobic
* Lots of H surrounding side group
Amino Acid Classifications based on side group properties: Polar
- Hydrophilic: Presence of H accepting atoms (OH, S..)
- Positively Charged: Basic
- Negatively Charged: Acidic
Proteins are:
String of amino acids linked by peptide bonds
What are Peptide Bonds?
A covalent bond between the carboxyl group of one amino acid and the amino group of another amino acid.
* One molecule of water is produced. BYPRODUCT
* C then bonds to N
N-terminus / Amino End:
Very end of amino acid sequence **containing the amino group **
* +H3N
C-Terminus / Carboxyl End:
Very end of amino acid sequence containing the carboxyl group
* COO-
t-RNA:
Holds the key for translation: bind both mRNA and amino acids
* amino acid attached to the 3’ end of t-RNA
* Allows translation of nucleotide sequence (DNA) into amino acid sequence (Protein).
Degeneracy or redundancy
One aminoacid can be encoded by multiple codons
Wobbling Hypothesis
Degeneracy seems to be more prevalent for the third position of the codon
* The third nucleotide of the codon is less constraint than the other two.
Translation Mechanism Pt. 1: INITIATION
- Small ribosome subunit (30S) recognize certain sequences near the 5’ end of mRNA (Ribosome recognition sequence) around the initial AUG start codon.
- 3OS INITIATION COMPLEX. Once small subunit of the ribosome is bound, **Methionine-charged t-RNA **that recognizes AUG start codon bind the codon.
- 70S INITIATION COMPLEX. Next, Large subunit of ribosome (50S) is recruited and binds t-RNA in the P site.
Shine-Dalgarno Sequence
Typical ribosome recognition sites in bacteria.
Located around 8 base pairs before the start codon
Sites in 70S Initiation Complex Ribosome:
- E (Exit) Site
- P (Peptide) Site
- A (Aminoacyl) Site
Translation Mechanism Pt. 2: ELONGATION
- MET-tRNA occupies P-Site of ribosome
- EF-Tu, GTP, and the next charged tRNA form a complex.
- Complex enters A Site of the ribosome
- After charged tRNA is placed, GTP is cleaved to GDP. EF-Tu-GDP complex is released.
- EF-Ts regenerates the EF-Tu-GTP complex. Complex is ready to combine with another charged tRNA.
- Peptide bond forms between amino acids in P and A sites. tRNA in P site releases its amino acid.
- Ribosome moves down mRNA to next codon (translocation). Requires EF-G and GTP.
- tRNA that was in P site is now in E site, which it now moves into the cytoplasm.
- tRNA that occupied A site is now in P site. A site open and ready to receive another tRNA.
CONCLUSION: At the end of each cycle of elongation, the amino acid that was in the A site is added to the polypeptide chain and the A site is free to accept another tRNA.
SLIDE 25 DIAGRAM
Polyribosome structures
Often, more ribosomes can bind to the mRNA even before other ribosomes have finished translating the mRNA, forming the so called polyribosome structures
Proteins have four different structure levels:
- Primary
- Secondary
- Tertiary
- Quaternary
Protein Primary Structure
Initial sequence of amino acids
Protein Secondary Structure
Interactions betweenn amino acids cause folding of two sub-structures:
1. Pleated Beta-Sheet
2. Alpha-Helix
Protein Tertiary Structure
Established by folding of primary and secondary structure
Protein Quaternary Structure
Two or more polypeptide chains may associate. Protein made of more than one subunit.
* Refers to assembly of all subunits
