1. 7.3 Translation
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2. Definition of translation
The process of changing something from 1 form to another

3. Understanding: Initiation of translation involves assembly of the components that carry out the process
Steps of Initiation:
mRNA binds to small ribosomal subunit
Initiator tRNA carrying MET binds its anticodon to the start codon on mRNA (P site)
Large ribosomal subunit then binds to small one
Another tRNA binds to A site
Peptide bond forms between the 2 amino acids

4. Understanding: Synthesis of the polypeptide involves a repeated cycle of events
Steps of Elongation:
1. ribosome moves over 3 bases along mRNA from 5’ to 3’ end
2. tRNA in P site is moved to E site
3. tRNA in A site is moved to P site
4. Another tRNA moves into vacant A site

5. Understanding: Disassembly of the components follows termination of translation
Steps of Termination:
Ribosome reaches a stop codon (UAG, UAA or UGA)
Release factor binds to stop codon
Peptidyl transferase causes polypeptide release
Ribosome disassembles & RF released

6. Understanding: Free ribosomes synthesize proteins for use primarily within the cell
2 different places ribosomes appear in eukaryotic cell:
Free-floating in the cytoplasm
Bound to the rER
Translation can occur at both
occurs more often at free ribosomes
Free ribosomes synthesize proteins that will be used in the cytoplasm, mitochondria or chloroplast

7. Understanding: Bound ribosomes synthesize proteins primarily for secretion or for use in lysosomes
Proteins are synthesized by ribosomes bound to rER if they will be used:
In the ER
In the Golgi body
In lysosomes
In the cell membrane
Outside the cell

8. All ribosomes start FREE
* All ribosomes start FREE! * Become bound if signal sequence present on protein being translated. * SRP (signal receptor protein) binds to signal sequence, and stops translation until it can bind to receptor on ER surface. * Then translation continues. * Protein moves into rER lumen.

9. Understanding: Translation can occur immediately after transcription in prokaryotes dues to absence of nuclear membrane
Eukaryotes
Prokaryotes
Compartmentalized
mRNA modification occurs after transcription
Delay between transcription & translation
Not compartmentalized (no membrane-bound organelles)
No mRNA modification
No delay between transcription & translation

10. Skill: The use of molecular visualization software to analyse structure of eukaryotic ribosomes & tRNA molecule
PDB = protein data bank = public database containing data on 3-D structures for many biological molecules 2000 – Ramakrishnan, Steitz & onath made first data about ribosome subunits available on PDB 2009 – received Nobel Prize for their work on ribosome structure Activity: Visit the PDB. 1. Search Thermus thermophilus ribosome (Images 1jgo and 1giy) 2. Search tRNA molecule

11. Ribosome structure Protein + rRNA A large & small subunit
3 binding sites for tRNA
E site = exit
P site = peptidyl (holds tRNA carrying growing protein)
A site = aminoacyl (hold tRNA carrying next amino acid to be added)
mRNA binding site on small subunit

12. tRNA structure Sections that are single-stranded
Sections that are double-stranded (creates loops)
Anticodon on one end (3 bases, complementary to codon)
“Anticodon loop” = 7 bases
3 loops total to form a “cloverleaf” shape
CCA at 3’ end = site of attachment of amino acid (CCA is read 5’ to 3’)

13. Application: tRNA activating enzymes illustrate enzyme-substrate specificity and the role of phosphorylation
Base sequence of tRNA varies
tRNA activating enzyme = activates tRNA by attaching a specific amino acid to 3’ end of tRNA
20 different tRNA activating enzymes
Energy from ATP needed for attaching amino acid

14. Skill: Identification of polysomes in electron micrograph
Polysomes = polyribosomes = many ribosomes
Look like beads on a string
Multiple ribosomes attach to single mRNA, each translating same protein at the same time, so large amounts of same protein are made simultaneously!

15. In which direction is translation occurring?

16. Nature of Science: developments in scientific research following improvements in computing: use of computers has enabled scientists to make advances in bioinformatics applications such as locating genes within genomes and identifying conserved sequences.
Bioinformatics
= interdisciplinary field that develops methods & software for understanding biological data
= combines computer science, statistics, math & engineering to analyze biological data.
Databases:
GenBank
DDBJ = DNA databank of Japan
EMBL = European molecular biology Laboratory

17. Understanding: The sequence & number of amino acids in the polypeptide is the primary structure.
Primary structure = sequence of amino acids in a polypeptide
Polypeptide = chain of amino acids
20 commonly occurring amino acids can be combined in any sequence
Huge diversity of proteins

18. Understanding: The secondary structure is the formation of alpha helices & beta pleated sheets stabilized by hydrogen bonding.
Secondary structure = α-helix and β-pleated sheets
Forms because of folding caused by polar covalent bonds
Held together by H bonds (dotted lines)

19. Understanding: The tertiary structure is the further folding of the polypeptide stabilized by interactions between R groups.
Tertiary structure = 3-D shape
Results from interaction between R groups (and between R groups & H2O)

20. Understanding: The quaternary structure exists in proteins with more than one polypeptide chain.

21. 4 levels of protein structure (summary)