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Dr Zahid Azeem
Assistant Professor
Biochemistry
AJK Medical College, Muzaffarabad
MBBS-2019--- CMB Module
RNA for translation
Exists in 3 forms:
mRNA (messenger) made by eukaryotic RNAP II
tRNA (transfer) made by eukaryotic RNAP III
rRNA (ribosomal) made by eukaryotic RNAP I
made (transcribed) in the nucleus, used in the
cytoplasm
Single stranded
Genetic Codes
Specificity
Universality
Degeneracy
Nonverlapping and Commaless
mRNA
RNA nucleotides transcribed from DNA
Codons: mRNA nucleotide triplets that code for
amino acids
tRNA
tRNA carries the amino
acid to make the
polypeptide chain
Anticodon:
complementary sequence
on tRNA
Fig. 17.12
Codon
tRNA Structure
Hydrogen bond base pairing
between nucleotides of the
same single strand of RNA (80
nucleotides)
Fig. 17.13
Cloverleaf
L-shape
Anticodon loop:
H-bonds with
mRNA codon
3’ end
3’ end
tRNA Activation
Enzyme aminoacyl-tRNA
synthetase
 attach appropriate amino acid to
tRNA
 catalyze covalent joining of
amino acid to tRNA
 tRNA + amino acid = aminoacyl-
tRNA (aatRNA)
20 different aatRNA synthetases
for each of the 20 different
amino acids
tRNA molecule is reactivated
many times (recycled)
Fig. 17.14
http://www.bio.davidson.edu/courses/genomics/2005/drysdale/molecular%20function.jpg
Ribosome Structure
2 subunits:
large (60S) and small (40S)
Final size is 80S
S (Svedberg): a unit of
measure of size based on
how quickly an object
sediments in a centrifuge
Ribosome Binding Sites
Ribosome binds mRNA
binding site
3 tRNA binding sites
E, P, A
Ribosome tRNA binding sites
A site:
aminoacyl-tRNA site
holds the aatRNA carrying the next
amino acid to be added
P site:
peptidyl-tRNA site
holds the tRNA molecule carrying
the growing polypeptide chain
E site:
Exit site
where tRNA molecules leave the
ribosome
Translation Mechanism
Initiation
Elongation
Termination
Post-translational modifications
Initiation step 1: Ribosome finds and
binds to the mRNA strand
Prokaryotes:
mRNA transcript has a Shine-Dalgarno sequence
upstream of initiation AUG codon
16S rRNA on ribosome small 30s subunit has a
complementary sequence: anti Shine-Dalgarno sequence
Eukaryotes
Ribosome small subunit recognizes and bind to mRNA at 5’
cap
Initiation step 2: Ribosome locates
translation start site
Ribosome small subunit moves along 5’ leader of
mRNA until reach translation start site (start codon
AUG)
Factors that help ribosome small subunit find start
codon:
Prokaryotes: Initiation factors
Eukaryotes: Kozak sequence on the mRNA
Fig. 17.8
Initiation step 3: Initator tRNA binds
Once ribosome
small subunit reach
AUG, initiator
tRNA attaches
AUG
H bonds forms
between the
mRNA codon and
tRNA anticodon
Initiation step 3: Initator tRNA binds
Starting amino acid:
Prokaryotes: formyl-methionine (fmet)
Eukaryotes: regular methionine (met)
Initiation step 4: Ribosome large
subunit binds
= complete ribosome
+ initiator tRNA
+ mRNA at AUG
Forming
complex
requires
energy
Final position of
initiator tRNA is
in P site
Elongation Step 1:
Codon recognition
Incoming aa-tRNA to A
site
H bonds form between
the mRNA codon and
tRNA anticodon
Energy is required
Elongation Step 2:
Peptide bond formation
Ribosome catalyzes the formation of
a peptide bond
between the amino acid in the P-site to
the amino acid in the A-site
involves the carboxyl end of the
polypeptide chain
Result:
polypeptide chain is longer by one
amino acid
polypeptide chain is transferred to
tRNA at the A site
Elongation Step 3: Translocation
Translocation requires
energy
Ribosome moves:
tRNA from P site to E site:
leaves ribosome
tRNA from A site to P site:
polypeptide returns to P site,
ready for next polymerization
A site is now empty
next aatRNA can bind
Unidirectional Translocation
mRNA bound to tRNA
Translocates by 1 codon (3
nucleotides)
Ribosome reads mRNA 5’  3’
mRNA moved through ribosome
unidirectionally
Termination
At stop codon a protein called release factor binds to A site
(no tRNA for stop codon, thus no aatRNA)
Release factor:
adds water molecule instead of amino acid to polypeptide
polypeptide hydrolyzed from tRNA in P site and released
Translation complex disassembles
Fig. 17.19
Wobble Mechanism
tRNA can recognize more than one codon for
particular amino acid- Wobble hypothesis
First base of tRNA pairs non-stringently
Hence, no need of 61 tRNA for 61 codons
Wobble standards for Non-
standard pairing
Polyribosomes
A single strand of mRNA can be used to make
many copies of a polypeptide simultaneously
Polyribosomes: when 1 molecule of mRNA has
multiple ribosomes simultaneously translating the
mRNA
Fig. 17.20
Protein Synthesis in Prokaryotes
Prokaryotes don’t
have a nucleus
How does that
change protein
synthesis?
Fig. 17.22
Post-Translational Modifications
Addition: of sugars, lipids, or phosphate groups
Removal (Cleavage): of some amino acids (such
as the methionine) or whole polypeptide chains.
Polymerization: Two or more polypeptides may
join to form a protein. Example: hemoglobin
Folding
1- Triming
Example: Insulin
Covalent Modification
Phosphorylation
Glycosylation
Hydroxylation
Other covalent modification; that include
biotinylated enzymes and carboxylation
Protein folding
Molecular chaperones
Gro ES and Gro EL
Maintaining native confirmation
Protein degration
Ubiquitinylation
Proteosome
E1, E2, E3
THE END

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Translation lgis

  • 1. Dr Zahid Azeem Assistant Professor Biochemistry AJK Medical College, Muzaffarabad MBBS-2019--- CMB Module
  • 2. RNA for translation Exists in 3 forms: mRNA (messenger) made by eukaryotic RNAP II tRNA (transfer) made by eukaryotic RNAP III rRNA (ribosomal) made by eukaryotic RNAP I made (transcribed) in the nucleus, used in the cytoplasm Single stranded
  • 3.
  • 5. mRNA RNA nucleotides transcribed from DNA Codons: mRNA nucleotide triplets that code for amino acids
  • 6. tRNA tRNA carries the amino acid to make the polypeptide chain Anticodon: complementary sequence on tRNA Fig. 17.12 Codon
  • 7. tRNA Structure Hydrogen bond base pairing between nucleotides of the same single strand of RNA (80 nucleotides) Fig. 17.13 Cloverleaf L-shape Anticodon loop: H-bonds with mRNA codon 3’ end 3’ end
  • 8. tRNA Activation Enzyme aminoacyl-tRNA synthetase  attach appropriate amino acid to tRNA  catalyze covalent joining of amino acid to tRNA  tRNA + amino acid = aminoacyl- tRNA (aatRNA) 20 different aatRNA synthetases for each of the 20 different amino acids tRNA molecule is reactivated many times (recycled) Fig. 17.14 http://www.bio.davidson.edu/courses/genomics/2005/drysdale/molecular%20function.jpg
  • 9. Ribosome Structure 2 subunits: large (60S) and small (40S) Final size is 80S S (Svedberg): a unit of measure of size based on how quickly an object sediments in a centrifuge
  • 10. Ribosome Binding Sites Ribosome binds mRNA binding site 3 tRNA binding sites E, P, A
  • 11. Ribosome tRNA binding sites A site: aminoacyl-tRNA site holds the aatRNA carrying the next amino acid to be added P site: peptidyl-tRNA site holds the tRNA molecule carrying the growing polypeptide chain E site: Exit site where tRNA molecules leave the ribosome
  • 13. Initiation step 1: Ribosome finds and binds to the mRNA strand Prokaryotes: mRNA transcript has a Shine-Dalgarno sequence upstream of initiation AUG codon 16S rRNA on ribosome small 30s subunit has a complementary sequence: anti Shine-Dalgarno sequence Eukaryotes Ribosome small subunit recognizes and bind to mRNA at 5’ cap
  • 14. Initiation step 2: Ribosome locates translation start site Ribosome small subunit moves along 5’ leader of mRNA until reach translation start site (start codon AUG) Factors that help ribosome small subunit find start codon: Prokaryotes: Initiation factors Eukaryotes: Kozak sequence on the mRNA Fig. 17.8
  • 15. Initiation step 3: Initator tRNA binds Once ribosome small subunit reach AUG, initiator tRNA attaches AUG H bonds forms between the mRNA codon and tRNA anticodon
  • 16. Initiation step 3: Initator tRNA binds Starting amino acid: Prokaryotes: formyl-methionine (fmet) Eukaryotes: regular methionine (met)
  • 17. Initiation step 4: Ribosome large subunit binds = complete ribosome + initiator tRNA + mRNA at AUG Forming complex requires energy Final position of initiator tRNA is in P site
  • 18. Elongation Step 1: Codon recognition Incoming aa-tRNA to A site H bonds form between the mRNA codon and tRNA anticodon Energy is required
  • 19. Elongation Step 2: Peptide bond formation Ribosome catalyzes the formation of a peptide bond between the amino acid in the P-site to the amino acid in the A-site involves the carboxyl end of the polypeptide chain Result: polypeptide chain is longer by one amino acid polypeptide chain is transferred to tRNA at the A site
  • 20. Elongation Step 3: Translocation Translocation requires energy Ribosome moves: tRNA from P site to E site: leaves ribosome tRNA from A site to P site: polypeptide returns to P site, ready for next polymerization A site is now empty next aatRNA can bind
  • 21.
  • 22. Unidirectional Translocation mRNA bound to tRNA Translocates by 1 codon (3 nucleotides) Ribosome reads mRNA 5’  3’ mRNA moved through ribosome unidirectionally
  • 23.
  • 24. Termination At stop codon a protein called release factor binds to A site (no tRNA for stop codon, thus no aatRNA) Release factor: adds water molecule instead of amino acid to polypeptide polypeptide hydrolyzed from tRNA in P site and released Translation complex disassembles Fig. 17.19
  • 25.
  • 26. Wobble Mechanism tRNA can recognize more than one codon for particular amino acid- Wobble hypothesis First base of tRNA pairs non-stringently Hence, no need of 61 tRNA for 61 codons
  • 27. Wobble standards for Non- standard pairing
  • 28. Polyribosomes A single strand of mRNA can be used to make many copies of a polypeptide simultaneously Polyribosomes: when 1 molecule of mRNA has multiple ribosomes simultaneously translating the mRNA Fig. 17.20
  • 29. Protein Synthesis in Prokaryotes Prokaryotes don’t have a nucleus How does that change protein synthesis? Fig. 17.22
  • 30. Post-Translational Modifications Addition: of sugars, lipids, or phosphate groups Removal (Cleavage): of some amino acids (such as the methionine) or whole polypeptide chains. Polymerization: Two or more polypeptides may join to form a protein. Example: hemoglobin Folding
  • 33. Covalent Modification Phosphorylation Glycosylation Hydroxylation Other covalent modification; that include biotinylated enzymes and carboxylation
  • 34. Protein folding Molecular chaperones Gro ES and Gro EL Maintaining native confirmation Protein degration Ubiquitinylation Proteosome E1, E2, E3