8-15 Protein Synthesis Flashcards
What are 4 MAIN DIFFERENCES between prokaryote vs. EUKARYOTE Protein synthesis
- prokaryotes use F-MET as Starting AA while EUKARYOTES have only MET
- prokaryotes ribosomes are 50s+30s->70S
- ***** EUKARYOTES: 60s+40s—> 80s
- prokaryotes are fully polycistronic
EUKARYOTES ARE MONOCISTRONIC - prokaryotes: 3 rRNAs //// EUKARYOTES: 4 rRNAs
What are the Elongation Factors of translation for prokaryotic cells?
EF-Tu , EF-G
[T or F] prokaryotic cells undergo mRNA processing Just like Eukaryotic Cells
FAALSE!!!! PROKARYOTIC CELLS DO NOOOT AT ALL UNDERGO mRNA PROCESSING!!!
What are the translation “initiation” factors for Prokaryotes specifically?
IF2 and IF3
Prokaryotes use _____Polyermase during protein synthesis/translation
Prokaryotes ONLY USE RNA POL 1! During protein synthesis/translation
In regards to [aminoacyl tRNA synthetase] what is the difference between Prokaryotes and EUKARYOTES?
prokaryotes may use ONLY 1 aminoacyl tRNA synthetase to bring different types of AA to their corresponding tRNA
**EUKARYOTES HAVE A DIFFERENT SYNTHETASE FOR EACH AA WHEN BINDING THEM TO THEIR tRNA
What’s the relationship between a DNA template and the protein sequences it ultimately codes for?
DNA Template(daughter strand) is THE SAME SEQ./Co-linear with the Protein AA seq.
THe Genetic Code is “____” which means =….
Genetic code is DEGENERATE!–>this means Multiple codons will possibly encode for the same AA
Genetic Code
Code where each AA is represented by at least 1 codon. Note: Some AA can be made by multiple codons[degenerate]
1: What codon (___) produces the START Amino Acid (____)
2: What 3 codons (____, _____ or ______) produces the stoppp amino acids
- START codon (AUG) = Methionine AA
2. UAA, UAG or UGA codons = stoppp AA
1) What makes tRNAs?
2) What does tRNAs contribute to protein synthesis other than AA?
1) tRNAs are made by RNA POL 3
2) tRNA binding to AA by synthetases INC fidelity of the process –> good thing!
What parts of the EUKARYOTIC tRNA allows it to be “distinguished” from other tRNAs when binding to its correct aminoacetyl tRNA synthetase?
tRNAS have specific:
1-anticodon loop
2-acceptor stem
3-specific aminoacetyl-tRNA that it binds to only[EUKRYTOC}
Describe the rxn by which AA are actually covalently attached to tRNAs? [2]
Aminoactyl tRNA synthetase activates AA with ATP hydrolysis –>
AA is then ESTER bonded to (OH) of 3’ on tRNA
How do Aminoactyl-tRNA synthetase ensure the CORRECT AA is being ester bonded to tRNA
Hydrolytic Editing of the Aminoactyl-tRNA synthetase removes its own coupling errors by rejecting wrong AA at the “editing site” [CORRECT AA should NOT be able to fit into this editing site!]
Which base of the codon contributes MOST to Degeneracy??
THe WOBBLE BASE “3rd Base” allows for multiple codon seq. to sometimes code for the SAME AA = DEGENERACY
What may prevent the wrong reading frame from being used in translation
frequent premature STOP codons
[T or F] the first 2 bases of a codon have to have STRICT MATCHING while the 3rd can have variability
TRUE!
Describe the Process of prokaryote Translation? [4]
1) 16s sRibosomal[brought by IF-3] subunit binds to upstream Shine-Delgarno sequence
2) Ribosome assembles at Trnsltion start site with Psite right on point! [due to SD sequence]
3) binds to ]—>Placed @ P site
4) IF-2 is hydrolyzed by large ribosome so that initiation factors can DETACH from the initiating tRNA
When does the Lrge ribosomal subunit during EUKARYOTIC translation actually bind to the mRNA?
Large ribosomal unit binds to mRNA AFTER eIF2(carrying the tRNA and GTP) is HYDROLYZED and initiator MET is in P-site!
Describe the process of Translation ELONGATION?
1) EFTU (with an attached GTP) binds to a floating tRNA*with its Amino Acid attached and hooks it up with the GROWING CHAIN!–>2 lags occur when EFTU GTP is hydrolyzed and EFTU is released= which allow for correctness check
2) EFG then comes and binds to ribosome w/GTP and is hydrolyzed to ACTUALLY SHIFT the Ribosome downward
How is translation Terminated? [3]
STOP Codon—->Release factor (looks similar to tRNA) binding to A site————–>water is added to end of chain which releases polypep chain and disassembles ribosome!
What are the 4 Fidenlity/Check Points for ensuring Amino Acids are paired correctly?
1) Aminoactyl-tRNA synthetase has to recognize correct tRNA with correct AA [Hydrolytic editing]
2) mRNA has to be fully processed[5’cap/3’polyA tail]
3: Codon and ANTI-codon matched correctly produces stronger affinity. THey have to match !
4: EFTU introduces 2 lags as time for tRNA to be corrected* happens when EFTU GTP is hydrolyzed and EFTU released
How can less than 64 tRNAs recognize ALL 64 codons??
WOBBLE pairing of the 3rd base allows a small group of tRNAs to still be able to recognize MULTIPLE codons
Prokaryotic Tx and TL occur in which compartment?
Prokaryotic Tx and TL BOTH occur in the SAME Compartment!
Eukaryotes are MONOcistronic!
Eukaryotes are MONOcistronic [1 protein message per mRNA strand] due to the tedious task of having to scan for AUG start codon during TL initiation!
Puromycin
Mimics tyrosyl-tRNA with “Molecular Mimicry” and binds to
(A site) of Lrge ribosome STOPPING any further peptide bond growth because it LACKS [OH] for protein chain growth
Why don’t abx that affect ribosomal sites of Bacteria affect us as Eukaryotes as well?
Ribosomes between Bact and Eukaryote Are Different in Size! [Eukaryotes= 60s + 40s–>80s]
What Eukaryotic Organisms CAN be possibly affected by abx?
Ribosomes of Mitochondria/Chloroplast resemble Bacteria and are sensitive to Rbsme inhibitors
deleterious effect on human mitochondria
When and WHY does folding of a protein occur?
Protein folding occurs AS Polypeptide Chain is being MADe due to hydrophobic AA folding inward to protect themselves from aqueous environment of blood
Why when eIF2 is Phosphorylated eIF2B is unable to do its job?
When eIF2 is phosphorylated “[eIF2P]” then eIF2B WILL BIND IRREVERSIBLY to [eIF2P] and not be able to help other regular eIF2 become recharged!
1) What does the AP1 element of a gene do?
2) Explain the ENTIRE PROCESS of the AP1 gene activation?
1)AP1 element of a gene INDUCES CANCER METASTASIS
2) A: URK phosphorylates Fos and Junk phosphorylates Jun
B: Jun-P, Fos-P and ETS tx factor all bind to AP1 element
C: AP1 element gene is activated!
WHat does PERK do in the Endoplasmic Reticulum ?
After BIP leaves from PERKs side..PERK STOPS TRANSLATION! in order to prevent any more misfolded proteins from happening while the ER problem is reprimanded!
The intermembrane space of the mitochondria is _____
[+ / - ] .WHat does this have to do with cargo proteins?
mitochondrial intermembrane space is [+]!! and Cargo protein that’s mitochondria bound will electrophoresis across this [+] space to eventually get to TIM for the matrix
During Translation, mRNA molecules are read_____
mRNA molecules during Translation are read 5’–>3’
Which site of the tRNA is responsible for the initial attachment of an AA for delivery to a protein?
3’ end ACCEPTOR STEM on tRNA grabs the AA so that it can be delivered
Second Genetic Code
Refers to the recognizing of a tRNA by its appropriate aminoacyl-tRNA synthetase
The Shine-Dalgarno box is a ___-rich sequences in _______ that’s located ____nucleotides upstream of initiator [___ or ____]. Shine-Dalgarno box sequence is complementary to what part of the incoming Prokaryote ribosome?
*Shine-Dalgarno box is a PURINE-rich sequence in PROKARYOTES located 10 nucleotides upstream of initiator [AUG or GUG]
**Shine-Dalgarno box sequence is complementary and pairs to the
3’ end of the 16s-ribosomalRNA THAT’S APART OF the Prokaryotic 30s Ribosomal subunit
eIF4F?
2)What is eIF4F job during translation?
eIF4F= (eIF4E cap binding protein) + (eIF4G) and (eIF4A helicase used for AUG scanning by mRNA unwinding)
2)eIF4F includes the cap binding protein that is needed to
During Protein Synthesis mRNA transcripts are read by ribosomes from ____—->___ and the __-terminal end of the protein is the end the new amino acid is added to
During Protein Synthesis mRNA transcripts are READ from 5—->3 and the C-TERMINAL end is the protein end AA will be added to.
{n-terminal is the end made first}
How does Translation Elongation MOVEMENT FORWARD occur
Upon contact w/ribosome, EF-G GTPase ability is activated and the GTP hydrolysis causes a confirmational change in EF-G that moves an “in the middle” A/P tRNA FULLY into the P-site.–>This moves the previous P site-tRNA into the
E site
When does the tRNA occupying the E-site of Lrge ribosome actually get pushed off??
E-site tRNA is ejected when the next aminoacyl-tRNA is delivered to the A site and is pushed fully into that A site from the dissociation of EF-Tu*GDP
Why exactly are Bacteria/Prokaryotes Polycistronic
in Eukaryotes our ribosomes HAVE to bind near the
1 5’end cap and scan for the AUG but Prokaryotes have a 5’end cap that is NOT significant so Prokary.Ribosomes can bind to multiple site/SD and start codons
What are some common post-translational modifications
Most frequent post-TL modifications are covalent Glycosylation, phosphorylation and acetylation
When does Protein Folding occur and what is it for?
Proteins are FOLDED while they’re MADE!=
Co-translationally fold with N-terminal folding first.
2)Proteins FOLD are important for a mature functional state
