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48 Cards in this Set

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What does mRNA do in protein synthesis?
Encodes the genetic info tt specifies the order of a.a's in the protein in the form of a sequence of nucleotide bases
What does tRNA do in protein synthesis?
Deciphers or "translates" the nucleic acid base sequence code into the a.a. order of the protein. It also shuttles the necessary energy to the synthetic rxn
How does tRNA translate the nucleic acid base sequence code into the a.a. order of the protein?
Via shape specific coupling to an a.a. w/base order specific nucleic acid hybridization
What does rRNA do in protein synthesis?
Provides a "core" able to bind proteins, thereby creating the Ribosome. Ts organelle provides a "platform" to organize the rxns of protein synthesis.
What makes up the "PeptidylTransferase enzyme"?
rRNA
What is a Codon?
The three bases on the mRNA that are read together, dictating which amino acid is attached
How many codons are possible (with the 4 nucleotides)?
64 codons are possible
What are the three nonsense codons (non-coding) that are used as a STOP?
1. UAA
2. UAG
3. UGA
What is the only codon that has double duty? What does it code for?
AUG: codes for Methionine and for START here
The code is degenerate or redundant, why?
To minimize mistakes and provide extra codons for high use a.a's.
All tRNA's actually have two functions, what are they?
1. Chemically links w/one and only one a.a
2. Recognizes and binds w/the corresponding codon in mRNA, bring its a.a into the growing protein
tRNA's have a unique characteristic that gives them their shape, describe it
Ty contain stretches of complementary sequences tt allows internal hybridization tt results in a "cloverleaf" 2D structure
About how large is a tRNA?
Small: ~70-90 nucleotides long
What causes the 3D L-shape structure of tRNA?
Ty contain a # of invariant and chemically modified bases tt disrupt of alter H-bonding patterns. **These modified bases provide specific binding sites for enzymes and factors
There are 4 distinct regions of the 2D structure of tRNA, what are they (exclude functions)
1. Acceptor Arm
2. Pseudouridine (TψCG) stem/loop
3. Dihydrouridine (D) stem/loop
4. Anticodon stem/loop
What is the function of the Acceptor are of the tRNA?
The 3' end of the tRNA is modified by the addition of non-coding bases CCA 3'OH. The a.a. is coupled to this modification (see pic)
What is the function of the pseudouridine (TψCG) stem/loop and the dihydrouridine (D) stem/loop?
Provide special binding sites/regions
What is the function of the Anticodon stem/loop of the tRNA?
The central 3 of seven bases of ts loop constitute the anticodon. Wn read 3'-5', it's complementary to codon mRNA sequence
What two ways can tRNA compensate for the redundancy of the genetic code?
1. Modification of the bases alters and expands the H-bonding pattern of the anticodon sequence
2. The Wobble hypothesis
Explain the Wobble hypothesis.
Since the 3 anticodon bases extend out fm a bend in the loop, tr position in space is not constrained by stacking against neighboring bases (like in a helix). Ts allows the 1st anticodon base to "swing" taking up alternate H-bonding patterns w/3rd codon base
What does Aminoacyl tRNA synthetases do?
*It carries out amino acid activation; the attachment of an a.a to its corresponding tRNA
*Provides major portion of energy for peptide bond formation
How many Aminoacyl tRNA synthetases are there for each a.a?
20 (written as 20 one)
There are two steps in amino acid activation, what are they?
1. The recognition Step, which ensures specificity
2. The Coupling step, wc conserves the energy of ATP
What is the first part of the Recognition Step in a.a. activation?
Synthetase selects its particular a.a. via a specifically configured binding pocket & reacts it w/ATP form the intermediate aminoacyl AMP (aka AA-AMP)
What is the second part of the Recognition Step in a.a. activation?
The tRNA binds. Specificity is ensured by recognition of anticodon loop-does it correspond to the particular amino acid in the pocket & by the config. of the ψ or D loop. Wn tRNA and a.a match, enzyme undergoes a conformational change tt allows continued rxn. If no match found, AA-AMP bond is hydrolyzed and components released
WHat is the most abundant organelle in the cytoplasm? What is its general purpose?
The Ribosomes. They increase the efficiency of protein synthesis by acting as a platform upon wc all the components necessary for translation can gather.
What's the difference between prokaryotic and eukaryotic ribosomes?
Size: In Eukaryotes, they're 80S and in prokaryotes, they're 70S
In Prokaryotes, what are the lg and sm subunits denoted as? They are broken down even farther, what are their subunits?
small subunit= 30S: consists of the 16S RNA and 21 proteins
Large subunit= 50S: consists of 23S and 5S rRNAs and 34 proteins
In Eukaryotes, what are the lg and sm subunits denoted as? They are broken down even farther, what are their subunits?
Sm= 40S: composed of the 18S rRNA and ~30 proteins
Lg= 60S: 28S, 5.8S, and 5S rRNAs and ~45 (he put 49) proteins
How are the proteins and rRNA's of the ribosomes organized?
the RNAs form the "core" of the organelle w/the proteins on outer surface, stabilizing the structure and providing binding surfaces
What is the second step in the activation of ATP? (The Coupling Step)
The a.a. of the AA-AMP intermediate is transferred to the 2' or 3' OH group of terminal A-base of the tRNA. Ts forms a covalently linked aminoacyl-tRNA (aa tRNA). Much of the energy originally in the ATP or aa-AMP link is actually retained in the aa-tRNA link. Hydrolysis of ts "high energy" link is later used to drive peptide bond formation during protein synthesis
Descrive the "Madonna with Child" image
1. the infant (sm subunit) is carried in a pouch suspended fm mother's chest w/mother kissing infant's forehead.
- mRNA wd appear as a scarf passed around the infant's neck and the tRNAs as two straps connecting the pouch to mother's shoulders(anticodon loop at baby's neck and acceptor stem on mother)
-Active site b/w mother and child, it's relatively devoid of proteins, showing the ribosome acts as a ribozyme
- Mother (lg sub) has a tunnel running thrgh fm active site to lower back, its the exit for new peptide
The 5' cap on mRNA has three functions, what are they?
1. Inhibit 5'-3' degradation
2. Transport
3. Recognition site for factors in initiation of protein synthesis
The mRNA contains numerous features that affect the protein synthetic process, what are the 5? (Don't need to memorize this card, it's just to set up the "big pic")
1. 5' cap
2. 5' untranslated segment
3. Coding sequence
4. 3' untranslated sequence
5. Poly A tail
What does the 5' untranslated segment of mRNA do and what is it?
A sequence of nucleotides before the start site for translation. Regulation may occur here.
What does the coding sequence in mRNA do?
-Ts starts w/AUG and ends at "stop" codon
-determines the protein's a.a. sequence
What is the 3' Untranslated sequence of mRNA and what does it do?
Is a variable length of nucleotide sequence beyond the stop codon. It may function in regulation or locating the RNA in cytoplasm
What is the Poly A tail of mRNA and what does it do?
~200A nucleotides. Once in cytoplams, tail becomes wrapped around another poly A binding protein (PAB I). Ts protects the mRNA fm nucleolytic attack. A's are slowly lost and timing of the losses serves to determine the "life expectancy" of the mRNA
During initiation of translation, a special tRNA is used to begin the initiation, what's it called and describe the process
Initiator tRNA. MET has only 1 codon, but tr r 2 different tRNAs tt bind MET and recognize AUG. 1 of ts is ordinary variety, wc will deliver MET at any pnt. 2nd tRNA will only use it to begin translation. Its distinct structure allows it to be recognized by certain initiation factors tt deliver it to a unique binding site on ribosome (P site). In bacteria, MET a.a is formylated to make it look like a peptide (fMET)
Describe initiation in Prokaryotes (pic on pg 293)
-IF2 forms a complex w/GTP and the fMETtRNA
-IF1 &IF3 bind the 30S displacing the 50S & promoting ternary complex association
-30S "initiation complex" can now locate start site on mRNA. Ts is done by two RNA/RNA hybrids; 16S rRNA w/the "Shine-Dalgarno"sequence upstream start codon & initiator tRNA w/start codon itself.
-Once start site located, IF2 hydrolyzes its GTP causing the IFs to be released and allowing the 50S subunit to join completing initiation process
Describe initiation in Eukaryotes.
1.eIF1 & eIF3 maintain 40S subunit in free form
2.eIF2 forms a "ternary complex" w/GTP & METtRNA[f] and couples it to the 40S
3. eIF4 binds to 40S complex. Ts factor hs 2 critical functions; locates & binds 5' cap, and uses ATP to move 40S along mRNA until initiator tRNA locates and binds to AUG. Called scanning
4. eIF5 promotes binding of lg subunit to properly orientated complex
5. eIF2 hydrolyzes its GTP causing release of all factors & allowing the 2 subunits to lock into place and complete initiation
What are the four sites on the ribosome used in elongation?
F = factor binding site
A = aminoacyl tRNA binding site
P = peptidyl tRNA binding site
E = tRNA exit site
**We're only concerned w/A and P
There are 3 main steps in Elongation. What is the first step? (translation)
-aa-tRNAa are prepared for translation by forming a ternary complex w/elongation factor Tu (EF1 in euk). Ts factor delivers the aa-tRNA to A-site. If proper codon/anticodon match is made Tu hydrolyzes its GTP to lock the aa-tRNA into active site of A-site
What is the 2nd step of Elongation during translation?
-"Peptidyl transferase" enzyme (actually RNA of lg subunit) transfers the peptide held by tRNA at P-site to a.a. held by the tRNA at A site. The enrgy required for peptide bond formation is supplied by hydrolysis of "high energy" peptide-tRNA bond
What is the 3rd step of Elongation during translation?
-Translocation step; promoted by elongation factor, EF-G (EF2 in euk). An EF-G/GTP complex binds the ribosome. Ts change pulls the codon/anticodon pair fm A to P site, ejecting now empty initiator peptidyl-tRNA & exposing a new codon in now empty A site. Ts also ejects G factor and resets ribosome for a new cycle
What happens when the ribosomal translocation process exposes a "stop" codon?
There is no aa-tRNA tt can fill the A-site. Instead a release factor (RF/GTP) binds at A. Ts induces the peptidyltransferase activity to transfer the peptide/protein to a non-existent aa-tRNA and thus releases it fm the ribosome
**the ribosome falls off and is recycled
Can there be more than one ribosome translating 1 mRNA strand?
Yes, there can be multiple ones. The more there are, the faster translation goes and the more copies of the protein you have
What are several ways to regulate translation?
1. Activity of eIF2 or eIF4 is modulated. Ts cd result in a complete shutdown of synthesis or a modulation of rate of initiation.
2. Synthesis fm individ. mRNAs can be modulated by binding regulatory proteins to 5' untranslated region, interfering w/40S's "scan" for AUG