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130 Cards in this Set

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  • Back
What occurs in translation?
The cell interprets the mRNA's code to make proteins.
What is the basic scheme of translation?
mRNA acts as a template for interaction of ribosomes and tRNA.
What enzyme is responsible for attaching amino acids to tRNA?
Aminoacyl synthetase
What direction (in terms of chemical bonds) are proteins made?
Amino to carboxyl direction.
Where in the cell does protein translation occur?
In the cytosol.
List the 7 components of Protein Synthesis:
1. Amino acids
2. tRNAs
3. mRNAs
4. aa-tRNA synthetases
5. Ribosomes
6. Initiation, elongation & termination factors
7. ATP/GPT energy sources
How many tRNAs are actually in humans?
What are the 2 important sites on a tRNA?
1. AA Attachment site (3' end)
2. Anticodon sequence
In E.coli, where does regulation of translation take place primarily?
At the level of TRANSCRIPTION
What are aa-tRNA synthetases?
A family of enzymes that attach AA's to their tRNAs in a very specific 2-step rxn.
What are ribosomes?
Ribonucleoprotein complexes consisting of TWO subunits.
What ribosome is for
Prok: 70S

Euk: 80S
What subunits make up the ribosomes in
Prok: 30S + 50S

Euk: 60S + 40S
Where in euks are ribosomes found (3 places)?
-RER - rough endopl. reticulum
What is RER for?
Rough endoplasmic reticulum synthesizes exported and membrane-bound proteins.
How much energy is required for the addition of one amino acid?
4 ATP and GTP; more for added elongation and termination.
How is energy obtained for elongation?
Via the cleavage of high energy bonds of ATP/GTP.
What makes up the 50S subunit of proks?
rRNA: 23S + 5S

Proteins: L1/L2/L3 (31 total)
What makes up the 30S subunit of proks?
rRNA: 16S

Proteins: S1/S2/S3 (21 total)
What does binding of the 50S and 30S subunits make?
The 70S Assembled ribosome!
What makes up the 60S subunit of euks?
rRNA: 28S + 5.8S

Proteins: L1/L2/L3 (50 total)
What makes up the 40S subunit of euks?
rRNA: 18S

Proteins: S1/S2/S3 (33 total)
What are codons?
Triplet sequences that make up the genetic code.
How many different combinations of bases are there in the genetic code?
64 -> 4^3
How many of the possible codons code for amino acids?
What do the other 3 do?
Act as nonsense/termination codons.
How many amino acids are there?
So what does it mean that there are 61 codons for 20 amino acids?
The genetic code is redundant - more than one codon exists for each amino acid.
List the 4 properties of the Genetic Code:
1. Specific - codons always encode same amino acid.
2. Universal
3. Redundant
4. Non-overlapping and commaless.
What are the 3 termination codons?
What are 3 types of alterations that can occur in codons?
1. Silent mutations
2. Missense mutations
3. Nonsense mutations
What are silent mutations and their result?
Change in codon base to a different base that results in a different codon - BUT it encodes the same amino acid.
What are missense mutations and their result?
Replacement of a codon base that results in a DIFFERENT amino acid being encoded.
What are nonsense mutations and their result?
Base replacement that results in a Termination codon being encoded. (UAA/UGA/UAG)
How do tRNA molecules read mRNA?
Anticodons are 'flipped' so they read mRNA 5'->3'
So which base sequence dictates the amino acid? mRNA or the anticodon?
mRNA!!! That's where the codon is. If you read the anticodon, it's backward.
Where is the wobble position?
-In the Anticodon
-In the Codon
Anticodon: 5' position
Codon: 3' position
How many codons can be recognized if the wobble position is occupied by
How many codons can be recognized if the wobble position is occupied by
What codons can be recognized when wobble is occupied by
Uracil: Adenine or Guanine

Guanine: Cytosine or Uracil
What residue confers capability of recognizing 3 codons when in wobble pos?
What bases can be recognized by inosine?
There are 61 anticodons for 20 amino acids; do there have to be 61 tRNA's then?
No; by using the wobble position, fewer tRNAs have to exist in order to READ all 61 codons, and still polymerize 20 amino acids.
Nutshell: what is the use of the Wobble hypothesis?
There need not be 61 tRNAs to read all 61 codons.
What is a nonsense suppressor tRNA?
A tRNA that has mutated
When looking at mRNA to see how it's read, which direction directs codon?
What are Suppressor tRNA's?
TransferRNA molecules that have mutated, so that their anticodons recognize STOP (nonsense)codons, but yet they transfer an amino acid to the growing chain.
What is the result of suppressor tRNA in the overall translation scheme?
Normal suppression (stopping) does not occur; the chain keeps on growing instead.
What are the 5 steps in protein synthesis?
1. Activation of Amino Acids
2. Initiation
3. Elongation
4. Termination/Release
5. Folding/Processing
What are the 5 essential components of Amino Acid Activation?
1. 20 Amino Acids
2. 20 Aminoacyl-tRNA synthetases
3. 20 or more tRNAs
4. ATP
5. Mg2+
What are the 8 essential components of Initiation (step 2)?
1. mRNA
2. N-formylmethionyl-tRNA
3. Start Codon in mRNA (AUG)
4. 50S ribosome subunit
5. 30S ribosome subunit
6. Initiation Factors 1/2/3
7. GTP
8. Mg2+
List the 5 essential components of Elongation:
1. Functional 70S ribosome
2. AA-tRNAs specific to codons
3. Elongation Factors Te/Ts/G
4. GTP
5. Mg2+
What are the 3 essential components of Termination and Release (step 4)?
1. Termination codon in mRNA
2. Polypeptide release factors
3. ATP
What are the polypeptide release factors called?
how fitting!
How do AA-tRNA synthetases are so specific and accurate?
They recognize not only the Anticodon arm, the AA attachment point, and also motifs on other arms of the tRNA
Why do amino acids have to be charged prior to attachment to their tRNA?
Because they are not naturally in an energy state that favors the transfer.
What provides the energy for amino acid activation?
PPi hydrolysis
What is the actual reaction that takes place in activating amino acids?
Nucleophilic attack of the alpha phosphate by the terminal O of the carboxyl group on the amino acid; subsequent release of PPi.
How are activated amino acids put onto their tRNAs?
The AMP is a good leaving group; the 2' or 3' -OH on the tRNA's adenine residue attacks the carbonyl group on the AA with release of AMP.
What's the difference between Class I and Class II AA-tRNA synthetases?
Class I uses the 2' OH
Class II uses the 3' OH
What's the primary difference to remember between Prok and Euk mRNAs?
Prok = polycistronic

Euk = monocistronic
How many rRNA molecules are contained in:
-Prokaryotic ribosomes
-Eukaryotic ribosomes
Prok: 3 - 23S, 5S, and 16S

Euk: 4 - 28S, 5S, 5.8S, & 18S
What are the APE sites on ribosomes?
The binding sites for tRNA
In bacteria, how do ribosomes know which AUG encoding MET is really the start point?
By recognizing the Shine Dalgarno sequence
What is the Shine Dalgarno sequence?
Sequence 6-10 nucleotides upstream the REAL start codon; purine rich (UAAGGAGG)
What component of the ribosome recognizes the Shine Dalgarno sequence?
The 3' end of the 16S ribosome (on 30S subunit);
Where is the Shine Dalgarno sequence located?
Near the 5' end of the prokaryotic mRNA; upstream the first start codon (aug)
How do eukaryotic ribosomes know when to start translating the mRNA?
There's only one start because their genes are monocistronic.
What signals eukaryotic ribosomes to assemble for translation?
The 40S ribosomal subunit binds and moves down the mRNA until it encounters AUG.
Why is it important that prokaryotic 16S ribosomes bind the Shine Dalgarno sequence?
So that the start codon is put into the P site, not the A site.
What is always the first amino acid in protein?
What special tRNA puts the methionine into the P site in bacteria?
Initiator tRNA
What is special about the initiator tRNA?
It carries N-formyl methionine
Why do prokaryotes need the first AA to be N-formyl methionine?
Because the N is blocked from making a peptide bond and so this can only be placed at initiator P sites.
What enzyme is responsible for formylating the methionine?
what's important to remember about how transformylase works?
It only recognizes fmet-tRNA the special initiator tRNA for protein synth in proks.
What is different about translation inititation in eukaryotes?
There is no shine-dalgarno sequence and no formylated methionine; just normal MET.
What else aids in initiation?
Which IF helps recognition of the initiation codon in both euks and proks?
Euks: eIF-2

Proks: IF-2
What does IF3 do?
-Promotes dissociation of 50S and 30S ribosome subunits
-Aids in 30S binding mRNA
What does IF1 do?
Helps IF3 by increasing the dissociation rate of the subunits.
What does IF2 do?
Complexed w/ GTP; Binds fmet-tRNA and puts it in the P site.
How do the IF molecules leave when initiation is done?
IF3 leaves and makes GTP hydrolyze to GDP. That makes IF2-GDP release; the hydrolysis also helps IF1 release, and the 50S unit can now associate with 30S.
What antibiotic interferes with protein initiation and how?
Streptomycin; binds the 30S subunit, distorting it so it can't bind mRNA.
What are the 3 steps in Translation Elongation?
1. 2nd Aminocyl-tRNA binds at the A site.
2. Peptide bond formation between the 2 amino acids.
3. Release of uncharged AA and Translocation.
What aids in the first step of elongation?
EF-Tu-GTP; GTP hydrolyzes when the AA-tRNA binds A site.
What happens to EF-Tu-GDP?
EF-Ts binds to make it release GDP; then GTP binds and causes EF-TS to release. Generates a fresh EF-Tu-GTP
How does EF-Tu actually help protein synthesis?
By a mechanism called kinetic proofreading.
What is kinetic proofreading?
When AA-tRNA binds the A site, the anticodon must bp with mRNA; otherwise it will leave the A site before GTP hydrolysis can occur.
What forms the peptide bond in the 2nd step of elongatn?
Attack of the already-present aa's ester bond between tRNA and AA by the amino group on the incoming aa.
What catalyzes transpeptidation?
Probably the 23S ribozyme peptidyl transferase
What else happens in step 2, transpeptidation?
The 3' and 5' ends of the uncharged tRNA bend into the E site, and the growing amino acid chain bends into the P site; their anticodons remain in the A and P sites though.
What happens in translocation?
Dissociation of the uncharged tRNA; Then, complete shift of the ribosome on the mRNA so that the A site is empty and P/E are now occupied.
What allows for translocation to take place?
GTP hydrolysis on EF-G
Which steps of elongation require GTP?
steps 1 and 3.
What signals termination of protein synthesis to occur?
The presence of a termination codon on the mRNA in the A site.
What happens when a termination codon is encountered in the A site?
A release factor RF binds the A site, breaking the ester bond of the peptide chain and the tRNA in the P site.
What is required for termination?
ATP (as well as termination codon and release factors)
What is protein targeting?
Incorporation of specific sequences encoding signals in proteins, to help them get to their functional destination after cytosolic production.
What does it mean to say protein elongation is fast and accurate?
Fast: 15-20 AA added / sec
Accurate: ~1 mistake for every 10000 AA added.
What is EIF4?
Eukaryotic Initiation Factor 4
What does EIF4 do?
Guides mRNA to bind the pre-Initiation complex for translation by recognizing the 5' Cap on mRNA.
What happens after the mRNA binds to the small subunit?
The initiation complex scans the mRNA for AUG; when it finds it, the Met-tRNA is positioned and eIF5 helps the 60S subunit bind 40S.
Why is EIF4 so gosh darn important?
It's a key step in regulating the translatability of mRNA; if there's no eIF4, the pre-initiation complex won't recognize the cap
What is required for the scanning-for-AUG action during eukaryotic initiation?
Helicases and Energy (ATP)
What feature re: eIF4 allows us to manipulate its effectiveness for recognizing mRNA's cap?
the fact that it must be phosphorylated to be active.
By manipulating eIF4 through phosphorylation, what power does that give us?
The ability to regulate the translatability of a eukaryotic cell's RNA.
HOW do we manipulate eIF4?
Phosphorylate: activates eIF4, makes it recognize cap, guide mRNA to 30S ribosome. Translation then ensues.
Name 8 factors that stimulate translation by phosphorylating eIF4:
1. TNF-alpha
2. Insulin
3. Epidermal growth factor
4. Plt-derived growth factor
5. Nerve growth factor
6. IL-1
7. pp5 src
8. p21 ras
Name one thing that inhibits eIF4 (cap binding protein):
Polio virus
How does polio virus inhibit eIF4?
By proteolysing it; this allows the virus' own uncapped RNA to be translated.
When is eIF4 not phosphorylated?
In the eggs of urchins and frogs, and in Heat Shock.
How does Diphtheria toxin work?
It inhibits translocation during eukaryotic protein translation.
How does the diphtheria toxin inhibit translocation?
It ribosylates EF-2 translocase, which prevents elongation.
What is EF-2?
The eukaryotic analog to EF-G in proks, which translocates the ribosomal machinery.
Why is the diphtheria toxin so potent?
It is catalytic; it inactivates ALL EF-2 molecules in the host cell.
What molecule does the diphtheria toxin take advantage of?
Diphthamide; a modified His residue within the EF-2 molecule.
How is Diphthamide made?
It's essentially a His residue, but with ADP (minus a nicotinamide) on it.
So name 3 antibiotics that inhibit prokaryotic translation.
Name an antibiotic that inhibits eukaryotic translation.
What type of an antibiotic is streptomycin?
An aminoglycoside.
How do aminoglycosides and streptomycin work?
By inhibiting translation INITIATION, and misreading of mRNA.
How does Tetracycline work?
Binds the 30S subunit and inhibits binding of aa-tRNAs.
How does Chloramphenicol work?
Inhibits peptidyl transferase activity of 50S subunit in prokaryotes..
How does Cyclohexamide work?
Inhibits the peptidyl transferase activity of 60S subunit in eukaryotes.
How does Erythromycin work?
Binds the 50S subunit and inhibits translocation.
How does Puromycin work?
Acts as an analog of aa-tRNAs in proks/euks, causes premature chain termination.
Why does Puromycin terminate translation?
It results in an amide linkage between the puromycin molecule and the AA in the P sites; this disrupts the peptide bond formation.
How do bacteria become resistant to erythromycin?
They contain a plasmid-born methylase, which converts a single adenosine in 23S rRNA to N6-dimethyl adenosine, which blocks the binding site of the drug.
What are 6 types of post-translational modification?
1. Proteolytic processing
2. Phosphorylation
3. Glycosylation
4. Hydroxylation
5. Additional modifications
6. Ubiquitination