Term
| Components of translation machinery (7) |
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Definition
1)amino acids: all a.a. present in a protein. must be present at the time of protein synthesis; essential amino acids
2) tRNAs: a.k.a. adaptor molecules. At least one per amino acid, actually >50 in humans. Two important sites a) aa attachment site; b)anticodon sequence. Have highly ordered structure
3) mRNAs: translated in the 5’—>3’ direction; in E.coli transcription and translation are closely coupled, regulation of protein expression largely controlled at transcriptional level.
4) aa-tRNA synthetases: Family of enzymes, attach a.a. to corresponding tRNAs.
5)ribosomes: ribonucleoprotein complexes; consist of two subunits: prok.- 70S = 30S + 50S; euk. -80S= 60S + 40S.
6)initiation, elongation, and termination factors
7)ATP and GTP- energy sources: cleavage of four high Energy bonds (ATP and GTP) are required for addition of one aa. Initiation and termination require additional ATP and GTP. |
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Term
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Definition
1)Ribosomal RNA component, large and small subunit. (e.g. for pro, it's 23S and 16S)
2) Proteins adhere to RNA to form subunits, you have L1-L3 and S1-S3 proteins for formation of large and small subunit respectively. |
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Term
| Physical properties of Ribosomal RNA subunits (an example: 16S) |
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Definition
1)Not typical W-C double stranded helix, e.g.: some triple-stranded regions
2)Modified bases
3)Bulges |
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Term
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Definition
18S-Small
28S and 5.8S-Large
in eukaryotes! |
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Term
| Genetic Code (4 properties) |
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Definition
The code is read as a sequence of triplets called codons. There are 64 different combinations of 3 base codons (43). Sixty one of these code for 20 common amino acids.
The code has the following properties:
1)It is specific-a specific codon always codes for the same amino acid.
2)It is essentially universal.
3)It is redundant (or degenerate). A given amino acid may have more than one codon.
4)It is non-overlapping and comma-less. The code is read from a fixed starting point as a continuous sequence of bases, three at a time. Frameshift mutations occur if the reading frame is altered. |
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Term
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Definition
1. Termination codons: UAG, UGA, UAA (3 of the 64 AAs) do not code for aa.
2. Altered codons:
a)Silent mutations - codon base is changed to codon that codes for the same aa.
b)Missense - codon base is changed to codon that codes for a different aa.
c)Nonsense - codon changed to become a termination codon. |
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Term
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Definition
1)tRNA anticodon recognizes codon
a)binding follows the rules of complementary base pairing, mRNA is read 5’—>3’ by a flipped anticodon (1 to 3 position).
2) WOBBLE HYPOTHESIS
a)tRNAs can recognize more than one codon for a specific amino acid due to ‘wobble’ at the 5’ end of the tRNA anticodon, forming non-traditional base pairs; result is that need not be 61 tRNAs to read 61 codons
3)SUPPRESSOR tRNAs
a)Nonsense Suppressors are tRNAs whose anticodons have been mutated such that they incorporate an amino acid at termination codons (i.e., they suppress the normal termination of a protein.) *It essentially reverses or the neutralizes the effect of a nonsense mutation* |
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Term
| Five steps of Protein Synthesis |
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Definition
1.Activation of Amino Acids
2.Initiation
3.Elongation
4.Termination and Release
5.Folding and Posttranslational modification |
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Term
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Definition
1. Looks like clover 2D but is really a L in 3D.
2. Anticodon arm binds to codon and AAs bind to 3' end.
3. Requires a)ATP b)AAs c)Mg2+ d)tRNA.
AA+tRNA+ATP (Mg2+)--> AA-tRNA + AMP + PPi
*Two notes: Mg2+ is coupled with ATP reactions and aminoacyl attached to 3' of the sugar residue--adenine attached to 1'.*
4.Mechanism: oxyanion O of carboxyl group of AA attacks the gamma P of the 3'end tRNA phosphate group, the resulting high-energy phosphodiester bond powers the class II or class I rxn where the 3' and 2' Oxygen nucleophilically attacks the aminoacyl-AMP complex respectively. Final product has the complex on the 3' position. |
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Term
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Definition
1)Prokaryotes produce polycistronic mRNAs; eukaryotes produce polycistronic mRNAs.
2)tRNA recgonizes prokaryotic genes by Shine-Dalgrano (consensus) sequence (AGGAGGU with 16S, S subunit) where translation is more efficient when binding of small subunit of ribosome to SD sequence is tighter.
-also aligns translate to start at a specific AUG.
3.eIF and no formylation in humans, IF (1&3) and initiator tRNA carries N-formyl methionine (which is removed before protein is translated) in bacteria and mitochondria.
4.AUG placed in polymerizing site of 16S, small subunit
5.Methionine residue attached to tRNA attaches to subunit matching anticodon with the AUG codon with help of IF-2, GTP needed for met addition.
6. Hydrolysis of GTP results in release of all 3 IFs followed by binding of large subunit. |
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Term
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Definition
1)Incoming aminoacyl-tRNA-GTP complex undergoes a cycle before it reaches the acceptor (A) site (1.TU-GTP (EFTU) hydrolyzed 2)TU-GDP 3)TS-GDP EFTS 4)TS-GTP 5)TU-GTP. EFTU guides complex to A site. (2 GTPs hyrolyzed for elongation, 1 GTP for initiation)
2)Dipeptide formed on A site, nucleophilic attack of AA on P site by AA on A site, both tRNAs shift to the left (the translation requires ATP, so that's 1 GTP for initiation, 2 for elongation, and 1 for translocation; 4 in total).
3. Repeat 1. |
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Term
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Definition
1. Once you reach Stop codon, a RF (1 or 2 depending on which stop codon) factor binds instead of another tRNA. Protein can also bind to mRNA codon through H-bonding.
2. The machinery disassembles and gets recycled. |
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Term
| Differences between eukaryotic and prokaryotic |
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Definition
1. Ribosomes
a) Eukaryotic
80S, can be dissociated into:
-60S large subunit (5S, 28S RNAs, and unique 5.8S)
-40S small subunit (18S RNA)
b)Prokarotic
70S, can be dissociated into:
a)50S large subunit (5S, 28S RNAs)
b)30S small subunit (16S RNA)
2. Initiator tRNA
In eukaryotes, the initiator amino acid is methionine and it is encoded by MET-tRNAi.
In prokaryotes, proteins start with N-formylmethionine (Met modified by tetrahydrofolate).
3.The selection of AUG (Met codon) to initiate translation differs in prokaryotes and eukcaryotes.
a)In prokaryotes, initation occurs at an AUG adjacent to a purine rich sequence called the Shine-Dalgarno sequence, which base pairs with the 16S RNA.
b)In eukaryotes, the AUG nearest the 5’ end of the mRNA is generally utilized as the initiator MET. The 40S ribosomes loads at the 5’ end of the message and ‘scans’. This stepwise
movement requires energy (ATP) and helicases. |
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Term
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Definition
Similar to prokaryotic initiation except you have EIF instead of IF.
1)You also have EIF-4 which guides mRNA to complex at its 5' cap. *KEY POINT, REGULATION OF EIF-4 CAN REGULATE TRANSLATION, EIF-4 NEEDS TO BE PHOSPHORYLATED TO BE ACTIVE. POLIO VIRUS PROTEOLYSIS EIF-4 SO ITS UNCAPPED RNA CAN BE TRANSLATED MORE EFFICIENTLY*
2)Scanning begin and you see a similar release of all the EIF (except for 2), ATP hydrolysis.
3)Once the 40S places the AUG codon in its polymerization site, the EIF-2 is released. |
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Term
Inhibitors of Protein Synthesis
mnemonic: Stupid Teachers Can't Elongate (prokaryotes) [SPACE] Dumb Protein Complexes (eukaryotes except for Puromycin which does both) |
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Definition
Diptheria Toxin: blocks eukaryotic translation by inhibiting translocation; ADP ribosylation of EF2-translocase (eukaryotic version of EF-G).
-Inactivation of all of the host cell EF-2 molecules causes death of the cell. Attachment of the ADP ribosyl group occurs at an unusual derivative of histadine called diphthamide. |
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Term
| Streptomcycin and other aminoglycosides |
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Definition
Prokaryotes.
Inhibits Initiation & causes misreading of mRNA. |
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Term
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Definition
Prokaryotes.
Binds to 30S and inhibits binding of amino-acyl tRNAs. |
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Term
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Definition
Prokaryotes.
Inhibits peptidyl transferase activity of the 50S ribosomal subunit. |
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Term
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Definition
Eukaryotes.
Inhibits peptidyl transferase activity of the 60S ribosomal subunit. |
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Term
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Definition
Prokaryotes.
Binds to 50S ribosomal subunit. Inhibits translocation. |
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Term
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Definition
Prokaryotes and Eukaryotes.
Causes earlier termination by acting as an analog of aminoacyl-tRNA.
Amide linkage as opposed to ester linkage and can't be cleaved in this system. |
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