Essay on Protein and Amino Acid

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CH 273 Exam 3 Study Guide/Annotated chapter list

Ch 22: Section 22.1

(tRNA aminoacylation): isoacceptor tRNA: tRNAs that bear the same amino acid but have different anticodons
Many tRNA bases pair intramolecularly gnereating short stems and loops of what is commonly called a cloverleaf secondary structure
Acceptor system—segement at the 5’ end of the tRNA pairs with the bases near 3’
D loop- often contains the modified base dihydrouridine
Variable loop—ranges from 3-21 nucleotides in different tRNAs.
The various elements of tRNA secondary structure fold into a compact L shape that is stabilized by extensive stacking interactions that nonstandard base pairs
Elongated structure of tRNA molecules allow them to align side-by-side so that they can interact with adjacent mRNA codons during translation.

tRNA amino acylation consumes ATP:
Aminoacylation-attachment of an amino acid to a tRNA
AARS- aminoacyl-tRNA synthetase that catalyzes the attachment of an amino acid to a tRNA (most AARS interact with the tRNA anticodon as well as the aminoacylation site at the other end of the tRNA model)
To ensure accurate translation, the synthetase must attach the appropriate amino acid to the tRNA bearing the corresponding anticodon
An ester bond is created between an amino acid and an OH group of the ribose at the 3’ end of a tRNA to yield an aminoacyl-tRNA
Overall rxn: amino acid + tRNA + ATP  aminoacyl-tRNA + AMP + PPi
Step 1: the amino acid reacts with ATP to form an aminoacyl-adenylate (aminoacyl-AMP). The subsequent hydrolysis of the PPi product makes this step irreversible in vivo.
Step 2: the amino acid, which has been “activated” by its adenylation, reacts with tRNA to form an aminoacyl-tRNA and AMP
Class I enzymes: attach an amino acid to the 2’ OH group of the tRNA ribose
Class II enzymes: attach an amino acid to the 3’ OH group

Some synthetases have proofreading ability
Proofreading by AARS enhances the specificity of tRNA aminoacylation
Cognate tRNA and synthetase must be recognized
Once tRNA is charged with the wrong thing it cant be left
First u get charged tRNA –synthetase bind cognate tRNA and bind with correct amino acid and if it is small water will come and hydrolyze it – first layer of defense
Once its charged by right amino acid—the ribosome proofreads anticodon codon pair and the conserved bases will not allow the rxn
Proofreading in ribosome is from codon/anticodon
Wobble pair isn’t exact that’s why u can have more than one codon code for the same amino acid (directionality and third is wobble)

tRNA anticodons pair with mRNA codons tRNA molecules line up with mRNA codons (antiparallel) many isoacceptor tRNAs can bind to more than one of the codons that specify their amino acid wobble hypothesis- the third codon position and the 5’ anticodon position experience some flexibility, or wobble, in the geometry of their hydrogen bonding.

Section 22.2
(only general idea of structure/components, not specific numbers) the two subunits of the ribosome consist largely of rRNA that binds mRNA and three tRNAs during protein synthesis contains protein and RNA large and small subunit (50S, 30S)

Section 22.3

Initiation requires an initiator tRNA protein synthesis begins at an mRNA codon (AUG) in prokaryotes , this initiation codon lies about 10 bases downstream of a conserved mRNA sequence called a Shine-Dalgarno sequence eukaryotic mRNA lacks a Shine-Dalgarno sequence the initiation codon is recognized by an initiator tRNA that has been charged with methionine initiation factors (Ifs) –IF1, IF2, IF3
IF3-binds to the small ribosomal subnit to promote the dissociation of the large and small subunits
IF2- helped bind fMet-tRNA to the 30S subunit (gtp binding protein)
IF1-sterically blocks the A site of the small subunit, thereby forcing the initiator tRNA to the P site
Translation initiation in E.Coli:
Step 1:mRNA and fMet-tRNA in complaex with…