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Attachment of Amino Acid to Transfer RNA
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The function of transfer RNA is to ensure that each amino acid incorporated into a protein corresponds to a particular codon (a group of three consecutive nucleotides) in the messenger RNA. The transfer RNA serves this function through its structure: It has an anticodon at one end and an amino acid attachment site at the other end.The correct amino acid, the amino acid corresponding to the anticodon, is attached to the transfer RNA by enzymes known as aminoacyl-tRNA synthetases (e.g., arginyl-tRNA synthetase, leucyl-tRNA synthetase).A transfer RNA with an amino acid attached is said to be charged. An aminoacyl-tRNA synthetase joins a speci c amino acid to its transfer RNA in a two-stage reaction that takes place on the surface of the enzyme. In the rst stage, the amino acid is activated with ATP.In the second stage of the reaction, the amino acid is attached with a high-energy bond to the 2 or 3 carbon of the ribose sugar at the 3 end of the transfer RNA ( g.11.6).In the gure,we denote high-energy bonds, bonds that liberate a lot of free energy when hydrolyzed, as ~. Thus, during the process of protein synthesis, the energy for the formation of the peptide bond will be present where it is needed, at the point of peptide bond formation.
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Before proceeding to the details of translation,a sketch of the beginning of the process may be helpful ( g. 11.5).
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In bacteria, there are twenty aminoacyl-tRNA synthetases, one for each amino acid.A particular enzyme recognizes a particular amino acid, as well as all the transfer RNAs that
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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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11. Gene Expression: Translation
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The McGraw Hill Companies, 2001
Eleven
Gene Expression: Translation
Nonpolar L-Alanine (Ala,A) H H General amino acid H H N H
L-Valine (Val,V) O H H O N H
L-Proline (Pro,P) O C O H H N
H C CH CH3
H C CH2 C
O O
C CH3
CH2 CH2
H C R C
H3C O O L-Leucine (Leu,L) H H N H
L-Phenylalanine (Phe,F) O H H O N H
L-Tryptophan (Trp,W) H H N H
H C CH2 CH C
H C CH2 C
O O
H C CH2 C C
O O CH2 NH
Acidic L-Aspartic acid (Asp,D) H H N H
L-Glutamic acid (Glu,E) H H N H
H C CH2 C C
O O
H C CH2 CH2 C
O H3C O CH3
C L-Methionine (Met,M) O H H
L-Isoleucine (IIe,I) H H N H
L-Glycine (Gly,G) H H N H
O C O
H C CH CH2 CH3 C
O O
H C H C
O O
Basic L-Lysine (Lys,K) H H N H
H L-Arginine (Arg,R) O C O H H N H
C CH2 CH2 S
H C CH2 CH2 CH2
H C CH2 CH2 C
O O
NH CH2 H3N+ C NH
Polar (uncharged) L-Cysteine (Cys,C) H H C CH2 SH L-Asparagine (Asn,N) C O O H L-Serine (Ser,S) H N H
H3N+
L-Threonine (Thr,T) O H H O N H
L-Histidine (His,H) H H N H
H C CH2 OH C
H C HC OH C
O O CH3
H C CH2 C HC N C
O O
N+ H
L-Glutamine (Gln,Q) H H N H
L-Tyrosine (Tyr,Y) H H N H
CH N H H
H N H
H C CH2 C NH2 C
O O
H C CH2 CH2 C O NH2 C
O O
H C CH2 C
O O
The twenty amino acids found in proteins and their three- and one-letter abbreviations. At physiological pH, the amino acids usually exist as ions. Note the classi cation of the various R groups.
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
11. Gene Expression: Translation
The McGraw Hill Companies, 2001
Information Transfer
H H N+ H
R1 C H C
O H O
H N+ H
R2 C H C
Cysteine O O H H N H H C H S H
H C C
O H O H N H H C H S S
H C C
O O
AMP + PP H2O Cysteine H H H N H
S O H
H C H H C H O C N+ H
R1 C H
O C N H
R2 C H C
H C H O O O C O Figure 11.3 C H N
H H Cystine
N Terminal Figure 11.2
C Terminal
Protein synthesis: formation of a peptide bond between two amino acids. The bond is between the carboxyl group of one amino acid and the amino group of the other.
A disul de bridge can form when two cysteines are brought into apposition. If the two amino acids are in the free form, the new structure is called cystine. When the two cysteines are in the same or different polypeptides, the disul de bridge creates stability.
(a) Figure 11.4
Three different ways of depicting a protein, the enzyme phosphoglycerate kinase. At left is a bond diagram; all the lines shown represent bonds between the various atoms of the molecule. In the middle is a ribbon diagram that emphasizes the secondary structure of the protein. Shown are alpha helices (spiral ribbons) and beta pleated sheets ( at arrows). Finally, on the right is a space- lling diagram that emphasizes the volume the molecule lls. The space- lling diagram is what the molecule would generally look like if it were magni ed eight million times. (Images by David S. Goodsell, the Scripps Research Institute.)
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
11. Gene Expression: Translation
The McGraw Hill Companies, 2001
Eleven
Gene Expression: Translation
BOX 11.1
rotein-sequencing techniques have been known since 1953, when F. Sanger worked out the complete sequence of the protein hormone insulin.The basic strategy is to purify the protein and then sequence it, beginning at one end. However,since most proteins contain too many amino acids to do this successfully, proteins are rst broken into small peptides in several different ways. These peptides are sequenced, and the whole protein sequence can be determined by the overlap pattern of the sequenced subunits. A protein can be broken into peptide fragments by many different methods, including acid and alkaline hydrolysis. For the most part, proteolytic enzymes (proteases) that hydrolyze the peptides at speci c
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