Protein Synthesis and Genetics Help
There are two major steps in protein synthesis: transcription and translation. The first step is the transcription of DNA to an NA molecule. This process is carried out by the enzyme RNA polymerase. This enzyme attaches to the DNA at a specific nucleotide sequence called a promoter ahead of (upstream from) the gene to be translated. A number of enzymes stimulate the local unwinding of DNA, and this allows RNA polymerase to begin transcription of one of the DNA strands. Within a gene, only one of the DNA strands is transcribed into mRNA. This DNA strand is called the anticoding strand or antisense strand; the DNA strand that is not transcribed is called the coding strand or sense strand. Some other gene on that same DNA molecule may use the other strand as a template for RNA synthesis. Within a gene, however, RNA polymerase does not jump from one DNA strand to another to transcribe the RNA molecule. Termination of transcription occurs when RNA polymerase encounters a "terminator nucleotide sequence" at the end of a structural gene.
In eukaryotic cells, primary mRNA transcripts are "processed" before they are released from the nucleus as mature mRNA molecules. Initially, most eukaryotic primary transcripts (pre-mRNAs) are mosaics of coding regions (exons) and non-coding regions (introns). Before the mRNA leaves the nucleus to become mature cytoplasmicm RNA, the noncoding regions must be precisely removed and the exons must be spliced together. In addition, an unusual guanine nucleotide (called a cap) is attached to the 5' end, and a string of adenine nucleotides (called a poly-A tail) is attached to the 3' end of the mRNA. In prokaryotic cells, however, there is no nuclear membrane, and mRNA processing does not occur. Except for the archaebacteria, bacterial genes do not contain introns. Thus, translation of mRNA into protein can commence in bacteria even before them RNA has been completely transcribed from the DNA.
In the second major step of protein synthesis, ribosomes and tRNA-methionine complexes (called "charged" methionyl tRNAs) attach near the 5' end of the mRNA molecule at the first start codon or initiation codon (AUG) and begin to translate its ribonucleotide sequence into the amino acid sequence of a protein. Ribosomes consist of three different rRNA molecules and about 50 different proteins. Each amino acid is coded for by at least one tRNA molecule. Because the genetic code is degenerate, many more than 20 tRNAs are actually involved in protein synthesis. Each amino acid becomes attached at its carboxyl terminus to the 3' end of its own species of tRNA (Fig. 3-8) by a specific enzyme (amino-acyl synthetase). Thus, there are at least 20 different synthetases. Once the amino acid is attached, the tRNA is said to be charged. A loop of unpaired bases near the middle of the tRNA carries a triplet of adjacent bases called the anti-codon. Other parts of the tRNA form complementary base pairs with rRNA of the ribosome during protein synthesis or to act as recognition sites for a specific amino-acyl synthetase.
Translation of most proteins begins with the start codon 5' AUG 3', which specifies the amino acid methionine (refer to Fig. 3-9 throughout the following discussion). Two sites exist on a ribosome for activated tRNAs: the peptidyl site (P site) and the amino-acyl site (A site). The initiating methionineloaded tRNA enters the P site (perhaps by passing through the A site). The 3' UAC 5' anticodon of the tRNA pairs with the complementary 5' AUG 3' codon in the mRNA. The ribosome holds all of the reactants in the proper alignment during translation. A second activated tRNA (e.g., one loaded with threonine) enters the A site (again by specific codon-anticodon base pairing). A peptide bond is formed between the two adjacent amino acids by the action of an enzymatic portion of the ribosome called peptidyl transferase. In bacteria, it appears that ribosomal RNA is responsible for peptide bond formation. This is an example of ribozyme activity. The amino-acyl bond that held the methionine to its tRNA is broken when the peptide bond forms. The now "unloaded" methionyl-tRNA in the P site leaves (usually to become activated again). The ribosome shifts (translocates) three nucleotides along the mRNA to position a new open codon in the vacant A site while at the same time moving the thr-loaded tRNA (now attached to a dipeptide) from the A to the P site. The third tRNA (e.g., one loaded with phenylalanine) enters the A site; a peptide bond forms between the second and the third amino acids; the second tRNA exits the P site; translocation of the ribosome along the mRNA displays the next codon for arginine in the A site while shifting the phe-loaded tRNA (now carrying a tripeptide) from the A to the P site; and so on. Eventually the system reaches one or more nonsense or stop codons (UAA, UAG, or UGA) causing the polypeptide chain to be released from the last tRNA, the last tRNA to be released from the ribosome, and the ribosome to be released from the mRNA Thus, the 5' end of mRNA corresponds to the amino terminus of the polypeptide chain; the 3' end of the mRNA corresponds to the carboxyl terminus of the polypeptide chain.
The preceding description of protein synthesis is only a broad outline of the process. Some important aspects of this process are performed differently in bacteria and in eukaryotes.
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