The Flow of Information from Stored to Active Form (Genetics & Inherited Conditions)
The cell can be viewed as a unit that assembles resources from the environment into biochemically functional molecules and organizes these molecules in three-dimensional space in a way that allows cellular growth and replication. In order to carry out this organizational process, a cell must have a biosynthetic means to assemble resources into useful molecules, and it must contain the information required to produce the biosynthetic and structural machinery. DNA serves as the stored form of this information, whereas protein is its active form. Although there are thousands of different proteins in cells, they either serve a structural role or are enzymes that catalyze the biosynthetic reactions of a cell. Following the discovery of the structure of DNA in 1953 by James Watson and Francis Crick, scientists began to study the process by which the information stored in this molecule is converted into protein.
Proteins are linear, functional molecules composed of a unique sequence of amino acids. Twenty different amino acids are used as the protein building blocks. Although the information for the amino acid sequence of each protein is present in DNA, protein is not synthesized directly from this source. Instead, RNA serves as the intermediate form from which proteins are synthesized. RNA plays three roles during protein synthesis. Messenger RNA (mRNA) contains the information for the amino acid...
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The Translation Process: Initiation (Genetics & Inherited Conditions)
Translation occurs in three phases: initiation, elongation, and termination. The function of the 40s ribosomal subunit is to bind to an mRNA and locate the correct AUG as the initiation codon. It does this by binding close to the cap at the 5′ end of the mRNA and scanning the nucleotide sequence in its 5′ to 3′ direction in search of the initiation codon. Marilyn Kozak identified a certain nucleotide sequence surrounding the initiator AUG of eukaryotic mRNAs that indicates to the ribosome that this AUG is the initiation codon. She found that the presence of an A or G three nucleotides prior to the AUG and a G in the position immediately following the AUG were critical in identifying the correct AUG as the initiation codon. This is referred to as the “sequence context” of the initiation codon. Therefore, as the 40s ribosomal subunit scans the leader sequence of an mRNA in a 5′ to 3′ direction, it searches for the first AUG in this context and may bypass other AUGs not in this context.
Nahum Sonenberg demonstrated that the scanning process by the 40s subunit can be impeded by the presence of stem-loop structures present in the leader sequence. These form from base pairing between complementary nucleotides present in the leader sequence. Two nucleotides are said to be complementary when they join together by hydrogen bonds. For instance, the nucleotide (or base) A is complementary to U, and...
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The Translation Process: Elongation and Termination (Genetics & Inherited Conditions)
During the elongation phase, tRNAs bind to the 80s ribosome as it passes over the codons of the mRNA, and the amino acids attached to the tRNAs are transferred to the growing polypeptide. Binding of the tRNAs to the ribosome is assisted by an accessory protein called eukaryotic elongation factor 1 (eEF1). A codon is decoded by the appropriate tRNA through base pairing between the three nucleotides that make up the codon in the mRNA and three complementary nucleotides within a specific region (called the anticodon) within the tRNA. The tRNA binding sites in the 80s ribosome are located in the 60s subunit. The ribosome moves over the coding region one codon at a time, or in steps of three nucleotides, in a process referred to as “translocation.” When the ribosome moves to the next codon to be decoded, the tRNA containing the appropriate anticodon will bind tightly in the open site in the 60s subunit (the A site). The tRNA that bound to the previous codon is present in a second site in the 60s subunit (the P site). Once a new tRNA has bound to the A site, the ribosomal RNA itself catalyzes the formation of a peptide bond between the growing polypeptide and the new amino acid. This results in the transfer of the polypeptide attached to the tRNA present in the P site to the amino acid on the tRNA present in the A site. A second elongation factor, eEF2, catalyzes the movement of the ribosome to the...
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Impact and Applications (Genetics & Inherited Conditions)
The elucidation of the process and control of protein synthesis provides a ready means by which scientists can manipulate these processes in cells. In addition to infectious diseases, insufficient dietary protein represents one of the greatest challenges to world health. The majority of people now living are limited to obtaining their dietary protein solely through the consumption of plant matter. Knowledge of the process of protein synthesis may allow molecular biologists to increase the amount of protein in important crop species. Moreover, most plants contain an imbalance in the amino acids needed in the human diet that can lead to disease. For example, protein from corn is poor in the amino acid lysine, whereas the protein from soybeans is poor in methionine and cysteine. Molecular biologists may be able to correct this imbalance by changing the codons present in plant genes, thus improving this source of protein for those people who rely on it for life.
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Further Reading (Genetics & Inherited Conditions)
Crick, Francis. “The Genetic Code III.” Scientific American 215 (October, 1966): 57. The codiscoverer of DNA’s helical structure provides a good summary of the code specifying the amino acids.
Lake, James. “The Ribosome.” Scientific American 245 (August, 1981): 84-97. Summarizes information about the structure and function of ribosomes.
Lewin, Benjamin. Genes IX. Sudbury, Mass.: Jones and Bartlett, 2007. Details the translational process.
Liljas, Anders. Structural Aspects of Protein Synthesis. Hackensack, N.J.: World Scientific, 2004. Summarizes the translation process for bacterial ribosomes and explains the functions of ribosomes. Illustrations.
Rich, Alexander, and Sung Hou Kim. “The Three-Dimensional Structure of Transfer RNA.” Scientific American 238 (January, 1978): 52-62. Presents a structural description of tRNA.
Tropp, Burton E., and David Freifelder. Molecular Biology: Genes to Proteins. 3d ed. Sudbury, Mass.: Jones and Bartlett, 2008. Includes two chapters about protein synthesis: “Protein Synthesis: The Genetic Code” and “Protein Synthesis: The Ribosome.”
Whitford, David. “Protein Synthesis, Processing, and Turnover.” In Proteins: Structure and Function. Hoboken, N.J.: John Wiley and Sons, 2005. This chapter of the textbook discusses the cell cycle, transcription, an outline of and the...
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Web Sites of Interest (Genetics & Inherited Conditions)
Natural Science Pages, DNA and Protein Synthesis. http://web.jjay.cuny.edu/~acarpi/NSC/12-dna.htm. One of the natural science pages created by Anthony Carpi, a professor at John Jay College in New York City, offers an explanation of DNA and protein synthesis, with links to additional information.
Online Biology Book. http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html#Links. Michael J. Farabee, a professor at the Maricopa Community Colleges, includes a page on protein synthesis, with links to additional information, in his online book.
Public Broadcasting Service (PBS), DNA Workshop Activity. http://www.pbs.org/wgbh/aso/tryit/dna/index.html. The workshop includes a page of information about protein synthesis and an interactive activity enabling users to become involved with the process of DNA replication and protein synthesis.
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Protein Synthesis (World of Microbiology and Immunology)
Protein synthesis represents the final stage in the translation of genetic information from DNA, via messenger RNA (mRNA), to protein. It can be viewed as a four-stage process, consisting of amino acid activation, translation initiation, chain elongation, and termination. The events are similar in both prokaryotes, such as bacteria, and higher eukaryotic organisms, although in the latter there are more factors involved in the process.
To begin with, each of the 20 cellular amino acids are combined chemically with a transfer RNA (tRNA) molecule to create a specific aminoacyl-tRNA for each amino acid. The process is catalyzed by a group of enzymes called aminoacyltRNA synthetases, which are highly specific with respect to the amino acid that they activate. The initiation of translation starts with the binding of the small subunit of a ribosome, (30S in prokaryotes, 40S in eukaryotes) to the initiation codon with the nucleotide sequence AUG, on the mRNA transcript. In prokaryotes, a sequence to the left of the AUG codon is recognized. This is the Shine-Delgrano sequence and is complementary to part of the small ribosome subunit. Eukaryotic ribosomes start with the AUG nearest the 5'-end of the mRNA, and recognize it by means of a "cap" of 7-methylguanosine triphosphate. After locating the cap, the small ribosome subunit moves along the mRNA until it meets the first AUG codon, where it combines with the large ribosomal subunit.
In both prokaryotes and eukaryotes, the initiation complex is prepared for the addition of the large ribosomal subunit at the AUG site, by the release of initiation factor (IF) 3. In bacteria, the large 50S ribosomal subunit appears simply to replace IF, with IF and IF. In eukaryotes, another factor eIF (eukaryotic initiation factor 5), catalyses the departure of the previous initiation factors and the joining of the large 60S ribosomal subunit. In both cases, the release of initiation factor 2 involves the hydrolysis of the GTP bound to it. At this stage, the first aminoacyl-tRNA, Met-tRNA, is bound to the ribosome. The ribosome can accommodate two tRNA molecules at once. One of these carries the Met-tRNA at initiation, or the peptide-tRNA complex during elongation and is thus called the P (peptide) site, while the other accepts incoming aminoacyl-tRNA and is therefore called the A (acceptor) site. What binds to the A site is usually a complex of GTP, elongation factor EF-TU, and aminoacyl-tRNA. The tRNA is aligned with the next codon on the mRNA, which is to be read and the elongation factor guides it to the correct nucleotide triplet. The energy providing GTP is then hydrolysed to GDP and the complex of EF-TU:GDP leaves the ribosome. The GDP is released from the complex when the EF-TU complexes with EF-TS, which is then replaced by GTP. The recycled EF-TU: GTP is then ready to pick up another aminoacyl-tRNA for addition to the growing polypeptide chain. On the ribosome, a reaction is catalysed between the carboxyl of the P site occupant and the free amino group of the A site occupant, linking the two together and promoting the growth of the polypeptide chain. The peptidyl transferase activity which catalyses this transfer is intrinsic to the ribosome. The final step of elongation is the movement of the ribosome relative to the mRNA accompanied by the translocation of the peptidyl-tRNA from the A to the P. Elongation factor EF-G is involved in this step and a complex of EF-G and GTP binds to the ribosome, GTP being hydrolysed in the course of the reaction. The de-acylated tRNA is also released at this time.
The end of polypeptide synthesis is signalled by a termination codon contacting the A site. Three prokaryotic release factors (RF) are known: RF is specific for termination codons UAA and UAG, while RF is specific for UAA and UGA. RF stimulates RF and RF, but does not in itself recognize the termination codons. RF also has GTPase activity and appears to accelerate the termination at the expense of GTP. Only one eukaryotic release factor is known and it has GTPase activity.
At any one time, there can be several ribosomes positioned along the mRNA and thus initiation, elongation and termination proceed simultaneously on the same length of mRNA. The three dimensional structure of the final protein begins to appear during protein synthesis before translation is completed. In many cases, after the synthesis of the amino acid chain, proteins are subjected to further reactions which convert them to their biologically active forms, e.g., by the attachment of chemical groups or by removal of certain amino acids processes known as post-translational modification.
See also Deoxyribonucleic acid (DNA); Genetic code; Molecular biology and molecular genetics; Ribonucleic acid (RNA)