Protein Synthesis

Protein Synthesis Follows a Plan Proteins Are Gene Products Decoding the Genetic Code

Transfer RNA Forms a Flat Cloverleaf Shape and a Folded "L" Shape

Modified Bases Are Present in Transfer RNA

Some tRNA Molecules Read More Than One Codon

Charging the tRNA with the Amino Acid

The Ribosome: The Cell's Decoding Machine

Three Possible Reading Frames Exist

The Start Codon Is Chosen

The Initiation Complexes Must Be Chosen

The tRNA Occupies Three Sites During Elongation of the Polypeptide

Termination of Protein Synthesis Requires Release Factors

Several Ribosomes Usually Read the Same Message at Once

Bacterial Messenger RNA Can Code for Several Proteins

Transcription and Translation Are Coupled in Bacteria

Some Ribosomes Become Stalled and Are Rescued

Differences between Eukaryotic and Prokaryotic Protein Synthesis

Initiation of Protein Synthesis in Eukaryotes

Protein Synthesis Is Halted When Resources Are Scarce

A Signal Sequence Marks a Protein for Export from the Cell

Molecular Chaperones Oversee Protein Folding

Protein Synthesis Occurs in Mitochondria and Chloroplasts

Proteins Are Imported into Mitochondria and Chloroplasts by Translocases Mistranslation Usually Results in Mistakes in Protein Synthesis The Genetic Code Is Not "Universal"

Unusual Amino Acids are Made in Proteins by Post-Translational Modifications

Selenocysteine: The 21st Amino Acid

Pyrrolysine: The 22nd Amino Acid

Many Antibiotics Work by Inhibiting Protein Synthesis

Degradation of Proteins

Ribosomes use the information carried by messenger RNA to make proteins.

Protein Synthesis Follows a Plan

Each protein is made using the genetic information stored in the chromosomes (see Ch. 3 for a brief overview). The genetic information is transmitted in two stages. First the information in the DNA is transcribed into messenger RNA (mRNA). The next step uses the information carried by the mRNA to give the sequence of amino acids making up a polypeptide chain. This involves converting the nucleic acid "language," the genetic code, to protein "language," and is therefore known as translation. This overall flow of information in biological cells from DNA to RNA to protein is known as the central dogma of molecular biology (see Chapter 3, Fig. 3.17) and was first formulated by Sir Francis Crick.

The decoding of mRNA is carried out by a submicroscopic machine called a ribo-some, which binds the mRNA and translates it. The ribosome moves along the mRNA reading the message and synthesizing a new polypeptide chain. Bacterial protein synthesis will be discussed first. The process is similar in higher organisms, but some of the details differ and will be considered later.

Gene products include proteins as well as non-coding RNA.

Proteins Are Gene Products

An early rule of molecular biology was Beadle and Tatum's dictum: "one gene—one enzyme" (see Ch. 1). This rule was later broadened to include other proteins in addition to enzymes. Proteins are therefore often referred to as "gene products." However, it must be remembered that some RNA molecules (such as tRNA, rRNA, small nuclear RNA) are never translated into protein and are therefore also gene products.

Furthermore, instances are now known where one gene may encode multiple proteins (Fig. 8.01). Two relatively widespread cases of this are known—alternative splicing and polyproteins. In eukaryotic cells, the coding sequences of genes are often interrupted by non-coding regions, the introns. These introns are removed by splicing at the level of messenger RNA. Alternative splicing schemes may generate multiple mRNA molecules and therefore multiple proteins from the same gene. This is especially frequent in higher eukaryotes, in particular vertebrates (see Ch. 12).A set of proteins generated in this manner shares much of their sequence and structure.

gene product End product of gene expression;usually a protein but includes various untranslated RNAs such as rRNA, tRNA, and snRNA messenger RNA The type of RNA molecule that carries genetic information from the genes to the rest of the cell ribosome The cell's machinery for making proteins translation Making a protein using the information provided by messenger RNA

Decoding the Genetic Code 199

FIGURE 8.01 How Many Proteins Per Gene?

A) Normally each gene is transcribed giving one mRNA and this is translated into a single protein. Variations in the normal theme are B) alternative splicing, C) polyproteins and D) multiple proteins due to the use of different reading frames.

One mRMA

One protein

B) Alternative splicing

One mRMA

One protein

C) POLYPROTEIN

Multiple different mRNAs Multiple proteins

D) FRAMESHIFT

One mRNA Multiple proteins

RNA of Polyprotein Smaller proteins virus are cut out from polyprotein

Although there are exceptions, most genes give rise to a single protein.

In eukaryotic cells, mRNA only carries information from a single gene and therefore can only be translated into a single protein.This causes problems for certain viruses that infect eukaryotic cells and which have RNA genomes (see Ch. 17). To circumvent the problem, these viruses make a huge "polyprotein" from an extremely long coding sequence in their RNA. This polyprotein is then cut up into several smaller proteins.

Finally, there are occasional oddities, such as the generation of two proteins from the same gene due to frameshifting (see below). Despite these exceptions, it is still generally true that most genes give rise to a single protein.

Just as the total genetic information of a cell is the genome, so the total number of different proteins that a cell can produce is sometimes known as the proteome. In bacteria there is an almost one-for-one correspondence between genes and proteins. However, in higher organisms where alternative splicing is common, there may be an average of two or three final proteins per gene and so the proteome may be significantly larger than the genome.

Each amino acid in a protein is encoded by three bases in the DNA or RNA sequence.

Decoding the Genetic Code

There are 20 amino acids in proteins but only four different bases in the mRNA. So one cannot simply use one base of a nucleic acid to code for a single amino acid when making a protein. During translation, the bases of mRNA are read off in groups of three, which are known as codons. Each codon represents a particular amino acid. Four different bases gives 64 possible groups of three bases; that is, 64 different codons in the genetic code. Because there are only 20 different amino acids, some are encoded by more than one codon. In addition, three of the codons are used for punctuation. Those are the stop codons that signal the end of a polypeptide chain.Figure 8.02 shows nature's genetic code.

To read the codons, a set of adapter molecules that recognize the codon on the mRNA at one end and carry the corresponding amino acid attached to their other end codon Group of three RNA or DNA bases that encodes a single amino acid genetic code System for encoding amino acids as groups of three bases (codons) of DNA or RNA

proteome The set of all proteins that an organism can make stop codon Codon that signals the end of a protein

FIGURE 8.02 Code

The Genetic

2nd (middle) base

The 64 codons as found in messenger RNA are shown with their corresponding amino acids. As usual, bases are read from 5' to 3' so that the first base is at the 5' end of the codon. Three codons (UAA, UAG, UGA) have no cognate amino acid but signal stop. AUG (encoding methionine) and, less often, GUG (encoding valine) act as start codons. To locate a codon, find the first base in the vertical column on the left, the second base in the horizontal row at the top and the third base in the vertical column on the right.

2nd (middle) base

1st base

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