Protein Biosynthesis

The information that tells a cell how to build the proteins it needs to survive is coded in the structure of the DNA in the nucleus of that cell. This code can't be based on a one-to-one match between nucleotides and amino acids because there are only four nucleotides and there are 20 amino acids that must be coded. If the nucleotides are grouped in threes, however, there are 64 possible triplets, or codons, which is more than enough combinations to code for the 20 amino acids.

To understand how proteins are made, we have to divide the decoding process into two steps. DNA only stores the genetic information, it isn't involved in the process by which the information is used. The first step in protein biosynthesis therefore has to involve transcribing the information in the DNA structure into a useful form. In a separate step, this information can be translated into a sequence of amino acids.

Before the information in DNA can be decoded, a small portion of the DNA double helix must be uncoiled. A strand of RNA is then synthesized that is a complementary copy of one strand of the DNA.

Assume that the section of the DNA that is copied has the following sequence of nucleotides, starting from the 3´ end.

When we predict the sequence of nucleotides in the RNA complement, we have to remember that RNA uses U where T would be found in DNA. We also have to remember that base pairing occurs between two chains that run in opposite directions. The RNA complement of this DNA should therefore be written as follows.

Since this RNA strand contains the message that was coded in the DNA, it is called messenger RNA, or mRNA.

The messenger RNA now binds to a ribosome, where the message is translated into a sequence of amino acids. The amino acids that are incorporated into the protein being synthesized are carried by relatively small RNA molecules known as transfer RNA, or tRNA. There are at least 60 tRNAs, which differ slightly in their structures, in each cell. At one end of each tRNA is a specific sequence of three nucleotides that can bind to the messenger RNA. At the other end is a specific amino acid. Thus, each three-nucleotide segment of the messenger RNA molecule codes for the incorporation of a particular amino acid. The relationship between the triplets, or codons, on the mRNA and the amino acids is shown in the table below.

First Position (5' End)	Second Position				Third Position (3' End)
First Position (5' End)	U	C	A	G	Third Position (3' End)
	Phe	Ser	Tyr	Cys	U
U	Phe	Ser	Tyr	Cys	C
	Leu	Ser	^a	^a	A
	Leu	Ser	^a	Trp	G
	Leu	Pro	His	Arg	U
C	Leu	Pro	His	Arg	C
	Leu	Pro	Gln	Arg	A
	Leu	Pro	Gln	Arg	G
	Ile	Thr	Asn	Ser	U
A	Ile	Thr	Asn	Ser	C
	Ile	Thr	Lys	Arg	A
	Met	Thr	Lys	Arg	G
	Val	Ala	Asp	Gly	U
G	Val	Ala	Asp	Gly	C
	Val	Ala	Glu	Gly	A
	Val	Ala	Glu	Gly	G
^aThere are three triplets code for termination of the polypeptide chain: UAA, UGA, and UAG.

Practice Problem 4:

Assume that the DNA chain that codes for the synthesis of a particular protein contains the triplet A-G-T (reading from the 3´ to the 5´ end). Predict the sequence of nucleotides in the triplet, or codon, that would be built in the messenger RNA constructed on this DNA template. Then predict the amino acid that would be incorporated at this point in the protein.

Click here to check your answer to Practice Problem 4

The signal to start making a polypeptide chain in simple, prokaryotic cells is the triplet AUG, which codes for the amino acid methionine (Met). The synthesis of every protein in these cells therefore starts with a Met residue at the N-terminal end of the polypeptide chain. After the tRNA that carries Met binds to the start signal on the messenger RNA, a tRNA carrying the second amino acid binds to the next codon. A dipeptide is synthesized when the Met residue is transferred from the first tRNA to the amino acid on the second tRNA. If the DNA described in this section were translated, the dipeptide would be Met-Phe (reading from the N-terminal to the C-terminal amino acid).

The messenger-RNA now moves through the ribosome, and a tRNA carrying the third amino acid (Val) binds to the next codon. The dipeptide is then transferred to the amino acid on this third tRNA to form a tripeptide. This sequence of steps continues until one of three codons is encountered: UAA, UGA, or UAG. These codons give the signal for terminating the synthesis of the polypeptide chain, and the chain is cleaved from the last tRNA residue.

The sequence of DNA described in this section would produce the following sequence of amino acids.

This polypeptide is not necessarily an active protein. All proteins in prokaryotic cells start with Met when synthesized, but not all proteins have Met first in their active form. It is often necessary to clip off this Met after the polypeptide has been synthesized to give a protein with a different N-terminal amino acid.

Modifications to the polypeptide often have to be made before an active protein is formed. Insulin, for example, consists of two polypeptide chains connected by disulfide linkages. In theory, it would be possible to make these chains one at a time and then try to assemble them to make the final protein. Nature, however, has been more subtle. The polypeptide chain that is synthesized contains a total of 81 amino acids. All of the disulfide bonds that will be present in insulin are present in this chain. The protein is made when a sequence of 30 amino acids is clipped out of the middle of this polypeptide chain.

3´		T-A-C-A-A-G-C-A-G-T-T-G-G-T-C-G-T-G...		5´		DNA
5´		A-U-G-U-U-C-G-U-C-A-A-C-C-A-G-C-A-C...		3´		mRNA