Sequence
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Structure

Primary structure is the distinct sequence of amino acid residues that make up a polypeptide or protein.

If two peptides differ by only a single residue, they are different peptides, may have different charges, and different biochemical activities and effects.

Can you draw the structure of Nutrasweet? (Asp-Phe-Me) Hint: the Me indicates a methyl ester of the carboxyl group on the Phe residue.

How important is the primary sequence (the specific sequence of residues)?


Consider two similar peptides (the C-terminal NH2 is an amide):

Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH2 Vasopressin

Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2 Oxytocin

Both peptides are produced in the brain.

Vasopressin is produced in males by sexual arousal and during sexual intercourse. Elevated levels of this hormone in the brain seem to cause male bonding to the female and cause the male to act in an aggressive fashion toward other males. In Europe, vasopressin is used as a prescription drug inhaled through the nose to enhance brain performance and memory.

Oxytocin in produced in women during sexual intercourse and contributes to the muscle contractions of the orgasmic response. These contractions cause a greater proportion of the sperm to be retained in the vagina and delivered to the upper reproductive tract for fertilization. It has also been suggested that high levels of oxytocin contribute to multiple orgasms in women. If an ovum is fertilized and a fetus develops for the full term, oxytocin is again produced and is involved in the uterine contractions that are part of birth. The high levels of oxytocin cause a feeling of calmness and serenity following the birth and seem to cause the bonding of the mother to the child. When nursing, the nipple stimulation causes more oxytocin to be produced, which again causes a pleasant calmness and serenity and stimulates expulsion of the milk. This milk has high concentrations of oxytocin and may be involved in bonding the child to the mother.

The small changes in the sequence of these polypeptides gives them very different biological properties. A change in a single amino acid residue in a protein can alter or halt biological activities, causing disease or death.


Protein sequencing is normally accomplished via the Edman Degrdation method. The reagent phenylisothiocyanate is used to modify the N-terminus of the polypeptide. The modified residue is removed by hydrolysis and the next residue on the shortened chain is again modified in a cyclic process. Because the number of residues that can be sequentially identified is limited, proteins are specifically hydrolyzed by cyanogen bromide [local] or protease enzymes to produce smaller internal fragments that can be sequenced. Sequencing of fragments produced by two different methods produces the necessary overlapping sequence information to deduce the sequence of the protein.

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