Introduction to Proteins PDF

Introduction to proteins  The second product of genome expression is the proteome-------- ----the cell’s collection of proteins, which specifies the nature of the biochemical reactions that the cell is able to carry out. These proteins are synthesized by translation of the mRNA molecules t...

Introduction to proteins  The second product of genome expression is the proteome-------- ----the cell’s collection of proteins, which specifies the nature of the biochemical reactions that the cell is able to carry out. These proteins are synthesized by translation of the mRNA molecules that make up the transcriptome. Protein structure A protein, like a DNA molecule, is a linear, unbranched polymer. In proteins, the monomeric subunits are called amino acids and the resulting polymers, or polypeptides, are rarely more than 2000 units in length. History – As with DNA, the key features of protein structure were determined in the first half of the twentieth century, this phase of protein biochemistry ending in the 1940s and early 1950s with the elucidation by Pauling and Corey of the major conformations, or secondary structures, taken up by polypeptides. – In recent years, interest has focused on how these secondary structures combine to produce the complex, three-dimensional shapes of proteins. The general structure of an amino acid. All amino acids have the same general structure, comprising a central α-carbon attached to a hydrogen atom, a carboxyl group, an amino group, and an R group. The R group is different for each amino acid The drawing shows the chemical reaction that results in two amino acids becoming linked together by a peptide bond.  The four levels of protein structure The primary structure of the protein is formed by joining amino acids into a polypeptide. The amino acids are linked by peptide bonds that are formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of a second amino acid(see fig.). As with a polynucleotide, the two ends of the polypeptide are chemically distinct: one has a free amino group and is called the amino, NH2–, or N terminus; the other has a free carboxyl group and is called the carboxyl, COOH–, or C terminus. The direction of the polypeptide can therefore be expressed as either N C (left to right, fig.) or C N (right to left fig.) The secondary structure refers to the different conformations that can be taken up by the polypeptide. The two main types ᵦ of secondary structure are the a α-helix and b -sheet (see in fig.). These are stabilized mainly by hydrogen bonds that form between different amino acids in the polypeptide  The two main secondary structural units found in proteins: (A) the a a-helix, and (B) the b b-sheet. The polypeptide chains are shown in outline. The R groups have been omitted for clarity. Each structure is stabilized by hydrogen (H) bonds between the C=O and N–H groups of different peptide bonds. The b-sheet conformation that is shown is anti- parallel, the two chains running in opposite directions. Parallel b- sheets can also occur.  The tertiary structure results from folding the secondary structural components of the polypeptide into a three-dimensional configuration (see fig.). The tertiary structure is stabilized by various chemical forces, – Hydrogen bonding between individual amino acids, – electrostatic interactions between the R groups of charged amino acids and – hydrophobic forces, which dictate that amino acids with nonpolar (“water-hating”) side-groups must be shielded from water by embedding within the internal regions of the protein. – There may also be covalent linkages called disulfide bridges between cysteine amino acid residues at various places in the polypeptide.  The tertiary structure of a protein. This imaginary protein structure comprises three α-helices, shown as coils, and a four-stranded b-sheet, indicated by the arrows.  The quaternary structure involves the association of two or more polypeptides, each folded into its tertiary structure, into a multi-subunit protein. Not all proteins form quaternary structures, but it is a feature of many proteins Some quaternary structures are held together by – disulfide bridges between the different polypeptides, resulting in stable multi-subunit proteins that cannot easily be broken down to the component parts. – Other quaternary structures comprise looser associations of subunits stabilized by hydrogen bonding and hydrophobic effects, which means that these proteins can revert to their component polypeptides, or change their subunit composition, according to the functional requirements of the cell. Proteoms  Comprises all the proteins present in a cell at a particular time. A “typical” mammalian cell,e.g. liver cell contain 10,000-20,000 different proteins, approx. 0.5 ng of protein or 18%–20% of the total cell weight. The copy numbers of individual proteins vary enormously – Any protein that is present at a copy number of >50,000 per cell is considered to be relatively abundant, and in the average mammalian cell some 2000 proteins fall into this category. – Most of protein are housekeeping proteins that perform general biochemical activities that occur in all cells. – The proteins that provide the cell with its specialized function are often quite rare (copy number is