Chapter 14 Proteins

Peptides and Proteins Proteins behave as zwitterions. isoelectric point, pI Proteins also have an isoelectric point, pI. ◦ At its isoelectric point, the protein has no net charge. ◦ At any pH above (more basic than) its pI, it has a net negative charge. ◦ At any pH below (more acidic than) its pI, it has a net positive charge. ◦ Hemoglobin, for example, has an almost equal number of acidic and basic side chains; its pI is 6.8. ◦ Serum albumin has more acidic side chains; its pI is 4.9. ◦ Proteins are least soluble in water at their isoelectric points and can be precipitated from solution at this pH.

Levels of Structure Primary structure: Primary structure: The sequence of amino acids in a polypeptide chain. Read from the N-terminal amino acid to the C-terminal amino acid. Secondary structure: Secondary structure: Conformations of amino acids in localized regions of a polypeptide chain. Examples are  -helix,  -pleated sheet, and random coil. Tertiary structure: Tertiary structure: The complete three-dimensional arrangement of atoms of a polypeptide chain. Quaternary structure: Quaternary structure: The spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.

Primary Structure Primary structure: Primary structure: The sequence of amino acids in a polypeptide chain. The number peptides possible from the 20 protein-derived amino acids is enormous. ◦ There are 20 x 20 = 400 dipeptides possible. ◦ There are 20 x 20 x 20 = 8000 tripeptides possible. n 20 n ◦ The number of peptides possible for a chain of n amino acids is 20 n. ◦ For a small protein of 60 amino acids, the number of proteins possible is = 10 78, which is possibly greater than the number of atoms in the universe!

Primary Structure Figure 14.8 The hormone insulin consists of two polypeptide chains, A and B, held together by two disulfide bonds. The sequence shown here is for bovine insulin.

Primary Structure How important is the exact amino acid sequence? ◦ Human insulin consists of two polypeptide chains having a total of 51 amino acids; the two chains are connected by two interchain disulfide bonds. ◦ In the table are differences between four types of insulin.

Primary Structure ◦ Vasopressin and oxytocin are both nonapeptides but have quite different biological functions. ◦ Vasopressin is an antidiuretic hormone. ◦ Oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk.

Figure 22.9 The structures of vasopressin an oxytocin. Differences are shown in color.

Secondary Structure Secondary structure: Secondary structure: describes the repetitive conformation assumed by the segment of the backbone of a peptide or protein ◦ The most common types of secondary structure are  -helix and  -pleated sheet. ◦ -Helix: ◦ -Helix: A type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral. ◦ -Pleated sheet: ◦ -Pleated sheet: A type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel.

Secondary Structure: The  -Helix Figure 14.10(a) The  -Helix.

 -Helix  -Helix In a section of  -helix ◦ There are 3.6 amino acids per turn of the helix. ◦ The six atoms of each peptide bond lie in the same plane. ◦ The N-H groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix. ◦ The C=O groups of peptide bonds point in the opposite direction, also roughly parallel to the axis of the helix. ◦ The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it. ◦ All R- groups point outward from the helix.

 -Helix The model is an  -helix section of polyalanine, a polypeptide derived entirely from alanine. The intrachain hydrogen bonds that stabilize the helix are visible as the interacting C=O and N-H bonds.

 -Pleated Sheet Figure 14.10(b) The  -pleated sheet structure.

 -Pleated sheet  -Pleated sheet In a section of  -pleated sheet; ◦ The polypeptide backbone is extended in a zigzag structure resembling a series of pleats. ◦ The six atoms of each peptide bond of a  -pleated sheet lie in the same plane. ◦ The C=O and N-H groups of the peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them. ◦ All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.

β-Pleated Sheet

Secondary Structure Many globular proteins contain all three kinds of secondary structure in different parts of their molecules:  -helix,  -pleated sheet, and random coil Figure Schematic structure of the enzyme carboxypeptidase. The  -pleated sheet sections are shown in blue, the  -helix portions in green, and the random coils as orange strings.

Random Coil Figure The rest of the molecule is a random coil.

Tertiary Structure Tertiary structure: Tertiary structure: the overall conformation of an entire polypeptide chain. Tertiary structure is stabilized in four ways: ◦ Covalent bonds ◦ Covalent bonds, as for example, the formation of disulfide bonds between cysteine side chains. ◦ Hydrogen bonding ◦ Hydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine. ◦ Salt bridges ◦ Salt bridges, as for example, the attraction of the - NH 3 + group of lysine and the -COO - group of aspartic acid. ◦ Hydrophobic interactions ◦ Hydrophobic interactions, as for example, between the nonpolar side chains of phenylalanine and isoleucine.

The Collagen Triple Helix Figure The collagen triple helix.

Non covalent interactions that stabilize the tertiary and quaternary structures of protein: a) Hydrogen bonding, b) salt bridge, c) hydrophobic interaction, and d) Metal ion coordination

Tertiary Structure Figure Forces that stabilize tertiary structures of proteins.

Quaternary Structure Quaternary structure: Quaternary structure: The threee-dimension arrangement of every atom in the molecule. ◦ The individual chains are held together by hydrogen bonds, salt bridges, and hydrophobic interactions. Hemoglobin ◦ Adult hemoglobin: ◦ Adult hemoglobin: Two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each. ◦ Fetal hemoglobin: ◦ Fetal hemoglobin: Two alpha chains and two gamma chains. Fetal hemoglobin has a greater affinity for oxygen than does adult hemoglobin. ◦ Each chain surrounds an iron-containing heme unit.

Quaternary Structure Figure The quaternary structure of hemoglobin. The structure of heme is shown on the next screen.

Quaternary Structure Figure The structure of heme

Quaternary Structure Integral membrane proteins form quaternary structures in which the outer surface is largely nonpolar (hydrophobic) and interacts with the lipid bilayer. Two of these are shown on the next screens. Figure Integral membrane protein of rhodopsin, made of  - helices.

Quaternary Structure Figure An integral membrane protein from the outer mitochondrial membrane forming a  - barrel from eight  -pleated sheets.

Denaturation Denaturation Denaturation: The process of destroying the native conformation of a protein by chemical or physical means. ◦ Some denaturations are reversible, while others permanently damage the protein. Denaturing agents include: ◦ Heat: ◦ Heat: heat can disrupt hydrogen bonding; in globular proteins, it can cause unfolding of polypeptide chains with the result that coagulation and precipitation may take place.

Denaturation ◦ 6 M aqueous urea: ◦ 6 M aqueous urea: Disrupts hydrogen bonding. ◦ Surface-active agents: ◦ Surface-active agents: Detergents such as sodium dodecylbenzenesulfate (SDS) disrupt hydrogen bonding. ◦ Reducing agents: ◦ Reducing agents: 2-Mercaptoethanol (HOCH 2 CH 2 SH) cleaves disulfide bonds by reducing -S-S- groups to -SH groups. ◦ Heavy metal ions: ◦ Heavy metal ions: Transition metal ions such as Pb 2+, Hg 2+, and Cd 2+ form water-insoluble salts with -SH groups; Hg 2+ for example forms -S-Hg-S-. ◦ Alcohols: ◦ Alcohols: 70% ethanol penetrates bacteria and kills them by coagulating their proteins. It is used to sterilize skin before injections.