Chemistry 110. Bettelheim, Brown, Campbell & Farrell. Introduction to General, Organic and Biochemistry Chapter 22 Proteins

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1 hemistry 110 Bettelheim, Brown, ampbell & Farrell Ninth Edition Introduction to General, rganic and Biochemistry hapter 22 Proteins Step-growth polyamide (polypeptide) polymers or oligomers of L-α-aminoacids. Proteins have Many Functions Structure: Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails. atalysts: atalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes. Movement: muscles are made up of proteins called myosin and actin. Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes. ormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone. Protection: the body used proteins called antibodies to fight disease; blood clotting involves the protein fibrinogen. Storage: Storage: casein in milk and ovalbumin in eggs store nutrients for infants and birds; ferritin, a protein in the liver, stores iron. egulation: specific proteins control the expression of genes, others control when gene expression takes place. Peptides & Proteins Emil Fischer proposed in 1902 that proteins are long chains of amino acids joined by amide bonds. The special name given to the amide bond between the α-carboxyl group of one amino acid and the α-amino group of another is called a peptide bond. A short polymer of amino acids joined by peptide bonds are classified by the number of amino acids in the chain. A dipeptide is a molecule containing two amino acids joined by a peptide bond. A tripeptide is a molecule containing three amino acids joined by two peptide bonds. A A polypeptide is a macromolecule containing many amino acids joined by peptide bonds. A protein is defined as A protein is defined as a biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds. 1

2 Proteins and Amino Acids Proteins are step-growth polymers of alpha aminoacids. Proteins are of two types, fibrous and globular. Amino acid are compound that contains both an amino group and a carboxyl group. In α-amino acids the amino group is on the carbon adjacent to the carboxyl group. Although α-amino acids are commonly written in the unionized form, they are more properly written in the zwitterion (internal salt) form. With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral. Two α aminoacids, threonine and isoleucine, have a second stereocenter. The vast majority of α-amino acids have the L-configuration at the α-carbon. Proteins - Polymers of Alpha Aminoacids When a pure aminoacid is dissolved in water it has this form. The p will be a value called the pi. N 3 acidic solution p < 2.0 In strong Acid the aminoacid will be a cation, net positive. N 3 Aminoacids are ionic at all p values and remain soluble in aqueous solution. This is the isoelectric form. The molecule has no net charge. A zwitterion or internal salt. N 2 basic solution p > 10 In strong base the aminoacid will be an anion, net negative. The Standard Set of Amino Acids Always shown at the isoelectric point The "non-polar" side chain group: = N Glycine Gly G Phenylalanine Phe F Alanine Ala A Valine Val V Leucine Leu L 2 2 S 3 N Tryptophan Methionine Trp W Met M Isoleucine Ile I N 6.30 Proline Pro P 2

3 The Standard Set of Amino Acids Always shown at the isoelectric point N 3 The side chain has a polar, but neutral, group: = 2 2 N N Serine Ser S Threonine Thr T 5.41 Asparagine Asn N 5.65 Glutamine Gln Q These groups will orient in a protein so that they project toward the aqueous layer, and will not associate with nonpolar groups. They can form hydrogen bonds with water and with each other. The Standard Set of Amino Acids Always shown at the isoelectric point The side chain is acidic: = Aspartic Acid Glutamic Acid Asp D Glu E The side chain is basic: = N Lysine Lys K NN Arginine Arg N 3 2 S 5.63 Tyrosine 5.07 ysteine Tyr Y ys N 2 N N 7.64 istidine is Protein Behavior & Levels of Structure Proteins behave as zwitterions and have an isoelectric point, pi, because their side groups can be acidic and basic. emoglobin 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 their solutions. The primary structure is the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the - terminal amino acid. The secondary structure is the conformations of amino acids in localized regions of a polypeptide chain; examples are α-helix, β- pleated sheet, and random coil. The The tertiary structure is the overall conformation of a polypeptide chain. A quaternary structure is the arrangement of two or more polypeptide chains into a non-covalently bonded aggregation. 3

4 The Primary Structure of Proteins N N ' N " 2 2 N N N ' " N-terminal residue Peptide Bonds -terminal residue The primary structure of proteins is the specific sequence of aminoacids in the protein chain. Proteins are always written with the N-terminus on the left. Secondary Structure of Proteins N N N ' " N N N ' " ydrogen Bonds can form between adjacent strands of polypeptide or with different portions of the same strand. A stable alpha-helix has the hydrogen bonds forming between each peptide residue and the fourth peptide removed. In structural proteins a left-handed helix may form. A beta-pleated sheet has the hydrogen bonds between adjacent segments. The Alpha elix In a section of α-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- groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix. The = groups of peptide bonds point in the direction opposite the N- groups, also roughly parallel to the axis of the helix. The = group of each peptide bond is hydrogen bonded to the N- group of the peptide bond four amino acid units away from it. All the - groups of the aminoacids point outward from the helix 4

5 The Beta Pleated Sheet In a section of β-pleated sheet the six atoms of each peptide bond lie in the same plane. The = and N- groups of peptide bonds from adjacent chains point toward each other and are in the same plane so that hydrogen bonding is possible between them. All -groups on any one chain alternate, first above, then below the plane of the sheet, etc. The distinction between secondary structure (α-helix, β-pleated sheets) and tertiary structure is that secondary structures are stabilized only by hydrogen bonds arising through the peptide units, while tertiary structure may utilize more varied elements. Usually only certain portions of protein molecules, especially globular proteins, are α-helix or β-pleated sheets. The remainder is commonly random coil. Some proteins, e.g. keratin, are predominately α-helix. The ollagen Triplehelix ollagen consists of three polypeptide chains wrapped around each other in a ropelike twist to form a triple helix called tropocollagen. 30% of amino acids in each chain are proline and L- hydroxyproline (yp); L-hydroxylysine (yl) also occurs. Every third position is glycine and repeating sequences are X- Pro-Gly and X-yp-Gly. Each polypeptide chain is a helix, called an extended helix, but not an α-helix. The three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine. With age, the collagen helices become cross linked by covalent bonds formed between lysine residues. This is a factor in aging, muscle stiffness, etc. Tertiary Structure of Proteins The The tertiary structure of a protein is the overall conformation of a polypeptide chain caused by side-group interaction. The side-groups of proteins project outward from either the helices or the sheets. Side-groups in contact with the aqueous medium tend to cause folding of the helical strands or sheets. ydrophobic side-chains aggregate to minimize contact with water. They tend to tuck inside away from water. ydrophilic side-groups extend themselves in order to hydrogen-bond with the aqueous medium. 5

6 Tertiary Structure of Proteins The tertiary structure of a protein is stabilized in four ways: ovalent ovalent bonds, most commonly the formation of disulfide bonds between cysteine side chains. 2 S 2 N 3 [] 2 S S 2 N 3 N 3 ydrogen bonding between polar groups of side chains, such as between the - groups of serine and threonine. Salt Salt bridges, formation of ionic bonds, most commonly the attraction of the side group ammonium ions of one of the basic aminoacids, (lysine, arginine) and the - - in the side-group of one of the acidic aminoacids (aspartic acid, glutamic acid). ydrophobic interactions, such as between the nonpolar side chains of phenylalanine, leucine, isoleucine. Quaternary Structures of Proteins The The quaternary structure is the arrangement of polypeptide chains into a noncovalently bonded aggregation. The individual chains are held in together by hydrogen bonds, salt bridges, and hydrophobic interactions. Prosthetic Groups often get incorporated. 1) In one case, collagen, three helical coils form a triple helix, like a steel cable. Although the lysine side chain residues are linked together by covalent bonds, the triple strands of tropocollagen eventually overlap lengthwise to form fibrils or micro-fibres. 2) In another case, adult hemoglobin, two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each combine with each chain surrounding an iron-containing heme prosthetic group unit. Fetal hemoglobin is slightly different. Glycoproteins A A glycoprotein is a protein to which one or more carbohydrate units are bonded. There are two common types: xygen-linked saccharides in which a glycosidic bond between the anomeric carbon of a saccharide and the group of serine, threonine, or hydroxylysine has been formed. Example: the mucins which coat and protect mucous membranes. Nitrogen-linked saccharides in which an N-glycosidic bond between the anomeric carbon of N-acetyl-D-glucosamine and the nitrogen of the side chain amide group of asparagine has been formed. Examples are the proteoglycans. 2 2 N N 3 β-n-acetyl-d-glucosyl-serine 2 N 2 N N β-n-acetyl-d-glucosyl-asparagine 3 6

7 Denaturation Denaturation is the process of destroying the native shape or conformation of a protein by chemical or physical means. Some denaturations are reversible, while others permanently damage the protein. Methods involve both physical and chemical means. Few methods change the primary structure of proteins. Physical denaturing agents include: eat eat can disrupt hydrogen bonding; in globular proteins unfolding of the polypeptide chains may occur resulting in coagulation and precipitation. Sonic disruption or whipping can disrupt tertiary and quaternary structure. Dehydration removal of water, drying-out can change tertiary and quaternary structure. Denaturation hemical denaturing agents include: 66 M aqueous urea will disrupt hydrogen bonding. Surface-active active agents such as detergents disrupt hydrogen bonding. educing educing agents commonly 2-mercaptoethanol ( 2 2 S) cleaves disulfide bonds by reducing -S-Sgroups to -S groups. Permanent wave processes do this. eavy eavy metal ions such as: Pb 2+, g 2+, and d 2+ form waterinsoluble salts with -S groups on cysteine. g 2+ for example forms -S-g-S-. Alcohols Alcohols affect the water content and hydrophobic/hydrophilic relationships. 70% ethanol, for example, which denatures proteins, is used to sterilize skin before injections Digestion of Proteins ydrolysis (breakdown) ecovers onstituent Amino Acids. Peptide Bonds N + 2 N ' + 2 N " N N ' N " Essential aminoacids, ones our bodies cannot make, are obtained this way from our diet. All the others can be obtained too. 7

8 ommon Properties of Proteins Protein shape is essential to its function. Sometimes changing its shape can be lethal Prions Proteinaceous Infectuous Particles are altered proteins that can cause natural proteins to change shape Mad ow disease or Bovine Spongiform Encephalopathy, Scrapie, Kuru, reutzfeldt-jacob disease. Sometimes a single aminoacid substitution can cause a protein to have the wrong shape. Sickle cell anemia is an example. Proteins have isoelectric points just like amino acids. At the isoelectric points proteins are uncharged (net neutral, dipolar) and clump together (precipitate, denature). Away from the isoelectric point they have a like charge, either positive or negative and repel each other thus remaining in solution. At the isoelectric point neither proteins nor amino acids will drift toward either electrode (anode or cathode) in an electric field. 8