Peptides and Proteins

PEPTIDES

Peptide - unbranched chain of amino acids; further classified by number of amino acids present in chain

  • Dipeptide - 2

  • tripeptide - 3

  • Oligopeptide - peptides with 10 to 20 amino acid residues

  • Polypeptide - long unbranched chain of amino acids

Peptide bond - covalent bond between the carboxyl group of one amino acid and the amino group of another amino acid

  • N-terminal end (H3N)

  • C-terminal end (COO-)

Amino acid residue - portion of amino acid structure that remains, after the release of H2O during peptide bond formation

Peptide nomenclature

  • Rule 1: C-terminal amino acid residue keep its full name

  • Rule 2 : All other amino acid residue end in -yl

    • except (tryptophol, cysteinyl, glutaminyl and asparaginyl)

  • Rule 3: Amino acid naming sequence begins at N-terminal end

    • A. Glu-Ser-Ala = Glutamylserylalanine

    • B. Gly-Tyr-Leu-Val = Glycyltyrosylleucylvaline

BIOCHEMICALLY IMPORTANT SMALL PEPTIDES

Small Peptide Hormones - nonapeptide; 6 residues held in form of loop by disulfide bond from cysteine residues

  • Oxytocin - regulates uterine contractions and lactations

  • Vasopressin (ADH - Antidiuretic Hormone) - function in kidneys, decrease

    urine output, to decrease H2O eliminated during dehydration

Small peptide neurotransmitters

  • Enkephalins - pentapeptide neurotransmitters, bind at receptor sites of brain

    to reduce pain

Small peptide Antioxidants

  • Glutathione - tripeptide, regulator of redox reaction, protect cells from

    peroxides and superoxides

GENERAL STRUCTURE OF PROTEINS

Protein- peptide with at least 40 amino acid residues; protein and polypeptide used interchangeably.

  • 10,000 amino acid on most proteins, 400-500 amino acid residues on

    some proteins, 40-100 on small proteins.

    • Monomeric protein - one peptide chain

    • Multimeric Protein - more than 1 peptide chain

Simple Protein - only Amino Acid is present, may have sub unit as long as amino acid is present

Conjugated Protein - more than one peptide chain and contain non amino acid entities

  • Lipoproteins - lipid prosthetic groups,

  • glycoproteins - carbohydrate groups,

  • metalloproteins - specific metal,

Prosthetic group - non amino acid group present in conjugated protein

PRIMARY STRUCTURE OF PROTEINS

Primary Protein Structure - order in which amino acid are linked together in proteins

  • Order of attachment in peptide bonds

  • Same regardless of where protein is found in organism.

  • Peptide bonds = backbone of protein

  • C and N atoms arranged in zigzag

Peptide linkages can be planar or zigzag

Secondary Structure of Proteins

  • The α-helix - protein chain = coiled spring; maintained by H bonds (intramolecular), Hydrogen bonds between every fourth amino acid

    • H bond between C=O and N-H are parallel to axis of helix

    • H bond involves C=O and N-H group of amino acid

    • four amino acid residues along the spiral;

    • 1 turn of spiral is = 3.6 amino acid residue

    • Amino acid R groups extend outward from spiral, no room for R group within

  • (β-pleated sheet)- two extended protein segments in same or different

    molecules held together by H bonds

    • Either in single chain that folds back to itself (intrachain), or atoms of different

      peptide chain (interchain)

    • In molecules where β-pleated sheet involves single molecule, U-turns are

      needed to form structure

  • Unstructured segments - contain neither (α-helix) or (β-pleated sheet)

Tertiary Structure of Proteins

Interactions Responsible for Tertiary Structure

  • Disulfide Bonds - strongest bond for tertiary structure,-SH of two cysteine to form covalent bond ; intramolecular or intermolecular disulfide bond

  • Electrostatic Interaction (Salt Bridges) - acidic R group and basic R group: at

    different pH carry charges -COO- and NH3+, cation and anion

  • Hydrogen Bonds - occur in amino acids with polar R groups; weak, disrupted

    by pH changes

  • Hydrophobic interactions - two nonpolar side chains, polar group outward

    (toward solvent), nonpolar side chains inward and interact;

Quaternary Structure of Proteins- Only in multimeric proteins, sub units independent, not covalently bonded

  • Organization among peptide sub units on multimeric proteins

  • Two subunits = dimer, four subunits = tetramer; non covalent interactions contribute to structure; Hydrophobic interactions most important

Protein Hydrolysis

- When protein in solution of strong base and strong acid is heated, peptide bonds are hydrolyzed and free amino acids are produced

Complete protein hydrolysis - all peptide bonds are broken, Amino acids are the only products

Partial protein hydrolysis, - some peptide bonds are broken , Amino acids and small peptides are produced

Protein Denaturation

  • partial or complete disorganization of 3d structure, disruption of secondary, tertiary and quaternary structural interactions

  • cannot affect the primary structure

  • biochemical function of protein depends on 3D structure, loss of

  • biochemical function = denaturation

  • some refold 3D structure = renaturation; extensive denaturation is irreversile

  • loss of water solubility = consequence of denaturation ; coagulation =precipitation out of solution of denatured protein

Protein Classification Based on Shape

Fibrous protein - molecules w/ elongated shape & one dimension much longer - Linear and form aggregate to form macromolecular structure

  • α-Keratin - Fibrous protein, major constituent of hair, feathers, wool, fingernails and

    toenails, claws, scales, horns, turtle shells, quills, and hooves Coiling @ higher levels produce strength, intercoil disulfide bridge

  • Collagen - most abundant of all proteins in humans (30% of total body protein), is a

    major structural material in tendons, ligaments, blood vessels, and skin Rich proline content = triple helix conformation; form fibrils with cross linking on helices; stiffening of skin associated with aging

Globular protein - peptide chains folded into spherical or globule shapes Hydrophilic side chains on outside; hydrophobic in interior

Protein Classification Based on Function

Catalytic proteins - Role of biochemical catalysts = enzymes

Defense proteins - immunoglobulins or antibodies fxn in immune system

Transport proteins- Bind to small biomolecules and transport e.g. hemoglobin

Messenger proteins - transmit signals to coordinate biochemical processes between different cells, tissues, and organ ex. Hormones

Contractile proteins - Necessary for movement. Filament like proteins in muscles, flagella of sperm

Structural proteins - Stiffness and rigidity ex. Collagen & keratin

Transmembrane proteins - cell membrane and control movement

Storage proteins - Bind & store molecules for future use ex ferritin

Nutrient proteins - Important in early stages of life e.g. Casein in milk

Regulatory proteins - Site of binding for messenger proteins & enact function

Fluid-balance proteins - Maintain fluid balance between blood & tissue; e.g. albumin and globulin in capillary beds

Glycoproteins -conjugated proteins that contain carbohydrates or carbohydrate derivatives in addition to amino acids.

Lipoproteins - conjugated proteins that are composed of both lipids and amino acids. Lipoproteins are classified on the basis of their density

  • plasma lipoprotein - involved in the transport system for lipids in the bloodstream

  • Chylomicrons - transport dietary triacylglycerols from the intestine to the liver and to adipose tissue.

  • Very-low-density lipoproteins (VLDL) - Transport triacylglycerols synthesized in the liver to adipose tissue.

  • Low-density lipoproteins (LDL) - transport cholesterol synthesized in the liver to cells throughout the body.

  • High-density lipoproteins (HDL) - collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.