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Chapter 14. Proteins. Proteins. Proteins serve many functions, including the following. Given are examples of each. Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails

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Chapter 14
Chapter 14

Proteins


Proteins
Proteins

  • Proteins serve many functions, including the following. Given are examples of each.

    • Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails

    • Catalysts: 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

    • Hormones: many hormones are proteins, among them insulin and human growth hormone


Proteins1
Proteins

  • Protection: blood clotting involves the protein fibrinogen; the body uses proteins called antibodies to fight disease

  • Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron

  • Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place

  • Proteins are divided into two types:

    • fibrous proteins (water insoluble)

    • globular proteins (more soluble)


  • Amino acids
    Amino Acids

    • Amino acid: a compound that contains both an amino group and a carboxyl group

      • -amino acid: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group

      • although -amino acids are commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt) form


    Chirality of amino acids
    Chirality of Amino Acids

    • With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the -carbon) and are chiral

      • the vast majority of -amino acids have the L-configuration at the -carbon


    Chirality of amino acids1
    Chirality of Amino Acids

    • A comparison of the stereochemistry of L-alanine and D-glyceraldehyde


    20 protein derived aa
    20 Protein-Derived AA

    • Nonpolar side chains (at pH 7.0)


    20 protein derived aa1
    20 Protein-Derived AA

    • Polar side chains (at pH 7.0)


    20 protein derived aa2
    20 Protein-Derived AA

    • Acidic and basic side chains (at pH 7.0)


    20 protein derived aa3
    20 Protein-Derived AA

    1. All 20 are -amino acids (10 are essential)

    2. For 19 of the 20, the -amino group is primary; for proline, it is secondary

    3. With the exception of glycine, the a-carbon of each is a stereocenter

    4. Isoleucine and threonine contain a second stereocenter


    Ionization vs ph
    Ionization vs pH

    • The net charge on an amino acid depends on the pH of the solution in which it is dissolved

      • if we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion

      • if we now add a strong acid such as HCl to bring the pH of the solution to 2.0 or lower, the strong acid donates a proton to the -COO- of the amino acid turning the zwitterion into a positive ion


    Ionization vs ph1
    Ionization vs pH

    • if we add a strong base such as NaOH to the solution and bring its pH to 10.0 or higher, a proton is transferred from the NH3+ group to the base turning the zwitterion into a negative ion

    • to summarize


    Isoelectric point
    Isoelectric Point

    • Isoelectric point, pI:

      the pH at which the majority of molecules of a compound in solution have no net charge


    Characteristics of amino acids
    Characteristics of amino acids

    • The functions of the amino acids and their polymers and proteins are ultimately determined by their side chains (polar, nonpolar, acidic, basic, aromatic, etc.)

    • One of the 20 common amino acids, cysteine, has a chemical property not shared by any of the others.


    Cysteine
    Cysteine

    • The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide)


    Peptides
    Peptides

    • In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds

      • peptide bond: the special name given to the amide bond between the -carboxyl group of one amino acid and the -amino group of another


    Peptides1
    Peptides

    • peptide: a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain

    • dipeptide: a molecule containing two amino acids joined by a peptide bond

    • tripeptide: a molecule containing three amino acids joined by peptide bonds

    • polypeptide: a macromolecule containing many amino acids joined by peptide bonds

    • protein: a biological macromolecule containing at least 30 to 50 amino acids joined by peptide bonds


    Writing peptides
    Writing Peptides

    • by convention, peptides are written from the left, beginning with the free -NH3+ group and ending with the free -COO- group on the right

    • C-terminal amino acid: the amino acid at the end of the chain having the free -COO- group

    • N-terminal amino acid: the amino acid at the end of the chain having the free -NH3+ group


    Peptides and proteins
    Peptides and Proteins

    • proteins behave as zwitterions

    • proteins also have an isoelectric point, pI

      • hemoglobin 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

      • at any pH above the isoelectric point, the protein molecules have a net negative charge; below the isoelectric point the net charge is positive

      • proteins are least soluble in water at their isoelectric points and can be precipitated from their solutions


    Levels of structure
    Levels of 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: conformations of amino acids in localized regions of a polypeptide chain; examples are a-helix, b-pleated sheet, and random coil

    • Tertiary structure: the overall conformation of a polypeptide chain

    • Quaternary structure: the arrangement of two or more polypeptide chains into a noncovalently bonded aggregation


    Primary structure
    Primary Structure

    • Primary structure: the sequence of amino acids in a polypeptide chain

    • The number peptides derived 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

      • the number of peptides possible for a chain of n amino acids is 20n

      • for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078, which is possibly greater than the number of atoms in the universe


    Primary structure1
    Primary Structure

    • Just 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 disulfide bonds

      • in the table are differences between four types of insulin


    Bovine

    insulin

    Fig 21.4, p.533


    Primary structure2
    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 that aid in the secretion of milk


    Secondary structure
    Secondary Structure

    • Secondary structure: conformations of amino acids in localized regions of a polypeptide chain

      • the most common types of secondary structure are a-helix and b-pleated sheet

      • a-helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral

      • b-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


    A helix
    a-Helix

    Pink = O, Blue = N


    A helix1
    a-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

      • N-H groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix

      • 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


    B pleated sheet
    b-Pleated Sheet


    B pleated sheet1
    b-Pleated Sheet

    • In a section of b-pleated sheet

      • the six atoms of each peptide bond lie in the same plane

      • the C=O and N-H 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 R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.


    Random coil

    Another secondary

    structure

    Fig 21.7, p.538


    Enzyme

    with all

    three

    structures

    Fig 21.8, p.538


    Collagen triple helix
    Collagen Triple Helix

    • 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 Pro and L-hydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs

    • every third position is Gly and repeating sequences are X-Pro-Gly and X-Hyp-Gly

    • each polypeptide chain is a helix but not an a-helix

    • the three strands are held together by hydrogen bonding involving hydroxyproline and hydroxylysine

    • with age, collagen helices become cross linked by covalent bonds formed between Lys residues



    Tertiary structure
    Tertiary Structure

    • Tertiary structure: the overall conformation of a polypeptide chain

    • Tertiary structure is stabilized in four ways

      • covalent bonds, as for example the formation of disulfide bonds between cysteine side chains

      • hydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine

      • salt bridges, as for example the attraction of the -NH3+ group of lysine and the -COO- group of aspartic acid

      • hydrophobic interactions, as for example between the nonpolar side chains of phenylalanine and isoleucine




    Quaternary structure
    Quaternary Structure

    • Quaternary structure: 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

    • Hemoglobin

      • adult hemoglobin: two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each

      • each chain surrounds an iron-containing heme unit

      • fetal hemoglobin: two alpha chains and two gamma chains; fetal hemoglobin has a greater affinity for oxygen than does adult hemoglobin




    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 can disrupt hydrogen bonding; in globular proteins, it can cause unfolding of polypeptide chains with the result that coagulation and precipitation may take place


    Denaturation1
    Denaturation

    • 6 M aqueous urea: disrupts hydrogen bonding

    • surface-active agents: detergents such as sodium dodecylsulfate (SDS) disrupt hydrogen bonding

    • reducing agents: 2-mercaptoethanol (HOCH2CH2SH) cleaves disulfide bonds by reducing -S-S- groups to -SH groups

    • heavy metal ions: transition metal ions such as Pb2+, Hg2+, and Cd2+ form water-insoluble salts with -SH groups; Hg2+ for example forms -S-Hg-S-

    • alcohols: 70% ethanol, for example, which denatures proteins, is used to sterilize skin before injections


    Permanent wave

    or hair straightening.

    Hair = protein

    keratin

    Fig 21.UN, p.547



    Proteins2
    Proteins

    End

    Chapter 14


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