Chapter 14 Proteins

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Chapter 14 Proteins
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Peptides and Proteins

• Proteins behave as zwitterions.
• 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.

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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 complete
  three-dimensional arrangement of atoms of a
  polypeptide chain.
• Quaternary structure The spatial relationship
  and interactions between subunits in a protein
  that has more than one polypeptide chain.

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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.
• 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!

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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.

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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.

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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.

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Figure 22.9 The structures of vasopressin an
oxytocin. Differences are shown in color.
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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
  a-helix and b-pleated sheet.
• a-Helix A type of secondary structure in which a
  section of polypeptide chain coils into a spiral,
  most commonly a right-handed 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.

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Secondary Structure The ?-Helix

• Figure 14.10(a) The ?-Helix.

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?-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 CO groups of peptide bonds point in the
  opposite direction, also roughly parallel to the
  axis of the helix.
• The CO 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.

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??-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 CO and N-H
  bonds.

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?-Pleated Sheet

• Figure 14.10(b) The ?-pleated sheet structure.

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?-Pleated sheet

• In a section of b-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 b-pleated
  sheet lie in the same plane.
• The CO 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.

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ß-Pleated Sheet
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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 14.12 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.
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Random Coil

• Figure 14.11
• The rest of the molecule is a random coil.

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Tertiary Structure

• Tertiary structure the overall conformation of
  an entire 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.

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The Collagen Triple Helix

• Figure 14.13 The collagen triple helix.

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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
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Tertiary Structure

• Figure 14.20 Forces that stabilize tertiary
  structures of proteins.

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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 Two alpha chains of 141 amino
  acids each, and two beta chains of 146 amino
  acids each.
• 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.

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Quaternary Structure

• Figure 14.22 The quaternary structure of
  hemoglobin. The structure of heme is shown on the
  next screen.

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Quaternary Structure

• Figure 14.18 The structure of heme

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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 14.19 Integral membrane protein of
rhodopsin, made of ?-helices.
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Quaternary Structure

• Figure 14.20 An integral membrane protein from
  the outer mitochondrial membrane forming a
  ?-barrel from eight ?-pleated sheets.

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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.

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Denaturation

• 6 M aqueous urea Disrupts hydrogen bonding.
• Surface-active agents Detergents such as sodium
  dodecylbenzenesulfate (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 penetrates bacteria and
  kills them by coagulating their proteins. It is
  used to sterilize skin before injections.

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