Proteins are the most plentiful organic compounds in the body, making up more than half its dry weig

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• Proteins are the most plentiful organic compounds
  in the body, making up more than half its dry
  weight.
• The functions of proteins can be categorized
• Catalytic proteins, or enzymes
• Catalyze the synthesis and utilization of
  proteins (themselves), carbohydrates, lipids,
  nucleic acids, and almost all other biomolecules.
• Transport proteins
• Bind and carry specific molecules from place to
  place.
• Regulatory proteins
• Control cellular activity.

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• Structural proteins
• Give physical shape, and the strength to maintain
  it, to structures in animals.
• Contractile proteins
• Provide cells and organisms with the ability to
  change shape and move.
• Protective proteins
• Defend against invaders and prevent or minimize
  damage after injury.
• Storage proteins
• Provide a reservoir of nitrogen and other
  nutrients, especially when external sources are
  low or absent.

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• The building blocks of proteins are ?-amino acids

• Nearly all polypeptides and proteins are
  constructed from twenty common amino acids.
• Three letter abbreviations, based on the name of
  the amino acid are used to identify them glycine
  GLY with R H.
• The R- group is the only difference in the
  general structures of amino acids except for
  proline (PRO).

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• Mammals require all 20 amino acids for protein
  synthesis but can synthesize only 10 of them.
• There are 10 essential amino acids that must be
  obtained from the diet.
• Phenylalanine, Valine, Tryptophan, Threonine,
  Isoleucine, Methionine, Histidine, Arginine,
  Lysine, Leucine
• The amino acids are categorized by their
  R-groups
• Nonpolar neutral
• Polar neutral
• Polar acidic
• Polar basic

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• Except for glycine (R -H), the ?-carbon of all
  amino acids is a tetrahedral stereocenter and
  each amino acid exists as a pair of enantiomers.

• With very rare exceptions, only the L-?-amino
  acids exist in the proteins of plants and animals.

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Exercise 20.4 Using Table 20.1, give the three
letter abbreviation for the amino acid below that
has ____ no tetrahedral stereocenter ____ a
basic side group ____ a polar side group and two
carboxylic acids ____ the amine group is part of
hydrocarbon ring
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• The actual structure of an amino acid in neutral
  solution and in the solid is a charged molecule,
  containing a -COO- group and an NH3 group,
  called a zwitterion and the net charge is zero

• The presence of the charged groups in the
  zwitterion result in very strong secondary forces
  between the positive and negative charges

MP 314C MP 53C

• Amino acids are also soluble in water due to the
  strong secondary forces between the zwitterionic
  charge centers of the amino acids and the dipolar
  water molecules.

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• Amino acids exist exclusively in the zwitterionic
  form in the solid state.
• In solution, an equilibrium exists between the
  cationic, zwitterionic, and anionic forms of the
  amino acid

• At low pH, the equilibrium position is at the
  left (cation), and at high pH, the equilibrium
  position is at the right (anion).
• Compounds with the ability to both release
  (acids) and absorb (bases) protons are called
  amphoteric compounds.

• Each amino acid has a pH at which almost all of
  the molecules are present in the zwitterionic
  form (0 net charge), called the isoelectric
  point, pI.

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• At physiological pH, the neutral ?-amino acids
  exist as zwitterions with zero net charge,
  whereas the acidic and basic amino acids have
  overall charges of -1 and 1, respectively

• Amino acids are least soluble in their
  zwitterionic form, although even this form is
  fairly soluble.

• Neutral amino acids act as strong buffers,
  keeping the pH of the solution relatively
  constant as acids or bases are added.
• Most amino acids have isoelectric points in the
  range 5.05-6.30.
• Acidic amino acids (ASP, GLU) have isoelectric
  points of 2.77 and 3.22, respectively.
• Basic amino acids (LYS, ARG, HIS) have
  isoelectric points of 9.74, 10.76, and 7.59,
  respectively.

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• Electrophoresis can be used to analyze mixtures
  of ?-amino acids. In this procedure, a strong
  electric field causes anions (acidic amino acids)
  to move towards the anode (positive electrode)
  and cations (basic amino acids) to move towards
  the cathode (negative electrode).
• Amino acids whose isoelectric pH is close to the
  pH of the solution remain stationary in the
  electric field.
• A form of electrophoresis called paper
  electrophoresis is often used for this analysis

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• Exercise 20.7
• Show the structure of of alanine at its
  isoelectric point, at pH 7, at low pH (lt1) and
  very high pH (gt12).
• At what pH does alanine have its lowest
  solubility?
• To which electrode does alanine migrate in
  electrophoresis at its pI at pH7?

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• Peptides are polyamides formed by ?-amino acids
  reacting with one another.
• The reaction can be conceptually viewed as a
  dehydration reaction between the carboxyl and
  amino groups of different ?-amino acid molecules

• The amino acid residues, or monomers, in the
  peptide are linked together by peptide bonds.

• Peptides are referred to as di-, tri-, tetra-,
  penta-, hexapeptides, etc.
• When the size exceeds 10-20 amino acid residues,
  the term polypeptide is used. The term
  oligopeptide is used to loosely refer to peptides
  smaller than polypeptides.

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Peptides are often distinguished from proteins by
the number of amino acid residues molecules
having fewer than 50 amino acid residues are
generally called peptides, regardless of
physiological activity.
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Amino Acid Sequences and Constitutional Isomers

• Two different dipeptides are possible from the
  reaction of Gly and Ala

• Different constitutional isomers are possible
  whenever amino acids react to form peptides.
• All peptides have one free ?-amino group
  (N-terminal or amino-terminal residue), and one
  free ?-carbonyl group (C-terminal or
  carboxyl-terminal residue).
• When drawing (or naming) peptides the standard
  convention is to place the N-terminal residue at
  the left and the C-terminal residue to the right.

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The Peptide Bond

• The peptide bond is usually drawn as a single
  bond, but actually has considerable double bond
  character which prevents free rotation about the
  bond

• Almost all peptide bonds are in the trans
  configuration which is sterically more stable
  than the cis configuration.
• The atoms of the double bond, and those directly
  attached to it, all lie in the same plane.
• The trans-planar nature of the peptide bond
  accounts for the very high melting and boiling
  points and a lack of basicity in the simple
  amides, and plays an important role in
  determining three-dimensional structure and
  function in polypeptides.

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• There is a pI at which each peptide is
  electrically neutral.

The pI value of a peptide containing only
neutral amino acid residues or equal numbers of
acidic and basic residues or both is in the range
of pI values for neutral amino acids (pH
5.056.30). The pI of a peptide containing
acidic and basic amino acid residues is on the
acidic side (lower than 5.056.30) if there is an
excess of acidic residues and on the basic side
(higher than 5.056.30) if there is an excess of
basic residues. All amino and carboxyl groups,
including those on side groups of acidic and
basic amino acids, are charged at physiological
pH.
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• Peptides have solubility and electrophoresis
  properties that are pH dependent.
• Peptide solubility is lowest at its isoelectric
  point.
• At a given pH, each peptide has a particular
  electrical charge depending upon its isoelectric
  point and the number of ionizable groups it
  contains.
• Electrophoresis can be used to separate peptides
  of differing charges.

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• The amino acid cysteine contains a sulfhydryl
  group, -SH. Pairs of cysteine residues often link
  two peptide chains or two parts of one peptide
  chain through disulfide bridges

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Digestion or laboratory hydrolysis of peptides
containing disulfide bridges results in the
formation of cystine
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• Reduction of cystine in the liver results in the
  formation of two cysteine residues

• Disulfide bridges in peptides represented using
  the 3 letter amino acid abbreviations are written

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• Exercise 20.26
• Write the structures of the products obtained, if
  any, when the peptide below is
• Digested
• Subjected to selective oxidizing conditions
• Subjected to selective reducing conditions

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Each amino acid sequence (100,000 different
proteins, each with a unique physiological
function) produces a unique 3-D structure, which
in turn determines the unique physiological
function of the protein.
The 3-D structure of a protein is determined by
the conformations of the bonds in the individual
amino acid residues within the protein.
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The formation of a proteins 3-D structure by
conformational changes within its amino acid
residues is called protein folding. The overall
folding of a protein is described at four levels
Primary structure is the amino acid sequence of
a polypeptide Secondary structure is the
conformation in a local region of a polypeptide
molecule. The conformations are the same in
different regions of the molecule for some
polypeptides but are different in different
regions for other polypeptides. (beta sheet,
alpha helix, beta turn, loop) Tertiary
structure exists when the polypeptide has
different secondary structures in different local
regions. Tertiary structure describes the
three-dimensional relation among the different
secondary structures in different regions.
Quaternary structure exists only in proteins in
which two or more polypeptide molecules aggregate
together. It describes the three-dimensional
relation among the different polypeptides.
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Determinants of Protein Conformation
The most stable conformation of a protein is
determined by The bonds in the linear chain No
free rotation about the peptide bond. Rotations
about C?-NH and C?-CO are limited by steric
contacts between atoms within the polypeptide
chain at certain angles of rotation. The
interactions of the side groups with each other
and with the surrounding aqueous solvent.
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• Exercise 20.34
• What attractive interaction (hydrogen bond, salt
  bridge, hydrophobic or none) can take place
  between the side groups for each of the following
  pairs of amino acid residues under physiological
  conditions
• Met and Agr
• Met and Ile
• Thr and Tyr
• Asp and Glu
• Thr and Phe
• Arg and Asp

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Basic Patterns of Protein Conformation
The most important secondary structures in
naturally occurring polypeptides are
?-Helix The polypeptide chain is arranged like a
coiled spring with a hydrogen bond between each
peptide groups CO oxygen and the hydrogen of
the N-H group of the fourth residue farther down
the chain.
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?-Pleated sheet Peptide chains are extended and
run side-by-side each other in either a parallel
or an antiparallel arrangement. Neighboring
chains are held together by hydrogen bonds
between an N-H on one chain and a CO on a
neighboring chain.
Side chains extend alternately above and below
the plain of the sheet.
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?-Turn, or ?-bend Occurs where the polypeptide
chain abruptly changes direction. ?-Turns are
often found where the polypeptide chain of an
antiparallel pleated sheet changes
direction. Loop conformations Segments of
polypeptide chain that are less ordered than
?-turns and much less ordered than ?-helices and
?-pleated sheets.
Lysozyme hydrolyzes bacterial cell walls which
then are susceptible to cell lysis or breaking
open. It contains 129 amino acids which are
organized into all four types of secondary
structure
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Certain amino acid residues favor or disfavor
specific conformations
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Exercise 20.91 Part X of a polypeptide
containing considerable amounts of Pro and Glu
and very little Gly, Ala and Ser. What is the
secondary structure of X? Explain.
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Fibrous proteins are elongated, water insoluble,
proteins that serve structural and contractile
functions. Fibrous proteins have no tertiary
structure, but generally possess a single
conformational pattern throughout all or most of
the chain (secondary structure). Fibrous proteins
almost always have a quaternary structure
involving the aggregation of two or more
polypeptide chains into a specific conformational
pattern.
?-Keratins
?-Keratins are the structural component of hair,
horn, hoofs, nails, skin, and wool. These
materials have a hierarchical structure
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?-Keratins
The packing within the ?-keratins is stabilized
by disulfide bridges and secondary forces between
different polypeptide molecules. Disulfide
bridges are more important than secondary forces
in imparting insolubility, strength, and
resistance to stretching. Interchain disulfide
bonds are often called cross-links.
The degree of hardness of an ?-keratin depends
upon its degree of cross-linking. High cysteine
content results in increased hardness (hair,
horn, nail) compared to low cysteine content
(skin, callus).
Permanent waving of hair is accomplished by
breaking and reforming cysteine cross-links
within the hair fiber.
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Collagen

• The most abundant protein in vertebrates a
  stress-bearing component of connective tissues
  such as bone, cartilage, cornea, ligament, teeth,
  tendons, skin and blood vessels.
• Collagen contains much more glycine and proline
  and much less cysteine than does ?-keratin. Much
  of the proline present is converted into
  hydroxyproline.

• A single collagen molecule forms a left-handed
  helical structure, more elongated than an
  ?-helix.
• Three left-handed collagen helices twist around
  each other to form a right-handed superhelix
  called a triple-helix or tropocollagen.
• In bone and teeth, collagen fibrils are embedded
  in hydroxyapatite, Ca5(PO4)3OH, which is an
  inorganic calcium phosphate polymer, to form a
  high physical strength structure.

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Globular proteins do not aggregate into
macroscopic structures but remain soluble in
order to carry out their metabolic functions
catalysis, transport, regulation, and
protection. Globular proteins remain soluble by
folding up in such a way as to segregate their
hydrophobic amino acid side chains in the
interior of the molecule, and their hydrophilic
amino acid side chains on the exterior of the
molecule, in contact with water.
Myoglobin and Hemoglobin

• Hemoglobin in red blood cells binds oxygen in the
  lungs, transports it through the blood stream,
  and releases it in the tissues.
• Myoglobin has a higher affinity for oxygen than
  does hemoglobin and is found in muscle tissue.
  Myoglobin serves as a storage reserve for oxygen
  within the muscle.

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• Myoglobin consists of a single polypeptide chain
  containing 153 amino acid residues, organized
  into 8 ?-helical regions that surround a
  prosthetic group called a heme

• The iron atom on the heme group is the site of
  attachment of the O2 molecule.

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• Hemoglobin has 4 polypeptide chains, 2 ?-chains
  (141 residues each), and 2 ?-chains (146 residues
  each).
• Each ? and ? chain is folded in a manner similar
  to that of myoglobin and each contains a heme
  group capable of carrying oxygen.

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• The surfaces of the ? and ? chains contain some
  hydrophobic residues which cause all 4 chains to
  aggregate into a tetramer.
• A space at the center of the tetrameric structure
  can bind a molecule of 2,3-bisphosphoglycerate
  (BPG) which regulates the affinity of the
  hemoglobin molecule for oxygen.
• Carbon monoxide binds more strongly than oxygen
  to the heme groups in hemoglobin and exposure can
  result in death from asphyxiation.
• Heavy smokers tie up a significant fraction of
  their hemoglobin with carbon monoxide resulting
  in shortness of breath.

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Denaturation is the loss of native conformation
due to a change in environmental conditions. The
non-functioning protein is called a denatured
protein. Denaturation results from the
disruptions of the weak secondary forces holding
a protein in its native conformation. Disulfide
bridges confer considerable resistance to
denaturation because they are much stronger than
the weak secondary forces.

• A variety of denaturing conditions or agents lead
  to protein denaturation
• Increased temperature (or microwave radiation)
• Ultraviolet and ionizing radiation
• Mechanical energy
• Changes in pH
• Organic chemicals
• Heavy metal salts
• Oxidizing and reducing agents