Amino Acids, Peptides and Proteins
• Amino acids share a common structure
• R groups provide different chemical properties
• Amino acids can ionize in aqueous solutions
• Proteins can be purified and studied in a variety of
• Protein structure has four levels of organization
• Sequence homology generally translates to shared
• Proteins serve many functions:
– 1.Structure: collagen and keratin are the chief
constituents of skin, bone, hair, and nails.
– 2. Catalysts: virtually all reactions in living systems are
catalyzed by proteins called enzymes.
– 3. Movement: muscles are made up of proteins called
myosin and actin.
– 4. Transport: hemoglobin transports oxygen from the
lungs to cells; other proteins transport molecules across
– 5. Hormones: many hormones are proteins, among
them insulin, oxytocin, and human growth hormone.
– 6. Protection: blood clotting involves the protein
fibrinogen; the body used proteins called antibodies to
– 7. Storage: casein in milk and ovalbumin in eggs store
nutrients for newborn infants and birds; ferritin, a
protein in the liver, stores iron.
– 8. Regulation: certain proteins not only control the
expression of genes, but also control when gene
expression takes place.
•Have an alpha- carbon
• an amino group
• carboxyl group
• a hydrogen
• an R group
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 protein-derived amino acids have
Each R group
properties of the amino
R groups can be
Hundreds of modified
Each R group
properties of an amino
R groups can be
amino acids can act as acids and bases
• Amino acids exist in solution as dipolar ions (Zwitterions)
• Like buffers, AA’s can act as proton donors or acceptors
– “Amphoteric” compounds or “amphoteric electrolytes”
titration of amino acids
Ex. Glycine Deprotonation
• Two distinct
deprotonation of glycine
• Titration curves can be
used to predict AA
charge at a given pH
• The isoelectric point (pI)
is the pH at 0 charge
formation of peptide bonds
Peptides and proteins are
polymers of amino acids
• Two amino acids are
covalently joined in
Peptides: how aa are linked
• proteins are long chains of amino acids joined by amide
– amino acids become linked together to form peptide
bonds with the elimination of water
– The reaction takes place between the -COOH of one
amino acid and the -NH2
α-carbons separated by 3 covalent bonds
Partial sharing of
• A small electric dipole results from the partial negative charge on
oxygen and the partial positive charge on nitrogen
• The shared electrons result in some double bond character and the
lack of rotation
planar nature of peptide bonds
• The N-Cα and Cα-C bonds can rotate
• Just how important is the exact amino acid
– Human insulin consists of two polypeptide chains
having a total of 51 amino acids.
– In the table are differences between four types of
– 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
proteins contain prosthetic groups
Non-amino acid part of proteins
protein purification (chromatography)
Uses protein characteristics, such as charge, size and binding affinity to separate the protein
blot the gel
Migration of charged proteins in an electric field
Gel slows migration in proportion to mass
2D gel electrophoresis
1. Isoelectric focusing
2. SDS PAGE
1. First treat isolated
protein with a protease
2. Mixture is vaporized
3. One peptide is
selected and further
4. MS measures m/z
ratios for all the
Levels of Structure
• Primary structure: the sequence of amino acids
• Secondary structure: conformations of amino acids
in localized regions of a polypeptide chain;
examples are -helix, -pleated sheet, and random
• 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.
4 levels of protein structure
• Primary – sequence of amino acids
• Secondary – interactions between adjacent amino
• Tertiary – 3D folding of the polypeptide
• Quaternary – arrangements of multiple polypeptides
• conformations of amino acids in localized regions
of a polypeptide chain.
– The most common types of secondary structure are helix and -pleated sheet.
-Helix: a type of secondary structure in which a
section of polypeptide chain coils into a spiral, most
commonly a right-handed spiral.
-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 -helix structure: held together by hydrogen
• In a section of -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
– All R- groups point
outward from the helix.
• Note the position of the
purple R groups relative
to the backbone of the
all α helices are right handed
• But some
right-handed = clockwise
β sheet secondary structure
• More extended
• H-bonds may occur between amino acids some
distance from one another
• Adjacent chains can run parallel or anti-parallel
to each other
β sheets require β turns
• One third of amino acids are in turns or loops
• Gly and Pro are frequently found in turns
• In a section of -pleated sheet;
– The C=O and N-H groups of peptide bonds from
adjacent chains point toward each other 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.
• the overall conformation of an entire polypeptide
• Tertiary structure is stabilized in several 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.
– Electrostatic interaction or Salt bridges, as for example, the
attraction of the -NH3+ group of lysine and the -COO- group of
– Hydrophobic interactions, as for example, between the nonpolar
side chains of phenylalanine and isoleucine.
• The -SH (sulfhydryl) group of cysteine is easily
oxidized to an -S-S- (disulfide).
the permanent wave that isn’t
New S-S bonds
• Forces that stabilize 3° structure of proteins
Tertiary Structures of Proteins
• the three dimensional shape of proteins that results
from further crosslinking, folding and interaction between
ribbon + side chains
relative compactness of proteins
• Hypothetical chain length of a protein if it were to
appear either as an α helix or β sheet
Common Motifs stable folding patterns in globular proteins
• the arrangement of polypeptide chains into a
noncovalently bonded aggregation.
– The individual chains are held together by hydrogen
bonds, electrostatic interactions, and hydrophobic
– Adult hemoglobin: two chains of 141 amino acids
each, and two chains of 146 amino acids each.
– Each chain surrounds an iron-containing heme unit.
• The 4° structure of hemoglobin: made up of 4
Fibrous proteins: α keratin
• Evolved for strength (hair, wool, nails, claws, quills…)
• Right handed α helix
• Coiled-coil provides added strength (like a twisted rope)
Fibrous proteins: collagen
• Like keratin, collagen also evolved to provide strength
• Left-handed a chain (not an α helix)
• Right handed coiled coils – 3-stranded coil
Fibrous protein: silk
• Fibroin, the silk protein is in the β conformation
• Rich in Ala and Gly (for close packing)
• More extended than α helix conformation
• 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.
protein folding and misfolding
• Molecular chaperones
assist in protein folding
• Interact with partially
folded or improperly
• Misfolded proteins can
• Protein function often includes reversible binding
interactions with other molecules.
• Complementary interactions between proteins
and ligands are the basis of self vs non-self
recognition by the immune system.
• Specific protein interactions modulated by
chemical energy are the basis of muscle
oxygen-binding proteins have a
heme prosthetic group
oxygen-binding proteins have a
heme prosthetic group
protein-ligand interactions can be measured
association equilibrium: Ka = [PL] / [P] [L]
dissociation equilibrium: Kd = [P] [L] / [PL]
O2 binding to myoglobin
θ = fraction of ligand-binding sites
Which protein (X or Y) has greater
affinity for ligand A?
Binds O2 is a cooperative process.
Binding affinity of Hb for O2 is increased by the O2
saturation of the molecule
with the first O2 bound influencing the shape of the
binding sites (conformation change) for the next O2
hemoglobin-O2 binding is influenced by pH
Hb, binds H+ and CO2 as well as
O2, but all at different sites.
Binding of H+ and CO2 is inversely
related to binding of O2.
Low pH = high [H+] = lower O2
hemoglobin-O2 binding allosterically
modulated by 2,3-bisphosphoglycerate
BPG reduces the affinity of
Hb for O2.
BPG binds at a site distant
from the O2-binding site
and regulates the affinity of
Hb for O2.
immune responses are mediated by protein
interactions that distinguish self and non-self
Cellular immune response - T cells destroy host cells infected by
Humoral immune response – B cells produce antibodies or
immunoglobulins against bacteria, viruses and foreign molecules
muscle contraction is also based on protein
interactions and conformational changes
Muscle contraction occurs by the
sliding of the thick (myosin) and thin
(actin) filaments past each other
changes in the
are coupled to
What 2 functional groups are present in all amino acids?
Name the simplest amino acid. Is it a chiral molecule?
Approximately how many amino acids are needed to make the proteins found in the
What is meant by the primary, secondary and tertiary structures of proteins?
What type of bonds are responsible for the helix structure of some proteins?
Linus Pauling and Robert Corey found that the C—N bond in the peptide link is
intermediate in length between a single and double bond. They also found that the
peptide bond is planar.
a) What does the length of the bond tell us about the strength and bond order?
b) What does the observations tell us about the ease of rotation about the C—N
9. What is the effect of the following changes on the O2 affinity of hemoglobin?
Drop in pH of blood plasma
A decrease of partial pressure of CO2 in the lungs
Increase in BPG levels
Increase in CO
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