Proteins serve many functions, including the following:
• 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 cell membranes.
• 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
fight disease.
• 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.
• Proteins are divided into two types:
• Fibrous proteins
• Globular proteins
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
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 Lconfiguration at the -carbon.
Chirality of -Amino Acids
A comparison of the configuration of L-alanine and Dglyceraldehyde (as Fischer projections):
Protein-Derived -Amino Acids
Nonpolar side chains. Each ionizable group is shown in the
form present in highest concentration at pH 7.0).
Protein-Derived -Amino Acids
• Polar side chains (at pH 7.0)
Protein-Derived -Amino Acids
Acidic and basic side chains (at pH 7.0)
Protein-Derived -Amino Acids
1. For 19 of the 20, the -amino group is primary; for
proline, it is secondary.
2. With the exception of glycine, the -carbon of each is a
3. Isoleucine (left) and threonine (right) contain a second
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 add a strong acid such as HCl to bring the pH of
the solution to 0.0, the strong acid donates a proton to
the -COO- of the amino acid turning the zwitterion into a
positive ion.
Ionization vs. pH
• If we add a strong base such as NaOH to the solution
and bring its pH to 14, a proton is transferred from the
NH3+ group to the base turning the zwitterion into a
negative ion.
• To summarize:
Isoelectric Point (pI)
• Isoelectric
point, pI:
The pH at
which the
majority of
molecules of a
compound in
solution have
no net charge.
Nonpolar &
polar side chains
Side Chains
aspartic acid 2.77
glutamic acid 3.22
Side Chains
The -SH (sulfhydryl) group of cysteine is easily oxidized to
an -S-S- (disulfide).
Phe, Trp, and Tyr
The amino acids phenylalanine, tryptophan, and tyrosine
have aromatic rings on their side chains.
Tryptophan is the precursor to the neurotransmitter
Tyr and Phe
Phenylalanine and tyrosine are precursors to
norepinephrine and epinephrine, both of which are
Other Amino Acids
Figure 22.3
(oxidation) of proline,
lysine, and tyrosine,
respectively and
iodination for
tyrosine, give these
uncommon amino
In 1902, Emil Fischer proposed that proteins are long
chains of amino acids joined by amide bonds.
• Peptide bond (peptide linkage): The special name given
to the amide bond between the -carboxyl group of one
amino acid and the -amino group of another.
• 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.
• The individual amino acid units are often referred to as
Peptide Bond
• A peptide bond is typically written as a carbonyl group
bonded to an N-H group. Linus Pauling, however,
discovered that there is about 40% double bond character
to the C-N bond and that a peptide bond between two
amino acids is planar, which Pauling explained using the
concept of resonance.
Writing Peptides
By convention, peptides are written from the left to right,
beginning with the free -NH3+ group and ending with the
free -COO- group.
• 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.
Figure 22.4 A small peptide showing the direction of the
peptide chain (N-terminal to C-terminal).
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
• Proteins are least soluble in water at their isoelectric
points and can be precipitated from solution
at this pH.
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
-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.
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!
Primary Structure
Figure 22.8 The
hormone insulin
consists of two
chains, A and B,
held together by
two disulfide
bonds. The
sequence shown
here is for bovine
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
A Chain
positions 8-9-10
B Chain
position 30
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.
• The structures of vasopressin and oxytocin.
Differences are shown in color.
Primary Structure
Secondary Structure
Secondary structure: Conformations of amino acids in
localized regions of a polypeptide chain.
• The most common types of secondary structure are
-helix and b-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.
• 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.
Secondary Structure: The -Helix
The -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
• The N-H groups of peptide bonds point in the same
direction, roughly parallel to the axis of the helix.
• The 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.
• 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 C=O and N-H bonds.
b-Pleated Sheet
Figure 22.10(b)
The b-pleated
b-Pleated sheet
In a section of b-pleated sheet;
• The six atoms of each peptide bond of a b-pleated
sheet lie in the same plane.
• The C=O 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.
Random Coil
Figure 22.11 A
random coil.
Secondary Structure
Schematic structure of the enzyme carboxypeptidase. The
b-pleated sheet sections are shown in blue, the -helix
portions in green, and the random coils as orange strings.
Many globular proteins contain -helices, b-pleated
sheets, and random coils.
The Collagen Triple Helix
The collagen triple helix.
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.
Tertiary Structure
Forces that stabilize tertiary structures of proteins.
Quaternary Structure
Quaternary structure: the arrangement of polypeptide
chains into a noncovalently bonded aggregation.
• The individual chains are held together by hydrogen
bonds, salt bridges, and hydrophobic interactions.
• Adult hemoglobin: Two alpha chains of 141 amino
acids each, and two beta chains of 146 amino acids
• 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.
Quaternary Structure
The quaternary structure of hemoglobin. The structure of
heme is shown on the next screen.
Quaternary Structure
The structure of heme
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.
Quaternary Structure
Integral membrane
protein of rhodopsin,
made of -helices.
Quaternary Structure
An integral membrane protein from the outer
mitochondrial membrane forming a b-barrel from eight
b-pleated sheets.
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.
• 6 M aqueous urea: Disrupts hydrogen bonding.
• Surface-active agents: Detergents such as sodium
dodecylbenzenesulfate (SDS) disrupt hydrogen
• 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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