UNIT 2 PROTEINS

Proteins
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.
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Proteins
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

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Amino Acids
Amino acid: A compound that contains both an amino
group and a carboxyl group.
• α-Amino acid: An amino acid in which the amino group is on the
carbon adjacent to the carboxyl group.
• Although α-amino acids are commonly written in the un-ionized
form, they are more properly written in the zwitterion (internal salt)
form.

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Chirality of α-Amino Acids
With the exception of glycine, all protein-derived amino
acids have at least one stereocenter (the α-carbon) and are
chiral.
• The vast majority of α-amino acids have the L-configuration at the
α-carbon.

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Chirality of α-Amino Acids
A comparison of the configuration of L-alanine and D-
glyceraldehyde (as Fischer projections):

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 Protein-Derived α-Amino Acids
Nonpolar side
chains. Each
ionizable group is
shown in the form
present in highest
concentration at
pH 7.0).

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 Protein-Derived α-Amino Acids

• Polar side chains (at pH 7.0)

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Protein-Derived α-Amino Acids
Acidic and basic side chains (at pH 7.0)

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Protein-Derived α-Amino Acids

1. For 19 of the 20, the α-amino group is primary; for proline, it is

secondary.
2. With the exception of glycine, the α-carbon of each is a stereocenter.
3. Isoleucine (left) and threonine (right) contain a second stereocenter.

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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 zwitterion
turning it into a positive ion.

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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:

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 Isoelectric Point (pI)
• Isoelectric point, pI:
The pH at which the
majority of molecules
of a compound in
solution have no net
charge.

14
Isoelectric
Point (pI)

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

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 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 serotonin.

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 Tyr and Phe
Phenylalanine and tyrosine are precursors to norepinephrine
and epinephrine, both of which are stimulatory
neurotransmitters.

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Other Amino Acids

Hydroxylation
(oxidation) of proline,
lysine, and tyrosine,
respectively and
iodination for tyrosine,
give these uncommon
amino acids.

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Peptides
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 α-carboxyl group of one amino acid and the α-amino
group of another.

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Peptides
Peptide: A short polymer of amino acids joined by peptide bonds;
they are c 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 individual21 amino acid units are often referred to as “residues”.

 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.

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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.
• Alternatively they are referred to as the C-terminus and the N-terminus.

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 Peptides
A small peptide showing the direction of the peptide chain (N-terminal
to C-terminal)

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Peptides and Proteins
Proteins behave as zwitterions.
Proteins 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 when pH = pI.

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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
α-helix, β-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
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.

• 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.
• The structures of vasopressin an oxytocin.

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Primary Structure

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Secondary Structure
Secondary structure: Conformations of amino acids in
localized regions of a polypeptide chain.
• The most common types of secondary structure are
α-helix and β-pleated sheet.
• α-Helix: A type of secondary structure in which a section of polypeptide
chain coils into a spiral, most commonly a right-handed spiral.
• β-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 α-Helix

The α-Helix.

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 α-Helix
In a section of α-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 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.

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 α-Helix

• The model is an α-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.

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Kinds of α – helix
Right – Handed α-helix
Left – Handed α-helix
R grp: outside the helix
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 β-Pleated Sheet
The β-pleated
sheet
structure.

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 β-Pleated sheet
In a section of β-pleated sheet;
• The six atoms of each peptide bond of a β-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.

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β – Pleated
Sheets
• Intrachain or
interchain H-bond
• Two types:
• Parallel pleated
sheet
• Antiparallel pleated
sheet

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Random Coil
A random coil is a polymer
conformation where the
monomer subunits are oriented
randomly while still being bonded
to adjacent units.

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 Secondary Structure
• Many globular proteins contain all three kinds of secondary
structure in different parts of their molecules: α-helix, β-
pleated sheet, and random coil

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Secondary Structure
Schematic structure of the enzyme
carboxypeptidase. The β-pleated
sheet sections are shown in blue,
the α-helix portions in green, and
the random coils as orange strings.

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The Collagen Triple Helix
The collagen triple helix.

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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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 Tertiary Structure
Forces that stabilize tertiary structures of proteins.

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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.
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
The quaternary
structure of
hemoglobin.

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 Quaternary Structure
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.

Integral membrane protein of

rhodopsin, made of α-helices.

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Quaternary Structure
An integral membrane protein from the
outer mitochondrial membrane forming a
β-barrel from eight β-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.

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Denaturatio
n
q Loss of high level of structural organization of protein
q Denaturing agents:
Ø Heat
Ø Change in pH
Ø Organic solvents e.g. alcohols, urea
Ø Detergents
Ø Salts of Heavy metals
Ø Performic acid and 2-mercaptoethanol

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 Denaturating Agents
• 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 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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