MODULE 5

PROTEINS Dr. Johanne Baluyut

Internal Disease Specialist
Diplomate in Internal Medicine
 Objectives:
❖ Discuss the different functions of protein
❖ Illustrate the molecular composition of protein
❖ Illustrate the : a. Types of amino acids b. Structure of
peptides
❖ Discuss the functions of enzymes
❖ Present videos showing the functions and how enzymes
work
 FUNCTION OF PROTEINS
❖ Enzymes and polypeptide
hormones direct and regulate
metabolism in the body
❖ Contractile proteins in muscle
permit movement
❖ In bone, the protein collagen
forms a framework for the
deposition of calcium
phosphate crystals, acting like
the steel cables in reinforced
concrete.
 FUNCTION OF PROTEINS

❖ In the bloodstream, proteins,

such as hemoglobin and
plasma albumin, shuttle
molecules essential to life
❖ Immunoglobulins ght
infectious bacteria and viruses
❖ Enzymes catalyzes chemical
reactions.
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 COMPOSTION OF PROTEINS
❖ 300 amino acids have been described in nature but only
20 amino acids are commonly found as components of
mammalian protein.
❖ These 20 amino acids are the only amino acids coded for
by our DNA
❖ Each amino acid has a carboxyl group, a primary amino
group (except for proline, which has a secondary amino
group), and a distinctive side chain (“R group”) bonded
to the α-carbon atom
COMPOSTION OF PROTEINS
 COMPOSTION OF PROTEINS
❖ At physiologic pH (approximately 7.4), the carboxyl group
is dissociated, forming the negatively charged carboxylate
ion (–COO–), and the amino group is protonated (–NH3+)
❖ In proteins, almost all of these carboxyl and amino groups
are combined through peptide linkage and, in general, are
not available for chemical reaction except for hydrogen
bond formation.
❖ The nature of the side chains that ultimately dictates the
role an amino acid plays in a protein
- all 20 common amino
acids are essential to
ensure health.

- Of these 20 amino
acids, 10 must be
present in the human
diet, and thus are
best termed
“nutritionally
essential.” The other
12 amino acids are
“nutritionally
nonessential” since
they need not be
present in the diet
BIOMEDICAL IMPORTANCE
OF PROTEINS
BIOMEDICAL IMPORTANCE OF PROTEINS

Kwashiokor - results when

a child is weaned onto a
starchy diet poor in protein
BIOMEDICAL IMPORTANCE OF PROTEINS

Marasmus - both caloric

intake and speci c amino
acids are de cient
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BIOMEDICAL IMPORTANCE OF PROTEINS

Short bowel syndrome - individual is unable to absorb

suf cient quantities of calories and nutrients suffer from
signi cant nutritional and metabolic abnormalities
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BIOMEDICAL IMPORTANCE OF PROTEINS

Scurvy - a dietary de ciency of

vitamin C, and speci c genetic
disorders are associated with an
impaired ability of connective
tissue to form peptidyl 4-
hydroxyproline and peptidyl 5-
hydroxylysine. The resulting
conformational instability of
collagen is accompanied by
bleeding gums, swelling joints,
poor wound healing, and
ultimately in death
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BIOMEDICAL IMPORTANCE OF PROTEINS

Menkes Syndrome -
characterized by kinky hair
and growth retardation, results
from a dietary de ciency of
copper, an essential cofactor
for the enzyme lysyl oxidase
that functions in formation of
the covalent cross-links that
strengthen collagen bers.
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BIOMEDICAL IMPORTANCE OF PROTEINS

Osteogenesis Imperfecta -
Genetic disorders of
collagen biosynthesis
characterized by fragile
bones
BIOMEDICAL IMPORTANCE OF PROTEINS

Ehlers-Danlos Syndrome -
a group of connective tissue
disorders that result in
mobile joints and skin
abnormalities due to defects
in the genes that encode
enzymes, including
procollagen-lysine 5-
hydroxylase.
 AMINO ACIDS
can be classi ed according to the properties of their side
chains, that is, whether they are nonpolar (have an even
distribution of electrons) or polar (have an uneven
distribution of electrons, such as acids and bases)
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Amino acids with non-polar side chains

❖ Each of these amino acids has a nonpolar side chain that

does not gain or lose protons or participate in hydrogen
or ionic bonds.
❖ The side chains of these amino acids can be thought of
as “oily” or lipid-like, a property that promotes
hydrophobic inter-actions.
NOTE: Proline differs from other amino acids in that its side chain and α-amino N form a rigid, ve-
membered ring structure. Proline, then, has a secondary (rather than a primary) amino group. It is
frequently referred to as an “imino acid.” The unique geometry of proline contributes to the formation
of the brous structure of collagen and often interrupts the α-helices found in globular proteins.
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Amino acids with polar side chains

❖ uncharged or charged, considered hydrophilic

STRUCTURE OF PROTEINS
- The 20 amino acids commonly found in proteins are joined together by
peptide bonds.
- The linear sequence of the linked amino acids contains the information
necessary to generate a protein molecule with a unique three-
dimensional shape.
- The complexity of protein structure is best analyzed by considering the
molecule in terms of four organizational levels: primary, secondary,
tertiary, and quaternary
 I. PRIMARY STRUCTURE

❖ The sequence of amino acids in a protein is called the primary

structure of the protein.
❖ If the primary structures of the normal and the mutated proteins are
known, this information may be used to diagnose or study the
disease.
 I. PRIMARY STRUCTURE

Peptide bond - In proteins, amino acids are joined covalently by peptide

bonds, which are amide linkages between the α-carboxyl group of one
amino acid and the α-amino group of another. Peptide bonds are
resistant to conditions that denature proteins, such as heating and high
concentrations of urea. Prolonged exposure to a strong acid or base at
elevated temperatures is required to break these bonds non-enzymically.
 II. SECONDARY STRUCTURE

❖ The polypeptide backbone does not assume a random three-

dimensional structure but, instead, generally forms regular
arrangements of amino acids that are located near each other in the
linear sequence.
❖ These arrangements are termed the secondary structure of the
polypeptide. The α-helix, β-sheet, and β-bend (β-turn) are examples
of secondary structures commonly encountered in proteins.
 α-Helix
❖ most common helix found in
nature.
❖ An α-helix is stabilized by
extensive hydrogen bonding
between the peptide-bond
carbonyl oxygens and amide
hydrogens that are part of the
polypeptide backbone
❖ Each turn of an α-helix
contains 3.6 amino acids.
❖
 β-Sheet
❖ The β-sheet is another form of
secondary structure in which all
of the peptide bond components
are involved in hydrogen
bonding
❖ The surfaces of β-sheets appear
“pleated,” and these structures
are, therefore, often called β-
pleated sheets.
❖ Note also that the hydrogen
bonds are perpendicular to the
polypeptide backbone in β-sheets
 III. TERTIARY STRUCTURE
❖ The primary structure of a polypeptide chain determines its
tertiary structure.
❖ “Tertiary” refers both to the folding of domains (the basic units
of structure and function) and to the nal arrangement of
domains in the polypeptide.
❖ The structure of globular proteins in aqueous solution is
compact, with a high density (close packing) of the atoms in the
core of the molecule. Hydrophobic side chains are buried in the
interior, whereas hydrophilic groups are generally found on the
surface of the molecule.
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 III. TERTIARY STRUCTURE

❖ Domains - Domains are the

fundamental functional and
three-dimensional structural
units of polypeptides.
 INTERACTION STABILIZING THE TERTIARY
STRUCTURE

❖ Disul de bonds - A disul de bond is a

covalent linkage formed from the
sulfhydryl group (–SH) of each of two
cysteine residues to produce a cystine
residue
❖ Hydrophobic interactions - Amino
acids with nonpolar side chains tend to
be located in the interior of the
polypeptide molecule, where they
associate with other hydrophobic amino
acids. In contrast, amino acids with
polar or charged side chains tend to be
located on the surface of the molecule in
contact with the polar solvent.
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 INTERACTION STABILIZING THE TERTIARY
STRUCTURE

❖ Hydrogen bonds - Amino acid side chains

containing oxygen- or nitrogen-bound
hydrogen, such as in the alcohol groups of
serine and threonine, can form hydrogen
bonds with electron-rich atoms, such as the
oxygen of a carboxyl group or carbonyl group
of a peptide bond. Formation of hydrogen
bonds between polar groups on the surface of
proteins and the aqueous solvent enhances
the solubility of the protein.
❖ Ionic Interactions - Negatively charged
groups, such as the carboxylate group (–
COO-) in the side chain of aspartate or
glutamate, can interact with positively
charged groups such as the amino group (–
NH3+) in the side chain of lysine.
PROTEIN MISFOLDING
- Protein folding is a complex process that can sometimes result in
improperly folded molecules. These misfolded proteins are usually tagged
and degraded within the cell. However, this quality control system is not
perfect, and intracellular or extracellular aggregates of misfolded proteins
can accumulate, particularly as individuals age.
- Deposits of misfolded proteins are associated with a number of diseases.
DISEASE ASSOCIATED WITH PROTEIN MISFOLDING

❖ Amyloid Disease - Misfolding of proteins may occur

spontaneously or be caused by a mutation in a particular gene,
which then produces an altered protein. In addition, some
apparently normal proteins can, after abnormal proteolytic
cleavage, take on a unique conformational state that leads to the
formation of long, brillar protein assemblies consisting of β-
pleated sheets.
❖ Accumulation of these insoluble, spontaneously aggregating
proteins, called amyloids, has been implicated in degenerative
diseases such as Parkinson and Huntington and particularly in
the age-related neurodegenerative disorder, Alzheimer disease.
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DISEASE ASSOCIATED WITH PROTEIN MISFOLDING

❖ Prion Disease - The prion protein (PrP) has been

strongly implicated as the causative agent of
transmissible spongiform encephalopathies (TSEs),
including Creutzfeldt-Jakob disease in humans, scrapie
in sheep, and bovine spongiform encephalopathy in
cattle (popularly called “mad cow” disease).
 ENZYMES
- Virtually all reactions in the body are mediated by enzymes,
which are protein catalysts that increase the rate of
reactions without being changed in the overall process.

- Among the many biologic reactions that are energetically

possible, enzymes selectively channel reactants (called
substrates) into useful pathways. Enzymes thus direct all
metabolic events.
 I. NOMENCLATURE

❖ Each enzyme is assigned two names.

❖ The rst is its short, recommended name, convenient
for everyday use.
❖ The second is the more complete systematic name,
which is used when an enzyme must be identi ed
without ambiguity.
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 I. NOMENCLATURE

❖ Recommended name - Most commonly used enzyme names have the suf x “-ase” attached to the
substrate of the reaction (for example, glucosidase and urease) or to a description of the action
performed (for example, lactate dehydrogenase and adenylyl cyclase).
❖ [Note: Some enzymes retain their original trivial names, which give no hint of the associated enzymic
reaction, for example, trypsin and pepsin.]
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 I. NOMENCLATURE
❖ Systematic name - In the systematic naming system, enzymes are
divided into six major classes, each with numerous subgroups. For
a given enzyme, the suf x -ase is attached to a fairly complete
description of the chemical reaction catalyzed, including the names
of all the substrates, for example, lactate:NAD+ oxidoreductase.

❖ [Note: Each enzyme is also assigned a classi cation number.

Lactate:NAD+ oxidoreductase, for example, is 1.1.1.27.] The
systematic names are unambiguous and informative but are
frequently too cumbersome to be of general use.
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PROPERTIES OF ENZYMES
Enzymes are protein catalysts that increase the velocity of a
chemical reaction and are not consumed during the reaction.
 PROPERTIES OF ENZYMES
❖ Active sites - Enzyme molecules contain a special
pocket or cleft called the active site.
❖ The active site, formed by folding of the protein,
contains amino acid side chains that participate in
substrate binding and catalysis.
❖ The substrate binds the enzyme, forming an
enzyme–substrate (ES) complex.
❖ Binding is thought to cause a conformational
change in the enzyme (induced t model) that
allows catalysis.
❖ ES is converted to an enzyme–product (EP) complex
that subsequently dissociates to enzyme and
product.
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 PROPERTIES OF ENZYMES

❖ Catalytic ef ciency - Enzyme-catalyzed reactions are

highly ef cient, proceeding from 103–108 times faster
than uncatalyzed reactions.
❖ Speci city - Enzymes are highly speci c, interacting
with one or a few substrates and catalyzing only one
type of chemical reaction. The set of enzymes made in a
cell determines which reactions occur in that cell.
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 PROPERTIES OF ENZYMES
❖ Holoenzymes, apoenzymes, cofactors, and coenzymes
❖ Some enzymes require molecules other than proteins for enzymic activity.
A. Holoenzyme - refers to the active enzyme with its nonprotein component,
B. Apoenzyme - inactive enzyme without its nonprotein moiety.
C. Co-factor - the nonprotein moiety is a metal ion, such as Zn2+ or Fe2+
D. Co-enzyme - the nonprotein moeity is a small organic molecule. Coenzymes that
only transiently associate with the enzyme are called cosubstrates. Cosubstrates
dissociate from the enzyme in an altered state (NAD+ is an example). If the
coenzyme is permanently associated with the enzyme and returned to its original
form, it is called a prosthetic group (FAD is an example). Coenzymes commonly
are derived from vitamins. For example, NAD+ contains niacin, and FAD contains
ribo avin
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 PROPERTIES OF ENZYMES
❖ Regulation - Enzyme activity can be
regulated, that is, increased or decreased, so
that the rate of product formation responds
to cellular need.
❖ Location within the cell - Many enzymes are
localized in speci c organelles within the
cell. Such compartmentalization serves to
isolate the reaction substrate or product from
other competing reactions. This provides a
favorable environment for the reaction and
organizes the thousands of enzymes present
in the cell into purposeful pathways.
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CARPE DIEM