Proteins and enzymes

Dr Sana Javaid Awan

PhD Molecular Biology
Proteins

Atoms: C, H, O, N, P, S
Basic units: amino acids (20)
Provide energy & structure, repairs body tissues
Some are called hormones, enzymes,
neurotransmitters, etc.
Foods high in protein: meat, eggs, poultry, milk &
milk products, nuts, dried beans, peas, & lentils
Peptides, Proteins and Enzymes

Proteins are the workhorses in living systems. Their

many roles include providing structure, catalyzing
nearly all the reactions that take place in a living cell,
transporting and storing materials, and controlling and
defending living systems. Like carbohydrates, proteins
are polymers, but unlike the polysaccharides, proteins
are able to assume a much wider range of 3-
dimensional structures and a functions.
 Amino Acids
-Amino acids are the building blocks (monomers) for
polypeptides and proteins.
Every amino acid contains,
A carboxylic acid group
An amino group
A side chain (R)

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 Amino Acids
Net charge
At pH 7, amino acids are in their
zwitterionic form. +1
There is no pH value at which
there are no charges on an
amino acids.
However, there is a pH value at
which the net charge is zero. 0
This pH value is called the
isoelectric point.

-1

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 Amino Acids
There are 20 different sidechains for the amino acids that are
used to build proteins.
These are classified according to their physical properties
as
Non-polar
Polar acidic (negatively charged at pH 7)
Polar basic (positively charged at pH 7)
Polar neutral (polar, but not charged at pH 7)

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 Amino Acids
Non polar
sidechains
Most of these
sidechains
are
hydrocarbons

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 Amino Acids
Polar acidic sidechains
Sidechains contain
carboxylic acids
Negatively charged
at pH 7

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 Amino Acids
Polar basic sidechains
Sidechains contain
amines
Positively charged at pH 7

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 Amino Acids
Polar neutral sidechains
Sidechains contain polar
groups that are capable of
hydrogen bonding
alcohols
phenols
amides
Uncharged at pH 7

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 Peptides, Proteins, and pH
Amino acids are joined together to form polymers of amino
acids called oligopeptides (2-10 amino acids) and
polypeptides (more than 10 amino acids).

Collectively, oligopeptides and polypeptides are called

peptides.

The amino acids are joind together by an amide bond

called a peptide bond, which is analogous to the
glycosidic bond found in oligosaccharides and
polysaccharides.

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 Peptides, Proteins, and pH
The amide bond that
connects the amino
acids together in a
peptide is called a
peptide bond.

Proteins are long

polypeptide chains,
usually with 50 or
more amino acids,
which fold into a well
defined structure. The protein
ubiquitin

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 Peptides, Proteins, and pH
Proteins are sensitive to the pH because they contain
numberous acid and base groups
The pH affects the charge on a proteins, which in turn, can
have a marked effect on a proteins structure and function.

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 Protein Structure
Proteins are polypeptides that fold to adopt a well-defined,
three-dimensional structure.
There two general classifications of proteins
Fibrous proteins exist as long fibers that are usually
tough and insoluble in water; examples include
collagen (skin and bones)
Keratin (hair)
Globular proteins are spherical, highly folded, and usually
soluble in water; examples include
enzymes
antibodies
transport proteins like hemoglobin and myoglobin

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 Protein Structure
Fibrous versus globular

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 Protein Structure
Proteins display up to four levels of structure
Primary structure
This is the amino acid sequence, which is unique for each protein
This defines the covalent structure of a protein
Secondary structure
Regular, periodic structures, that involve hydrogen bonding between

the backbone amides
H O H O
N C C N C C N
hydrogenbonds H R H R H
betweenamides
O H O H O

C N C C N C C
H R H R

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 Protein Structure
Proteins display up to four
levels of structure
Tertiary structure
The 3-dimensional fold of the
the polypeptide in which the
backbone twists and turns its
way through the folded structure
of the protein.

It involves interactions between

the sidechains of the the amino
acids and is highly influenced by
the amino acid sequence. The protein
ubiquitin

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 Protein Structure
Primary Structure

A proteins amino acid sequence is referred to as its

primary structure.

Every protein has a unique primary structure that is

determined by the gene for that protein.

The primary structure defines the covalent structure

of a protein.

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 Protein Structure
Primary structure
The Central Dogma
DNA mRNA Polypeptide
The genetic code is
used to match up the
DNA/mRNA sequence
to the sequence of
amino acids in a
protein
All living organisms
use the same code

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 Protein Structure
Secondary structure
The polypeptide backbone can take on regular shapes that
allow the backbone amides to hydrogen bond to one
another.
The primary forms of secondary structure include
-helix
-sheet

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 Protein Structure
Secondary structure

-Helix

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 Protein Structure
Secondary Structure

-Sheet

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Proteins

Tertiary Structure Quaternary Structure

Interaction between alpha Small globular proteins

helices and beta-sheets. form protein aggregates.
A famous example is
These protein domains hemoglobin.
for small globular
proteins.
 Protein Denaturation
Because the secondary, tertiary and quaternary structures of
proteins are stabilized by weak, non-covalent interactions,
these structures are easily disrupted by agents that disrupt
theses interactions, including:
Changes in temperature
Changes in pH
Mechanical stress (agitation)
Soaps and detergents
These agents typically cause the protein to unfold
Only the primary structure remains
The protein loses it function
The process is called protein denaturation.

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 Enzymes
Nearly every reaction that takes place in a living cell has an
enzyme associated with it.

Enzymes are biological catalysts

Most enzymes are proteins
Many human diseases involve enzymes misbehaving

Many treatments for diseases involve drugs that target

enzymes.

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Enzymes

Are proteins
Speed up chemical reactions without being
consumed or using energy
Enzymes
Amylase - breaks down sugar
Proteases - break down proteins
Lipases - break down lipids
Catalase - breaks down hydrogen peroxide
Enzyme Action Models
Models
Enzyme Action Models
lock and key model substrate & the enzyme fit together
perfectly

induced-fit model Enzyme changes shape slightly to

accommodate the substrate
Factors that affect enzyme action:
1. Temperature 37oC best for human enzymes
2. pH different for each enzyme
a. 7 for amylase in the mouth
b. 2 for pepsin in the stomach
c. 8 for trypsin in the intestines
3. Concentration of enzyme and substrate
4. Coenzymes helpers such as minerals and vitamins
 Enzymes
The common names for enzymes often describe the
substrate (reactant) for the reaction and a description of the
reaction that is being carried out on that substrate.
The names usually end with -ase.
Example: alcohol dehydrogenase

alcohol
alcohol aldehyde
aldehyde

NADH +
NAD+
NAD+ NADH ++ HH+ O
O
CH
CH33 CH
CH22 OH
OH CH
CH33 C C H H
ethanol alcohol
alcohol dehydrogenase
dehydrogenase ethanal
ethanal
ethanol enzyme
enzyme (acetaldehyde)
(acetaldehyde)

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 Enzymes
Specificity
Absolute spectificity - enzyme only accepts one specific
substrate.
Relative specificity - enzyme accepts a range of related
substrates.

alcohol
alcohol aldehyde
aldehyde
NADH +
NAD+
NAD+ NADH ++ HH+ O
O
R
R CHCH22 OH
OH CH
CH33 C C H H
ethanol alcohol
alcohol dehydrogenase
dehydrogenase ethanal
ethanal
ethanol enzyme
enzyme (acetaldehyde)
(acetaldehyde)

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 Enzymes
Catalysis
As catalysis, enzyme have no effect on the change in free
energy, G, for a reaction
Ezymes speed up reactions by decreasing the activation
energy, Eact.
Enzymes do this by binding the substrates and by directing the
reaction

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 Enzymes
Cofactors and Coenzymes
Sometimes enzymes need some help with catalzying the
reactions.
Cofactors are non-protein components of an enzyme
Metal ions
Organic molecules (Coenzymes)
Many of the coenzymes are derived from the vitamins that
we take in in our diet.

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 Enzymes
pH and Temperature
Enyzme activity is often critically dependent on the pH and
temperature.

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 Control of Enzyme-Catalyzed Reactions
Enzyme Inhibition
Can be a normal
event used by the cell
to control enzyme
activity.
Can also be exploited
in the design of drugs.
Example, the
irreversible
inhibition of COX
enzymes by aspirin

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 Control of Enzyme-Catalyzed Reactions
Enzymes that are inhibited by a substance binding to a site
other than the active site are called allosteric enzymes.
The enzymes that are regulated by noncompetive inhibition
in feedback inhibition are examples of allosteric enzyme.
The substance that inhibits the enzyme in this way is called
a negative effector.

Some allosteric enzymes are activated instead of inhibited by

as substance binding at their allosteric site.
These substances are called positive effectors.

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The End