Amino Acids, Proteins, and Enzymes

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Chemistry 203
Chapter 21 Amino Acids, Proteins, and Enzymes
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Function of proteins
Fibrinogen helps blood clotting
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Function of proteins
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Proteins
- Proteins account for 50 of the dry weight of
the human body.
- Unlike lipids and carbohydrates, proteins are
not stored, so they must be consumed daily.
- Current recommended daily intake for adults is
0.8 grams of protein per kg of body weight (more
is needed for children).
- Dietary protein comes from eating meat and milk.
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Proteins
100,000 different proteins in human body
Fibrous proteins Insoluble in water used for
structural purposes (Keratin Collagen).
Globular proteins More or less soluble in water
used for nonstructural purposes.
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Amino acids

• Are the building blocks of proteins.
• Contain carboxylic acid and amino groups.
• Are ionized in solution (soluble in water).
• They are ionic compounds (solids-high melting
  points).
• Contain a different side group (R) for each.
• side chain
• H2N C COOH H3N C COO-

Zwitterion
R
R

H
H
a-carbon
Ionized form (Salt)
This form never exist in nature.
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Amino acids
Only difference containing a different side
chain (R) for each.
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Amino acids

• Amino acids are classified as
• Nonpolar (Neutral) amino acids (hydrophobic) with
  hydrocarbon (alkyl or aromatic) sides chains.
• Polar (Neutral) amino acids (hydrophilic) with
  polar or ionic side chains.
• Acidic amino acids (hydrophilic) with acidic side
  chains (-COOH).
• Basic amino acids (hydrophilic) with NH2 side
  chains.

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Amino acids
There are many amino acids.
There are only 20 different amino acids in the
proteins in humans.
They are called a amino acids.
- Humans cannot synthesize 10 of these 20 amino
acids. (Essential Amino Acids) - They must be
obtained from the diet (almost daily basis).
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Nonpolar (Neutral) amino acids
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Polar (Neutral) amino acids
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Acidic and basic amino acids
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Fischer projections
All of the a-amino acids are chiral (except
glycine)
Four different groups are attached to central
carbon (a-carbon).
L isomers is found in the body proteins and in
nature.
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Ionization and pH
pH 6 to 7
Isoelectric point (pI)
Positive charges Negative charges No net charge
(Neutral) - Zwitterion
pH 3 or less
-COO- acts as a base and accepts an H
pH 10 or higher
-NH3 acts as an acid and loses an H
-
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Ionization and pH
The net charge on an amino acid depends on the
pH of the solution in which it is dissolved.
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Ionization and pH
Each amino acid has a fixed and constant pI.
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Peptide

• A dipeptide forms
• When an amide links two amino acids (Peptide
  bond).
• Between the COO- of one amino acid and
• the NH3 of the next amino acid.

(amide bond)
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Peptide

• 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 40 amino acids joined by peptide bonds.

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Naming of peptides
C-terminal amino acid the amino acid at the end
of the chain having the free -COO- group (always
written at the left). N-terminal amino acid
the amino acid at the end of the chain having
the free -NH3 group (always written at the
right).
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Naming of peptides

• - Begin from the N terminal.
• Drop -ine or -ic acid and it is replaced by
  -yl.
• Give the full name of amino acid at the C
  terminal.

-
From alanine alanyl
From glycine glycyl
From serine serine
Alanylglycylserine (Ala-Gly-Ser)
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Biologically Active Peptides
- Enkephalins, pentapeptides made in the brain,
act as pain killers and sedatives by binding to
pain receptors.
- Addictive drugs morphine and heroin bind to
these same pain receptors, thus producing a
similar physiological response, though longer
lasting.
- Enkephalins belong to the family of
polypeptides called endorphins (16-31 amino
acids), which are known for their pain reducing
and mood enhancing effects.
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Biologically Active Peptides
Enkephalins
Met-enkephalin It contains a C-terminal
methionine.
Leu-enkephalin It contains a C-terminal leucine.
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Biologically Active Peptides
Oxytocin and vasopressin are cyclic nonapeptide
hormones, which have identical sequences except
for two amino acids.
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Biologically Active Peptides
Oxytocin stimulates the contraction of uterine
muscles, and signals for milk production it is
often used to induce labor.
Vasopressin, antidiuretic hormone (ADH) targets
the kidneys and helps to limit urine production
to keep body fluids up during dehydration.
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Structure of proteins
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
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Primary Structure of proteins

• The order of amino acids held together by
  peptide bonds.
• Each protein in our body has a unique sequence
  of amino acids.
• The backbone of a protein.
• - All bond angles are 120o, giving the protein a
  zigzag arrangement.

C
H
3
S
C
H
3
C
H
C
H
S
H
C
H


2
3


C
H
C
H
C
H
O
O
O
O
C
H

2
2
3

-
C
C
H
N
C
C
H
N
C
C
H
N
C
C
H
H
N
O
3
H
H
H


Ala-Leu-Cys-Met
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Cysteine

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

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Primary Structure of proteins

• The primary structure of insulin
• - Is a hormone that regulates the glucose level
  in the blood.
• - Was the first amino acid order determined.
• - Contains of two polypeptide chains linked by
  disulfide bonds (formed by side chains (R)).
• - Chain A has 21 amino acids and
• chain B has 30 amino acids.
• - Genetic engineers can produce it for treatment
  of diabetes.

C
O
O-
C
O
O-
Chain A
Chain B
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Secondary Structure of proteins
Describes the way the amino acids next to or near
to each other along the polypeptide are arranged
in space.
1. Alpha helix (a helix)
2. Beta-pleated sheet (?-pleated sheet)
3. Triple helix (found in Collagen)
4. Some regions are random arrangements.
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Secondary Structure - a-helix

• A section of polypeptide chain coils into a rigid
  spiral.
• Held by H bonds between the H of N-H group and
  the O of CO of the fourth amino acid down the
  chain (next turn).
• looks like a coiled telephone cord.
• All R- groups point outward from the helix.
• Myosin in muscle and a-Keratin in hair
• have this arrangement.

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Secondary Structure - ?-pleated sheet

• Consists of polypeptide chains (strands) arranged
  side by side.
• Has hydrogen bonds between the peptide chains.
• Has R groups above and below the sheet
  (vertical).
• Is typical of fibrous proteins such as silk.

O
H
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Secondary Structure Triple helix (Superhelix)

• - Collagen is the most abundant protein.
• - Three polypeptide chains (three a-helix) woven
  together.
• - It is found in connective tissues bone, teeth,
  blood vessels, tendons, and cartilage.
• - Consists of glycine (33), proline (22),
  alanine (12), and smaller amount of
  hydroxyproline and hydroxylysine.
• - High of glycine allows the chains to lie
  close to each other.
• - We need vitamin C to form H-bonding (a special
  enzyme).

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Tertiary Structure
The tertiary structure is determined by
attractions and repulsions between the side
chains (R) of the amino acids in a polypeptide
chain.
Interactions between side chains of the amino
acids fold a protein into a specific
three-dimensional shape.
-S-S-
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Tertiary Structure

• Disulfide (-S-S-)
• (2) salt bridge (acid-base)
• (3) Hydrophilic (polar)
• (4) hydrophobic (nonpolar)
• (5) Hydrogen bond

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Tertiary Structure
Shorthand symbols on a protein Ribbon diagram
Lysozyme (an enzyme)
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Globular proteins

• Have compact, spherical shape.
• Almost soluble in water.
• - Carry out the work of the cells
• Synthesis, transport, and metabolism

Myoglobin
Stores oxygen in muscles. 153 amino acids in a
single polypeptide chain (mostly a-helix).
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Fibrous proteins

• Have long, thin shape and insoluble in water.
• - Involve in the structure of cells and tissues.

a-keratin skin, nail, hair, and bone
Superhelix
Collagen
?-keratin feathers of birds
Large amount of ?-pleated sheet
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Fibrous proteins
a-keratin hair, wool, skin, and nails
- They are made of two mainly a-helix chains
coiled around each other in a superhelix
(supercoil).
- These coils wind around other coils making
larger and stronger structures (like hair).
- a-helix chains bond together by disulfide bond
(-S-S-)
- More disulfide bonds, more rigid materials
(horns nails).
Collagen
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Quaternary Structure

• Occurs when two or more protein units
  (polypeptide subunits) combine.
• Is stabilized by the same interactions found in
  tertiary structures (between side chains).
• Hemoglobin consists of four polypeptide chains as
  subunits.
• Is a globular protein and transports oxygen in
  blood (four molecules of O2).
• CO is poisonous because it binds 200 times more
  strongly to the Fe2 than does O2 (Cells can die
  from lack of O2).

? chain
a chain
? chain
a chain
Hemoglobin
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Conjugated Proteins
They are composed of a protein unit and a
nonprotein molecule.
Myoglobin Hemoglobin
Heme a complex organic compound containing the
Fe2.
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Sickle Cell Hemoglobin
Sickle cell anemia is a disease where a single
amino acid of both ß subunits is changed from
glutamic acid to valine.
- A genetic mutation in the DNA sequence that is
responsible for synthesis of hemoglobin.
- Red blood cells containing these mutated
hemoglobin units become elongated and crescent
(sickle) shaped (more fragile).
- These red blood cells will rupture
capillaries, causing pain and inflammation,
leading to organ damage, and eventually a
painful death.
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Summary of protein Structure
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Summary of protein Structure
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Denaturation

• - Is a process of destroying a protein
• by chemical and physical means.
• We can destroy secondary, tertiary,
• or quaternary structure but the primary
• structure is not affected.
• - Denaturing agents heat, acids and bases,
• organic compounds, heavy metal ions, and
• mechanical agitation.
• Some denaturations are reversible,
• while others permanently damage the protein.

Ovalbumin
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Denaturation

• Heat H bonds, Hydrophobic interactions
• Detergents H bonds
• Acids and bases Salt bridges, H bonds.
• Reducing agents Disulfide bonds
• Heavy metal ions (transition metal ions Pb2,
  Hg2) Disulfide bonds
• Alcohols H bonds, Hydrophilic interactions
• Agitation H bonds, Hydrophobic interactions

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Enzymes
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Enzyme
- Like a catalyst, they increase the rate of
biological reactions (106 to 1012 times faster).
- But, they are not changed at the end of the
reaction.
- They are made of proteins.
- Lower the activation energy for the reaction.
- Less energy is required to convert reactants to
products.
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Enzyme

• Most of enzymes are globular proteins (water
  soluble).
• Proteins are not the only biological catalysts.
• Most of enzymes are specific.
• (Trypsin cleaves the peptide bonds of
  proteins)
• Some enzymes are localized according to need.
• (digestive enzymes stomach)

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Names of Enzymes

• By replacing the end of the name of reaction or
  reacting compound
• with the suffix -ase .

Oxidoreductases oxidation-reduction reactions
(oxidase-reductase). Transferases transfer a
group between two compounds. Hydrolases
hydrolysis reactions. Lyases add or remove
groups involving a double bond without
hydrolysis. Isomerases rearrange atoms in a
molecule to form a isomer. Ligases form bonds
between molecules.
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Enzyme

• - Substrate the compound or compounds whose
  reaction an enzyme catalyzes.
• - Active site the specific portion of the enzyme
  to which a substrate binds during reaction.

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Enzyme catalyzed reaction

• An enzyme catalyzes a reaction by,
• Attaching to a substrate at the active site (by
  side chain (R) attractions).
• Forming an Enzyme-Substrate
• Complex (ES).
• Forming and releasing products.
• E S ES E P

Enzyme globular protein
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1. Lock-and-Key model

• Enzyme has a rigid, nonflexible shape.
• An enzyme binds only substrates that
• exactly fit the active site.
• The enzyme is analogous to a lock.
• - The substrate is the key that fits into the lock

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2. Induced-Fit model

• - Enzyme structure is flexible, not rigid.
• - Enzyme and substrate adjust the shape of the
  active site to bind substrate.
• - The range of substrate specificity increases.
• - A different substrate could not induce these
  structural changes and no catalysis would occur.

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Factors affecting enzyme activity
Activity of enzyme how fast an enzyme catalyzes
the reaction.
1. Temperature
2. pH
3. Substrate concentration
4. enzyme concentration
5. Enzyme inhibition
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Temperature

• Enzymes are very sensitive to temperature.
• At low T, enzyme shows little activity (not an
  enough amount of energy for
• the catalyzed
  reaction).
• - At very high T, enzyme is destroyed (tertiary
  structure is denatured).
• - Optimum temperature 37C or body temperature.

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pH

• Optimum pH is 7.4 in our body.
• Lower or higher pH can change the shape of
  enzyme.
• (active site change and substrate cannot fit
  in it)
• But optimum pH in stomach is 2.
• Stomach enzyme (Pepsin) needs an acidic pH to
  digest the food.
• - Some damages of enzyme are reversible.

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Substrate and enzyme concentration
Enzyme concentration ?
Rate of reaction ?
Substrate concentration ?
First Rate of reaction ?
End Rate of reaction reaches to its maximum all
of the enzymes are combined with substrates.
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Enzyme inhibition
Inhibitors cause enzymes to lose catalytic
activity.
Competitive inhibitor
Noncompetitive inhibitor
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Competitive Inhibitor

• Inhibitor has a structure that is so similar to
  the substrate.
• It competes for the active site on the enzyme.
• Solution increasing the substrate concentration.

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Noncompetitive Inhibitor

• Inhibitor is not similar to the substrate.
• It does not compete for the active site.
• When it is bonded to enzyme, change the shape
• of enzyme (active site) and substrate cannot
  fit in
• the active site (change tertiary structure).
• Like heavy metal ions (Pb2, Ag, or Hg2) that
• bond with COO-, or OH groups of amino acid
• in an enzyme.
• Penicillin inhibits an enzyme needed for
  formation
• of cell walls in bacteria infection is
  stopped.
• Solution some chemical reagent can remove the
• inhibitors.

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Competitive and Noncompetitive Inhibitor
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Enzyme cofactors
Metal ions bond to side chains.
obtain from foods. Fe2 and Cu2 are
gain or loss electrons in redox reactions.
Zn2 stabilize amino acid side chain during
reactions.
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Enzyme cofactors

• Enzyme and cofactors work together.
• Catalyze reactions properly.

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Vitamins and Coenzymes
Vitamins are organic molecules that must be
obtained from the diet. (our body cannot make
them)
Water-soluble vitamins have a polar group (-OH,
-COOH, or )
- They are not stored in the body (must be
taken). - They can be easily destroyed by heat,
oxygen, and ultraviolet light (need care).
Fat-soluble vitamins have a nonpolar group
(alkyl, aromatic, or )

• - They are stored in the body (taking too much
  toxic).
• A, D, E, and K are not coenzymes, but they are
  important
• vision, formation of bone, proper blood
  clotting.

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Zymogens (Proenzymes)
Zymogen (Proenzyme) an inactive enzyme that
becomes an active enzyme after a chemical change
(remove or change some polypeptides).
Trypsinogen (inactive enzyme) Trypsin (active
enzyme)
Pancreas
Small intestine
Digestive enzyme (hydrolyzes the peptide bonds of
proteins)
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Enzymes in medicine

• - Most of enzymes are in cells.
• Small amounts of them are in body fluids (blood,
  urine,).

Level of enzyme activity can be monitored.
Find some diseases
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Enzymes in medicine
Certain enzymes are present in higher amounts in
particular cells.
If these cells are damaged or die, the enzymes
are released into the bloodstream and can be
detected.
Enzyme
Condition
Creatine phosphokinase
Heart attack
Alkaline phosphatase
Liver or bone disease
Acid phosphatase
Prostate cancer
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Enzymes in medicine
Inhibitors can be useful drugs.
Penicillin inhibits the enzyme that forms cell
walls of bacteria, destroying the bacterium.
ACE (angiotensin-converting enzyme) causes blood
vessels to narrow, increasing blood pressure.
ACE inhibitors are given to those with high blood
pressure to prevent ACEs synthesis from its
zymogen.
HIV protease is an essential enzyme that allows
the virus to make copies of itself.
HIV protease inhibitors interfere with this
copying, decreasing the virus population in the
patient.