Chapter 21

Amino Acids, Proteins, and Enzymes

Chemistry 203

Function of proteins

Fibrinogen helps blood clotting

Function of proteins

- 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.

Proteins

- Proteins account for 50% of the dry weight of the human body.

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.

• 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−

Amino acids

+Zwitterion

α-carbon

H H

Ionized form (Salt)

R R

This form never exist in nature.

Amino acids

H │

H3N—C —COO−

│ H glycine

CH3 │

H3N—C —COO−

│ H alanine

+

+

Only difference: containing a different side chain (R) for each.

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.

Amino acids

There are only 20 different amino acids in the proteins in humans.

There are many amino acids.

Amino acids

They are called α amino acids.

- Humans cannot synthesize 10 of these 20 amino acids. (Essential Amino Acids)

- They must be obtained from the diet (almost daily basis).

Nonpolar (Neutral) amino acids

NH3+

COO-

NH3+

COO-

NH3+

COO-

NH3+

COO-

NH3+

COO-S

NH3+

COO-

NH H

COO-

NH3+

COO-

NH

COO-

NH3+

Alanine (Ala, A)

Glycine (Gly, G)

Isoleucine (Ile, I)

Leucine (Leu, L)

Methionine (Met, M)

Phenylalanine (Phe, F)

Proline (Pro, P)

Tryptophan (Trp, W)

Valine (Val, V)

NH3+

COO-

HS

NH3+

COO-

HO

Cysteine (Cys, C)

Tyrosine (Tyr, Y)

NH3+

COO-H2N

O

NH3+

COO-

H2N

O

NH3+

COO-

HO

NH3+

COO-OH

Asparagine (Asn, N)

Glutamine (Gln, Q)

Serine (Ser, S)

Threonine (Thr, T)

Polar (Neutral) amino acids

NH3+

COO--O

O

NH3+

COO--O

O NH3+

COO-

NH

H2N

NH2+

NH3+

COO-

N

NH

NH3+

COO-H3N

Glutamic acid (Glu, E)

Aspartic acid (Asp, D)

Histidine (His, H)

Lysine (Lys, K)

Arginine (Arg, R)

+

Acidic and basic amino acids

Fischer projections

All of the α-amino acids are chiral (except glycine)

Four different groups are attached to central carbon (α-carbon).

H NH3+

COO-

CH3

+H3N H

COO-

CH3

D-Alanine L-Alanine

(Fischer projections)

H NH3+

COO-

CH3

+H3N H

COO-

CH3

D-Alanine L-Alanine

(Fischer projections)

CH2SH CH2SH

D-cysteine L-cysteine

L isomers is found in the body proteins and in nature.

Ionization and pH

pH: 6 to 7 Isoelectric point (pI)

Positive charges = Negative chargesNo net charge (Neutral) - Zwitterion

pH: 3 or less -COO- acts as a base and accepts an H+

+

RH3N-CH-C-O

-O

+ H3O+ +

RH3N-CH-C-OH

O+H2O

pH: 10 or higher -NH3+ acts as an acid and loses an H+

+

RH3N-CH-C-O

-O

+ OH-

RH2N-CH-C-O

-O

+H2O

+

RH3N-CH-C-O

-O

+ OH-

RH2N-CH-C-O

-O

+H2O

-

Ionization and pH

The net charge on an amino acid depends on the pH of the solution in which it is dissolved.

pH 2.0 pH 5.0 - 6.0 pH 10.0Net charge +1 Net charge 0 Net charge -1

+

RH3N-CH-C-O

-O+

RH3N-CH-C-OH

O

RH2N-CH-C-O

-OOH-

H3O+

OH-

H3O+

6.015.41

5.655.976.026.025.745.486.485.685.87

5.895.97

pI

valinetryptophan

threonineserineprolinephenylalaninemethionineleucineisoleucineglycineglutamine

asparaginealanine

Nonpolar &polar side chains

10.76

2.77

5.073.22

7.599.74

5.66

pI

tyrosine

lysinehistidine

glutamic acidcysteine

aspartic acid

arginine

AcidicSide Chains

BasicSide Chains pI

Ionization and pH

Each amino acid has a fixed and constant pI.

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.

Peptide

O

O-H3N

CH3H3N O-

CH2OH

O

H3NN

CH3

O CH2OH

O

O-

H

H2O+

Alanine (Ala) Serine (Ser)

++

+

peptide bond

Alanylserine (Ala-Ser)

+

(amide bond)

•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.

Peptide

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).

H3N

OH

NH O

HN

COO-

O-

OC6H5O

+

C-terminalamino acid

N-terminalamino acid

Ser-Phe-Asp

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.

H3N-CH-C-NH-CH2-C-NH-CH-C-O

CH3 CH2OH

O O O

From alaninealanyl

From glycineglycyl

From serineserine

Alanylglycylserine(Ala-Gly-Ser)

+ -

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.

Biologically Active Peptides

Enkephalins:

Met-enkephalin:It contains a C-terminal methionine.

Leu-enkephalin:It contains a C-terminal leucine.

Biologically Active Peptides

Oxytocin and vasopressin are cyclic nonapeptide hormones, which have identical sequences except for two amino acids.

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.

Biologically Active Peptides

Structure of proteins

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure

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.

Ala─Leu─Cys─Met

+

CH3

S

CH2

CH2

SH

CH2

CH3

CH3CH

CH O

O-CCH

H

N

O

CCH

H

N

O

CCH

H

N

O

C

CH3

CHH3N

+

Cysteine

The -SH (sulfhydryl) group of cysteine is easily oxidized

to an -S-S- (disulfide).

+

CH2

H3N-CH-COO-

SH

oxidation

reduction

+

CH2

H3N-CH-COO-

S

+H3N-CH-COO

-CH2

S

CysteineCystine

2

a disulfidebond

Primary Structure of proteins

Chain A

CO

O-

NH3+ NH3

+

CO

O-

Chain B

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.

Secondary Structure of proteins

Describes the way the amino acids next to or near to each otheralong the polypeptide are arranged in space.

1. Alpha helix (α helix)

2. Beta-pleated sheet (-pleated sheet)

3. Triple helix (found in Collagen)

4. Some regions are random arrangements.

Secondary Structure - α-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 C=O 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 α-Keratin in hair

have this arrangement.

H-bond

Secondary Structure - -pleated sheet

O H

• 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.

Secondary Structure – Triple helix (Superhelix)

- Collagen is the most abundant protein.

- Three polypeptide chains (three α-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).

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-

Tertiary Structure

(1) Disulfide (-S-S-)

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

Shorthand symbols on a protein Ribbon diagram:

Tertiary Structure

Lysozyme (an enzyme)

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 α-helix).

Fibrous proteins

α-keratin: skin, nail, hair, and bone

- Have long, thin shape and insoluble in water.

- Involve in the structure of cells and tissues.

-keratin: feathers of birds

Large amount of -pleated sheet

Superhelix:

Collagen

- They are made of two mainly -helix chains coiled around each other in a superhelix (supercoil).

- These coils wind around other coils making larger and stronger structures (like hair).

Fibrous proteins

α-keratin: hair, wool, skin, and nails

- α-helix chains bond together by disulfide bond (-S-S-)

- More disulfide bonds, more rigid materials (horns & nails).

Collagen

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

chain

α chain

α chain

Hemoglobin

Conjugated Proteins

They are composed of a protein unit and a nonprotein molecule.

Myoglobin & Hemoglobin

Heme: a complex organic compound containing the Fe2+.

Sickle Cell Hemoglobin

Sickle cell anemia is a disease where a single amino acid of both β subunits is changed from glutamic acid to valine.

- 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.

- A genetic mutation in the DNA sequence that is responsible for synthesis of hemoglobin.

Summary of protein Structure

Summary of protein Structure

Denaturation

Active protein

Denatured protein

- 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

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

Enzymes

Enzyme

Eact

Eact

- Like a catalyst, they increase the rate of biological reactions (106 to 1012 times faster).

- Lower the activation energy for the reaction.

2HIH2 + I2 H…H

I … I

… …

- Less energy is required to convert reactants to products.

- But, they are not changed at the end of the reaction.

- They are made of proteins.

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)

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.

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.

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

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

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.

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

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: 37°C or body temperature.

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.

Substrate and enzyme concentration

Maximum activity

Enzyme concentration ↑ Rate of reaction ↑

Substrate concentration ↑ First: Rate of reaction ↑

End: Rate of reaction reachesto its maximum: all of the enzymesare combined with substrates.

Enzyme inhibition

Inhibitors cause enzymes to lose catalytic activity.

Competitive inhibitor

Noncompetitive inhibitor

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.

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.

Inhibitor

Site

Competitive and Noncompetitive Inhibitor

Enzyme cofactors

protein

protein

protein

Metal ion

Organicmolecules

(coenzyme)

Simple enzyme (apoenzyme)

Enzyme + Cofactor

Enzyme + Cofactor (coenzyme)

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.

Enzyme cofactors

- Enzyme and cofactors work together.

- Catalyze reactions properly.

Vitamins and Coenzymes

Water-soluble vitamins: have a polar group (-OH, -COOH, or …)

Vitamins are organic molecules that must be obtained from the diet.(our body cannot make them)

Fat-soluble vitamins: have a nonpolar group (alkyl, aromatic, or …)

- They are not stored in the body (must be taken).

- They can be easily destroyed by heat, oxygen, and ultraviolet light (need care).

- 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.

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)

Digestive enzyme (hydrolyzes the peptide bonds of proteins)

Pancreas

Small intestine

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

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

Enzymes in medicine

Penicillin inhibits the enzyme that forms cell walls of bacteria, destroying the bacterium.

ACE inhibitors are given to those with high blood pressure to prevent ACE’s synthesis from it’s zymogen.

ACE (angiotensin-converting enzyme) causes blood vessels to narrow, increasing blood pressure.

HIV protease inhibitors interfere with this copying, decreasing the virus population in the patient.

HIV protease is an essential enzyme that allows the virus to make copies of itself.

Enzymes in medicine

Inhibitors can be useful drugs.