Copyright © Houghton Mifflin Company. All rights reserved.3–13–1 16.1 Intro to Proteins Proteins are polymers in which the monomer units are amino acids.

Copyright © Houghton Mifflin Company. All rights reserved. 3–1

16.1 Intro to Proteins

Proteins are polymers in which the monomer units are amino acids.

The name “protein” comes from the Greek, and means “of first importance.”

Proteins are the most abundant biomolecules in animals (including humans) and have the widest variety of structures.

Proteins contain nitrogen; carbohydrates and lipids generally do not.


16.2 Amino AcidsAn amino acid contains both an amino group

(–NH2) and a carboxylic acid (–COOH).

Both groups are on the same carbon, the -carbon. The carbon also carries an R group and a hydrogen atom.

CCN

RH

O

O

H

HH


16.2 Amino AcidsThere are 20 standard amino acids, each

with a different R group. There are four categories of amino acids.


16.2 Amino AcidsPolar neutral amino acids.


16.2 Amino Acids

Polar acidic and basic amino acids.


16.2 Amino Acids

Polar acidic and basic amino acids.


16.2 Amino AcidsTen amino acids cannot be produced by the

body, and must be obtained through the diet. These are the essential amino acids.


16.3 HandednessThe -carbon in an amino acid is chiral. Most

amino acids have the L-configuration.


16.4 Acid-Base PropertiesAmino acids undergo intramolecular proton

transfer. They always exist as zwitterions (double, or hybrid) ions.

Zwitterions have no net electrical charge.

CCN

RH

O

O

H

H CCN

RH

O

O

H

HH

H

Neutral Molecule Zwitterion


16.4 Acid-Base Properties

In acidic solution, the carboxylate group is protonated. This produces a cation.

CCN

RH

O

O

H

HH

+ H3O CCN

RH

O

OH

H

HH

+ H2O

Zwitterion + acid Positive net charge



In basic solution, the ammonium group is deprotonated. This produces an anion.

CCN

RH

O

O

H

HH

+ OH

Zwitterion + base

CCN

RH

O

OHH

+ H2O

Negative net charge



The pH at which an amino acid exists as its uncharged zwitterion is called the isoelectric point. Neutral amino acids have isoelectric points about pH 6.

Acidic amino acids have low isoelectric points, because the carboxylate group must be protonated.

Basic amino acids have high isoelectric points, because the amino group must be deprotonated.


16.5 Peptide FormationAmino acids condense to form amide, or

peptide, bonds. The reactions are cat-alyzed by enzymes.

N C C

H

R1

O

O

H

H

H

+ N C C

H

R2

O

O

H

H

H

N C C

H

R1

O

N

H

H

H

H

C

H

R2

C

O

O

+ H2O

enzyme

a dipeptide


16.5 Peptide Formation

A chain of any length can form.

A polypeptide contains 50 or fewer amino acid residues.

A protein contains more than 50 amino acid residues.

Central Dogma of Molecular BiologyProtein synthesis is directed by RNA (ribonu-

nucleic acid). DNA (deoxyribonucleic acid) acts as a template for RNA synthesis.


16.6 - 16.10 Protein Structure

The structure of pro-teins and peptides is critical to their func-tion in organisms. It is divided into four levels.

Primary structure of proteins refers to the sequence of amino acid residues.


16.6 - 16.10 Protein StructureThe structure of pro-

teins and peptides is critical to their func-tion in organisms. It is divided into four levels.

Primary structure of proteins refers to the sequence of amino acid residues. The illustration shows hu-man myobglobin.



Secondary structure of proteins refers to the arrangement adopted by the backbone por-tion of the protein. It results from hydrogen bonding between N–H and C=O groups.

Two major secondary structures are seen:

the -helix, formed by a coiled chain

the -pleated sheet, formed by hydrogen bonds between extended chains

or segments of a single chain



Views of the -helix, formed by a coiled chain



Views of the -pleated sheet, formed by hydro-gen bonds between extended chains or seg-ments of a single chain



Views of the -pleated sheet, formed by hydro-gen bonds between extended chains or seg-ments of a single chain



Tertiary structure re-fers to the overall three-dimensional shape of a protein.

This illustration shows the struc-ture of myoglobin.



Four types of attractive forces give rise to the tertiary structure of proteins.

Disulfide bonds

Electrostatic interactions, a.k.a. salt bridges

Hydrogen bonds

Hydrophobic interactions


16.6 - 16.10 Protein StructureDisulfide bonds form between –SH groups of

cysteine residues. They are covalent bonds.

C

C CH2H

N

O

SH

H

C

C H

N

O

H

CH2+ HSenzyme

C

C CH2H

N

O

S

H

C

C H

N

O

H

CH2S


16.6 - 16.10 Protein StructureDisulfide bonds between the two

chains of human insulin.



Electrostatic interactions between side-chain carboxylate and ammo-nium ions are ionic bonds. They are also called salt bridges.



Hydrogen bonds form between hydroxyl and amide functional groups on side chains of amino acid residues.



Hydrophobic interactions occur between nonpolar side chains on amino acid residues. They involve dispersion forces similar to those that form micelles.



Quaternary structure refers to the arrangement of polypeptide chains within a protein that are not covalently bound to each other.

The chains are bound by the same forces that give rise to tertiary structure.

The next slide shows the quaternary structure of hemoglobin.



Quaternary structure refers to the arrangement of polypeptide chains within a protein that are not covalently bound to each other.


16.11 Protein Classification

Proteins can be classified by composition or by morphology (shape/structure).

Classifications based on composition:

Simple proteins contain only amino acid residues. More than one chain may be present.

Conjugated proteins have prosthetic groups, components that are not made up of amino acids. These can be organic or inorganic.



Types of conjugated proteins:


16.11 Protein ClassificationClassifications based on morphology:

Fibrous proteins are rod-shaped or stringlike.They have structural or movement functions.They have very long chains.They are not water-soluble.

Globular proteins are “globby.”They have functions other than structure or movement.They have chains of moderate length.They dissolve in water or form colloids.



Types of fibrous and globular proteins:


16.11 Protein Functions

1. Catalysis: Proteins called enzymes catalyze biochemical reactions.

2. Structure: Proteins are the main structural molecules in animals.

Collagen is found in skin, bone, connective tissue (tendons, etc.)

Keratin in hair, nails, skin



3. Storage: Proteins provide a way to store small molecules or ions in

the organism.

Ovalbumin stores amino acids in bird eggs.

Casein stores amino acids in milk.

Ferritin stores iron ions in animal spleens.



4. Protection: Antibodies form complexes with foreign protein from viruses and bacteria, and help destroy them.

Fibrinogen and thrombin are proteins involved in

blood clot formation.



5. Regulation: Hormones trigger a specific process in target tissues.

Many are proteins or peptides.

Insulin regulates glucose metabolism.

Vasopressin regulates volume of urine and blood pressure.

Oxytocin regulates contraction of the uterus and lactating mammary glands.



6. Nerve Impulse Transmission:

Some proteins act as receptors of small molecules that pass across synapses, gaps between nerve cells.

Rhodopsin is a protein in the retina. It is activated by

isomer- ization of retinal, a molecule derived from Vitamin A.



7. Movement: Proteins in muscle are respon- sible for contraction and relax- ation.

Actin and myosin are fibrous proteins that slide

across each other in muscle movement.



8. Transport: Proteins transport ions and molecules through the blood stream and other body fluids.

Hemoglobin transports oxygen through the blood stream.

Serum albumin transports fatty acids through the blood

stream.

Lipoproteins transport lipids through various body fluids.


16.12 Protein Deactivation

Proteins can be deactivated by two processes, hydrolysis and denaturation.

Hydrolysis is the reverse of peptide bond for-mation. It reduces a protein to smaller poly-peptide molecules and free amino acids.

Hydrolysis can be caused by enzymes or strong acids or bases. It is part of the nor-mal digestion of proteins in the stomach.



Hydrolysis of a tripeptide to amino acids:

N C C

H

R1

O

N

H

H

H

H

C

H

R2

C

O

N

N C C

H

R1

O

O

H

H

H

+ N C C

H

R2

O

O

H

H

H

acid, base,or enzyme

H

C

R3

H

C

O

O

H2O

+ N C C

H

R3

O

O

H

H

H



Denaturation is the partial or complete disorganization of a protein’s three-dimensional shape.

Denaturation is caused by disruption of the attractive forces that produce this shape. Heat, acids or bases, deter-gents, organic solvents, ions of heavy metals, and violent whipping or shaking can denature proteins.


16.12 Protein DeactivationDenaturation of a protein:


16.13 Enzymes

Enzymes are catalysts for biochemical reactions. Most are globular proteins, although a few are ribonucleic acids.

Catalysts increase the rate of a chemical reaction, but they are not consumed in the reaction.

Enzymes can increase the rate of a reac-tion by a factor of 10 20 compared to that of the uncatalyzed reaction.


16.13 Introduction to Enzymes

Enzyme catalysis has three key characteristics:

Efficiency Reactions are very fast under mild conditions.

Specificity Enzymes catalyze reactions of just one compound, or a few

similar compounds (substrates).

Regulation Catalysis can be controlled by the cells in which reactions

occur.


16.14 Names and Classification

The name of a specific enzyme has three parts and ends in “-ase.”

1. Substrate Urea 2. Functional Group Amide 3. Reaction

Hydrolysis

H2NC

NH2

O Urea amidohydrolase

1 2 32 NH3 + CO2



Enzymes are named by the type of reaction they catalyze:

1. Oxoreductases Oxidation-reduction reactions

2. Transferases Move functional groups

3. Hydrolases Hydrolysis reactions

4. Lyases Addition across double bonds or the reverse

(elimination)

5. Isomerases Rearrange the substrate

6. Ligases Formation of bonds with ATP cleavage



Like other proteins, enzymes can be simple or conjugated.

Simple enzymes contain only amino acid residues. More than one chain may be present.

Conjugated enzymes have components that are not made up of amino acids. These can be organic or inorganic.



Conjugated enzymes consist of two parts:

An apoenzyme is the protein portion of a conjugated enzyme.

A cofactor is the nonprotein portion of a conjugated enzyme. There are three types:

Prosthetic groups Coenzymes Minerals


16.14 Names and ClassificationProsthetic groups, e.g. heme, are tightly

bound to the apoenzyme.


16.14 Names and ClassificationCoenzymes are small organic molecules that

are not tightly bound to the apoenzyme. They are often derived from vitamins.

N

COH

O

N

CNH2

O

R

N

C

R

H H O

NH2

Niacin,Vitamin B3 NAD+ NADH

NAD+ and NADH are cofactors for many oxoreductases



Minerals are inorganic ions that act as cofactors.

Common minerals:

Zn2+ Mg2+ Mn2+ Fe2+ Cl1−


16.15 How Enzymes Work

In catalysis, the substrate fits into the active site of the enzyme, where it is held in place while the reaction occurs.

This is called the enzyme-substrate complex, or ES complex. The reaction may then take place.

E + S ES E + P

enzyme substrate complex enzyme product



The active site is often a crevice-like region into which the sub-strate fits to form the ES complex.



The active site is often a crevice-like region into which the sub-strate fits to form the ES complex.

The specificity of en-zymes for substrates is attributed to the structures of active sites.



The “lock and key” model involves an active site with a fixed shape that accommodates only a certain substrate.



The “induced fit” model involves flexible active site that adapts to the structure of the sub-strate and binds to it.


16.16 Enzyme Activity

Enzymes activity is the rate at which an enzyme converts substrate to product.

“Turnover rate,” substrate molecules/minute or substrate molecules/second per molecule of enzyme

“Turnover time,” seconds per molecule of product per molecule of enzyme

Enzyme International Unit (EIU), concentration of enzyme that catalyzes 10–6 mole of substrate reaction per minute



Enzyme-catalyzed reactions are fast!



All chemical reaction rates increase with temperature. With enzymes, body tem-perature is optimal.

At higher temper-atures, the enzyme is denatured.


16.16 Enzyme ActivityAcidity affects enzyme

acitivity.

Optimal pH for most enzymes is 7.0 to 7.5.

Some digestive en-zymes function best outside this range.

Extremes in pH will denature the enzyme.


16.16 Enzyme ActivityAll chemical reaction

rates increase with increases in reactant and catalyst concen-tration.

If enzyme concentra-tion is constant, rate will increase with sub-strate concentration to a maximum.



Reaction rate will in-crease if enzyme concentration is increased.



Enzyme activity can be reduced by inhibitors. Inhibition may be caused by a substance that occurs naturally in an organism to regulate enzyme activity. It may also be caused by a medicine or a poison.

Enzyme inhibition can be irreversible or reversible.



Irreversible inhibitors form a covalent bond with a specific functional group of the enzyme and deactivate it. Cyanide binds to Fe3+ in cytochrome oxidase, so it can’t carry oxygen. Heavy metals bind to thiols.

Cyt ⏐ Fe3+ + CN1− Cyt⏐ Fe⏐ CN2+

cytochromeoxidase

stable complex

CN1− + S2O32− SCN1− + SO3

2−

thiosulfate thiocyanate sulfite

Cyt ⏐ Fe3+ + O2 Cyt⏐ Fe⏐ O23+

reversible complex



Some antibiotics inhibit bacterial enzymes.

Penicillin inhibits a transpeptidase that is used in bacterial cell wall construction.

Sulfa drugs interfere with synthesis of folic acid, which is required for growth of some bacteria. Folic acid is also essential to an-imals, but we get it in our diet. However, we need our intestinal bacteria! That’s why some antibiotics cause digestive distress.



Reversible inhibitors bind reversibly to enzymes. The enzyme-inhibitor complex is in equilibrium with its components.

Shifting the equilibrium frees the enzyme.There are two types of reversible inhibition, competitive and noncompetitive.

Enzyme + Inhibitor EI complex


16.16 Enzyme ActivityCompetitive inhibitors bind to the active site of

an enzyme and block it. They compete with the substrate molecules for the active site.

Noncompetitive inhibitors bind reversibly to an enzyme, but not at the active site. The inhibitor alters the shape of the active site. The enzyme cannot bind to the substrate.

Feedback inhibitors are metabolic products that inhibit enzymes that catalyze their production. They can be competitive or noncompetitive.

Copyright © Houghton Mifflin Company. All rights reserved.3–13–1 16.1 Intro to Proteins Proteins are polymers in which the monomer units are amino acids.

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amino acidsan amino

acidic amino acids

basic amino acids

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standard amino acids

essential amino acids

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