chemistry b11 chapters 16 proteins and enzymes€¦ · chemistry b11 chapters 16. proteins and...

Chemistry B11 Bakersfield College

Chemistry B11 Chapters 16

Proteins and Enzymes

Proteins: all proteins in humans are polymers made up from 20 different amino acids.

Proteins provide structure in membranes, build cartilage, muscles, hair, nails, and connective

tissue (wool, silk, feathers, and horns are some other proteins made by animals), transport

oxygen in blood and muscle, direct biological reactions as enzymes, defend the body against

infection, and control metabolic processes as hormones. They can even be a source of energy.

Different functions of proteins depend on the structure and chemical behavior of amino acids,

the building blocks of proteins.

Amino acids: proteins are composed of molecular building blocks called amino acids. An

amino acid contains two functional groups, an amino group (-NH2) and a carboxylic acid

group (-COOH). In all of the 20 amino acids found in proteins, the amino group, the

carboxylic group, and a hydrogen atom are bonded to a central carbon atom. Amino acids

with this structure are called α (alpha) amino acids. Although there are many amino acids,

only 20 different amino acids are present in the proteins in humans. The unique characteristics

of the 20 amino acids are due to a side chain (-R), which can be an alkyl, hydroxyl, thiol,

amino, sulphide, aromatic, or cyclic group.


Zwitterion: although it is convenient to write amino acids with carboxyl (-COOH) group and

amino (-NH2) group, they are usually ionized. At the pH of most body fluids, the carboxyl

group loses a H+, giving –COO

-, and the amino group accepts a H

+ to give an ammonium ion,

-NH3+. The dipolar form of an amino acid, called a Zwitterion, has a net charge of zero (it is

neutral).

Classification of Amino acids:

1. Nonpolar amino acids: which have alkyl or aromatic side chains, are hydrophobic

(“water-fearing”).

2. Polar amino acids: which have polar side chains such as hydroxyl (-OH), thiol (-SH), and

amide (-CONH2) that form hydrogen bonds with water, are hydrophilic (“water attracting”).

3. Acidic amino acids: have side chains that contain a carboxylic group (-COOH) and can

ionize as a weak acid.

4. Basic amino acids: have side chains that contain an amino group that can ionize as a weak

base.

D and L isomer: all of the α-amino acids (except for glycine) are chiral because the α carbon

is attached to four different atoms. Thus amino acids can exist as D and L isomers

(enantiomers). For the L isomer the amino group, NH2, is on the left, and in the D isomer, it is

on the right. In biological systems, only L amino acids are incorporated into proteins. There

are D amino acids found in nature, but not in proteins.

Ionization and pH: at a certain pH known as the isoelectric point (pI), the positive and

negative charges are equal, which gives an overall charge of zero (no net charge). The

zwitterions for polar and nonpolar amino acids typically exist at pH values of 5.0 to 6.0.

However, in a solution that is more acidic than the pI (pH about 2 or 3), the –COO- group acts

as a base and accepts an H+, which gives an overall positive charge to the amino acid (net

charge +1):

In a solution more basic than the pI (pH from 7.6 to 10.8), the –NH3+ group acts as an acid

and loses an H+, which gives the amino acid an overall negative charge (net charge –1):

+

R

H3N-CH-C-O-

O

+ H3 O+

+

R

H3N-CH-C-OH

O

+ H2 O

+

R

H3 N-CH-C-O-

O

+ OH-

R

H2 N-CH-C-O-

O

+ H2 O


As a result, the net charge on an amino acid depends on the pH of the solution in which it is

dissolved. Each amino acid has a constant pI (isoelectric point) and by comparison of values

of pI and pH of solution, we can find the charge of an amino acid.

Peptide: the linking of two or more amino acids forms a peptide. A peptide bond is an amide

bond that forms when the –COO- group of one amino acid reacts with the –NH3

+ group of the

next amino acid.

Note: Two amino acids linked together by a peptide bond form a dipeptide, three amino

acids from tripeptide, many amino acids form polypeptide. Protein is a biological

macromolecule containing at least 30 to 50 amino acids joined by peptide bonds.

Note: In a peptide, the amino acid written on the left with the unreacted or free amino group

(-NH3+) is called the N terminal amino acid. The C terminal amino acid is the last amino

acid in the chain with the unreacted or free carboxyl group (-COO-).

Naming of peptide: in naming a peptide, each amino acid beginning from the N terminal is

named with a “-yl” ending (we drop the “-ine” and we replace “-yl”) followed by the full

name of the amino acid at the C terminal. For example, a tripeptide consisting of alanine,

glycine, and serine is named as alanylglycylserine. For convenience, the order of amino acids

in the peptide is often written as the sequence of three-letter abbreviations.

pH 2.0 pH 5.0 - 6.0 pH 10.0

Net charge +1 Net charge 0 Net charge -1

+

R

H3 N-CH-C-O-

O+

R

H3 N-CH-C-OH

O

R

H2 N-CH-C-O-

OOH-

H3 O+

OH-

H3 O+

O

O-

H3N

CH3

H3NO-

CH2 OH

O

H3NN

CH3

O CH2 OH

O

O-

H

H2 O+

Alanine (Ala) Serine (Ser)

++

+

peptide

bond

Alanylseri ne

(Ala-Ser)

+


Levels of protein structure: Each protein in our cells has a unique sequence of amino acids

that determines in biological function. Four levels exist for structure of the proteins:

1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure

1. Primary Structure: The primary structure is the order of the amino acids held together by

peptide bonds.

The first protein to have its primary structure determined was insulin, which is a hormone that

regulated the glucose level in the blood. In the primary structure of human insulin, there are

two polypeptide chains. In the chain A, there are 21 amino acids, and chain B has 30 amino

acids. The polypeptide chains are held together by disulfide bonds formed by the side chains

of the cysteine amino acids in each of the chains. Today human insulin produced through

genetic engineering is used in the treatment of diabetes.

Note: The -SH (sulfhydryl) group of cysteine (an amino acid) is easily oxidized to an -S-S-

(disulfide).

Secondary structure: the secondary structure of a protein describes the way the amino acids

next to or near to each other along the polypeptide are arranged in space. The three most

common types of secondary structure are the alpha helix, the beta-pleated sheet, and the triple

helix found in collagen.

Alpha helix (α-helix): the corkscrew shape of an alpha helix is held in place by hydrogen

bonds between each N-H group and the oxygen of a C=O group in the next turn of the helix,

four amino acids down the chain. Because many hydrogen bonds form along the peptide

backbone, this portion of the protein takes the shape of a strong, tight coil that looks a

+

CH2

H3 N-CH-COO-

SH

oxidation

reduction

+

CH2

H3 N-CH-COO-

S

+H3 N-CH-COO

-CH2

S

Cysteine

Cystine

2

a disulfidebond


telephone cord or a Slinky toy. All the side chains (R groups) of the amino acids are located

on the outside of the helix.

Beta-pleated sheet (-pleated sheet): in a -pleated sheet, polypeptide chains are held

together side by side by hydrogen bonds between the peptide chains. In a -pleated sheet of silk fibroin, the small R groups of the prevalent amino acids, glycine, alanine, and serine,

extend above and below the sheet. This result in a series of -pleated sheets that are stacked

close together. The hydrogen bonds holding the -pleated sheets tightly in place account for the strength and durability of proteins such as silk.

Triple helix (Collagen): the most abundant protein, makes up as one-third of all the protein

in vertebrates. It is found in connective tissue, blood vessels, skin, tendons, ligaments, the

cornea of the eye, and cartilage. The strong structure of collagen is a result of three

polypeptides woven together like a braid to form a triple helix. Collagen has a high content of

glycine (33%), praline (22%), alanine (12%), and smaller amounts of hydroxyproline, and

hdroxylysine. The hydroxyl forms of praline and lysine contain –OH groups that form

hydrogen bonds across the peptide chains and give strength to the collagen triple helix.

Note: When a diet is deficient in vitamin C, collagen fibrils are weakened because the

enzymes needed to form hydoxyproline and hydroxylysine require vitamin C. Without the –

H-bond

O H


OH groups of hydroxyproline and hydroxylysine, there is less hydrogen bonding between

collagen fibrils. As a person ages, additional cross-links form between the fibrils, which make

collagen less elastic. Bones, cartilage, and tendons become more brittle, and wrinkles are seen

as the skin loses elasticity.

Tertiary structure: the tertiary structure of a protein involves attractions and repulsions

between the side chain groups of the amino acids in the polypeptide chain. As interactions

occur between different parts of the peptide chain, segments of the chain twist and bend until

the protein acquires a specific three-dimensional shape. The tertiary structure of a protein is

stabilized by interactions between the R groups of the amino acids in one region of the

polypeptide chain with R groups of amino acids in other regions of the protein.

There are five important interactions:

1. Hydrogen bond: occurs between H and O or N.

2. Hydrophobic interactions: are interactions between two nonpolar R groups. Within the

protein, the amino acids with nonpolar side chains push as far away from the aqueous

environment as possible, which forms a hydrophobic center at the interior of the molecule.

3. Hydrophilic interactions: are attractions between the external aqueous environment and

amino acids that have polar or ionized side chains. The polar side chains pull toward the outer

surface of globular proteins to hydrogen bond with water.

4. Salt bridges: are ionic bonds between side chains of basic and acidic amino acids, which

have positive and negative charges. The attraction of the oppositely charged side chains forms

a strong bond called a salt bridge. If the pH changes, the basic and acidic side chains lose their

ionic charges and cannot form salt bridge, which causes a change in the shape of the protein.

5. Disulfide bonds: are the strong covalent links between sulfur atoms of two cysteine amino

acids.

Globular proteins: a group of proteins known as globular proteins have compact, spherical

shapes because sections of the polypeptide chain fold over on top of each other. It is the

globular proteins that carry out the work of the cells: functions such as synthesis, transport,


and metabolism. Myoglobin is a globular protein that stores oxygen in skeletal muscle. High

concentrations of myoglobin are found in the muscles of sea mammals, such as seals and

whales, which allow them to stay under the water for long periods. Myoglobin contains 153

amino acids in a single polypeptide chain with about three-fourths of the chain in the α-helix

secondary structure. Within the tertiary structure, a pocket of amino acids and a heme group

binds and store oxygen.

Fibrous proteins: are proteins that consist of long, thin, fiber-like shapes. They are typically

involved in the structure of cells and tissue. Two types of fibrous protein are α- and -keratins. The α-keratins are the proteins that make up hair, wool, skin, and nails. In hair,

three α-helixes coil together like a braid to form a fibril. Within the fibril, the α-helices are

held together by disulfide (-S-S-) linkages between the R groups of the many cysteine amino

acids in hair. The -keratins are the type of proteins found in the feathers of birds and scales

of reptiles. In -keratins, the proteins consist of large amount of -pleated sheet structure.

Quaternary structure: when a biologically active protein consists of two or more

polypeptide subunits, the structure level is referred to as a quaternary structure. Hemoglobin,

a globular protein that transports oxygen in blood, consists of four polypeptide chains or

subunits, two α chains, and two chains. The subunits are held together in the quaternary by the same interactions that stabilized the tertiary structure, such as hydrogen bonds and salt

bridges between side groups, disulfide links, and hydrophobic attractions. Each subunit of the

hemoglobin contains a heme group that binds oxygen. In the adult hemoglobin molecule, all

four subunits must be combined for the hemoglobin to properly function as an oxygen carrier.

Therefore, the complete quaternary structure of hemoglobin can bind and transport four

molecules of oxygen.

Summary of structural level in proteins:

α chain

α chain chain

chain


Denaturation of proteins: denaturation of a protein occurs when there is a disruption of any

of the bonds that stabilize the secondary, tertiary, or quaternary structure. However, the

covalent amide bonds of the primary structure are not affected. When the interactions between

the R groups are undone or altered, a globular protein unfolds like a piece of spaghetti. With

the loss of its overall shape, the protein is no longer biologically active. Denaturation agents

include heat, acids and bases, organic compounds, heavy metal ions, and mechanical

agitation. The following table shows some examples of proteins denaturation. Some

denaturatins are reversible, while others permanently damage the protein.

Enzymes: as a catalyst, an enzyme increases the rate of a reaction by changing the way a

reaction takes place, but is itself not changed at the end of the reaction. An unanalyzed

reaction is a cell may take place eventually, but not at a rate fast enough for survival. For

example, the hydrolysis of proteins in our diet would eventually occur without a catalyst, but

not fast enough to meet the body’s requirements for amino acids. The chemical reactions in

our cells must occur at incredibly fast rates under the mild conditions pf pH 7.4 and a body

temperature of 37°C. To do this, biological catalysts known as enzymes catalyze nearly all the

chemical reactions that take place in the body. As catalysts, enzymes lower the activation

energy for the reaction (activation energy is the minimum energy necessary to cause a

chemical reaction to occur). As a result, less energy is required to convert reactant molecules

to products, which allows more reacting molecules to form product.


Names of enzymes: the names of enzymes describe the compound or the reaction that is

catalyzed. The actual names of enzymes are derived by replacing the end of the name of the

reaction or reacting compound with the suffix “-ase”. For example, an oxidase catalyzes an

oxidation reaction, and a dehydrogenase removes hydrogen atoms. The compound amylose is

hydrolyzed by the enzyme amylase, and a lipid is hydrolyzed by a lipase. Some early known

enzymes use names that end in the suffix “-in”, such as papain found in papaya, rennin found

in milk, and pepsin and trypsin, enzymes that catalyze the hydrolysis of proteins. There are

six classes of enzymes:

Enzyme action: Nearly enzymes are globular proteins. Each has a unique three-dimensional

shape that recognizes and binds a small group of reacting molecules, which are called

substrates. The tertiary structure of an enzyme plays an important role in how that enzyme

catalyzes reactions.

Active site: in a catalyzed reaction, an enzyme must first bind to a substrate in away that

favors catalysis. A typical enzyme is much larger that its substrate. However, within its large

tertiary structure, there is a region called the active site where the enzyme binds a substrate or

substrates and catalyzes the reaction. This active site is often a small pocket that closely fits

the structure of the substrate. Within the active site, the side chains of amino acids bind the

Eact

Eact


substrate with hydrogen bonds, salt bridges, or hydrophobic attractions. The active site of a

particular enzyme fits the shape of only a few types of substrates, which makes enzymes very

specific about the type of substrate they bind.

Enzyme catalyzed reaction: the proper alignment of a substrate within the active site forms

an enzyme-substrate (ES) complex. This combination of enzyme and substrate provides an

alternative pathway for the reaction that has a lower activation energy. Within the active site,

the amino acid side chains take part in catalyzing the chemical reaction. As soon as the

catalyzed reaction is complete, the products are quickly released from the enzyme so it can

bind to a new substrate molecule. We can write the catalyzed reaction of an enzyme (E) with

a substrate (S) to form product (P) as follows:

E (Enzyme) + S (Substrate) ES (Complex) E (Enzyme) + P (Product)

Let’s consider the hydrolysis of sucrose by sucrase (enzyme). When sucrose binds to the

active site of sucrase, the glycosidic bond of sucrose is placed into a geometry favorable for

reaction. The amino acid side chains catalyze the cleavage of the sucrose to give the products

glucose and fructose. Because the structures of the products are no longer attracted to the

active site, they are releases and the sucrase binds another sucrose substrate.

Sucrase (E) + Sucrose (S) Sucrase-Sucrose complex → Sucrase (E) + glucose (P2) + Fructose (P2)

There are two models for formation of ES Complex:

1. Lock-and-Key model: in this theory, the active site is described as having a rigid,

nonflexible shape. Thus only those substrates with shapes that fit exactly into the active site

are able to bind with enzyme. The shape of the active site is analogous to a lock, and the

proper substrate is the key that fits into the lock.

2. Induced-Fit model: certain enzymes have a broader range of activity that the lock and key

model allows. In the induced-fit model, enzyme structure is flexible, not rigid. There is an

interaction between both the enzyme and substrate. The active site adjusts to fit the shape of

the substrate more closely. At the same time the substrate adjusts its shape to better adapt to

the geometry of the active site. As a result, the reacting section of the substrate becomes

aligned exactly with the groups in the active site that catalyze the reaction. A different

substrate could not induce these structural changes and no catalysis would occur.


Factors affecting enzyme activity: the activity of an enzyme describes how fast an enzyme

catalyzed the reaction that converts a substrate to product. This activity is strongly affected by

reaction conditions, which include the temperature, pH, concentration of the substrate or

enzyme and the presence of inhibitors.

1. Temperature: enzymes are very sensitive to temperature. At low temperature, most

enzymes show little activity because there is not a sufficient amount of energy for the

catalyzed reaction to take place. At higher temperatures, enzyme activity increases as reacting

molecules move faster to cause more collisions with enzymes. Enzymes are most active at

optimum temperature, which is 37°C or body temperature for most enzymes. At

temperature above 50°C, the tertiary structure and thus the shape of most proteins is

destroyed, which causes a loss in enzyme activity. For this reason, equipment in hospitals and

laboratories is sterilized in autoclaves where the high temperatures denature the enzyme in

harmful bacteria.

2. pH: enzymes are most active at their optimum pH, the pH that maintains the proper tertiary

structure of the protein. A pH value above or below the optimum pH causes a change in he

three-dimensional structure of the enzyme that disrupts the active site. As a result the enzyme

cannot bind substrate properly and no reaction occurs. Enzymes in most cells have optimum

pH values at physiological pH values around 7.4. However, enzymes in the stomach have a

low optimum pH because they hydrolyze proteins at the acidic pH in the stomach. For

example, pepsin, a digestive enzyme in the stomach, has an optimum pH of 2. Between meals,

the pH in the stomach is 4 or 5 and pepsin shows little or no digestive activity. When food

enters the stomach, the secretion of HCl lowers the pH to about 2, which actives pepsin. If

small changes in pH are corrected, an enzyme can regain its structure and activity. However,

large variations from optimum pH permanently destroy the structure of the enzyme.


3. Substrate and enzyme concentration: in any catalyzed reaction, the substrate must first

bind with the enzyme to form the substrate-enzyme complex. When enzyme concentration

increases, the rate of catalyzed reaction increases because we produce more substrate-enzyme

complex. When enzyme concentration is kept constant, increasing the substrate concentration

increases the rate of the catalyzed reaction as long as there are more enzyme molecules

present than substrate molecules. At some point an increase in substrate concentration

saturates the enzyme. With all the available enzyme molecules bonded to substrate, the rate of

the catalyzed reaction reaches its maximum. Adding more substrate molecules cannot

increase the rate further.

4. Enzyme inhibition: many kinds of molecules called inhibitors cause enzymes to lose

catalytic activity. Although inhibitors act differently, they are all prevent the active site from

binding with a substrate. Inhibition can be competitive or noncompetitive.

Competitive inhibitor: a competitive inhibitor has a structure that is so similar to the

substrate it competes for the active site on the enzyme. As long as the inhibitor occupies the

active site, the substrate cannot bind to the enzyme and no reaction takes place. As long as the

concentration of the inhibitor is substantial, there is a loss of enzyme activity. However, increasing the substrate concentration displaces more of the inhibitor molecules. As more

enzyme molecules bind to substrate (ES), enzyme activity is regained.

Noncompetitive inhibitor: the structure of a noncompetitive inhibitor does not resemble the

substrate and does not compete for the active site. Instead, a noncompetitive inhibitor binds to

a site on the enzyme that is not the active site. When the noncompetitive inhibitor is bonded to

the enzyme, the shape of the enzyme is distorted. Inhibition occurs because the substrate

cannot fit in the active site, or it does not fit properly. Without the proper alignment of

substrate with the amino acid side groups, no catalysis can take place. Because a

noncompetitive inhibitor is not competing for the active site, the addition of more substrate

does not reverse this type of inhibition. Example of noncompetitive inhibitors are the heavy

Maximum activity


metal ions Pb2+

, Ag+, and Hg

2+ that bond with amino acid side groups such as –COO

-, or –

OH. Catalytic activity is restored when chemical reagents remove the inhibitors. Antibiotics

produced by bacteria, mold, or yeast are inhibitors used to stop bacterial growth. For example,

penicillin inhibits an enzyme needed for the formation of cell walls in bacteria, but not human

cell membranes. With an incomplete wall, bacteria cannot survive, and the infection is

stopped. However, some bacteria are resistant to penicillin because they produce

penicillinase, an enzyme that breaks down penicillin. Over the years, derivatives of penicillin

to which bacteria have not yet become resistant have been produced.

Enzyme cofactors: enzymes are known as simple enzyme when their function forms consist

only of proteins with tertiary structure. However, many enzymes require small molecules or

metal ions called cofactors to catalyze reactions properly. When the cofactor is a small

organic molecule, it is known as a coenzyme. If an enzyme requires a cofactor, neither the

protein structure nor the cofactor alone has catalytic activity.

Metal ions: many enzymes must contain a metal ion to carry out their catalytic activity. The

metal ions are bonded to one or more of the amino acid side chains. The metal ions from the

minerals that we obtain from foods in our diet have various functions in catalysis. Ions such as

Fe2+

and Cu2+

are used by oxidases because they lose or gain electrons in oxidation or

reduction reactions. Other metals ions such as Zn2+

stabilize the amino acid side chains during

hydrolysis reactions.

Site

Inhibitor

protein

protein

Metal ion

Organic molecules

(coenzyme)

Simple enzyme

Enzyme + Cofactor

Enzyme + Cofactor

protein


Vitamins and coenzymes: vitamins are organic molecules that are essential for normal health

and growth. They are required in trace amounts and must be obtained from the diet because

they are not synthesized in the body. Vitamins are classified into two groups by solubility:

water-soluble and fat-soluble.

Water-soluble vitamins: have polar groups such as –OH and –COOH, which make them

soluble in the aqueous environment of the cells. Most water-soluble enzymes are not stored in

the body and excess amounts are eliminated in the urine each day. Therefore, the water-

soluble vitamins must be in the foods of our daily diets. Because many water-soluble vitamins

are easily destroyed by heat, oxygen, and ultraviolet light, care must be taken in food

preparation, processing, and storage. The water-soluble vitamins are required by many

enzymes as cofactors to carry out certain aspects of catalytic action. The coenzymes do not

remain bonded to a particular enzyme, but are used over and over again by different enzymes

to facilitate an enzyme-catalyzed reaction. Thus, only small amounts of coenzymes are

required in the cells.

Fat-soluble vitamins: are nonpolar compounds, which are soluble in the fat (lipid)

components of the body such as fat deposits and cell membranes. The fat-soluble vitamins A,

D, E, and K are not involved as coenzymes, but they are important in processes such as

vision, formation of bone, protection from oxidation, and proper blood clotting. Because the

fat-soluble vitamins are stored in the body and not eliminated, it is possible to take too much,

which could be toxic.

chemistry b11 chapters 16 proteins and enzymes€¦ · chemistry b11 chapters 16. proteins and...

Documents