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"; Biochemistry Proteins Enzymes And Lipids Quiz Questions - Chem Homework Help
Biochemistry Proteins Enzymes and Lipids Quiz Questions

Proteins are the major structural molecules in living things for growth and repair (found in muscles, ligaments, tendons, bones, hair, skin). Proteins= membranes, enzymes, antibodies, non-steriod hormones, structural molecules, “MEANS”

Chemistry: An Introduction to General, Organic, and Biological Chemistry, Twelfth Edition

 

Aside from the protein found in animal sources…protein can also be found in

 

fruits, vegetables, grains, and nuts. (it just does not have as many amino acids)

word image 2622 word image 2623 word image 2624 word image 2625 word image 2626 word image 2627 word image 2628 word image 912

•

 

Found in plant foods

 

–

 

in the cell membranes

word image 916

•

 

Found in animal products

 

–

word image 919

in the cell membranes

 

–

 

in the

word image 922

muscles or living things

 

–

 

cows, chicken, fish…

Proteins are polymers that are made up of amino acid monomers.

At the atomic level, proteins are made up of carbon, hydrogen, oxygen, nitrogen and sometimes sulfur.

Proteins are most abundant molecules in the cells after water – account for about

15% of a cell’s overall mass

There are 3 classifications of proteins

based on structure: fibrous, globular, and membrane

Fibrous proteins have an elongated

shape (generally insoluble in water, tend to

word image 2629 aggregate together to form macromolecular structures, e.g., hair, nails, etc)

Globular proteins have peptide chains folded into spherical or globular shapes

(generally water soluble – hydrophobic amino acid residues are in the protein core; they function as enzymes and intracellular signaling molecules)

Membrane proteins are associated with cell membranes (generally insoluble in water – hydrophobic amino acid residues on the surface;

help in transport of molecules across the membrane)

There are numerous classifications of proteins based on function (proteios means of most importance)

L-AMINO ACIDS (found in nature)

word image 2630There are 20 common (standard) amino acids found in nature as well as in proteins and they are all L isomers.

word image 2631

hydrogen

19 of the 20 standard amino acids contain a chiral center (except glycine because the R group is

ALPHA AMINO ACIDS

An organic compound that contains both an amino (-NH2) and a carboxyl (COOH) group attached to same carbon atom. The position of carbon atom is Alpha (α)

word image 925

Common names assigned are currently used for amino acids .

Three letter abbreviations – widely used for naming:

First letter of amino acid name is compulsory and capitalized followed by next two letters not capitalized except in the case of Asparagine (Asn), Glutamine (Gln) and tryptophan (Trp).

One-letter symbols – commonly used for comparing amino acid sequences of proteins:

Usually the first letter of the name

When more than one amino acid has the same letter the most abundant amino acid gets the 1st letter.

  • All amino acids differ from one another by their R-groups
  • There are 20 common (standard) amino acids
  • Standard amino acids are divided into four groups based on the properties of the side chain R-groups (the most important aspect is their polarity (classified in 4 groups- nonpolar, polar but neutral, polar acidic and polar basic)
  • Non-polar amino acids have non-polar R groups (these amino acids are hydrophobic-water fearing and thus insoluble in water). When present in proteins, they are located in the interior of protein where there is no polarity
  • Polar amino acids have polar R-groups
  • (there are three types: Polar Neutral, Polar Acidic, and Polar Basic)
  • Polar-neutral: contains polar but neutral side chains
  • Polar acidic: Contain carboxyl group as part of the side chains
  • Polar basic: Contain amino group as part of the side chain

16.1 Proteins and Amino Acids

word image 2632 Protein molecules, compared with many of the compounds we have studied, can be gigantic.

The horns of animals are made of proteins.

Learning Goal Classify proteins by their functions. Give the name and abbreviation for an amino acid and draw its ionized structure.

Functions of Proteins

Proteins

  • in the body are polymers made from 20 different amino acids
  • differ in characteristics and functions that depend on the order of amino acids that make up the protein
  • form structural components such as cartilage, muscles, hair, and nails
  • function as enzymes to regulate biological reactions such as digestion and cellular metabolism
  • such as hemoglobin and myoglobin transport oxygen in the blood

Structural Classification of Proteins

word image 2633

Amino Acids

Amino acids, the molecular building blocks of proteins,

  • have a central carbon atom called the α-carbon bonded to two functional groups: an ammonium group (—NH3+) and a carboxylate group (—COO−)
  • have a central carbon atom bonded to a hydrogen atom and R group or side chain in addition to the carboxylate and ammonium groups

word image 2634

Structural Formulas of Amino Acids

An amino acid has

  • an α-carbon atom that is attached to three components: —NH3+,

—COO−, and —H group

  • a fourth component, an R group that differs for each particular amino acid (see Table 16.2 on next few slides)
  • a three-letter or one-letter abbreviation derived from its name

Core Chemistry Skill Drawing the Ionized Form for an

Amino Acid

Drawing Amino Acids

  • All amino acids have —NH3+, —COO−, and —H on the αcarbon.
  • Amino acids differ by their R groups.

word image 926 word image 927 word image 928 word image 929

R Group

 

Aspartic acid (Asp, D) Asparagine (Asn, N)

pH 2.8 pH 5.4

Classification of Amino Acids

Amino acids are classified as

  • nonpolar (hydrophobic) with hydrocarbon side chains
  • polar (hydrophilic) with polar or ionic side chains

word image 932 word image 2635

Nonpolar Polar

Valine Asparagine

Nonpolar Amino Acids

An amino acid is nonpolar when the R group is H, alkyl, or aromatic.

word image 2636

Polar Amino Acids

An amino acid is polar when the R group is an alcohol, a thiol, or an amide.

word image 2637 word image 2638

Acidic Amino Acids

An amino acid is acidic when the R group is a carboxylic acid.

word image 2639 word image 933

Basic Amino Acids

An amino acid is basic when the R group is an amine.

word image 2640 word image 934

Non-Polar Amino Acids (9)

word image 2641

Polar Neutral Amino Acids (5)

word image 2642

Polar Acidic (2) and Polar Basic (3)

Amino Acids

word image 2643

Amino Acid Stereoisomers

word image 2644 All the α-amino acids except for glycine are chiral.

  • The α-carbon is attached to four different atoms.
  • The —NH3+ group appears on the right or left of the chiral carbon to give D or L enantiomers.

Chemistry Link to Health:

Essential Amino Acids

Of the 20 amino acids used to build the proteins in the body,

  • only 11 can be synthesized in the body
  • the other 9 amino acids are essential amino acids that must be obtained from the proteins in the diet

word image 2645

Chemistry Link to Health:

Essential Amino Acids

word image 2646 Complete proteins such as eggs, milk, meat, and fish contain all of the essential amino acids.

Incomplete proteins from plants such as grains, beans, and nuts are deficient in one or more essential amino acids.

16.2 Amino Acids as Acids and Bases

word image 2647 When an amino acid with positive and negative charges is overall neutral in charge, it is said to be at its isoelectric point (pI).

Ball-and-stick model of glycine at its pI of 6.0.

Learning Goal Draw the condensed structural formula for an amino acid at pH values above or below its isoelectric point.

Isoelectric Point

The isoelectric point of an amino acid is the pH at which

  • the charged groups on an amino acid are balanced
  • the amino acid is neutral

An amino acid can exist as

  • a positive ion if a solution is more acidic (lower pH) than its pI
  • as a negative ion if a solution is more basic (higher pH) than its pI

The pI values for nonpolar and and polar neutral amino acids are from pH 5.1 to 6.3.

Alanine has a zero overall charge at its pI of 6.0 with a carboxylate anion (—COO−) and an ammonium cation (—NH3+).

Alanine adds an H+ to the carboxyl group (—COO−) when the solution is more acidic than its pI (pH < 6).

word image 2648

At a pH higher than 6.0, the —NH3+ group loses H+ and forms an amino group (—NH2) that has no charge.

word image 2649

Because the —COO− group has a charge of 1−, alanine has an overall negative charge (1−) at a pH higher than 6.0.

pH and Ionization

H+OH–

+

+

H3N–CH2–COOH

H3N–CH2–COO– H2N–CH2–COO–

Positive ion,

Negative ion,

low pH

pI high pH

Solution

CH3

CH3

|

+

|

H3N—CH—COOH

H2N—CH—COO–

(1)

Which structure represents

(2)

A. alanine at a pH above its pI?

(2)

B. alanine at a pH below its pI?

(1)

Study Check

Consider the amino acid leucine with a pI of 6.0.

  1. word image 935 At a pH of 3.0, how does leucine change?
  2. At a pH of 9.0, how does leucine change?

Solution

Consider the amino acid leucine with a pI of 6.0.

  1. At a pH of 3.0, how does leucine change?

Because the pH of 3.0 is more acidic than the pI at 6.0, the

—COO− group gains an H+ to give —COOH. The remaining —NH3+ gives leucine an overall positive charge (1+).

  1. At a pH of 9.0, how does leucine change?

Because a pH of 9.0 is more basic and above the pI of leucine, the —

NH3+ loses H+ to give —NH2. The remaining COO− gives leucine an overall negative charge (1−).

FORMATION OF A DIPEPTIDE- Under proper conditions, amino acids can bond together to produce an unbranched chain of amino acids. The reactions is between amino group of one amino acid and carboxyl group of another amino acid.The length of the amino acid chain can vary from a few amino acids to hundreds of amino acids. Such a chain of covalently-linked amino acids is called a peptide.The covalent bonds between amino acids in a peptide are called peptide bonds (amide).

word image 2650 word image 2651

PENTAPEPTIDE

S G Y A L

word image 2652

Primary structure of protein refers to the order in which amino acids are linked together in a protein. Every protein has its own unique amino acid sequence. In 1953, Frederick Sanger sequenced and determined the primary structure for the first protein – Insulin Secondary structure is the arrangement of atoms of backbone in space. It results due to hydrogen bonding between the backbone amino and carboxyl groups. The two most common types are alpha-helix (α-helix) and the beta-pleated sheet (β-pleated sheet). Tertiary structure is the overall three-dimensional shape of a protein. It results from the interactions between amino acid side chains (R groups) that are widely separated from each other. In general 4 types of interactions are observed: Disulfide bonding, Electrostatic interactions, Hydrogen-Bonding and Hydrophobic interactions.

Quaternary structure of protein refers to the organization among the various polypeptide chains in a multimeric protein. It is the highest level of protein organization and is present only in proteins that have 2 or more polypeptide chains (subunits).

word image 2653 word image 2654 word image 2655

16.3 Proteins: Primary Structure

word image 936 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.

The linking of two or more amino acids by peptide bonds forms a peptide.

Learning Goal Draw the condensed structural formula for a peptide and give its name. Describe the primary structure for a protein.

Formation of Peptides

The linking of two or more amino acids by peptide bonds forms a peptide.

Peptides formed from

  • two amino acids are called dipeptides
  • three amino acids are called tripeptides
  • four amino acids are called tetrapeptides

Formation of Peptides

A peptide bond

  • is an amide bond
  • forms between the —COO− group of one amino acid and the —NH3+ group of the next amino acid

word image 2656

Formation of a Dipeptide

word image 2657

A peptide bond between glycine and alanine forms the dipeptide glycylalanine.

Solution

Draw the dipeptide Ser–Thr.

word image 937

Naming Peptides

With the exception of the C-terminal amino acid, the names of all the other amino acids in a peptide end with yl.

word image 2658

Study Check

Write the three-letter abbreviation and name for the following tetrapeptide.

Alanine Leucine

Cysteine Methionine

Solution

Ala-Leu-Cys-Met Alanylleucylcysteinylmethionine

Alanine Leucine

Cysteine Methionine

Primary Structure of Proteins

A protein is a polypeptide of 50 or more amino acids that has biological activity.

The primary structure of a protein is the particular sequence of amino acids held together by peptide bonds.

word image 938

Ala–Leu–Cys–Met

Primary Structure

A thyroid hormone that stimulates the release of thyroxin is a tripeptide with the amino acid sequence Glu–His–Pro.

Although other amino acid sequences of these three amino acids are possible, only the specific sequence or primary structure of Glu−His−Pro produces hormonal activity.

word image 2659

Primary Structure of Insulin

word image 2660Insulin

  • was the first protein to have its primary structure determined
  • has a primary structure of two polypeptide chains linked by disulfide bonds
  • has a chain A with 21 amino acids and a chain B with

30 amino acids

Solution

Answer the questions for the tripeptide that is shown below:

  1. What is the N-terminal amino acid? Phe
  2. What is the C-terminal amino acid? Ala C. What is the name of the tripeptide? phenylalanylcysteinylalanine

16.4 Proteins: Secondary, Tertiary, and Quaternary Structures

word image 2661 The shape of an alpha helix is similar to that of a spiral staircase.

The α helix acquires a coiled shape from hydrogen bonds between the oxygen of the C O group and the hydrogen of the N—H group in the next turn.

Learning Goal Describe the secondary, tertiary, and quaternary structures for a protein; describe the denaturation of a protein.

Secondary Structure: Alpha Helix

word image 2662 In the secondary structure of an alpha helix (α helix),

  • hydrogen bonds form between the oxygen of the C O groups and the hydrogen of N—H groups of the amide bonds in the next turn of the α helix
  • the formation of many hydrogen bonds along the polypeptide chain gives the helical shape of a spiral staircase

Core Chemistry Skill Identifying the Primary, Secondary, Tertiary, and Quaternary Structures of Proteins

Secondary Structure: Beta-Pleated Sheet

word image 2663 In the secondary structure of a beta-pleated sheet (β-pleated sheet), hydrogen bonds form between the carbonyl oxygen atoms and hydrogen atoms in the amide groups bending the polypeptide chain into a sheet.

Secondary Structure: Triple Helix

In the secondary structure of a triple helix,

•three polypeptide chains are woven together

•hydrogen bonds hold the chains together, giving the polypeptide the added strength typical of collagen, connective tissue, skin, tendons, and cartilage

word image 939

Collagen fibers are triple helices of polypeptide chains held together by hydrogen bonds.

The tertiary structure of a protein

  • is an overall three-dimensional shape caused by interactions of different parts of the chain, causing it to bend and twist
  • is determined by cross-links, the attractions and repulsions between the side chains (R groups) of the amino acids in a peptide chain

Interactions between amino acid R groups fold a protein into a specific three-dimensional shape called its tertiary structure.

word image 2664

Sections of a protein interact to create the tertiary structure of a protein due to

  • hydrophobic interactions between two nonpolar amino acids
  • hydrophilic interactions between the external aqueous environment and the R groups of polar amino acids
  • salt bridges, ionic bonds between ionized R groups of basic and acidic amino acids
  • hydrogen bonds between H of a polar R group and the O or N of another amino acid
  • disulfide bonds — S— S — between the — SH groups of cysteine amino acids

Chemistry Link to Health:

Sickle-Cell Anemia

Sickle-cell anemia is caused by an abnormality in the shape of one of the subunits of the hemoglobin protein.

  • word image 2665 The sixth amino acid in the β-chain, polar acidic glutamic acid, is replaced by valine, a nonpolar amino acid.
  • The nonpolar R group on valine is attracted to the nonpolar regions within the beta hemoglobin chains.
  • The red blood cells change from a rounded shape to a crescent shape, like a sickle, which interferes with their ability to transport enough oxygen.

Chemistry Link to Health: Sickle-Cell Anemia

word image 2666 Hydrophobic interactions also cause sickle–cell hemoglobin molecules to stick together. They form insoluble fibers of sickle–cell hemoglobin that

  • clog capillaries
  • cause inflammation, pain, and organ damage
  • cause low oxygen levels in the affected tissues

Study Check

Indicate the type of protein structure.

primary alpha helix beta-pleated sheet triple helix

  1. polypeptide chains held side by side by H bonds
  2. sequence of amino acids in a polypeptide chain
  3. corkscrew shape with H bonds between amino acids
  4. three peptide chains woven like a rope

Solution

Select the type of tertiary interaction. disulfide ionic H bonds hydrophobic

A. leucine and valine

hydrophobic

B. two cysteines

disulfide

C. aspartic acid and lysine

ionic

D. serine and threonine

H bonds

Globular Proteins

word image 2667Globular proteins

•have compact, spherical shapes

•carry out synthesis, transport, and metabolism in the cells

•transport and store oxygen in muscle The ribbon structure represents the tertiary structure of myoglobin.

Myoglobin and hemoglobin transport and store oxygen in the body.

Fibrous Proteins

word image 2668Fibrous proteins consist of long, fiberlike shapes such as

  • alpha keratins, which make up hair, wool, skin, and nails
  • beta keratins in feathers, which contain large amounts of beta-pleated sheet structures

The fibrous proteins of α-keratin wrap together to for fibrils of hair and wool.

Quaternary Structure

word image 2669The quaternary structure

  • is the combination of two or more protein units
  • consists of four polypeptide chains as subunits in hemoglobin
  • is stabilized by the same interactions found in tertiary structures

In the ribbon structure of hemoglobin, the quaternary structure is made up of four polypeptide subunits: two (red) are α chains and two (blue) are βchains. The heme groups (green) in the four subunits bind oxygen.

Protein Structural Levels

word image 2670

The structural levels of protein are (a) primary, (b) secondary, (c) tertiary, and sometimes (d) quaternary.

Protein Structural Levels—Summary

word image 2671

Solution

Identify the level of protein structure. primary secondary tertiary quaternary

  1. beta-pleated sheet secondary
  2. order of amino acids in a protein primary
  3. a protein with two or more peptide chains quaternary

D. the shape of a globular protein

tertiary

E. disulfide bonds between R groups

tertiary

Denaturation of Proteins

Denaturation involves the disruption of bonds in the secondary, tertiary, and quaternary protein structures by

•heat and organic compounds that break apart H bonds and disrupt hydrophobic interactions

•acids and bases that break H bonds between polar R groups and disrupt ionic bonds

•heavy metal ions that react with S—S bonds to form solids

•agitation, such as whipping, that stretches peptide chains until bonds break

Applications of Denaturation

word image 2672Denaturation of protein occurs when an egg is cooked.

Denaturation of egg protein occurs when the bonds of the tertiary structure are disrupted.

Protein Denaturation

word image 2673

Solution

Tannic acid is used to form a scab on a burn. An egg is hard boiled by placing it in boiling water.

What is similar about these two events?

Acid and heat cause the denaturation of protein. They both break bonds in the secondary, tertiary, and quaternary structures of proteins.

16.5 Enzymes

Enzymes are proteins that act as biological catalysts. On the surface of an enzyme, a small region called an active site binds a substrate and catalyzes a specific reaction for that substrate.

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Learning Goal Describe enzymes and their role in enzymecatalyzed reactions.

Enzymes Are Biological Catalysts

Enzymes

  • word image 2675 catalyze nearly all the chemical reactions taking place in the cells of the body
  • increase the rate of reaction by lowering the energy of activation

The enzyme carbonic anhydrase lowers the activation energy for the reaction:

CO2 + H2O HCO3− + H+

Enzyme Names

The name of an enzyme

  • is derived by replacing the end of the name of the reaction or reacting compound with the suffix ase
  • identifies the reacting substance—for example, sucrase catalyzes the reaction of sucrose
  • describes the compound or the reaction that is catalyzed—for example, oxidase catalyzes an oxidation reaction
  • could be a common name, particularly for the digestion enzymes, such as pepsin and trypsin

Classification of Enzymes

Enzymes are classified by the reaction they catalyze. There are six main classes of enzymes.

Class Type of Reactions Catalyzed

Oxidoreductases Oxidation–reduction

Transferases Transfer groups of atoms

Hydrolases Hydrolysis

Lyases Add or remove atoms to or from a

double bond

Isomerases Rearrange atoms

Ligases Use ATP to combine small molecules

Solution

Match the type of reaction catalyzed with an enzyme class. hydrolases isomerases transferases ligases

A. form bonds between molecules using ATP energy

ligases

  1. rearrange atoms in a molecule to form an isomer

isomerases

  1. transfer a group between two compounds transferases
  2. hydrolysis reactions hydrolases

Active Site Binds the Substrate

On the surface of an enzyme, a small region called an active site binds a substrate and catalyzes a reaction of that substrate.

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Active Site Binds the Substrate

The active site

•is a region within an enzyme that fits the shape of the reacting molecule called a substrate

•contains amino acid R groups that bind the substrate

•releases products when the reaction is complete

Enzyme-Catalyzed Reaction

In an enzyme-catalyzed reaction,

  • word image 2677 a substrate attaches to the active site
  • an enzyme–substrate (ES) complex forms
  • reaction occurs and products are released
  • an enzyme is used over and over

E + S ES E + P

Binding of a substrate occurs when it interacts with the amino acids within the active site.

Enzyme-Catalyzed Reaction

In the hydrolysis of the disaccharide sucrose,

  • the ES complex is formed as sucrose binds to the active site of sucrase
  • the glycosidic bond of sucrose is in position for hydrolysis
  • the R groups on the amino acids in the active site catalyze the hydrolysis of sucrose, producing glucose and fructose
  • the product structures are no longer attracted to the active site, so they are released to allow sucrase to react with another sucrose molecule

E + S ES E + P sucrase + sucrose ES complex sucrase + product

Enzyme Action: Lock-and-Key Model

In the lock-and-key model, the

•active site has a rigid, nonflexible shape

•enzyme binds only substrates that exactly fit the active site like a lock

•substrate is the key that fits that lock

This model was a static one that did not include the flexibility of the tertiary shape of an enzyme and the way the active site can adjust to the shape of a substrate.

Enzyme Action: Induced-Fit Model

In the induced-fit model,

  • enzyme structure is flexible, not rigid, and adjusts to the shape of the active site in order to bind the substrate
  • the range of substrate specificity increases
  • shape changes improve catalysis during reaction

Enzyme Action: Induced-Fit Model

word image 2678 In the induced-fit model, substrate and enzyme work together to acquire a geometrical arrangement that lowers the activation energy of the reaction.

Study Check

  1. The active site is
    1. the enzyme
    2. a section of the enzyme
    3. the substrate
  2. In the induced–fit model, the shape of the enzyme when substrate binds
    1. stays the same
    2. adapts to the shape of the substrate

16.6 Factors Affecting Enzyme Activity

word image 2679 The activity of an enzyme

  • describes how fast an enzyme catalyzes the reaction that converts a substrate to product
  • is strongly affected by reaction conditions, which include temperature, pH, and the presence of inhibitors

Thermophiles survive in the high temperatures (50 °C to 120 °C) of a hot spring.

Learning Goal Describe the effect of temperature, pH, and inhibitors on enzyme activity.

Temperature and Enzyme Activity

word image 2680Enzymes

  • are most active at an optimum temperature (usually 37 °C in humans)
  • show little activity at low temperatures.
  • lose activity at temperatures above 50 °C as denaturation occurs with loss of catalytic activity

pH and Enzyme Activity

Enzymes

  • word image 2681 are most active at optimum pH
  • contain R groups of amino acids with proper charges at optimum pH
  • lose activity in low or high pH as tertiary structure is disrupted

Optimum pH Values

Enzymes in

  • the body have an optimum pH of about 7.4
  • certain organs operate at lower and higher optimum pH values

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Solution

Sucrase has an optimum temperature of 37 °C and an optimum pH of 6.2. Determine the impact of each change on the enzyme activity.

no change increases decreases

A. changing the pH to 4

decreases

B. running the reaction at 70 °C

decreases

Enzyme Inhibition

Inhibitors

  • are molecules that cause a loss of catalytic activity
  • prevent substrates from fitting into the active sites

E + S ES E + P

E + I EI no P

Competitive Inhibition

A competitive inhibitor

  • has a structure that is similar to that of the substrate
  • competes with the substrate for the active site
  • has its effect reversed by increasing substrate concentration

word image 2683

Competitive Inhibition

word image 2684

Noncompetitive Inhibition

A noncompetitive inhibitor

  • has a structure that is much different than that of the substrate
  • binds to an enzyme at a site other than the active site and distorts the shape of the enzyme by altering the shape of the active site
  • prevents the binding of the substrate
  • cannot have its effect reversed by adding more substrate

Noncompetitive Inhibition

word image 2685

Study Check

Identify each description as an inhibitor that is competitive or noncompetitive.

  1. Increasing substrate reverses inhibition.
  2. It binds to enzyme surface but not to the active site.
  3. Its structure is similar to that of substrate.
  4. Inhibition is not reversed by adding more substrate.

Solution

  1. Increasing substrate reverses inhibition. competitive
  2. It binds to enzyme surface but not to the active site. noncompetitive
  3. Its structure is similar to that of substrate. competitive
  4. Inhibition is not reversed by adding more substrate. noncompetitive

ENZYMES

  • The human body has 1000s of enzymes. They are usually proteins that act as a catalyst for biochemical reactions (they are not consumed in the reactions)
  • Enzymes are the most effective catalysts known (extremely specific)
  • Most enzymes are globular proteins; a few are now known to be RNA (ribozymes)
  • Enzymes don’t change the position of equilibrium but increase the reaction rate by lowering the activation energy
  • Names derived from reaction they catalyze and/or compound they act on
  • ENZYME TERMINOLOGY

activity– measurement of how much rates are increased

substrate– compound that binds to enzyme’s active site and is changed cofactors– nonprotein part of enzyme. It can be metal ions (Mg2+, Zn2+) ; organic cofactors are called coenzymes

apoenzyme– protein part of enzyme activation– initiation process for an enzyme

inhibition– process of making an active enzyme inactive

–competitive- Bind to the enzyme’s active site and inhibits the substrate from binding -noncompetitive- Binds elsewhere and changes the structure of the enzyme’s active site (thus inhibiting the substrate from binding)

  • word image 2686 The active site is a relatively small part of an enzyme’s structure that is actually involved in catalysis:
    • Place where substrate binds to enzyme
    • Formed due to folding and bending of the protein.
    • Usually a “crevice like” location in the enzyme
    • Some enzymes have more than one active site
  • ENZYME SUBSTRATE

COMPLEX – Intermediate

reaction species formed when substrate binds with the active site

  • It is needed for the activity of enzyme; its orientation and proximity is favorable and the reaction is fast

FACTORS AFFECTING ACTIVITY

  • The effect of concentration, temperature and pH on enzyme activity

(how much rate is increased)

1)If the [S] is kept constant, as long as [E] is less than [S], the rate will increase continuously and linearly (double [E], rate doubles)

2)If the [E] is kept constant, and you increase the [S] you will get a saturation curve. Once all of the enzyme active sites are occupied, increasing the [S] will not increase the rate.

    1. Temperature changes the structure of an enzyme. This hinders the substrate from fitting in the active site. Once the optimal temperature is reached, the rate of reaction will begin to decrease
    2. pH effects resemble temperature. All enzymes operate best at certain ph values (near 7). Drastically changing the pH can irreversibly alter the shape of a protein or enzyme.

Two Models for Substrate Binding to Enzyme

  • There are 2 common models for how Enzyme Substrate complexes are formed:
    1. LOCK AND KEY MODEL
      • Simplest (Enzyme has a pre-determined shape for the active site)lock is the active site and the key is the substrate
      • Enzyme is rigid body with an opening (active site)
      • Only substrate of specific shape can bind with active site (fit and open it)
      • Restrictive (E not static but dynamic; flexible active site)
    2. INDUCED FIT MODEL
        • Substrate enters and its contact with the enzyme causes the shape and size of its active site to change.
        • Latex glove and hand (gloves changes when hand is inserted)
        • More realistic (proteins are dynamic)
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