The Chemical Building Blocks of Life Chapter 3. 38 Biochemistry The study of the Chemistry of Life 4 Classes of Biological Molecules 1. Carbohydrates

The Chemical BuildingBlocks of Life

Chapter 3

38

Biochemistry

• The study of the Chemistry of Life

• 4 Classes of Biological Molecules1.Carbohydrates2.Nucleic Acids3.Proteins4.Lipids

• The Classes are determined by the proportions of C, H, O in the molecule

• We will distinguish the structures and functions of each in living cells

40

Biomolecules

• Organic Molecules – Composed of Carbon and Hydrogen– Elements Nitrogen, Oxygen, Phosphate, Sulfur

also included– These six elements compose 98.5% of body

weight (Saladin, 5th ed.)

• Some Inorganic molecules are incorporated as well – The Heme group in Hemoglobin contains Fe, for

example– Trace elements

4

Biological Molecules

Biological molecules are composed of:

1. A Central Carbon or Carbon Chain

2. Functional Groups

41

Organic Chemistry

• The carbon chain backbone of a molecule or Carbon Skeleton

CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH3

• Recall: Carbon makes 4 covalent bonds

42

Functional Groups

• Functional Groups are specific combinations of bonded atoms attached to a Carbon Skeleton

• The Functional Groups determine the chemistry of the molecule

• Functional groups behave in chemically predictable ways

7

8


• Biological molecules are typically Marcomolecules

- Very large molecules with high molecular weights

- DNA over a meter long

• Macromolecules are Polymers assembled from smaller Monomers

- Monomers - small, identical or similar subunits

- Polymers - covalently bonded monomers

Monomers and Polymers

• Proteins• Amino Acid monomers polymerize to form proteins

• Nucleotides• Nucleotide monomers polymerize to form DNA and

RNA Macromolecules

• Carbohydrates• Simple sugar monomers polymerize to form

complex sugars

• Monosaccharides polymerize to form disaccharides, polysaccharides

2-66

Polymerization• The joining monomers to form a polymer

• Dehydration Synthesis - the chemical reaction for how living cells form polymers

• A bond is formed between monomers and water is produced as a product of the reaction

• As the name implies, water is lost during the reaction

• Also known as Condensation

Dehydration Synthesis

• A hydroxyl (-OH) group is removed from one monomer, and a hydrogen (H+) from another

• A new bond is formed between the monomers

• Water is released as a by-product

2-67

Dehydration Synthesis• Monomers covalently bond together to form

a polymer with the removal of a water molecule– A hydroxyl group is removed from one monomer and a

hydrogen from the next

Monomer 1 Monomer 2

OH HO

OH– +

O

Dimer

(a) Dehydration synthesis

H+ H2O

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Figure 2.15a

Hydrolysis

• The reaction for the separation of joined monomers

• “Splitting with water”

• Opposite of dehydration synthesis– a water molecule ionizes into –OH and H+– the covalent bond linking one monomer to the other is

broken– the –OH is added to one monomer– the H+ is added to the other

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Hydrolysis• Splitting a polymer (lysis) by the addition of a water

molecule (hydro)– a covalent bond is broken

• All digestion reactions consists of hydrolysis reactions

OH HO

Monomer 1 Monomer 2

O

Dimer

(b) Hydrolysis

OH–+H+H2O


Figure 2.15b

15


2

1. Carbohydrates

The Saccharides (Sugars)

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1. CarbohydratesCarbohydrates

• Sugars, Starches, Fibers

• Names of carbohydrates often built from:– word root ‘sacchar-’ – the suffix ’-ose’– both mean ‘sugar’ or ‘sweet’

• monosaccharide or glucose

1. Carbohydrates

• Carbohydrates are composed of carbon backbones with Hydroxyl Groups and a Carboxyl Group– R-OH– R-COOH

• The carbon backbone may be a in straight line or a closed ring of carbon atoms

• Polar and therefore Hydrophilic Molecules

60

1. Carbohydrates

1. Carbohydrates

• The Proportions of C, H, and O for Carbohydrates follow the General Formula:

CnH2nOn – n = number of carbon atoms

– for glucose, n = 6, so formula is C6H12O6

– 2:1 ratio of hydrogen to oxygen

1. Carbohydrates

• Names of carbohydrates:– Carbohydrates are classified for the number of

carbon atoms in the carbon backbone• Pentose, Hexose

– Many carbohydrates have common names• Glucose, Fructose, Sucrose, Lactose

5

Carbohydrate Structure

• Numbering the C’s• Carbohydrates are classified by the number of

Carbon atoms they contain

• For Example: Ribose is a pentose sugar because it contains 5 carbon atoms Glucose is a hexose sugar

because it contains 6 carbon atoms

• Many Carbohydrates have informal names that do not provide information about the molecule

6

Carbohydrate Structure

• Numbering the Carbons• Numbering System allows the molecules to be

described efficiently

• The Carbons of Carbohydrates are numbered

• For Example:• Describing locations of covalent bonds• Ribose vs 2’ Deoxy-ribose

24

Carbohydrates

25

Carbohydrates

7

Carbohydrate StructureNumbering the Carbons Ribose vs. 2 Deoxyribose

• Ribose • 2’ Deoxyribose

27

1. Carbohydrates

1.Monosaccharides

2.Disaccharides

3.Polysaccharides

104

8

Carbohydrate Classification

1. Monosaccharides• Simple Sugars• Are not hydrolyzed into smaller carbohydrates

2. Disaccharides • On hydrolysis, are cleaved into two

monosaccharides

3. Polysaccharides • Are Hydrolyzed to more than 10 monosaccharides

9

10

1. Monosaccharidesa. Structure

• There are over 200 different monosaccharides

• Monosaccharides differ in the number of carbon atoms they contain in the C-C backbone (Ex. hexose vs. pentose)

• Monosaccharides also differ in their STEREOCHEMISTRY – the 3 dimensional shape of the molecule

67

Monosaccharides differ in their Stereochemistry - 3D shape

HexoseC6H12O6

PentoseC5H10O5

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Monosaccharides are Isomers

Glucose

HH

CH2OH

H

H

H

OH

OH

OH

O

HO

Galactose

H

H

H

H

H

OH

OH

OH

OHO

Fructose

HOCH2

OH

HO

OH

H

H

O

H

CH2OH

CH2OH


Figure 2.16

• Isomers – molecules with the same chemical

formula, but different structures

• 3 important monosaccharides– glucose, galactose and fructose

• Same molecular formula - C6H12O6

– isomers

33

Carbohydrates

34

Carbohydrates

35

Chiral Molecules• Isomers that are mirror images of each other

13

1. Monosaccharidesb. Functions

• Energy Source- Are efficiently oxidized for energy- The C-H bonds are high in energy- The C-H bonds are oxidized

• Most Important example: - Glucose in Cellular Respiration

C6H12O6 + 6 O2 6 H2O + 6 CO2 + EnergyGlucose Oxygen Water Carbon Dioxide

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2. Disaccharidesa. Structure

• Sugar molecule composed of 2 monosaccharides

• 3 important disaccharides– sucrose - table sugar

• glucose + fructose

– lactose - sugar in milk• glucose + galactose

– maltose - grain products• glucose + glucose

Sucrose

Lactose

Maltose

HO

H

H

H

H

H

H

H

H

H

H H

H

H HH

H

HH H

H

HH

H

H

H

H

H

H

HOOH

OH OH

OO

O

CH2OH

O

OH

HOOH OH

OH

OHOO

HO

OH

OH

OH

OH

OH

O

OO

CH2OH

CH2OH

CH2OH

CH2OH

CH2OHCH2OH


Figure 2.17

16

2. DisaccharidesPolymerization

• Monosaccharides are joined together into chains through a Dehydration Reaction

• A dimer of two monosaccharides is formed

• Water is lost in the polymerization reaction

39

Dehydration Synthesis

Glucose + Fructose = Maltose + H2O

Glucose + Glucose = Maltose + H2O

17

Dehydration Reaction•Carbon 1 on the left glucose exchanges its bond with the hydroxyl group for a bond with the oxygen of the hydroxyl group on carbon 4 of the glucose on the right (OH is released)

•The oxygen of hydroxyl group of carbon 4 exchanges its bond with H for a bond with carbon 1 (H is released)

• OH + H yields H2O

1 4

23

4

5

6

111 4

H2O

18

2. DisaccharidesHydrolysis Reaction

• Chains of Carbohydrates are cleaved into smaller chains and monosaccharides through Hydrolysis Reactions

• As the name implies, the complex carbohydrates are “cleaved by water”

19

2. DisaccharidesHydrolysis Reaction

Maltose + H2O = Glucose + Glucose

+ H2O

20

3. Polysaccharides

a. Structure1. Multiple Monosaccharides linked together

b. Functions1. Structural Molecules

2. Signaling Molecules

3. Energy Storage

44

3. Polysaccharides

• 3 Important Polysaccharides:1. Glucose2. Starch 3. Cellulose

Glycogen

• Glycogen: energy storage polysaccharide in animals– long, branching chains of glucose monomers

– made by cells of liver, muscles, brain, uterus, and vagina

– liver produces glycogen when glucose blood level is high, then breaks it down when needed to maintain blood glucose levels

– muscles store glycogen for own energy needs

– uterus uses glycogen to nourish embryo

2-73

GlycogenO

O

O

O

OO

O

O

OO

O

OO

O

O

O

O

O

O

OO

O

O

O

O O

O

OO

O OO

O

O

O

O

(a) (b)

CH2OHO

O O

O

O

O

O

CH2

O

O

O

OO

O

O

CH2OH

CH2OHCH2OH CH2OH


Figure 2.18

47

Glycogen

82

Glycogen Inclusions in a Liver Cell

Stryer's Biochemistry Fig. 23-2

3. Polysaccharides• Starch: energy storage polysaccharide in

plants– only significant digestible polysaccharide in the human

diet

• Cellulose: structural molecule of plant cell walls- fiber in our diet

22

3. Polysaccharides

b. Function

1. Structural MoleculesCellulose - plant cell walls

Chitin – Fungi cell walls

Peptidoglycan - Bacterial cell walls

51

Carbohydrates

52

Carbohydrates

53

Carbohydrates

Carbohydrate Functions

1.Structural:• Conjugated carbohydrates – covalently bound to lipid

or protein– glycolipids

• external surface of cell membrane

– glycoproteins• external surface of cell membrane

• mucus of respiratory and digestive tracts

– proteoglycans (mucopolysaccharides)

• gels that hold cells and tissues together

• forms gelatinous filler in umbilical cord and eye

• joint lubrication

• tough, rubbery texture of cartilage

24

Glycoproteins on Cell Surface

Viral Bioinformatics Resource Center athena.bioc.uvic.ca/.../copy9_of_sample/surface

23

3. Polysaccharides

Function

2. Signaling Molecules• GLYCOPROTEINS

– Carbohydrates bound to proteins – Example: Red Blood Cell Groups– Used by the Immune System to identify cells

• Antigenic – Are detected by the immune system and can cause an immune response

2-74

3. Polysaccharidesb. Functions

3.Energy Storage– Excess glucose stored as Glycogen– Hydrolyzed to Glucose as needed

149

2. Nucleic Acids

• DNA = Deoxyribonucleic Acid

• RNA = Ribonucleic Acid

• Function to store, transport, and control hereditary information

2-110

2. Nucleic Acids• DNA (deoxyribonucleic acid)

– constitutes genes • instructions for synthesizing all of the body’s proteins

• transfers hereditary information from cell to cell and generation to generation

• RNA (ribonucleic acid) – 3 types– messenger RNA, ribosomal RNA, transfer RNA– 70 to 10,000 nucleotides long– carries out genetic instruction for synthesizing proteins– assembles amino acids in the right order to produce

proteins

4-2

2. Nucleic Acids

• The Nucleic Acids are some of the largest organic compounds found in organisms

• Nucleic Acids are composed of Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorous atoms

• Nucleic Acids are components of DNA and RNA – the molecules responsible for the storage, transport and regulation of hereditary information

2-104

2. Nucleic Acids

• Nucleotides are the uilding blocks of bucleic acids (DNA and RNA) and ATP

• 3 components of nucleotides1.Nitrogenous base2.Ribose Sugar (monosaccharide)

3.Phosphate groups

62

2. Nucleic Acids

155

The Nitrogenous Bases of Nucleotides

• There are 5 different Nitrogenous Bases to choose from when building Nucleic Acids:

156

The Nitrogenous Bases of Nucleotides

• DNA is composed of the Nitrogenous Bases: Thymine, Cytosine, Adenine, and Guanine

• RNA is composed of the Nitrogenous Bases: Uracil, Cytosine, Adenine, and Guanine

4-5

Nitrogenous Bases of DNA

• Purines - double ring– Adenine (A)– Guanine (G)

• Pyrimidines - single ring– Cytosine (C)– Thymine (T)

• DNA bases - ATCG• RNA bases - AUCG

Figure 4.1b


C

NH2 N

NH

CCH

CH

N

N C

Adenine (A)

Purines

C

O N

NH

CCH

C N

HN C

NH2

Guanine (G)

HC

NH2

C

NH

C

HC N

O

Cytosine (C)

Uracil (U)

C

C

O

C

O

CH

HN CH

NH

NH

C

C

HC

CH3

NH

O

O

Thymine (T)

Pyrimidines

(b)

66

The Nitrogenous Bases

153

The Ribose Sugar of NucleotidesThe Nucleotides of DNA

• The name, Deoxyribonucleic Acid, tells us the structure of the ribose sugar in the Nucleotides of DNA

• It lacks a hydroxyl group at C2

The Nucleotides of RNA• The name, Ribonucleic acid, tells

us the structure of the ribose sugar in the RNA Nucleotides

157

The Phosphate Group of Nucleotides

• Both The Phosphate Group and the Nitrogenous Base attach to the central Ribose Sugar

• The Phosphate Group Attaches at the 5’ Carbon of the Nucleotide• The Nitrogenous Base Attaches at the 1’ Carbon of the Nucleotide

• The Phosphate Group is important in forming the “Backbone” of the Nucleic Acid Molecule

158

The Phosphate Group of Nucleotides

159

Polymerization of Nucleotides to Make Nucleic Acids (DNA and RNA)

• Nucleotides are covalently bound together into long strands through a Dehydration Reaction

• The Phosphate of one Nucleotide is bound to the Ribose Sugar of an adjacent nucleotide

• These Phosphate-Ribose bonds form the backbones of the Nucleic Acid Molecules

160

The Backbone is formed by multiple C3-C5 phospho-ribose linkages

161

The Backbone is formed by multiple C3-C5 phospho-ribose linkages

4-4

DNA Molecular Structure• DNA is a long threadlike

molecule with uniform diameter, but varied length– total length of 2 meters– average DNA molecule 2 inches

long

• 46 DNA molecules in the nucleus of most human cells (Chromosomes)

Figure 4.1a

HC

N C

N

NH2

NH

C

C

CH

N

H

CH2OHO

O

OH

P

H

HOH

HH

O

Adenine

Phosphate Deoxyribose(a)


74

DNA Molecular Structure

4-7

DNA Double Helix

• Two DNA strands are united by hydrogen bonds to form the double-helix

• DNA base pairing– A – T with 2 hydrogen bonds

– C – G with 3 hydrogen bonds

• Law of Complementary Base Pairing– one strand determines base sequence

of other

– One strand serves as the template for the complementary strand

Figure 4.2 partial

(b)

(c)

GC

Sugar–phosphatebackbone

Sugar–phosphatebackbone

G

A

C

T

AT

AT

GC

Hydrogenbond


163

Complementary Base Pairing

• To form the Double Stranded structure of DNA, two polynucleotide strands pair up through hydrogen bonds between specific Nitrogenous Bases:

• In DNA, Adenine pairs with Thymine via 2 Hydrogen bonds

• In DNA, Guanine pairs with Cytosine via 3 Hydrogen Bonds

• In RNA, Adenine pairs with Uracil via 2 Hydrogen Bonds

• A to T with two H-bonds, G to C with 3 H-bonds

164

Complementary Base Pairing

Fig. 3.16-1

79

Nucleic Acids

80

Nucleic Acids

RNA

• Contains ribose instead of deoxyribose

• Contains uracil instead of thymine

• Single polynucleotide strand

• Functions:

-Read the genetic information in DNA

-Direct the synthesis of proteins

Fig. 3.16-2

82

Nucleic Acids

Other nucleotides

• ATP: adenosine triphosphate

-primary energy currency of the cell

• NAD+ and FAD: electron carriers for many cellular reactions

The Chemical BuildingBlocks of Life

Chapter 3 Sec. 2 Proteins and Lipids

2-85

3. Proteins

• Protein - a polymer of amino acids

• Amino acids - the monomers of proteins

• 20 Amino acids are used to construct proteins

• Peptide Bonds form between adjacent amino acids

2-94

Protein Functions1. Structure

– keratin – tough structural protein• gives strength to hair, nails, and skin surface

– collagen – durable protein contained in deeper layers of skin, bones, cartilage, and teeth

2. Communication– some hormones and other cell-to-cell signals

– receptors to which signal molecules bind

1. ligand – any hormone or molecule that reversibly binds to a protein

• Membrane Transport– channels in cell membranes that governs what passes through

– carrier proteins – transports solute particles to other side of membrane

– turn nerve and muscle activity on and off

2-95

Protein Functions 4. Catalysis

– enzymes

5. Recognition and Protection– immune recognition

– antibodies

– clotting proteins

• Movement– motor proteins - molecules with the ability to change shape

repeatedly

4. Cell adhesion– proteins bind cells together

– immune cells to bind to cancer cells

– keeps tissues from falling apart

Amino Acid Structure

•A Central carbon with 4 attachments:

1.amino group (NH2)

2.carboxyl group (COOH)

3.radical group (R group)

4.hydrogen

• Properties of amino acid determined by -R group

Amino Acid Structure

• By definition, all amino acids have the amine and carboxyl groups in common

• Amino differ in the side chains

• Different side chains give amino acids different chemical properties (for example, some amino acids are hydrophobic, some are hydrophilic)

Page 46

2-86

Representative Amino Acids

• Note: they differ only in the R group

Some nonpolar amino acids

Methionine

Tyrosine

H

N

C

C

H

S

O

(a)

OH

H CH2 CH2 CH3

Some polar amino acids

Cysteine

Arginine

H

N

C

C

H

O OH

H CH2 SH

CH2 OH

H

N

C

C

H

O OH

H (CH2)3 NH

NH2

NH2+

H

N

C

C

C

H

O OH

H


Figure 2.23a

91

Proteins

The structure of the R group dictates the chemical properties of the amino acid.

Amino acids can be classified as:1. nonpolar2. polar3. charged4. aromatic5. special functions (acidic, basic)

Fig. 3.20

Fig. 3.20-1

Fig. 3.20-2

Fig. 3.20-3

Fig. 3.20-4

Fig. 3.20-5

2-87

Peptides• Peptide – any molecule composed of two or more

amino acids joined by peptide bonds

• Peptide Bond – joins the amino group of one amino acid to the carboxyl group of the next– formed by dehydration synthesis

• Peptides named for the number of amino acids– dipeptides have 2 – oligopeptides have fewer than 10 to 15 – polypeptides have more than 15– proteins have more than 50

99

Amino AcidPolymerization

The Formation of a Peptide Bond

Dehydration Reaction:The loss of water

The Peptide Bond

• Amino acids are joined together into polypeptide chains through a DEHYDRATION REACTION

• Similarly, Polypeptide chains are cleaved apart through a HYDROLYSIS REACTION

Hydrolysis Reaction

H2O

Hydrolysis Reaction:The Bond is Cleaved withwater

Find the Peptide Bond

Peptide BondTerminal Animo Group

Carboxyl Group

Amino GroupPeptide Bond

Side Chain

Side Chain

2-89

Protein Structure and Shape

• Protein properties and functions depend on Protein Conformation

• Conformation – unique three dimensional shape of protein crucial to function

• Because of unique conformations, proteins are very specific to their functions

• Protein conformation depends on the environment

2-89


• Four Level of Protein Structure

1.Primary structure 2.Secondary structure3.Tertiary structure4.Quaternary structure

2-89


1. Primary structure – protein’s sequence amino acid– encoded in the genes

Fig. 3.22-1

2-89


2. Secondary structure– coiled or folded shape held together by hydrogen

bonds– hydrogen bonds between slightly negative C=O

and slightly positive N-H groups

• Two secondary structure motifs: – Alpha Helix – springlike shape– Beta Helix – pleated, ribbonlike shape

Fig. 3.21a

Fig. 3.22-2

Fig. 3.22-3

2-89


3. Tertiary structure

– further bending and folding of proteins into globular and fibrous shapes

– further folding due to Hydrogen bonding or other R group interactions within the chain, hydrophobic/hydrophilic interactions

• globular proteins –compact tertiary structure well suited for proteins embedded in cell membrane and proteins that must move about freely in body fluid

• fibrous proteins – slender filaments better suited for roles as in muscle contraction and strengthening the skin

Fig. 3.21a

Fig. 3.21b

Fig. 3.21c

Fig. 3.21d

Fig. 3.21e

Fig. 3.22-4

2-89


3. Tertiary structure

• Tertiary Structure of polypeptides forms Domains

• Domains are 3D functional regions of a polypeptide strung together on the polypeptide chain

Fig. 3.23

2-89


• Quaternary structure– associations of two or more separate polypeptide chains– the chains are not covalently bonded

Fig. 3.22

2-92

• Proteins that contain a non-amino acid moiety called a prosthetic group

• Hemoglobin contains four complex iron containing rings called a heme moieties

Conjugated Proteins

Quaternary structure

Association of two ormore polypeptide chainswith each other

Beta chain

Betachain

Hemegroups

Alphachain

Alphachain


Figure 2.24 (4)

2-90

Structure of Proteins

C

C=O

C=O

C=O

HN

HN

HN

NH O=C

C

C

C

CC

C

CC

C

C

O=C

O=C

C

NH O=C

NH

NH

C=O HN

C=O HN

CH

N CC

O

O O

O

CC

OC

NH

CC

NH

NH

C

Amino acids

Peptidebonds

Primary structure

Sequence of aminoacids joined bypeptide bonds

Secondary structure

Alpha helix or betasheet formed byhydrogen bonding

Betasheet

Chain 1Chain 2

Alphahelix

Quaternary structure

Association of twoor more polypeptidechains with eachother

Beta chain

Betachain

Heme groups

Alphachain

Alphachain

Tertiary structure

Folding and coilingdue to interactionsamong R groups andbetween R groupsand surrounding water


Figure 2.24

C=O H N

127

Proteins

• Protein folding is aided by Chaperone Proteins• Endoplasmic Reticulum, Golgi Appartus

Fig. 3.24

2-91

Protein Denaturation

• A change in the shape of a protein, usually causing loss of function

• Caused by changes in the protein’s environment

- pH- temperature- concentration

• Protein ‘unfolding’- looses layers of structure as conditions deviate- Quaternary Tertiary Secondary Primary

129

Protein Denaturation

2-91

Protein ‘Renaturation’

• Protein conformation can be restored if conditions are returned to normal

Secondary Tertiary Quaternary

• Conformation cannot be restored if primary structure is lost

• Because protein function depends on conformation, proteins work best in their specific environments

Fig. 3.26

Protein ‘Renaturation’

2-96

Enzymes• Enzymes - special class of proteins that functions as

biological catalysts – facilitate chemical reactions

• The Rules to be an Enzyme

1. It is a protein molecule that speeds up a chemical reaction2. Enzymes are not changed during the reaction3. Enzymes can be re-used many times

2-96

Enzymes• Enzymes - proteins that function as biological

catalysts – facilitate chemical reactions – regulate chemical reactions– permit reactions to occur rapidly at normal body

temperature

• The Rules to be an Enzyme

1. It is a protein molecule that speeds up a chemical reaction• Enzymes are not changed during the reaction• Enzymes can be re-used many times

• Naming Convention– named for enzyme substrate with -ase as the suffix

• amylase enzyme digests amylose (a starch)

143

Enzyme Structure

• Substrate - substance an enzyme acts upon

• Active Site - area of an enzyme where the chemical activity takes place– The active site is specifically shaped to bind to a

certain substrate– The active site is usually a cleft or indented area of

a protein– The active site is lined with various R groups that

provide the chemical activity

How Enzymes Work:

• Enzymes Lower the Activation Energy - energy needed to get reaction started– enzymes facilitate molecular interaction

• Enzymes lower the Activation Energy by:1.Bringing the chemically active portions (functional

groups, for example) of Substrates together2.Destabilizing Substrates, making them more prone to

break or form bonds3.Decreasing Entropy – Enzymes hold substrates in

place, increasing the chance that chemical reactions will occur

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Enzymes and Activation Energy

Time

Free e

nerg

y c

onte

nt

Time

Energy levelof products

Energy levelof reactants

Activationenergy

Netenergyreleasedbyreaction

Activationenergy

Netenergyreleasedbyreaction

(a) Reaction occurring without a catalyst (b) Reaction occurring with a catalyst


Figure 2.26a, b

Enzyme Structure and Action

• Enzyme/Substrate Complex:

E + S ES EP E + P

1. The Enzyme and the Substrate come together (E+S)

2. The Enzyme/Substrate Complex is formed (ES)

3. The Enzyme’s Substrate is changed to the Enzyme’s

Product in the active site of the enzyme (EP)

4. The Enzyme and Product Separate (E+P)

5. The Enzyme is free to bind to another Substrate

2-98

Enzyme Structure and Action

• Substrate approaches active site on enzyme molecule

• Substrate binds to active site forming enzyme-substrate complex– highly specific fit –’lock and key’

• enzyme-substrate specificity

• Enzyme breaks covalent bonds between monomers in substrate

• adding H+ and OH- from water – Hydrolysis

• Reaction products released – glucose and fructose

• Enzyme remains unchanged and is ready to repeat the process

2-99

Enzymatic Reaction Steps

Sucrase (enzyme)

1 Enzyme and substrate

Sucrose (substrate)

Enzyme–substrate complex

2

Enzyme and reaction products

3

Glucose Fructose

O

O

Active site


Figure 2.27

2-100

• Reusability of enzymes– enzymes are not consumed by the reactions

• Astonishing speed– one enzyme molecule can consume millions of substrate

molecules per minute

• Factors that change enzyme shape– pH and temperature– alters or destroys the ability of the enzyme to bind to

substrate – enzymes vary in optimum pH

• salivary amylase works best at pH 7.0• pepsin works best at pH 2.0

– temperature optimum for human enzymes – body temperature (37 degrees C)

Enzymatic Action

The Allosteric Site

• The allosteric site is another binding area of the enzyme

• The allosteric site binds a substance other than the substrate

• Binding at the allosteric site can induce a change in the shape of the protein and affect the active site

• *Noncompetitive inhibitors bind to allosteric sites

29

Conformational Change

• The change in the shape of the protein induced by binding at an allosteric site is known as a CONFORMATIONAL CHANGE

Protein Specificity

• The Quaternary Shape of a Protein gives the Active Site Specificity

• Specific Receptors• Specific Antigens• Specific Antibodies• Specific Substrates

• Specificity is important for enzyme action and function

Protein Specificity

• Lock and Key Hypothesis:• The Substrates of Protein Active Sites fit like a key

fits into a lock

• Induced Fit Hypothesis:• The Active Site of a Protein changes shape as a it

binds to its substrate to create a very specific fit

Conformational Change Example:Hemoglobin

• Hemoglobin is the protein in Red Blood Cells that carries Oxygen

• One molecule of Hemoglobin has four active sites – each active site can bind to one molecule of oxygen

• Hemoglobin undergoes conformational changes at each of its oxygen binding sites as molecules of oxygen bind

Hemoglobin

Conformational Change Example:Hemoglobin

• As each oxygen binding site binds a molecule of oxygen, a conformational change is induced to the rest of the oxygen binding sites

• With the binding of every O2, the other O2 binding sites have a weaker attraction for O2

• How is this important physiologically?

2-101

Cofactors and Coenzymes• Cofactors

– about 2/3rds of human enzymes require a nonprotein cofactor

– inorganic partners (iron, copper, zinc, magnesium and calcium ions)

– some bind to enzyme and induces a change in its shape, which activates the active site

– essential to function

• Coenzymes– organic cofactors derived from water-soluble vitamins

(niacin, riboflavin)– they accept electrons from an enzyme in one metabolic

pathway and transfer them to an enzyme in another

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Coenzyme NAD+

• NAD+ transports electrons from one metabolic pathway to another

Pi+ADP

Glycolysis Aerobic respiration

Glucose Pyruvic acid

Pyruvic acid CO2 + H2O

ATP


Figure 2.28

e–NAD+ e–

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Metabolic Pathways• Chain of reactions, with each step usually catalyzed

by a different enzyme

• α β γ A → B → C → D

• A is initial reactant, B+C are intermediates and D is the end product

• Regulation of metabolic pathways – activation or deactivation of the enzymes – cells can turn on or off pathways when end products are

needed and shut them down when the end products are not needed

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4. Lipids

• Lipid molecules are composed of Carbon, Hydrogen, and Oxygen atoms

• The proportion of oxygen is much lower in lipids than it is in carbohydrates

• A high proportion of nonpolar C – H bonds causes the molecule to be hydrophobic

• Lipids are insoluble in water

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Lipids

• Two main categories of lipids

1. Fats (Triglycerides)2. Phospholipids

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1. Triglycerides

• Molecule for energy storage– store twice as much energy as carbohydrates

• Animal fats are are solid at room temperature

- Adipose tissue, waxes

• Plant fats (oils) are liquid at room temperature

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1. Triglycerides

• Composed of 2 Parts:a.Glycerol Molecule

b.Three Fatty Acids (tri)

• 3 fatty acids covalently bonded to a glycerol molecule – each bond formed by dehydration synthesis– broken down by hydrolysis

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a. Glycerol

• Glycerol is a 3 carbon molecule with 3 hydroxyl groups

• One, two, or three fatty acids can bind at the locations of the Hydroxyl Groups to form a lipid

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b. Fatty Acids• Chain of 4 to 24 carbon atoms

– carboxyl (acid) group on one end, methyl group on the other and hydrogen bonded along the side

Figure 2.19

C

H H H H H H H H H H H H H H HO

HOH H H H H H H H H H H H H H H

C C C C C C C C C C C C C C C H


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Fatty Acids

• Classes of Fatty Acids a.Saturated - carbon atoms saturated with hydrogen b.Unsaturated - contains C=C bonds without hydrogenc.Polyunsaturated – contains many C=C bonds

Figure 2.19Palmitic acid (saturated)CH3(CH2)14COOH

C

H H H H H H H H H H H H H H H

O

HO




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Fatty Acids

a. Saturated Fatty Acids- carbon backbone saturated with hydrogen - Contains C-C Single Bonds only

Figure 2.19Palmitic acid (saturated)CH3(CH2)14COOH

C


O

HO




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Saturation

A Saturated Fatty Acid

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Fatty Acids

b.Unsaturated Fatty Acids- contains C=C bonds, therefore fewer hydrogens

c.Polyunsaturated - contains many C=C bonds

Figure 2.19

C

H H H H H H H H H H H H H

O

HO

H H H H H H H H H H H H H



90

Saturation

• An Unsaturated Fatty Acid

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Examples of Fatty Acids

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Saturation

• The Saturation or Unsaturation of the Fatty Acids affects the properties of the lipid

• Unsaturations put “kinks” in the fatty acids

• Kinks in the fatty acids prevent them from stacking together, making them less stable solids

• Unsaturated Fats are usually liquids at room temperature – plant fats (oils)

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Saturation

• Saturated fats are not kinked• They stack together making the lipid more

stable solids

• Saturated Fats are usually solid at room temperature – animal fats and waxes

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Saturation

• Saturated Fatty Acids

• Unsaturated Fatty Acids

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Triglyceride Synthesis

A Dehydration Rxn.

A Triglyceride + 3H2OGlycerol + 3 Fatty Acids

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Saturated Fats

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Unsaturated Fats

2. Phospholipids

• Similar to triglycerides except that one fatty acid is replaced by a phosphate group

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Phospholipids• Phospholipids are Amphiphilic molecules

– fatty acid “tails” are hydrophobic– phosphate “head” is hydrophilic

Polar Head Group

Nonpolar Hydrocarbon Tail

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Phospholipids

• Because of Hydrophobic/ Hydrophilic Interactions, phospholipids spontaneously form micelles or lipid bilayers in water

• These structures cluster the hydrophobic tail regions of the phospholipid toward the inside and leave the hydrophilic head regions exposed to the water environment.

• Lipid bilayers are the basis of biological membranes

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Micelle

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Phospholipid Bilayer

Documents

The Chemical Building Blocks of Life Chapter 3. 38 Biochemistry The study of the Chemistry of Life 4 Classes of Biological Molecules 1. Carbohydrates