The Chemical Building
Blocks of Life
Chapter 3
Biochemistry
• The study of the Chemistry of Life
• 4 Classes of Biological Molecules
1.Carbohydrates
2.Nucleic Acids
3.Proteins
4.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
38
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
40
Biological Molecules
Biological molecules are composed of:
1. A Central Carbon or Carbon Chain
2. Functional Groups
4
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
41
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
42
7
Biological Molecules
• 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
8
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
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
2-66
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
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
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Dimer
Monomer 1
Monomer 2
O
OH HO
H+ + OH–
H2O
(a) Dehydration synthesis
Figure 2.15a
2-67
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
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
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Dimer
Monomer 1
Monomer 2
OH
O
H2O
HO
H+ + OH–
(b) Hydrolysis
Figure 2.15b
2-68
Biological Molecules
15
1. Carbohydrates
The Saccharides (Sugars)
2
1. Carbohydrates
Carbohydrates
• Sugars, Starches, Fibers
• Names of carbohydrates often built from:
– word root ‘sacchar-’
– the suffix ’-ose’
– both mean ‘sugar’ or ‘sweet’
• monosaccharide or glucose
2-69
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
1. Carbohydrates
60
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
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
5
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
6
Carbohydrates
24
Carbohydrates
25
Carbohydrate Structure
Numbering the Carbons
Ribose vs. 2 Deoxyribose
• Ribose
• 2’ Deoxyribose
7
1. Carbohydrates
1. Monosaccharides
2. Disaccharides
3. Polysaccharides
104
27
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
8
9
1. Monosaccharides
a. 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
10
shape of the molecule
Monosaccharides differ in their
Stereochemistry - 3D shape
Pentose
C5H10O5
Hexose
C6H12O6
67
Monosaccharides are Isomers
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Isomers
– molecules with the same chemical
formula, but different structures
• 3 important monosaccharides
– glucose, galactose and fructose
Glucose
CH2OH
H
HO
Galactose
HO
H
• Same molecular formula - C6H12O6
– isomers
O
H
H
OH
H
H
OH
OH
CH2OH
O
H
OH
H
H
OH
H
OH
Fructose
O
HOCH2
H
OH
H
HO
OH
H
Figure 2.16
CH2OH
2-70
Carbohydrates
33
Carbohydrates
34
Chiral Molecules
• Isomers that are mirror images of each other
35
1. Monosaccharides
b. 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
Glucose
Oxygen
6 H2O + 6 CO2 + Energy
Water
Carbon Dioxide
13
2. Disaccharides
a. Structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Sugar molecule composed
of 2 monosaccharides
Sucrose
CH2OH
O
H
H
OH
H
H
Lactose
– sucrose - table sugar
HO
• glucose + fructose
H
• glucose + galactose
– maltose - grain products
• glucose + glucose
H
HO
CH2OH
OH
OH
CH2OH
H
H
OH
O
H
OH
OH
O
OH
H
H
H
H
– lactose - sugar in milk
H
O
HO
• 3 important
disaccharides
CH2OH O
H
H
OH
H
O
H
CH2OH
Maltose
CH2OH
CH2OH
O
H
H
OH
H
HO
H
OH
H
O
H
O
H
OH
OH
H
H
H
Figure 2.17
OH
2-71
2. Disaccharides
Polymerization
• Monosaccharides are joined together into
chains through a Dehydration Reaction
• A dimer of two monosaccharides is formed
• Water is lost in the polymerization reaction
16
Dehydration Synthesis
Glucose + Fructose =
Maltose + H2O
Glucose + Glucose =
Maltose + H2O
39
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)
6
5
1
4
3
4
11
1
4
2
H2O
•
OH + H yields H2O
17
2. Disaccharides
Hydrolysis 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”
18
2. Disaccharides
Hydrolysis Reaction
Maltose + H2O = Glucose + Glucose
+ H2O
19
3. Polysaccharides
a. Structure
1. Multiple Monosaccharides linked together
b. Functions
1. Structural Molecules
2. Signaling Molecules
3. Energy Storage
20
3. Polysaccharides
• 3 Important Polysaccharides:
1. Glucose
2. Starch
3. Cellulose
44
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
Glycogen
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CH2OH
O
O
O
O
CH2OH
O
CH2OH
O
CH2
O
(a)
CH2OH
O
O
CH2OH
O
O
O
O
O
(b)
Figure 2.18
2-73
Glycogen
47
Glycogen Inclusions in a Liver Cell
Stryer's Biochemistry Fig. 23-2
82
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
3. Polysaccharides
b. Function
1. Structural Molecules
Cellulose - plant cell walls
Chitin – Fungi cell walls
Peptidoglycan - Bacterial cell walls
22
Carbohydrates
51
Carbohydrates
52
Carbohydrates
53
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
Glycoproteins on Cell Surface
Viral Bioinformatics Resource Center
athena.bioc.uvic.ca/.../copy9_of_sample/surface
24
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
23
3. Polysaccharides
b. Functions
3.Energy Storage
– Excess glucose stored as Glycogen
– Hydrolyzed to Glucose as needed
2-74
2. Nucleic Acids
• DNA = Deoxyribonucleic Acid
• RNA = Ribonucleic Acid
• Function to store, transport, and control
hereditary information
149
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
2-110
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
4-2
2. Nucleic Acids
• Nucleotides are the uilding blocks
of bucleic acids (DNA and RNA) and
ATP
• 3 components of nucleotides
1. Nitrogenous base
2. Ribose Sugar (monosaccharide)
3. Phosphate groups
2-104
2. Nucleic Acids
62
The Nitrogenous Bases of Nucleotides
• There are 5 different Nitrogenous Bases to
choose from when building Nucleic Acids:
155
The Nitrogenous Bases of Nucleotides
• DNA is composed of
• RNA is composed of
the Nitrogenous Bases:
the Nitrogenous
Thymine, Cytosine,
Bases: Uracil,
Adenine, and
Cytosine, Adenine,
Guanine
and Guanine
156
Nitrogenous Bases of DNA
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Purines
O
• Purines - double ring
NH2
C
– Adenine (A)
– Guanine (G)
N
C
N
C
CH
C
HN
C
C
H
N
NH
NH
C
C
N
CH
N
NH2
Adenine (A)
Guanine (G)
Pyrimidines
• Pyrimidines - single
ring
H
C
CH3
C
HC
C
N
N
H
– Cytosine (C)
– Thymine (T)
• DNA bases - ATCG
• RNA bases - AUCG
NH2
O
C
HC
C
NH
N
H
O
Cytosine (C)
C
O
Thymine (T)
O
HN
C
O
(b)
C
N
H
CH
CH
Uracil (U)
Figure 4.1b
4-5
The Nitrogenous Bases
66
The Ribose Sugar of Nucleotides
The Nucleotides of DNA
• The name, Deoxyribonucleic Acid,
tells us the structure of the ribose
sugar in the Nucleotides of DNA
The Nucleotides of RNA
• The name, Ribonucleic acid, tells
us the structure of the ribose sugar
in the RNA Nucleotides
• It lacks a hydroxyl group at C2
153
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
157
The Phosphate Group of Nucleotides
158
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
159
The Backbone is formed by multiple C3C5 phospho-ribose linkages
160
The Backbone is formed by multiple C3C5 phospho-ribose linkages
161
DNA Molecular Structure
• DNA is a long threadlike
molecule with uniform
diameter, but varied
length
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Adenine
NH2
N
HC
– total length of 2 meters
– average DNA molecule 2 inches
long
• 46 DNA molecules in the
nucleus of most human
cells (Chromosomes)
N
H
C
C
C
N
CH
N
O
HO
P
O
OH
O
CH2
H H
OH
Phosphate
H H
H
Deoxyribose
(a)
Figure 4.1a
4-4
DNA Molecular Structure
74
DNA Double Helix
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• Two DNA strands are united by
hydrogen bonds to form the
double-helix
(b)
T
• DNA base pairing
–
–
C
G
A – T with 2 hydrogen bonds
C – G with 3 hydrogen bonds
T
• Law of Complementary Base
Pairing
– one strand determines base
sequence of other
– One strand serves as the template
for the complementary strand
G
C
A
G
C
Hydrogen
bond
Sugar–phosphate
backbone
Sugar–phosphate
backbone
(c)
Figure 4.2 partial
4-7
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
163
Complementary Base Pairing
164
Fig. 3.16-1
Nucleic Acids
79
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
80
Fig. 3.16-2
Nucleic Acids
Other nucleotides
• ATP: adenosine triphosphate
-primary energy currency of the cell
• NAD+ and FAD: electron carriers for many
cellular reactions
82
The Chemical Building
Blocks of Life
Chapter 3
Sec. 2 Proteins and Lipids
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
2-85
Protein Functions
1. 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
• ligand – any hormone or molecule that reversibly binds to a protein
3. Membrane Transport
– channels in cell membranes that governs what passes through
– carrier proteins – transports solute particles to other side of membrane
2-94
– turn nerve and muscle activity on and off
Protein Functions
4. Catalysis
– enzymes
5. Recognition and Protection
– immune recognition
– antibodies
– clotting proteins
6. Movement
– motor proteins - molecules with the ability to change shape repeatedly
7. Cell adhesion
– proteins bind cells together
– immune cells to bind to cancer cells
– keeps tissues from falling apart
2-95
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
Representative Amino Acids
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Some nonpolar amino acids
Some polar amino acids
Methionine
H
Cysteine
H
H
N
N
C
H
CH2
CH2
S
C
H
CH3
O
OH
O
Tyrosine
H
SH
H
H
C
OH
Arginine
N
H
N
CH2
OH
H
C
O
CH2
C
C
H
H
C
NH2+
(CH2)3
O
C
NH2
C
OH
NH
Figure 2.23a
OH
(a)
• Note: they differ only in the R group
2-86
Proteins
The structure of the R group dictates the
chemical properties of the amino acid.
Amino acids can be classified as:
1. nonpolar
2. polar
3. charged
4. aromatic
5. special functions (acidic, basic)
91
Fig. 3.20
Fig. 3.20-1
Fig. 3.20-2
Fig. 3.20-3
Fig. 3.20-4
Fig. 3.20-5
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
2-87
Amino Acid
Polymerization
99
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
Hydrolysis Reaction:
The Bond is Cleaved with
water
H2O
Find the Peptide Bond
Peptide Bond
Terminal Animo Group
Side Chain
Carboxyl Group
Peptide
Bond
Amino Group
Side Chain
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
Protein Structure and Shape
• Four Level of Protein Structure
1.Primary structure
2.Secondary structure
3.Tertiary structure
4.Quaternary structure
2-89
Protein Structure and Shape
1. Primary structure
– protein’s sequence amino acid
– encoded in the genes
2-89
Fig. 3.22-1
Protein Structure and Shape
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
2-89
Fig. 3.21a
Fig. 3.22-2
Fig. 3.22-3
Protein Structure and Shape
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
2-89
Fig. 3.21a
Fig. 3.21b
Fig. 3.21c
Fig. 3.21d
Fig. 3.21e
Fig. 3.22-4
Protein Structure and Shape
3. Tertiary structure
• Tertiary Structure of polypeptides forms
Domains
• Domains are 3D functional regions of a
polypeptide strung together on the
polypeptide chain
2-89
Fig. 3.23
Protein Structure and Shape
• Quaternary structure
– associations of two or more separate polypeptide chains
– the chains are not covalently bonded
2-89
Fig. 3.22
Conjugated Proteins
• Proteins that contain a non-amino acid
moiety called a prosthetic group
• Hemoglobin contains four complex iron
containing rings called a heme moieties
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Figure 2.24 (4)
Beta chain
Alpha
chain
Association of two or
more polypeptide chains
with each other
Heme
groups
Alpha
chain
Quaternary structure
Beta
chain
2-92
Structure of Proteins
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Amino acids
Primary structure
Peptide
bonds
Tertiary structure
Sequence of amino
acids joined by
peptide bonds
Folding and coiling
due to interactions
among R groups and
between R groups
and surrounding water
C
C
Alpha
helix
Beta
sheet
C
C
C
C
C
C
Chain 1
Alpha helix or beta
sheet formed by
hydrogen bonding
C
C
Secondary structure
Beta chain
C
C
Chain 2
Alpha
chain
Heme
groups
Alpha
chain
Quaternary structure
Association of two
or more polypeptide
chains with each
other
Beta
chain
Figure 2.24
2-90
Proteins
• Protein folding is aided by Chaperone
Proteins
• Endoplasmic Reticulum, Golgi Appartus
Fig. 3.24
127
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 2-91
Protein Denaturation
129
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
2-91
Fig. 3.26
Protein ‘Renaturation’
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 reaction
2. Enzymes are not changed during the reaction
3. 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
2. Enzymes are not changed during the reaction
3. Enzymes can be re-used many times
• Naming Convention
– named for enzyme substrate with -ase as the suffix
• amylase enzyme digests amylose (a starch)
2-96
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
143
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 together
2. Destabilizing Substrates, making them more prone to
break or form bonds
3. Decreasing Entropy – Enzymes hold substrates in
place, increasing the chance that chemical reactions
will occur
Enzymes and Activation Energy
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Free energy content
Activation
energy
Activation
energy
Net
energy
released
by
reaction
Energy level
of reactants
Net
energy
released
by
reaction
Energy level
of products
Time
(a) Reaction occurring without a catalyst
Time
(b) Reaction occurring with a catalyst
Figure 2.26a, b
2-97
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
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
2-98
Enzymatic Reaction Steps
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Sucrose (substrate)
1 Enzyme and
substrate
O
Active site
Sucrase (enzyme)
2 Enzyme–substrate
complex
O
Glucose
3 Enzyme
and reaction
products
Fructose
Figure 2.27
2-99
Enzymatic Action
• 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)
2-100
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
Conformational Change
• The change in the shape of the protein
induced by binding at an allosteric site is
known as a CONFORMATIONAL
CHANGE
29
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?
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
2-101
pathway and transfer them to an enzyme in another
Coenzyme NAD+
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Aerobic respiration
Glycolysis
Pyruvic acid
Glucose
ADP + Pi
e–
NAD+
e–
ATP
Pyruvic acid
CO2 + H2O
Figure 2.28
• NAD+ transports electrons from one
metabolic pathway to another
2-102
Metabolic Pathways
• Chain of reactions, with each step usually catalyzed
by a different enzyme
•

 
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
2-103
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
29
Lipids
• Two main categories of lipids
1. Fats (Triglycerides)
2. Phospholipids
134
152
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
153
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
2-78
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
95
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
H
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
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
H
HO
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Figure 2.19
2-77
Fatty Acids
• Classes of Fatty Acids
a. Saturated - carbon atoms saturated with hydrogen
b. Unsaturated - contains C=C bonds without hydrogen
c. Polyunsaturated – contains many C=C bonds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
HO
C
H
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
H
H
H
H
H
H
H
H
H
H
H
H
H
H
Palmitic acid (saturated)
CH3(CH2)14COOH
Figure 2.19
H
2-77
Fatty Acids
a. Saturated Fatty Acids
- carbon backbone saturated with hydrogen
- Contains C-C Single Bonds only
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
HO
C
H
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
H
H
H
H
H
H
H
H
H
H
H
H
H
H
Palmitic acid (saturated)
CH3(CH2)14COOH
Figure 2.19
H
2-77
Saturation
A Saturated Fatty Acid
89
Fatty Acids
b.Unsaturated Fatty Acids
- contains C=C bonds, therefore fewer hydrogens
c.Polyunsaturated
-
contains many C=C bonds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
HO
C
H
H
H
H
H
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
C
C
C
H
H
C
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
Figure 2.19
H
2-77
Saturation
• An Unsaturated Fatty Acid
90
Examples of Fatty Acids
87
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)
92
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
93
Saturation
• Saturated Fatty Acids
• Unsaturated Fatty Acids
94
Triglyceride Synthesis
Glycerol + 3 Fatty Acids
A Triglyceride + 3H2O
A Dehydration Rxn.
96
Saturated Fats
167
Unsaturated Fats
168
2. Phospholipids
• Similar to triglycerides except that one fatty acid is
replaced by a phosphate group
Phospholipids
• Phospholipids are Amphiphilic molecules
– fatty acid “tails” are hydrophobic
– phosphate “head” is hydrophilic
Polar Head Group
Nonpolar Hydrocarbon Tail
101
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
171
Micelle
172
Phospholipid Bilayer
173