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Chapter 2 Part B
Chemistry
Comes Alive
© Annie Leibovitz/Contact Press Images
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PowerPoint® Lecture Slides
prepared by
Karen Dunbar Kareiva
Ivy Tech Community College
Part 2 – Biochemistry
• Biochemistry is the study of chemical
composition and reactions of living matter
• All chemicals either organic or inorganic
– Inorganic compounds
• Water, salts, and many acids and bases
• Do not contain carbon
– Organic compounds
• Carbohydrates, fats, proteins, and nucleic acids
• Contain carbon, are usually large, and are covalently
bonded
• Both equally essential for life
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2.6 Inorganic Compounds
Water
• Most abundant inorganic compound
– Accounts for 60%–80% of the volume of living
cells
• Most important inorganic compound because of
its properties
– High heat capacity
– High heat of vaporization
– Polar solvent properties
– Reactivity
– Cushioning
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Water
• High heat capacity
– Ability to absorb and release heat with little
temperature change
– Prevents sudden changes in temperature
• High heat of vaporization
– Evaporation requires large amounts of heat
– Useful cooling mechanism
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Water (cont.)
• Polar solvent properties
– Dissolves and dissociates ionic substances
– Forms hydration (water) layers around large
charged molecules
• Example: proteins
– Body’s major transport medium
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Figure 2.12 Dissociation of salt in water.
d+
H
d−
O
H
d+
Water molecule
Na+
Na+
Cl−
Salt
crystal
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Cl−
Ions in
solution
Water (cont.)
• Reactivity
– Necessary part of hydrolysis and dehydration
synthesis reactions
• Cushioning
– Protects certain organs from physical trauma
• Example: cerebrospinal fluid cushions nervous system
organs
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Salts
• Salts are ionic compounds that dissociate into
separate ions in water
– Separate into cations (positively charged
molecules) and anions (negatively charged)
• Not including H+ and OH– ions
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Salts (cont.)
• Salts (cont.)
– All ions are called electrolytes because they
can conduct electrical currents in solution
– Ions play specialized roles in body functions
• Example: sodium, potassium, calcium, and iron
– Ionic balance is vital for homeostasis
– Common salts in body
• NaCl, CaCO3, KCl, calcium phosphates
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Clinical – Homeostatic Imbalance 2.1
• Ionic balance is vital for homeostasis
• Kidneys play a big role in maintaining proper
balance of electrolytes
• If electrolyte balance is disrupted, virtually all
organ systems cease to function
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Acids and Bases
• Acids and bases are both electrolytes
– Ionize and dissociate in water
• Acids
– Are proton donors: they release hydrogen
ions (H+), bare protons (have no electrons) in
solution
• Example: HCl → H+ + Cl–
– Important acids
• HCl (hydrochloric acid), HC2H3O2 (acetic acid,
abbreviated HAc), and H2CO3 (carbonic acid)
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Acids and Bases (cont.)
• Bases
– Are proton acceptors: they pick up H+ ions in
solution
• Example: NaOH → Na+ + OH–
– When a base dissolves in solution, it releases a
hydroxyl ion (OH –)
– Important bases
• Bicarbonate ion (HCO3–) and ammonia (NH3)
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Acids and Bases (cont.)
• pH: Acid-base concentration
– pH scale is measurement of concentration of
hydrogen ions [H+] in a solution
– The more hydrogen ions in a solution, the more
acidic that solution is
– pH is negative logarithm of [H+] in moles per liter
that ranges from 0–14
– pH scale is logarithmic, so each pH unit
represents a 10-fold difference
• Example: a pH 5 solution is 10 times more acidic than
a pH 6 solution
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Acids and Bases (cont.)
• pH: Acid-base concentration (cont.)
– Acidic solutions have high [H+] but low pH
• Acidic pH range is 0–6.99
– Neutral solutions have equal numbers of H+ and
OH– ions
• All neutral solutions are pH 7
• Pure water is pH neutral
– pH of pure water  pH 7: [H+]  10–7 m
– Alkaline (basic) solutions have low [H+] but high
pH
• Alkaline pH range is 7.01–14
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Figure 2.13 The pH scale and pH values of representative substances.
Concentration (moles/liter)
[OH−] [H+]
Examples
1M Sodium
hydroxide (pH14)
10−14
14
10−1
10−13
13
10−2
10−12
12
10−3
10−11
11
10−4
10−10
10
10−5
10−9
9
10−6
10−8
8
Egg white (pH8)
10−7
10−7
7 Neutral
Blood (pH7.4)
10−8
10−6
6
Milk (pH6.3–6.6)
10−9
10−5
5
10−10
10−4
4
10−11
10−3
3
10−12
10−2
2
10−13
10−1
1
100
0
Increasingly acidic
Increasingly basic
100
10−14
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pH
Oven cleaner, lye
(pH13.5)
Household ammonia
(pH10.5–11.5)
Household bleach
(pH9.5)
Black coffee (pH5)
Wine (pH2.5–3.5)
Lemon juice; gastric
juice (pH2)
1M Hydrochloric
acid (pH0)
Acids and Bases (cont.)
• Neutralization
– Neutralization reaction: acids and bases are
mixed together
• Displacement reactions occur, forming water and a
salt
NaOH + HCl → NaCl + H2O
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Acids and Bases (cont.)
• Buffers
– Acidity involves only free H+ in solution, not H+
bound to anions
– Buffers resist abrupt and large swings in pH
• Can release hydrogen ions if pH rises
• Can bind hydrogen ions if pH falls
– Convert strong acids or bases (completely
dissociated) into weak ones (slightly dissociated)
• Carbonic acid–bicarbonate system (important buffer
system of blood):
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2.7 Organic Compounds: Synthesis and
Hydrolysis
• Organic molecules contain carbon
– Exceptions: CO2 and CO, which are inorganic
• Carbon is electroneutral
– Shares electrons; never gains or loses them
– Forms four covalent bonds with other elements
– Carbon is unique to living systems
• Major organic compounds: carbohydrates,
lipids, proteins, and nucleic acids
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2.7 Organic Compounds: Synthesis and
Hydrolysis
• Many are polymers
– Chains of similar units called monomers
(building blocks)
• Synthesized by dehydration synthesis
• Broken down by hydrolysis reactions
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Figure 2.14 Dehydration synthesis and hydrolysis.
Dehydration synthesis
Monomers are joined by removal of OH from one monomer
and removal of H from the other at the site of bond formation.
H2O
Monomer
1
Monomer
2
Monomers linked by covalent bond
Hydrolysis
Monomers are released by the addition of a water molecule,
adding OH to one monomer and H to the other.
H2O
Monomer
1
Monomer
2
Monomers linked by covalent bond
Example reactions
Dehydration synthesis of sucrose and its breakdown by hydrolysis
Water is
released
Water is
consumed
Glucose
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Fructose
H2O
H2O
Sucrose
2.8 Carbohydrates
• Carbohydrates include sugars and starches
• Contain C, H, and O
– Hydrogen and oxygen are in 2:1 ratio
• Three classes
– Monosaccharides: one single sugar
• Monomers: smallest unit of carbohydrate
– Disaccharides: two sugars
– Polysaccharides: many sugars
• Polymers are made up of monomers of
monosaccharides
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2.8 Carbohydrates
• Monosaccharides
– Simple sugars containing three to seven carbon
atoms
– (CH2O)n: general formula
• n  number of carbon atoms
– Monomers of carbohydrates
– Important monosaccharides
• Pentose sugars
– Ribose and deoxyribose
• Hexose sugars
– Glucose (blood sugar)
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Figure 2.15a Carbohydrate molecules important to the body.
Monosaccharides
Monomers of carbohydrates
Example
Example
Hexose sugars (the hexoses shown here are isomers)
Pentose sugars
Glucose
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Fructose
Galactose
Deoxyribose
Ribose
Carbohydrates (cont.)
• Disaccharides
– Double sugars
– Too large to pass through cell membranes
– Important disaccharides
• Sucrose, maltose, lactose
– Formed by dehydration synthesis of two
monosaccharides
• glucose + fructose → sucrose + water
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Figure 2.15b Carbohydrate molecules important to the body.
Disaccharides
Consist of two linked monosaccharides
Example
Sucrose, maltose, and lactose (these disaccharides are isomers)
Glucose
Fructose
Sucrose
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Glucose
Maltose
Glucose
Galactose
Glucose
Lactose
Carbohydrates (cont.)
• Polysaccharides
– Polymers of monosaccharides
• Formed by dehydration synthesis of many monomers
– Important polysaccharides
• Starch: carbohydrate storage form used by plants
• Glycogen: carbohydrate storage form used by animals
– Not very soluble
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Figure 2.15c Carbohydrate molecules important to the body.
Polysaccharides
Example
Long chains (polymers) of linked monosaccharides
This polysaccharide is a simplified representation of
glycogen, a polysaccharide formed from glucose molecules.
Glycogen
*Notice that in Figure 2.15 the carbon (C) atoms present at the angles of the carbohydrate ring
structures are not illustrated and in Figure 2.15c only the oxygen atoms and one CH2 group
are shown. The illustrations at right give an example of this shorthand style: The full structure of
glucose is on the left and the shorthand structure on the right. This style is used for nearly all
organic ringlike structures illustrated in this chapter.
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2.9 Lipids
• Contain C, H, O, but less than in carbohydrates,
and sometimes contain P
• Insoluble in water
• Main types:
– Triglycerides or neutral fats
– Phospholipids
– Steroids
– Eicosanoids
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Lipids (cont.)
• Triglycerides or neutral fats
– Called fats when solid and oils when liquid
– Composed of three fatty acids bonded to a
glycerol molecule
– Main functions
• Energy storage
• Insulation
• Protection
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Lipids (cont.)
• Triglycerides can be constructed of:
– Saturated fatty acids
• All carbons are linked via single covalent bonds,
resulting in a molecule with the maximum number of H
atoms (saturated with H)
• Solid at room temperature (Example: animal fats,
butter)
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Lipids (cont.)
– Unsaturated fatty acids
• One or more carbons are linked via double bonds,
resulting in reduced H atoms (unsaturated)
• Liquid at room temperature (Example: plant oils, such
as olive oil)
• Trans fats – modified oils; unhealthy
• Omega-3 fatty acids – “heart healthy”
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Figure 2.16a Lipids.
Triglyceride formation
Three fatty acid chains are bound to glycerol by dehydration synthesis.
3H2O
Glycerol
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3 fatty acid chains
Triglyceride, or neutral fat
3 water
molecules
Lipids (cont.)
• Phospholipids
– Modified triglycerides
• Glycerol and two fatty acids plus a phosphoruscontaining group
– “Head” and “tail” regions have different
properties
• Head is a polar region and is attracted to water
• Tails are nonpolar and are repelled by water
– Important in cell membrane structure
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Figure 2.16b Lipids.
“Typical” structure of a phospholipid molecule
Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone.
Example
Phosphatidylcholine
Polar “head”
Nonpolar “tail”
(schematic phospholipid)
Phosphorus-containing
group (polar “head”)
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Glycerol
backbone
2 fatty acid chains
(nonpolar “tail”)
Lipids (cont.)
• Steroids
– Consist of four interlocking ring structures
– Common steroids: cholesterol, vitamin D, steroid
hormones, and bile salts
– Most important steroid is cholesterol
• Is building block for vitamin D, steroid synthesis, and
bile salt synthesis
• Important in cell plasma membrane structure
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Figure 2.16c Lipids.
Simplified structure of a steroid
Four interlocking hydrocarbon rings form a steroid.
Example
Cholesterol (cholesterol is the basis for all steroids
formed in the body)
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Lipids (cont.)
• Eicosanoids
– Many different ones
– Derived from a fatty acid (arachidonic acid)
found in cell membranes
– Most important eicosanoids are prostaglandins
• Play a role in blood clotting, control of blood pressure,
inflammation, and labor contractions
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2.10 Proteins
• Comprise 20–30% of cell mass
• Have most varied functions of any molecules
– Structural, chemical (enzymes), contraction
(muscles)
• Contain C, H, O, N, and sometimes S and P
• Polymers of amino acid monomers held
together by peptide bonds
• Shape and function due to four structural
levels
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Amino Acids and Peptide Bonds
• All proteins are made from 20 types of amino
acids
– Joined by covalent bonds called peptide bonds
– Contain both an amine group and acid group
– Can act as either acid or base
– Differ by which of 20 different “R groups” is
present
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Unnumbered Figure 2.2_page47
Amine
group
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Acid
group
Figure 2.17 Amino acids are linked together by peptide bonds.
Amine
group
Dehydration synthesis:
The acid group of one amino
acid is bonded to the amine
group of the next, with loss of
a water molecule.
Acid
group
Peptide
bond
H2O
H2O
Amino acid
Amino acid
Dipeptide
Hydrolysis: Peptide bonds
linking amino acids together
are broken when water is
added to the bond.
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Structural Levels of Proteins
• Four levels of protein structure determine shape
and function
1. Primary: linear sequence of amino acids (order)
2. Secondary: how primary amino acids interact
with each other
• Alpha () helix coils resemble a spring
• Beta () pleated sheets resemble accordion ribbons
3. Tertiary: how secondary structures interact
4. Quaternary: how 2 or more different
polypeptides interact with each other
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Figure 2.18a Levels of protein structure.
Primary structure
The sequence of
amino acids forms the
polypeptide chain.
Amino acid
H
Amino acid
Amino acid
O
R
H
C
C
N
H
N
C
Amino acid
O
R
H
C
C
N
N
C
C
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H
O
H
H
N
H
R
Amino acid
C
C
C
O
R
H
O
R
H
Figure 2.18b Levels of protein structure.
Secondary structure
The primary chain forms
spirals (-helices) and
sheets (-sheets).
-Helix: The primary chain is coiled
to form a spiral structure, which is
stabilized by hydrogen bonds.
-Sheet: The primary chain
“zig-zags,” forming a “pleated”
sheet. Adjacent strands are held
together by hydrogen bonds.
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Figure 2.18c Levels of protein structure.
Tertiary structure
Superimposed on secondary
structure. -Helices and/or -sheets
are folded up to form a compact
globular molecule held together by
intramolecular bonds.
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Tertiary structure of transthyretin,
a protein that transports the thyroid
hormone thyroxine in blood and
cerebrospinal fluid.
Figure 2.18d Levels of protein structure.
Quaternary structure
Two or more polypeptide
chains, each with its own
tertiary structure, combine
to form a functional protein.
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Quaternary structure of a
functional transthyretin molecule.
Four identical transthyretin
subunits join to form a complex
protein.
Fibrous and Globular Proteins
• Shapes of proteins fall into one of two
categories: fibrous or globular
1. Fibrous (structural) proteins
•
•
•
•
Strandlike, water-insoluble, and stable
Most have tertiary or quaternary structure (3-D)
Provide mechanical support and tensile strength
Examples: keratin, elastin, collagen (single most
abundant protein in body), and certain contractile
fibers
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Fibrous and Globular Proteins (cont.)
2. Globular (functional) proteins
• Compact, spherical, water-soluble, and sensitive to
environmental changes
• Tertiary or quaternary structure (3-D)
• Specific functional regions (active sites)
• Examples: antibodies, hormones, molecular
chaperones, and enzymes
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Protein Denaturation
• Denaturation: globular proteins unfold and lose
their functional 3-D shape
– Fibrous proteins are more stable
– Active sites become deactivated
• Can be caused by decreased pH (increased
acidity) or increased temperature
• Usually reversible if normal conditions restored
• Irreversible if changes are extreme
– Example: cannot undo cooking an egg
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Enzymes and Enzyme Activity
• Enzymes: globular proteins that act as
biological catalysts
– Catalysts regulate and increase speed of
chemical reactions without getting used up in the
process
– Lower the energy needed to initiate a chemical
reaction
• Leads to an increase in the speed of a reaction
• Allows for millions of reactions per minute!
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Enzymes and Enzyme Activity (cont.)
• Characteristics of enzymes
– Most functional enzymes, referred to as
holoenzymes, consist of two parts
• Apoenzyme (protein portion)
• Cofactor (metal ion) or coenzyme (organic molecule,
often a vitamin)
– Enzymes are specific
• Act on a very specific substrate
– Names usually end in –ase and are often named
for the reaction they catalyze
• Example: hydrolases, oxidases
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Enzymes and Enzyme Activity (cont.)
• Enzyme action
– Enzymes lower activation energy, which is the
energy needed to initiate a chemical reaction
• Enzymes “prime” the reaction
– Enzymes allow chemical reactions to proceed
quickly at body temperatures
– Three steps are involved in enzyme action:
1. Substrate binds to enzyme’s active site, temporarily
forming enzyme-substrate complex
2. Complex undergoes rearrangement of substrate,
resulting in final product
3. Product is released from enzyme
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Figure 2.19 Enzymes lower the activation energy required for a reaction.
WITHOUT ENZYME
WITH ENZYME
Less activation
energy required
Energy
Energy
Activation
energy
required
Reactants
Reactants
Product
Progress of reaction
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Product
Progress of reaction
Slide 1
Figure 2.20 Mechanism of enzyme action.
Substrates (S)
e.g., amino acids
Energy is
absorbed;
bond is
formed.
Water is
released.
H2O
Product (P)
e.g., dipeptide
Peptide
bond
Active site
Enzyme-substrate
complex (E-S)
Enzyme (E)
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1 Substrates bind at
active site, temporarily
forming an enzymesubstrate complex.
2 The E-S complex
undergoes internal
rearrangements that
form the product.
Enzyme (E)
3 The enzyme
releases the
product of the
reaction.
Slide 2
Figure 2.20 Mechanism of enzyme action.
Substrates (S)
e.g., amino acids
Active site
Enzyme-substrate
complex (E-S)
Enzyme (E)
© 2016 Pearson Education, Inc.
1 Substrates bind at
active site, temporarily
forming an enzymesubstrate complex.
Slide 3
Figure 2.20 Mechanism of enzyme action.
Substrates (S)
e.g., amino acids
Energy is
absorbed;
bond is
formed.
Water is
released.
H2O
Active site
Enzyme-substrate
complex (E-S)
Enzyme (E)
© 2016 Pearson Education, Inc.
1 Substrates bind at
active site, temporarily
forming an enzymesubstrate complex.
2 The E-S complex
undergoes internal
rearrangements that
form the product.
Slide 4
Figure 2.20 Mechanism of enzyme action.
Substrates (S)
e.g., amino acids
Energy is
absorbed;
bond is
formed.
Water is
released.
H2O
Product (P)
e.g., dipeptide
Peptide
bond
Active site
Enzyme-substrate
complex (E-S)
Enzyme (E)
© 2016 Pearson Education, Inc.
1 Substrates bind at
active site, temporarily
forming an enzymesubstrate complex.
2 The E-S complex
undergoes internal
rearrangements that
form the product.
Enzyme (E)
3 The enzyme
releases the
product of the
reaction.
2.11 Nucleic Acids
• Nucleic acids, composed of C, H, O, N, and P,
are the largest molecules in the body
• Nucleic acid polymers are made up of
monomers called nucleotides
– Composed of nitrogen base, a pentose sugar,
and a phosphate group
• Two major classes:
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
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2.11 Nucleic Acids
• DNA holds the genetic blueprint for the
synthesis of all proteins
– Double-stranded helical molecule (double helix)
located in cell nucleus
– Nucleotides contain a deoxyribose sugar,
phosphate group, and one of four nitrogen
bases:
• Purines: adenine (A), guanine (G)
• Pyrimidines: cytosine (C) and thymine (T)
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2.11 Nucleic Acids
• DNA holds the genetic blueprint for the
synthesis of all proteins (cont.)
– Bonding of nitrogen base from strand to opposite
strand is very specific
• Follows complementary base-pairing rules:
– A always pairs with T
– G always pairs with C
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Figure 2.21 Structure of DNA.
Sugar:
Phosphate Deoxyribose
Base:
Adenine (A)
Thymine (T)
Sugar
Phosphate
P
P
Adenine nucleotide
Thymine nucleotide
Hydrogen
bond
A
T
C
G
A
Sugarphosphate
backbone
A
Deoxyribose
sugar
G
Phosphate
G
T
A
A
G
C
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
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G
C
T
A
2.11 Nucleic Acids
• RNA links DNA to protein synthesis and is
slightly different from DNA
– Single-stranded linear molecule is active mostly
outside nucleus
– Contains a ribose sugar (not deoxyribose)
– Thymine is replaced with uracil
– Three varieties of RNA carry out the DNA orders
for protein synthesis
• Messenger RNA (mRNA), transfer RNA (tRNA), and
ribosomal RNA (rRNA)
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2.12 ATP
• Chemical energy released when glucose is
broken down is captured in ATP (adenosine
triphosphate)
• ATP directly powers chemical reactions in cells
– Offers immediate, usable energy needed by
body cells
• Structure of ATP
– Adenine-containing RNA nucleotide with two
additional phosphate groups
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Figure 2.22 Structure of ATP (adenosine triphosphate).
High-energy phosphate
bonds can be hydrolyzed
to release energy.
Adenine
P
P
Phosphate groups
Ribose
Adenosine
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
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P
2.12 ATP
• Terminal phosphate group of ATP can be
transferred to other compounds that can use
energy stored in phosphate bond to do work
– Loss of phosphate group converts ATP to ADP
– Loss of second phosphate group converts ADP
to AMP
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Unnumbered Figure 2.3_page55
H2O
ATP
H2O
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ADP
+
Pi
+
energy
Figure 2.23 Three examples of cellular work driven by energy from ATP.
Solute
ADP
+
Pi
ATP
Membrane
protein
P
Pi
Transport work: ATP phosphorylates transport
proteins, activating them to transport solutes
(ions, for example) across cell membranes.
ATP
Relaxed smooth
muscle cell
Contracted smooth
muscle cell
ADP
+
Pi
Mechanical work: ATP phosphorylates
contractile proteins in muscle cells so the
cells can contract (shorten).
P
ATP
Pi
A
B
ADP
+
Pi
Chemical work: ATP phosphorylates key
reactants, providing energy to drive
energy-absorbing chemical reactions.
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