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Chapter 2
The Chemical Level
of Organization
Lecture Presentation by
Lee Ann Frederick
University of Texas at Arlington
An Introduction to the Chemical Level of
Organization
•  Chemistry
•  Is the science of change
•  Topics of this chapter include:
•  The structure of atoms
•  The basic chemical building blocks
•  How atoms combine to form increasingly complex
structures
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2-1 Atoms and Atomic Structure
•  Matter
•  Is made up of atoms
•  Atoms join together to form chemicals with different
characteristics
•  Chemical characteristics determine physiology at
the molecular and cellular levels
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2-1 Atoms and Atomic Structure
•  Subatomic Particles
•  Proton
•  Positive charge, 1 mass unit
•  Neutron
•  Neutral, 1 mass unit
•  Electron
•  Negative charge, low mass
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2-1 Atoms and Atomic Structure
•  Atomic Structure
•  Atomic number
•  Number of protons
•  Nucleus
•  Contains protons and neutrons
•  Electron cloud
•  Contains electrons
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Figure 2-1 The Structure of Hydrogen Atoms.
Electron shell
−
e
−
p+
Hydrogen-1
mass number: 1
a A typical hydrogen
nucleus contains a proton
and no neutrons.
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e
p+
n
e
p+
n
Hydrogen-2,
deuterium
Hydrogen-3,
tritium
mass number: 2
mass number: 3
b A deuterium
n
−
(2H)
nucleus
contains a proton and a
neutron.
c A tritium (3H) nucleus
contains a proton and two
neutrons.
2-1 Atoms and Atomic Structure
•  Elements and Isotopes
•  Elements are determined by the atomic number of
an atom
•  Remember, atomic number = number of protons
•  Elements are the most basic chemicals
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2-1 Atoms and Atomic Structure
•  Elements and Isotopes
•  Isotopes are the specific version of an element
based on its mass number
•  Mass number = number of protons plus the number
of neutrons
•  Only neutrons are different because the number of
protons determines the element
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2-1 Atoms and Atomic Structure
•  Atomic Weight
•  Exact mass of all particles
•  Measured in moles
•  Average of the mass numbers of the isotopes
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2-1 Atoms and Atomic Structure
•  Electrons and Energy Levels
•  Electrons in the electron cloud determine the
reactivity of an atom
•  The electron cloud contains shells, or energy
levels, that hold a maximum number of electrons
•  Lower shells fill first
•  Outermost shell is the valence shell, and it
determines bonding
•  The number of electrons per shell corresponds to
the number of atoms in that row of the periodic
table
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Figure 2-2 The Arrangement of Electrons into Energy Levels.
The first energy level
can hold a maximum
of two electrons.
−e
p+
−e
p+
a Hydrogen (H). A typical
b Helium (He). An
hydrogen atom has one
proton and one electron. The
electron orbiting the nucleus
occupies the first, or lowest,
energy level, diagrammed as
an electron shell.
e−
Helium, He
Atomic number: 2
Mass number: 4
(2 protons + 2 neutrons)
2 electrons
Hydrogen, H
Atomic number: 1
Mass number: 1
1 electron
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n
atom of helium has
two protons, two
neutrons, and two
electrons. The two
electrons orbit in the
same energy level.
Figure 2-2 The Arrangement of Electrons into Energy Levels.
The second and
third energy levels
can each contain
up to 8 electrons.
−e
−e
n
p+
e−
−e
−e
n
−e
c Lithium (Li). A lithium
atom has three protons,
three neutrons, and three
electrons. The first energy
level can hold only two
electrons, so the third
electron occupies a
second energy level.
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e−
p+
−e
Lithium, Li
Atomic number: 3
Mass number: 6
(3 protons + 3 neutrons)
3 electrons
e−
−e
e−
e−
e−
Neon, Ne
Atomic number: 10
Mass number: 20
(10 protons + 10 neutrons)
10 electrons
d Neon (Ne). A neon
atom has 10 protons, 10
neutrons, and 10 electrons. The second level
can hold up to eight
electrons; thus, both the
first and second energy
levels are filled.
2-2 Molecules and Compounds
•  Chemical Bonds
•  Involve the sharing, gaining, and losing of
electrons in the valence shell
•  Three major types of chemical bonds
1.  Ionic bonds
•  Attraction between cations (electron donor) and
anions (electron acceptor)
2.  Covalent bonds
•  Strong electron bonds involving shared electrons
3.  Hydrogen bonds
•  Weak polar bonds based on partial electrical
attractions
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2-2 Molecules and Compounds
•  Chemical Bonds
•  Form molecules and/or compounds
•  Molecules
•  Two or more atoms joined by strong bonds
•  Compounds
•  Two or more atoms OF DIFFERENT ELEMENTS
joined by strong or weak bonds
•  Compounds are all molecules, but not all molecules
are compounds
•  H2 = molecule only
•  H2O = molecule and compound
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Figure 2-4a The Formation of Ionic Bonds.
1
Formation of ions
2
Attraction between
opposite charges
3
Formation of an
ionic compound
Sodium atom
Sodium ion (Na+)
Na
Na
Na
+
+
−
−
Cl
Cl
Cl
Sodium chloride (NaCl)
a
Chlorine atom
a
Formation of an ionic bond.
Chloride ion (Cl−)
1
A sodium (Na) atom loses an electron, which is
accepted by a chlorine (Cl) atom. 2 Because the sodium ion (Na+) and chloride ion
(Cl−) have opposite charges, they are attracted to one another. 3 The association of
sodium and chloride ions forms the ionic compound sodium chloride.
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Figure 2-4b The Formation of Ionic Bonds.
Chloride ions
(Cl−)
b
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Sodium ions
(Na+)
Sodium chloride crystal.
Large numbers of sodium and
chloride ions form a crystal of
sodium chloride (table salt).
2-2 Molecules and Compounds
•  Covalent Bonds
•  Involve the sharing of pairs of electrons between
atoms
•  One electron is donated by each atom to make the
pair of electrons
•  Sharing one pair of electrons is a single covalent
bond
•  Sharing two pairs of electrons is a double
covalent bond
•  Sharing three pairs of electrons is a triple covalent
bond
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Figure 2-5 Covalent Bonds in Five Common Molecules.
Molecule
Hydrogen
(H2)
H − H
Oxygen
(O2)
O = O
Carbon
dioxide
(CO2)
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Electron Shell Model and
Structural Formula
O = C = O
Nitrogen
(N2)
N ≡ O
Nitric
oxide
(NO)
N = O
2-2 Molecules and Compounds
•  Covalent Bonds
•  Nonpolar covalent bonds
•  Involve equal sharing of electrons because atoms
involved in the bond have equal pull for the
electrons
•  Polar covalent bonds
•  Involve the unequal sharing of electrons because
one of the atoms involved in the bond has a
disproportionately strong pull on the electrons
•  Form polar molecules — like water
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Figure 2-6 Water Molecules Contain Polar Covalent Bonds.
Hydrogen
atom
Hydrogen
atom
Oxygen atom
a
Formation of a water
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molecule. In forming
δ+
Hydrogen
atom
a water molecule, an
oxygen atom completes
its outermost energy level Oxygen
δ+
atom
by sharing electrons with
a pair of hydrogen atoms.
2δ−
The sharing is unequal,
because the oxygen atom b
Charges on a water
holds the electrons more
molecule. Because the
tightly than do the
oxygen atom has two
hydrogen atoms.
extra electrons much of
the time, it develops a
slight negative charge,
and the hydrogen atoms
become weakly positive.
The bonds in a water
molecule are polar
covalent bonds.
2-2 Molecules and Compounds
•  Hydrogen Bonds
•  Bonds between adjacent molecules, not atoms
•  Involve slightly positive and slightly negative
portions of polar molecules being attracted to one
another
•  Hydrogen bonds between H2O molecules cause
surface tension
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Figure 2-7 Hydrogen Bonds Form between Water Molecules.
δ+
2δ−
δ+
δ+
2δ−
2δ−
δ+
δ+
δ+
2δ−
δ+
2δ−
KEY
Hydrogen
Oxygen
Hydrogen bond
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δ+
δ+
δ+
δ+
2δ−
2δ−
2-2 Molecules and Compounds
•  States of Matter
•  Solid
•  Constant volume and shape
•  Liquid
•  Constant volume but changes shape
•  Gas
•  Changes volume and shape
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2-3 Chemical Reactions
•  In a Chemical Reaction
•  Either new bonds are formed or existing bonds are
broken
•  Reactants
•  Materials going into a reaction
•  Products
•  Materials coming out of a reaction
•  Metabolism
•  All of the reactions that are occurring at one time
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2-3 Chemical Reactions
•  Basic Energy Concepts
•  Energy
•  The power to do work
•  Work
•  A change in mass or distance
•  Kinetic energy
•  Energy of motion
•  Potential energy
•  Stored energy
•  Chemical energy
•  Potential energy stored in chemical bonds
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2-3 Chemical Reactions
•  Decomposition Reaction (Catabolism)
•  Breaks chemical bonds
•  AB → A + B
•  Hydrolysis A-B + H2O → A-H + HO-B
•  Synthesis Reaction (Anabolism)
•  Forms chemical bonds
•  A + B → AB
•  Dehydration synthesis (condensation reaction)
A-H + HO-B → A-B + H2O
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2-3 Chemical Reactions
•  Exchange Reaction
•  Involves decomposition first, then synthesis
•  AB + CD → AD + CB
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2-3 Chemical Reactions
•  Reversible Reaction
•  A + B ↔ AB
•  At equilibrium the amounts of chemicals do not
change even though the reactions are still
occurring
•  Reversible reactions seek equilibrium, balancing
opposing reaction rates
•  Add or remove reactants
•  Reaction rates adjust to reach a new equilibrium
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2-4 Enzymes
•  Chemical Reactions
•  In cells, cannot start without help
•  Activation energy is the amount of energy needed
to get a reaction started
•  Enzymes are protein catalysts that lower the
activation energy of reactions
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Figure 2-8 Enzymes Lower Activation Energy.
Activation energy
required
Energy
1
Reactant(s)
Without
enzyme
2
With enzyme
3
Stable
product(s)
4
Progress of reaction
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2-4 Enzymes
•  Exergonic (Exothermic) Reactions
•  Produce more energy than they use
•  Endergonic (Endothermic) Reactions
•  Use more energy than they produce
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2-5 Inorganic and Organic Compounds
•  Nutrients
•  Essential molecules obtained from food
•  Metabolites
•  Molecules made or broken down in the body
•  Inorganic Compounds
•  Molecules not based on carbon and hydrogen
•  Carbon dioxide, oxygen, water, and inorganic
acids, bases, and salts
•  Organic Compounds
•  Molecules based on carbon and hydrogen
•  Carbohydrates, proteins, lipids, and nucleic acids
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2-6 Properties of Water
•  Water
•  Accounts for up to two-thirds of your total body
weight
•  A solution is a uniform mixture of two or more
substances
•  It consists of a solvent, or medium, in which
atoms, ions, or molecules of another substance,
called a solute, are individually dispersed
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2-6 Properties of Water
•  Solubility
•  Water’s ability to dissolve a solute in a solvent to
make a solution
•  Reactivity
•  Most body chemistry occurs in water
•  High Heat Capacity
•  Water’s ability to absorb and retain heat
•  Lubrication
•  To moisten and reduce friction
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2-6 Properties of Water
•  The Properties of Aqueous Solutions
•  Ions and polar compounds undergo ionization, or
dissociation, in water
•  Polar water molecules form hydration spheres
around ions and small polar molecules to keep
them in solution
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Figure 2-9 Water Molecules Surround Solutes in Aqueous Solutions.
Hydration
spheres
Negative
pole
2δ−
Glucose
molecule
Cl−
O
δ+
H
δ+
Positive
pole
Na+
a
Water molecule.
In a water
molecule, oxygen forms polar
covalent bonds with two
hydrogen atoms. Because
both hydrogen atoms are at
one end of the molecule, it has
an uneven distribution of
charges, creating positive and
negative poles.
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c
Glucose in solution.
b
Sodium chloride in solution.
Ionic
compounds, such as sodium
chloride, dissociate in water as the
polar water molecules break the
ionic bonds in the large crystal
structure. Each ion in solution is
surrounded by water molecules,
creating hydration spheres.
Hydration
spheres also form around an
organic molecule containing
polar covalent bonds. If the
molecule binds water strongly,
as does glucose, it will be
carried into solution—in other
words, it will dissolve. Note
that the molecule does not
dissociate, as occurs for ionic
compounds.
2-6 Properties of Water
•  The Properties of Aqueous Solutions
•  Electrolytes and body fluids
•  Electrolytes are inorganic ions that conduct
electricity in solution
•  Electrolyte imbalance seriously disturbs vital body
functions
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2-6 Properties of Water
•  The Properties of Aqueous Solutions
•  Hydrophilic and hydrophobic compounds
•  Hydrophilic
•  hydro- = water, philos = loving
•  Interacts with water
•  Includes ions and polar molecules
•  Hydrophobic
•  phobos = fear
•  Does NOT interact with water
•  Includes nonpolar molecules, fats, and oils
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2-6 Properties of Water
•  Colloids and Suspensions
•  Colloid
•  A solution of very large organic molecules
•  For example, blood plasma
•  Suspension
•  A solution in which particles settle (sediment)
•  For example, whole blood
•  Concentration
•  The amount of solute in a solvent (mol/L, mg/mL)
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2-7 pH and Homeostasis
•  pH
•  The concentration of hydrogen ions (H+) in a
solution
•  Neutral pH
•  A balance of H+ and OH•  Pure water = 7.0
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2-7 pH and Homeostasis
•  Acidic pH Lower Than 7.0
•  High H+ concentration
•  Low OH- concentration
•  Basic (or alkaline) pH Higher Than 7.0
•  Low H+ concentration
•  High OH- concentration
•  pH of Human Blood
•  Ranges from 7.35 to 7.45
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Figure 2-10 The pH Scale Indicates Hydrogen Ion Concentration.
1 mol/L
hydrochloric
acid
Beer,
vinegar,
wine, Tomatoes,
pickles grapes
Stomach
acid
Extremely
acidic
pH 0
[H+] 100
(mol/L)
1
10−1
Urine
Saliva,
milk
Increasing concentration of H+
2
10−2
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3
10−3
4
10−4
5
10−5
6
10−6
Blood Ocean
Pure Eggswater
water
Neutral
7
10−7
Household
bleach
Household
ammonia
Increasing concentration of OH−
8
10−8
9
10−9
10
10−10
11
10−11
12
10−12
1 mol/L
sodium
hydroxide
Oven
cleaner
Extremely
basic
13
10−13
14
10−14
2-8 Inorganic Compounds
•  Acid
•  A solute that adds hydrogen ions to a solution
•  Proton donor
•  Strong acids dissociate completely in solution
•  Base
•  A solute that removes hydrogen ions from a solution
•  Proton acceptor
•  Strong bases dissociate completely in solution
•  Weak Acids and Weak Bases
•  Fail to dissociate completely
•  Help to balance the pH
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2-8 Inorganic Compounds
•  Salts
•  Solutes that dissociate into cations and anions
other than hydrogen ions and hydroxide ions
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2-8 Inorganic Compounds
•  Buffers and pH Control
•  Buffers
•  Weak acid/salt compounds
•  Neutralize either strong acid or strong base
•  Sodium bicarbonate is very important in humans
•  Antacids
•  Basic compounds that neutralize acid and form a
salt
•  Alka-Seltzer, Tums, Rolaids, etc.
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2-9 Carbohydrates
•  Organic Molecules
•  Contain H, C, and usually O
•  Are covalently bonded
•  Contain functional groups that determine
chemistry
•  Carbohydrates
•  Lipids
•  Proteins (or amino acids)
•  Nucleic acids
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2-9 Carbohydrates
•  Carbohydrates
•  Contain carbon, hydrogen, and oxygen in a 1:2:1
ratio
•  Monosaccharide — simple sugar
•  Disaccharide — two sugars
•  Polysaccharide — many sugars
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2-9 Carbohydrates
•  Monosaccharides
•  Simple sugars with 3 to 7 carbon atoms
•  Glucose, fructose, galactose
•  Disaccharides
•  Two simple sugars condensed by dehydration
synthesis
•  Sucrose, maltose
•  Polysaccharides
•  Many monosaccharides condensed by
dehydration synthesis
•  Glycogen, starch, cellulose
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Figure 2-11 The Structures of Glucose.
a
The structural formula of b
The structural formula of
the ring form, the most
the straight-chain form
common form of glucose
KEY
= Carbon
= Oxygen
= Hydrogen
c
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A three-dimensional model that shows
the organization of the atoms in the ring
form
Figure 2-12a The Formation and Breakdown of Complex Sugars.
DEHYDRATION
SYNTHESIS
Glucose
Fructose
Sucrose
a
Formation of the disaccharide sucrose through dehydration synthesis. During dehydration
synthesis, two molecules are joined by the removal of a water molecule.
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Figure 2-12b The Formation and Breakdown of Complex Sugars.
HYDROLYSIS
Sucrose
Glucose
Fructose
b
Breakdown of sucrose into simple sugars by hydrolysis. Hydrolysis reverses the steps of dehydration
synthesis; a complex molecule is broken down by the addition of a water molecule.
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Figure 2-13 The Structure of the Polysaccharide Glycogen.
Glucose
molecules
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2-10 Lipids
•  Lipids
•  Mainly hydrophobic molecules such as fats, oils,
and waxes
•  Made mostly of carbon and hydrogen atoms
•  Include:
•  Fatty acids
•  Eicosanoids
•  Glycerides
•  Steroids
•  Phospholipids and glycolipids
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2-10 Lipids
•  Fatty Acids
•  Long chains of carbon and hydrogen with a
carboxyl group (COOH) at one end
•  Are relatively nonpolar, except the carboxyl group
•  Fatty acids may be:
•  Saturated with hydrogen (no covalent bonds)
•  Unsaturated (one or more double bonds)
•  Monounsaturated = one double bond
•  Polyunsaturated = two or more double bonds
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Figure 2-14a Fatty Acids.
Lauric acid (C12H24O2)
a
Lauric acid demonstrates two structural
characteristics common to all fatty acids: a long
chain of carbon atoms and a carboxyl group
(⎯ COOH) at one end.
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Figure 2-14b Fatty Acids.
Saturated
Unsaturated
b
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A fatty acid is either saturated (has single covalent
bonds only) or unsaturated (has one or more
double covalent bonds). The presence of a double
bond causes a sharp bend in the molecule.
2-10 Lipids
•  Eicosanoids
•  Derived from the fatty acid called arachidonic acid
•  Leukotrienes
•  Active in immune system
•  Prostaglandins
•  Local hormones, short-chain fatty acids
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2-10 Lipids
•  Glycerides
•  Fatty acids attached to a glycerol molecule
•  Triglycerides are the three fatty-acid tails
•  Also called triacylglycerols or neutral fats
•  Have three important functions
1.  Energy source
2.  Insulation
3.  Protection
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Figure 2-16 Triglyceride Formation.
Fatty acids
Glycerol
Fatty Acid 1
Saturated
Fatty Acid 2
Saturated
Fatty Acid 3
Unsaturated
DEHYDRATION
SYNTHESIS
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HYDROLYSIS
Triglyceride
2-10 Lipids
•  Steroids
•  Four rings of carbon and hydrogen with an
assortment of functional groups
•  Types of steroids
•  Cholesterol
•  Component of plasma (cell) membranes
•  Estrogens and testosterone
•  Sex hormones
•  Corticosteroids and calcitriol
•  Metabolic regulation
•  Bile salts
•  Derived from steroids
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Figure 2-17 Steroids Have a Complex Four-Ring Structure.
a
Cholesterol
b
Estrogen
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c
Testosterone
2-10 Lipids
•  Phospholipids and Glycolipids
•  Diglycerides attached to either a phosphate group
(phospholipid) or a sugar (glycolipid)
•  Generally, both have hydrophilic heads and
hydrophobic tails and are structural lipids,
components of plasma (cell) membranes
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Figure 2-18a Phospholipids and Glycolipids.
Nonlipid
group
Phosphate
group
Glycerol
Fatty
acids
a
The phospholipid lecithin. In a phospholipid, a phosphate group
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links a nonlipid molecule to a diglyceride.
Figure 2-18c Phospholipids and Glycolipids.
Hydrophilic
heads
c
In large numbers, phospholipids and glycolipids form
Hydrophobic
tails
micelles, with the hydrophilic heads facing the
water molecules, and the
hydrophobic tails on the
inside of each droplet.
Glycolipid
Phospholipid
WATER
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2-11 Proteins
•  Proteins
•  Are the most abundant and important organic
molecules
•  Contain basic elements
•  Carbon (C), hydrogen (H), oxygen (O), and
nitrogen (N)
•  Basic building blocks
•  20 amino acids
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2-11 Proteins
•  Seven Major Protein Functions
1.  Support
• Structural proteins
2.  Movement
•  Contractile proteins
3.  Transport
•  Transport (carrier)
proteins
4.  Buffering
•  Regulation of pH
5.  Metabolic Regulation
•  Enzymes
6.  Coordination and
Control
•  Hormones
7.  Defense
•  Antibodies
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2-11 Proteins
•  Protein Structure
•  Long chains of amino acids
•  Five components of amino acid structure
1. 
2. 
3. 
4. 
5. 
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Central carbon atom
Hydrogen atom
Amino group (—NH2)
Carboxyl group (—COOH)
Variable side chain or R group
Figure 2-19 Amino Acids.
Structure of an Amino Acid
Amino group
Central carbon
Carboxyl group
R group (variable side chain
of one or more atoms)
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2-11 Proteins
•  Hooking Amino Acids Together
•  Requires a dehydration synthesis between:
•  The amino group of one amino acid and the
carboxyl group of another amino acid
•  Forms a peptide bond
•  Resulting molecule is a peptide
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Figure 2-20 The Formation of Peptide Bonds
Peptide Bond Formation
Glycine (gly)
DEHYDRATION
SYNTHESIS
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Alanine (ala)
HYDROLYSIS
Peptide bond
2-11 Proteins
•  Protein Shape
•  Primary structure
•  The sequence of amino acids along a polypeptide
•  Secondary structure
•  Hydrogen bonds form spirals or pleats
•  Tertiary structure
•  Secondary structure folds into a unique shape
•  Quaternary structure
•  Final protein shape — several tertiary structures
together
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Figure 2-21 Protein Structure.
A1
A2
A3
A4
A5
A6
A7
A8
A9
Linear chain of amino acids
a
Primary structure. The
primary structure of a polypeptide is the sequence of amino
acids (A1, A2, A3, and so on)
along its length.
a
A2
A1
A
10
A6
A3
A5
A5
Hydrogen bond
Hydrogen
bond
A2
A4
A7
OR
A9
A9
A8
A7
A6
A11
A12
A13
A14
Alpha helix
Beta sheet
b
Secondary structure. Secondary structure is primarily the result of hydrogen
Alpha helix
bonding along the length of the polypeptide chain. Such bonding often produces a
simple spiral, called an alpha helix (α helix) or a flattened arrangement known as a
beta sheet (β sheet).
OR
Heme units
c
Tertiary structure. Tertiary
structure is the coiling and folding
of a polypeptide. Within the
cylindrical segments of this
globular protein, the polypeptide
chain is arranged in an alpha helix.
Hemoglobin
(globular protein)
Collagen
(fibrous protein)
d
Quaternary structure. Quaternary structure develops when separate
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polypeptide subunits interact to form a larger molecule. A single
hemoglobin molecule contains four globular subunits. Hemoglobin
transports oxygen in the blood; the oxygen binds reversibly to the heme
units. In collagen, three helical polypeptide subunits intertwine.
Collagen is the principal extracellular protein in most organs.
2-11 Proteins
•  Fibrous Proteins
•  Structural sheets or strands
•  Globular Proteins
•  Soluble spheres with active functions
•  Protein function is based on shape
•  Shape is based on sequence of amino acids
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2-11 Proteins
•  Enzyme Function
•  Enzymes are catalysts
•  Proteins that lower the activation energy of a
chemical reaction
•  Are not changed or used up in the reaction
•  Enzymes also exhibit:
1.  Specificity — will only work on limited types of
substrates
2.  Saturation Limits — by their concentration
3.  Regulation — by other cellular chemicals
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Figure 2-22 A Simplified View of Enzyme Structure and Function (Part 1 of 4).
1
Substrates bind to active
site of enzyme
S2
S1
Substrates
ENZY
M
E
Active
site
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Figure 2-22 A Simplified View of Enzyme Structure and Function (Part 2 of 4).
2
Once bound to the
active site, the
substrates are held
together and their
interaction facilitated
S1
S2
ENZYM
E
Enzyme-substrate
complex
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Figure 2-22 A Simplified View of Enzyme Structure and Function (Part 3 of 4).
3
Substrate binding
alters the shape
of the enzyme, and
this change promotes
product formation
PRO
DUC
ENZYM
E
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T
Figure 2-22 A Simplified View of Enzyme Structure and Function (Part 4 of 4).
4
Product detaches from enzyme;
entire process can now be
repeated
ENZYM
E
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2-11 Proteins
•  Cofactors and Enzyme Function
•  Cofactor
•  An ion or molecule that binds to an enzyme before
substrates can bind
•  Coenzyme
•  Nonprotein organic cofactors (vitamins)
•  Isozymes
•  Two enzymes that can catalyze the same reaction
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2-11 Proteins
•  Effects of Temperature and pH on Enzyme
Function
•  Denaturation
•  Loss of shape and function due to heat or pH
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2-11 Proteins
•  Glycoproteins and Proteoglycans
•  Glycoproteins
•  Large protein + small carbohydrate
•  Includes enzymes, antibodies, hormones, and
mucus production
•  Proteoglycans
•  Large polysaccharides + polypeptides
•  Promote viscosity
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2-12 Nucleic Acids
•  Nucleic Acids
•  Are large organic molecules, found in the nucleus,
which store and process information at the
molecular level
•  Deoxyribonucleic acid (DNA)
• 
• 
• 
• 
Determines inherited characteristics
Directs protein synthesis
Controls enzyme production
Controls metabolism
•  Ribonucleic acid (RNA)
•  Controls intermediate steps in protein synthesis
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2-12 Nucleic Acids
•  Structure of Nucleic Acids
•  DNA and RNA are strings of nucleotides
•  Nucleotides
•  Are the building blocks of DNA and RNA
•  Have three molecular parts
1.  A pentose sugar (deoxyribose or ribose)
2.  Phosphate group
3.  Nitrogenous base (A, G, T, C, or U)
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Figure 2-23a Nucleotides and Nitrogenous Bases.
a
Nucleotide structure
The nitrogenous base may be a purine or a pyrimidine.
Phosphate
group
Sugar
Nitrogenous
base
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Figure 2-23b Nucleotides and Nitrogenous Bases.
b
Purines
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A
Adenine
G
Guanine
Figure 2-23c Nucleotides and Nitrogenous Bases.
c
Pyrimidines
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C
Cytosine
T
Thymine
(DNA only)
U
Uracil
(RNA only)
2-12 Nucleic Acids
•  DNA and RNA
•  DNA is double stranded, and the bases form
hydrogen bonds to hold the DNA together
•  Sometimes RNA can bind to itself but is usually a
single strand
•  DNA forms a twisting double helix
•  Complementary base pairs
•  Purines pair with pyrimidines
•  DNA
•  Adenine (A) and thymine (T)
•  Cytosine (C) and guanine (G)
•  RNA
•  Uracil (U) replaces thymine (T)
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Figure 2-24 The Structure of Nucleic Acids.
Phosphate
group
Deoxyribose
Adenine
Thymine
Hydrogen bond
DNA strand 1
DNA strand 2
a
RNA molecule. An RNA
molecule has a single
nucleotide chain. Its shape
is determined by the
sequence of
nucleotides and by
the interactions
among them.
Cytosine
Guanine
b
DNA molecule. A DNA molecule
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has a pair of nucleotide chains
linked by hydrogen bonding
between complementary base pairs.
2-12 Nucleic Acids
•  Types of RNA
•  Messenger RNA (mRNA)
•  Transfer RNA (tRNA)
•  Ribosomal RNA (rRNA)
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2-13 High-Energy Compounds
•  Nucleotides Can Be Used to Store Energy
•  Adenosine diphosphate (ADP)
•  Two phosphate groups; di- = 2
•  Adenosine triphosphate (ATP)
•  Three phosphate groups; tri- = 3
•  Phosphorylation
•  Adding a phosphate group to ADP with a high-energy
bond to form the high-energy compound ATP
•  Adenosine triphosphatase (ATPase)
•  The enzyme that catalyzes the conversion of ATP to
ADP
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Figure 2-25 The Structure of ATP.
Adenine
Ribose
Phosphate
Phosphate
Phosphate
High-energy bonds
Adenosine
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
Adenine
Phosphate groups
Ribose
Adenosine
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2-14 Chemicals and Cells
•  Chemicals and Cells
•  Biochemical building blocks form functional units
called cells
•  Metabolic turnover lets your body grow, change,
and adapt to new conditions and activities
•  Your body recycles and renews all of its chemical
components at intervals ranging from minutes to
years
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Table 2-7 Classes of Inorganic and Organic Compounds.
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Table 2-8 Turnover Times.
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