Transcript 2-1 Atoms and Atomic Structure

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
• Learning Outcomes
• 2-1 Describe an atom and how atomic structure
affects interactions between atoms.
• 2-2 Compare the ways in which atoms combine
to form molecules and compounds.
• 2-3 Distinguish among the major types of
chemical reactions that are important for
studying physiology.
• 2-4 Describe the crucial role of enzymes in
metabolism.
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An Introduction to the Chemical Level of
Organization
• Learning Outcomes
• 2-5 Distinguish between organic and inorganic
compounds.
• 2-6 Explain how the chemical properties of water
make life possible.
• 2-7 Discuss the importance of pH and the role
of buffers in body fluids.
• 2-8 Describe the physiological roles of inorganic
compounds.
• 2-9 Discuss the structures and functions of
carbohydrates.
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An Introduction to the Chemical Level of
Organization
• Learning Outcomes
• 2-10 Discuss the structures and functions of
lipids.
• 2-11 Discuss the structures and functions of
proteins.
• 2-12 Discuss the structures and functions of
nucleic acids.
• 2-13 Discuss the structures and functions of
high-energy compounds.
• 2-14 Explain the relationship between chemicals
and cells.
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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
−
n
e
p+
n
Hydrogen-2,
deuterium
Hydrogen-3,
tritium
mass number: 2
mass number: 3
b A deuterium
(2H)
nucleus
contains a proton and a
neutron.
c A tritium (3H) nucleus
contains a proton and two
neutrons.
Table 2-1 Principal Elements in the Human Body
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Table 2-1 Principal Elements in the Human Body
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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
• 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+
Hydrogen, H
Atomic number: 1
Mass number: 1
1 electron
a Hydrogen (H). A typical
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.
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−e
n
p+
e−
Helium, He
Atomic number: 2
Mass number: 4
(2 protons + 2 neutrons)
2 electrons
b Helium (He). An
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
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
e
e−
n
−e
p+
−e
Lithium, Li
Atomic number: 3
Mass number: 6
(3 protons + 3 neutrons)
3 electrons
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
• Compounds are all molecules, but not all molecules
are compounds
• H2 = molecule only
• H2O = molecule and compound
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Figure 2-3 Chemical Notation (Part 4 of 4).
Ions
A superscript plus or minus sign following the symbol of an element indicates an ion. A single plus sign indicates
a cation with a charge of +1. (The original atom has lost one electron.) A single minus sign indicates an anion with
a charge of −1. (The original atom has gained one electron.) If more than one electron has been lost or gained, the
charge on the ion is indicated by a number preceding the plus or minus sign.
Na+
Cl−
Ca2+
sodium ion
chloride ion
calcium ion
the chlorine
the sodium
the calcium
atom has lost atom has gained atom has lost
one electron
one electron
two electrons
A sodium atom
becomes a sodium ion
Electron lost
+
Na
Na+
Sodium
atom (Na)
Sodium
ion (Na+)
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Na+
Cl−
sodium chloride
ion
ion
Ca2+
calcium
ion
2-2 Molecules and Compounds
• Covalent Bonds
• Involve the sharing of pairs of electrons between
atoms
• 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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2-2 Molecules and Compounds
• Covalent Bonds
• Nonpolar covalent bonds
• Involve equal sharing of electrons because atoms
• 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
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2-2 Molecules and Compounds
• Hydrogen Bonds
• Bonds between adjacent molecules, not atoms
• Hydrogen bonds between H2O molecules cause
surface tension
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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
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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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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
• The Properties of Aqueous Solutions
• Electrolytes are inorganic ions that conduct
electricity in solution
• Electrolyte imbalance seriously disturbs vital body
functions
• Water accounts for up to two-thirds of your total
body weight
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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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2-7 pH and Homeostasis
• pH Scale
• Has an inverse relationship with H+ concentration
• More H+ ions means lower pH, fewer H+ ions
means higher pH
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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
• Buffers
• Weak acid/salt compounds
• Neutralize either strong acid or strong base
• Antacids
• Basic compounds that neutralize acid and form a
salt
• Alka-Seltzer, Tums, Rolaids, etc.
• Salts
• Solutes that dissociate into cations and anions
other than hydrogen ions and hydroxide ions
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2-9 Carbohydrates
• Organic Molecules
• Contain H, C, and usually O
• Are covalently bonded
•
•
•
•
Carbohydrates
Lipids
Proteins (or amino acids)
Nucleic acids
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Table 2-3 Important Functional Groups of Organic Compounds.
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2-9 Carbohydrates
• Carbohydrates contain carbon, hydrogen, and
oxygen in a 1:2:1 ratio
• Monosaccharide — simple sugar 3 to 7 carbon
atoms,glucose, fructose, galactose
• Disaccharide — two sugars condensed by
dehydration synthesis ,sucrose, maltose
• Polysaccharide — many sugars condensed by
dehydration synthesis, glycogen, starch, cellulose
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Table 2-4 Carbohydrates in the Body.
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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 2-14b 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
• 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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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 2-18b Phospholipids and Glycolipids.
Carbohydrate
Glycerol
Fatty
acids
b
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In a glycolipid, a carbohydrate is
attached 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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Table 2-5 Representative Lipids and Their Functions in the Body.
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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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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
• 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
Hydrogen bond
Hydrogen
bond
A2
A1
A6
A3
A5
A7
OR
A9
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
• 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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2-12 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.
2.
3.
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A pentose sugar (deoxyribose or ribose)
Phosphate group
Nitrogenous base (A, G, T, C, or U)
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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2-12 Nucleic Acids
• DNA and RNA
• DNA is double stranded, and the bases form
hydrogen bonds to hold the DNA together
• RNA 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
has a pair of nucleotide chains
linked by hydrogen bonding
between complementary base pairs.
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2-12 Nucleic Acids
• Types of RNA
• Messenger RNA (mRNA)
• Transfer RNA (tRNA)
• Ribosomal RNA (rRNA)
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Table 2-6 Comparison of RNA with DNA.
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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
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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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