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2-1
CHAPTER 2
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The Chemical Elements
2-2
 Element = simplest form of matter with
unique chemical properties
24 elements have biological role

6 elements = 98.5% of body weight
 trace elements in minute amounts

 Atomic number = # of protons in nucleus
 periodic table

elements arranged by atomic number
2-3
 Atomic Mass
 Number of protons and neutrons in nucleus
 Atomic mass units (amu)

Number of neutrons determined by subtracting the atomic
number from the mass number
2-4
Atomic Structure
2-5
 Nucleus = center of atom
 protons: single + charge, mass = 1 amu
 neutrons: no charge, mass = 1 amu
 Electron shells surround the nucleus
 electrons: single negative charge, little mass
 electrons swarm about the nucleus in electron shells
(energy levels)
 valence electrons in the outermost shell
interact with other atoms
 determine chemical behavior

Planetary Models
of
Elements
2-6
p+ represents protons, no represents neutrons
Electron Energy Levels
2-7
 Each energy level can hold certain maximum
number of electrons
 Maximum number determined by formula

X=2(n squared)
Isotopes and2-8Radioactivity
 Isotopes
 differ in # of neutrons
 extra neutrons increase atomic weight
 isotopes of an element are chemically similar

have same valence electrons
 Atomic weight
 average atomic mass of the isotopes
Radioisotopes and
Radioactivity
2-9
 Isotopes
 same chemical behavior, differ in physical behavior
 breakdown gives off radiation
 Radioisotopes
 unstable isotopes
 every element has at least one radioisotope
 Radioactivity
 radioisotopes decay to stable isotopes releasing
radiation
 we are all mildly radioactive
Ions and Ionization
2-10
• Ions - carry a charge due to an unequal
number of protons and electrons
 Ionization =
transfer of
electrons from
one atom to
another
( stability of
valence shell)
Anions and Cations
• Anion
2-11
– atom that gained electrons (net negative charge)
• Cation
– atom that lost an electron (net positive charge)
• Ions with opposite charges are attracted to each
other
Electrolytes
2-12
 Salts that ionize in water to form body fluids

Form solutions capable of conducting electricity
 Electrolyte importance



chemical reactivity
osmotic effects (influence water movement)
electrical effects on nerve and muscle tissue
 Imbalances cause muscle cramps, brittle
bones, coma and death
2-13
Free Radicals
2-14
 Particle with an odd number of electrons
 Produced by
 normal metabolic reactions, radiation, chemicals
 Causes tissue damage
 reactions that destroy molecules
 causes cancer, death of heart tissue and aging
 Antioxidants
 neutralize free radicals
 in diet (vitamin E, carotenoids, vitamin C)
Molecules and 2-15
Chemical Bonds
 Molecules
 two or more atoms covalently bonded
 Compounds

two or more atoms of different elements covalently
bonded
 Molecular formula
 elements and how many atoms of each
 Structural formula
 location of each atom
 structural isomers revealed
Structural Formula of Isomers
2-16
 Molecular formulae are identical, but structural
formulas differ for grain alcohol and ether
Molecular
2-17 Weight
 MW of compound = sum of atomic weights
of atoms
 Calculate: MW of glucose (C6H12O6)
6 C atoms x 12 amu each = 72 amu
12 H atoms x 1 amu each = 12 amu
6 O atoms x 16 amu each = 96 amu
Molecular weight (MW) = 180 amu
Chemical
2-18 Bonds
 Ionic bonds
 Covalent bonds
 Hydrogen bonds
 Van der Waals force
Chemical Bonds Song
2-19
 http://www.youtube.com/watch?v=BCYrNU-
7SfA&feature=related
Ionic Bonds
2-20
 Attraction of oppositely charged ions
 No sharing of electrons
 Weak bond (easily dissociates in water)
Covalent
2-21 Bonds
 Formed by sharing of valence electrons
 Types of covalent bonds
 single = sharing of single pair electrons
 double = sharing of 2 pairs
 nonpolar
shared electrons (equal time around each nucleus)
 strongest of all bonds


polar

negative charge where electrons spend most time
Single Covalent Bond
2-22
 One pair of electrons are shared
Double covalent bonds:
Two pairs of electrons are shared each C=O bond
2-23
Nonpolar /Polar Covalent Bonds
2-24
electrons shared
equally
electrons
shared
unequally
Hydrogen Bonds
2-25
 Weakest bond = no sharing of electrons
 Attraction between polar molecules
 positive hydrogen atoms to negative oxygen atoms
in a 2nd molecule
 Physiological importance
 properties of water created by shapes of large
complex molecules
 determined by folding due to hydrogen bonds
Hydrogen Bonding in Water
2-26
Water animation
2-27
 http://www.youtube.com/watch?v=KiZJOTt3Dl0&f
eature=related
Van der Waals Forces
2-28
 Weak attractions between neutral atoms
 Fluctuations in electron density create
polarity
 Only 1% as strong as a covalent bond


folding of large molecules
significant when 2 large surfaces meet
Mixtures and Water
2-29
 Substances physically but not chemically combined
 Mixtures in our body contain water
 Water 50-75% of body weight
 Depends on age, sex, percentage body fat, etc
Solvency= ability to dissolve other chemicals
2-30
 Hydrophilic (charged substances) dissolve easily in
water
 Hydrophobic (neutral substances) do not easily
dissolve in water
 Water= universal solvent
 Metabolic reactions and transport of substances
Water as a Solvent
2-31
Polar water molecules overpower the ionic bond in Na+Cl-forming hydration spheres around each ion
-water molecules: negative pole faces Na+, positive pole
faces Cl-
Adhesion and Cohesion
2-32
 Adhesion- tendency of one substance to cling to
another
 Cohesion-tendency of like molecules to cling to each
other


water is very cohesive due to its hydrogen bonds
surface film on water formed by surface tension
Chemical Reactivity of Water
2-33
 Participation in chemical reactions
 Water ionizes into H+ OH Water ionizes other chemicals (acids and salts)
 Water involved in hydrolysis and dehydration synthesis
reactions
Thermal Stability of Water
2-34
 Water stabilizes internal temperature

Has high heat capacity

Hydrogen bonds inhibit temperature increases by inhibiting
molecular motion


Water absorbs heat without changing temperatures
Effective coolant

1 ml of perspiration removes 500 calories

Calorie: amount of heat required to raise temperature of 1 g of water
by 1 degree C
Solutions
2-35
 Mixture of a solute
into a solvent
 Small solute particles

Pass through cell membranes
 Solution transparent
 Remains mixed
Colloids
2-36
 Mixture of protein and water

Change from liquid to gel state within
and between cells
 Particles too large to pass
through cell membranes
 Cloudy
 Remains mixed
Suspensions and Emulsions
2-37
 Suspension

Particles suspended in a solvent

Particles exceed 100nm

Too large to pass through cell
membrane
Cloudy or opaque appearance
 Separates on standing

 Emulsion
-suspension of one liquid in
another
-fat in breast milk
Measures of Concentration
2-38
 Weight per Volume

weight of solute in given volume of solution

IV saline: 8.5 grams NaCl/liter of solution
 Percentages

Weight/volume of solute in solution

IV D5W (5% w/v dextrose in distilled water)
5
grams of dextrose and fill to 100 ml
water
 Molarity
 moles of solute/liter in solution
 physiologic effects based on number of
molecules in solution not on weight
Molarity
2-39
 Molecular weight in grams = 1 mole of
molecules
 1 mole = Avogadro’s number of molecules
 Molarity is the number of moles of solute/
liter of solution


MW of glucose is 180
one-molar (1.0M) glucose solution contains
180g/L
Percentage vs. Molar Concentrations
2-40
 Percentage
 # of molecules
unequal
 weight of solute
equal
 Molar
 # of molecules equal
 weight of solute
unequal
Electrolyte Concentrations
2-41
 Effect the body chemically, physically and
electrically

depends on charge and concentration
 Measured in equivalents

1 Eq will electrically neutralize 1 mole of H+ or
OH- ions
multiply molar concentration x valence of the ion
 1 M Na+ = 1 Eq/L
 1 M Ca2+ = 2 Eq/L

Acids, Bases and pH
2
4
2
 An acid is proton donor (releases H+
ions)
 A base is proton acceptor (accepts H+
ions)
 pH = the concentration of H+ ions in
solution
a pH of less than 7 is acidic solution
 a pH of greater than 7 is basic solution
 a pH of 7.0 is neutral pH

pH= -log [H+]
Acids
 Proton Donor
 HX H+ + X-
Bases
 Proton Acceptor
 YOH  Y+ + OH-
Strong acid
 Strong acid– ionizes completely in an aqueous




solution
H2O + HCl  H3O+ ClAlso sulphuric acid and nitric acid
Have pH around 0 to 1
The lower the pH the higher the conc of hydrogen
ions in the solution
Weak acid
 Does not ionize completely when it is dissolved in
water
 Ex. Ethanoic acid
 CH3COOH + H2O > CH3cOO- + H3O
 Most organic acids are weak
 Strong Base
 A base which hydrolyses completely, raising the pH
of the solution towards 14
 Weak Base
 A base that doesn’t convert fully into hydroxide ions
in solution
 Ex. ammonia
pH Scale
2-48
Buffers
 Maintains a constant pH upon the addition of small




amounts of either acid or base
2 parts to a buffer-weak acid and a weak base
Acid- can donate H+ ion if [H+] decreases
Base- can accept H+ ion if [H+] increases
Examples in body are bicarbonate buffer and
phosphate buffers
Salts
 Mixing an acid and a base results in water and salt
 A compound that yields ions other than hydrogen
ions is called a salt
Electrolytes
 Acids, bases, and salts are called electrolytes
 Solutions of electrolytes conduct electricity because
of the presence of ions
 Would a solution of hydrochloric acid be an
electrolyte?
 HCl  H+ + Cl-
Work and Energy
2-52
 Energy- capacity to do work
 Kinetic energy- energy of motion
 Heat is kinetic energy of molecular motion
 Potential energy- energy due to object’s position
(ions on one side only of cell membrane)

Chemical energy-potential energy stored in the molecular
bonds
Chemical Reaction
2-53
 Process that forms or breaks an ionic or
covalent bond
 Symbolized by chemical equation
reactants  products
Classes of reactions
 Synthesis reactions
 Decomposition reactions
 Exchange reactions
 Reversible reactions
Synthesis Reactions
2-54
 Two or more small molecules
combine to form a larger one
 A + B  AB
Decomposition Reactions
2-55
 Large molecules broken
down into smaller ones
 AB  A + B
Exchange Reactions
 Two molecules collide and exchange atoms or
2-56
group of atoms
 AB+CD  ABCD
Stomach acid
(HCl) and sodium
bicarbonate
(NaHCO3) from the
pancreas combine
to form NaCl and
H2CO3.

AC + BD
Exchange Reactions
2-57
Single exchange
AB+C  AC+B
Double exchange
AB+CD  AD + CB
Reversible Reactions
2-58
 Go in either direction (symbolized with
double-headed arrow)
A + B AB
CO2 + H2O <->
H2CO3 <->
carbonic acid
HCO3- + H+
bicarbonate
 Law of mass action determines direction
 side of equation with greater quantity of
reactants dominates
Reaction Rates
2-59
 Basis for reactions is molecular motion and
collisions

reactions occur when molecules collide with
enough force and the correct orientation
 Reaction Rates affected by:
 concentration


temperature


more concentrated, more collisions, faster rate
higher temperature, greater collision force, faster rate
Catalysts (enzymes)
speed up reactions without permanent change to itself
 holds reactant molecules in correct orientation

Metabolism
2-60
 All the chemical reactions of the body
 Catabolism
 energy releasing (exergonic) decomposition
reactions

breaks covalent bonds, produces smaller molecules,
releases useful energy
 Anabolism
 energy storing (endergonic) synthesis reactions

requires energy input
Oxidation-Reduction Reactions
2-61
 Oxidation
 molecule gives up electrons and releases energy
 accepting molecule is the oxidizing agent

oxygen is often the electron acceptor
 Reduction
 molecule gains electrons and energy
 donating molecule is the reducing agent
 Oxidation-reduction (redox) reactions
 Electrons are often transferred as hydrogen atoms
2-62
Organic Chemistry
2-63
 Study of compounds containing carbon
 4 categories of carbon compounds
 carbohydrates
 lipids
 proteins
 nucleotides and nucleic acids
Organic Molecules and Carbon
2-64
 Only 4 valence electrons
 bonds readily to gain more valence electrons
 Forms long chains, branched molecules and
rings

serve as the backbone for organic molecules
 Carries a variety of functional groups
Functional Groups
2-65
 Atoms attached to carbon
backbone
 Determines chemical
properties
Monomers and Polymers
2-66
 Macromolecules = very large molecules
 Polymers = macromolecules formed from
monomers bonded together
 Monomers = an identical or similar subunit
Polymerization
2-67
 Bonding of monomers together to form a
polymer
 Formed by dehydration synthesis


starch molecules are a polymer of 3000 glucose
monomers
protein molecules are a polymer of amino acids
Dehydration Synthesis
2-68
 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
Hydrolysis
2-69
 Splitting a polymer (lysis) by the addition of a
water molecule (hydro)

a covalent bond is broken
 All digestion reactions consists of hydrolysis
reactions
Organic Molecules: Carbohydrates
2-70
 Hydrophilic organic molecule
 General formula
 (CH2O)n
n = number of carbon atoms
 for glucose, n = 6, so formula is C6H12O6
 2:1 ratio of hydrogen to oxygen
 Names of carbohydrates
 word root sacchar- or the suffix -ose often used

monosaccharide or glucose
Monosaccharides
2-71
 Simple sugars
 General formula is C6H12O6

structural isomers
• Major monosaccharides
– glucose, galactose and
fructose
– produced by digestion of
complex carbohydrates
• glucose is blood sugar
Disaccharides
2-72
 Sugar molecule
composed of 2
monosaccharides
 Major disaccharides

sucrose = table sugar


Lactose = sugar in milk


glucose + fructose
glucose + galactose
Maltose = grain
products

glucose + glucose
Polysaccharides
2-73
 Chains of glucose subunits
 Starch: energy storage in plants
 digestible by humans for energy
 Cellulose: structural molecule of plant cell walls
 fiber in our diet
 Glycogen: energy storage in animals
 liver synthesizes after a meal and breaks down between
meals
Carbohydrate Functions
2-74
 All digested carbohydrates converted to
glucose and oxidized to make ATP
 Conjugated carbohydrate = bound to lipid or
protein

glycolipids


external surface of cell membrane
glycoproteins
external surface of cell membrane
 mucus of respiratory and digestive tracts


proteoglycans
gels that hold cells and tissues together
 joint lubrication
 rubbery texture of cartilage

2-75
Organic Molecules: Lipids
2-76
 Hydrophobic organic molecule
 composed of carbon, hydrogen and oxygen
 Less oxidized and thus has more calories/gram
 Five primary types in humans
 fatty acids
 triglycerides
 phospholipids
 eicosanoids
 steroids
Fatty Acids
2-77
 Chain of 4 to 24 carbon atoms
 carboxyl (acid) group on one end, methyl group on the
other and hydrogen bonded along the sides
 Classified
 saturated - carbon atoms saturated with hydrogen
 unsaturated - contains C=C bonds without hydrogen
Triglycerides (Neutral Fats)
2-78
 3 fatty acids bonded to glycerol molecule
(dehydration synthesis)
 At room temperature

when liquid called oils


often polyunsaturated fats from plants
when solid called fat

saturated fats from animals
 Function - energy storage, insulation and shock
absorption
Phospholipids
2-79
 Triglyceride with one fatty acid replaced by a
phosphate group
 Amphiphilic character
fatty acid “tails” are hydrophobic
 Phosphate “head” is hydrophilic

Eicosanoids
2-80
 Derived from arachidonic acid (a fatty acid)
 Hormone-like chemical signals between cells
 Includes prostaglandins – produced in all
tissues

role in inflammation, blood clotting, hormone
action, labor contractions, blood vessel diameter
Steroids and Cholesterol
2-81
 Steroid = lipid with carbon atoms in four
rings

all steroids are derived from cholesterol

cortisol, progesterone, estrogens, testosterone and bile
acids
 Cholesterol
 important component of cell membranes
 produced only in animal liver cells

naturally produced by our body
2-82
Organic Molecules: Proteins
2-83
• Protein = polymer of amino acids
• Combination determines structure and
function
• Amino acid = carbon with 3 attachments
– Amino (NH2), carboxy (COOH) and radical
group (R group)
• 20 unique amino acids
– -R groups differ
– properties determined by -R group
Naming of Peptides
2-84
 Peptide = polymer of 2 or more amino acids
 Named for the number of amino acids
 dipeptides have 2, tripeptides have 3
 oligopeptides have fewer than 10 to 15
 polypeptides have more than 15
 proteins have more than 100
Dipeptide Synthesis
2-85
•Dehydration synthesis creates a peptide bond that joins amino
acids
Protein Structure and Shape
2-86
 Primary structure
 amino acid sequence
 Secondary structure
 coiled or folded shape
 hydrogen bonds between negative C=O and positive
N-H groups
 Tertiary structure
 further folding and bending into globular and
fibrous shapes
 Quaternary structure
 associations of two or more separate polypeptide
chains
2-87
Conjugated Proteins
2-88
 Contain a non-amino acid moiety
 Hemoglobin contains complex iron
containing ring called a heme moiety
Protein Conformation and
Denaturation
2-89
 Conformation – unique 3-D shape crucial to
function

ability to reversibly change their conformation

opening and closing of cell membrane pores
 Denaturation
 conformational change that destroys function

extreme heat or pH
Protein Functions
2-90
 Structure
 collagen, keratin
 Communication
 some hormones, cell receptors
 Membrane Transport
 channels, carriers
 Catalysis
 enzymes
Protein Functions 2
2-91
 Recognition and protection
 antigens, antibodies and clotting proteins
 Movement
 molecular motor = molecules that can change shape
repeatedly
 Cell adhesion
 proteins bind cells together
Enzymes
2-92
 Proteins as biological catalysts
 promote rapid reaction rates
 Substrate - substance an enzyme acts upon
 Naming Convention
 named for substrate with -ase as the suffix

amylase enzyme digests starch (amylose)
 Lowers activation energy = energy needed to
get reaction started

enzymes facilitate molecular interaction
Enzymes and Activation Energy
2-93
Steps of an Enzyme Reaction
2-94
 Substrate approaches enzyme molecule
 Substrate binds to active site forming enzyme-
substrate complex

highly specific
 Enzyme breaks bonds in substrate
 Reaction products released
 Enzyme repeats process over and over
Enzymatic Reaction Steps
2-95
Enzymatic Action
2-96
 Reusability of enzymes
 enzymes are unchanged by the reactions
 Astonishing speed
 millions of molecules per minute
 Temperature and pH
 change shape of enzyme and alter its ability to
bind
 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
Cofactors and Coenzymes
2-97
 Cofactors
 nonprotein partners (iron, copper, zinc, magnesium or
calcium ions)
 bind to enzyme and change its shape
 essential to function
 Coenzymes
 organic cofactors derived from water-soluble vitamins
(niacin, riboflavin)
 transfer electrons between enzymes
Coenzyme NAD+
2-98
 NAD+ transports electrons from one metabolic
pathway to another
Metabolic Pathways
2-99
 Chain of reactions, each catalyzed by an 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
Organic Molecules: Nucleotides
2100
 3 components
 nitrogenous base
 sugar (monosaccharide)
 one or more phosphate groups
 Physiological important nucleotides
 ATP = energy carrying molecule
 cAMP = activates metabolic pathways
 DNA = carries genetic code
 RNA = assists with protein synthesis
ATP (Adenosine Triphosphate)
2101
ATP contains adenine, ribose and 3 phosphate groups
ATP
2102
 Holds energy in covalent bonds
 2nd and 3rd phosphate groups have high energy bonds ~
 ATPases hydrolyze the 3rd high energy
phosphate bond

separates into ADP + Pi + energy
 Phosphorylation
 addition of free phosphate group to another molecule
Overview of ATP Production
2103
 ATP consumed within 60 seconds
 Continually replenished
Other Nucleotides
2104
 Cyclic adenosine monophosphate (cAMP)
 formed by removal of both high energy Pi’s from ATP
 formation triggered by hormone binding to cell surface
 cAMP becomes “second messenger” within cell
 activates effects inside cell
Nucleic Acids
2105
 DNA (deoxyribonucleic acid)
 100 million to 1 billion nucleotides long
 contains genetic code

cell division, sexual reproduction, protein synthesis
 RNA (ribonucleic acid) – 3 types
 transfer RNA, messenger RNA, ribosomal RNA
 70 to 10,000 nucleotides long
 involved in protein synthesis coded for by DNA