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Chapter 2 Chemical Basis of LifeAnatomy & Physiology I (Dr. Rothschild)
2
2.1: Introduction
Why study chemistry in an Anatomy and Physiology class?
- Body functions depend on cellular functions
- Cellular functions result from chemical changes
- Biochemistry helps to explain physiological processes
3
Matter
• Atoms smallest unit of matter
• Elements- one type of atom
PropertiesMass, Volume
4
Atomic Structure
Atoms - composed of subatomic particles:• Proton – carries a single positive charge• Neutron – carries no electrical charge• Electron – carries a single negative charge
Nucleus• Central part of atom• Composed of protons and neutrons• Electrons move around the nucleus
Electron(e–)
Lithium (Li)
Proton(p+)
Neutron(n0)
Nucleus
0
0++
0+
0
-
-
-
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Chemical Behavior of an Atom1. Depends on electrons in
outermost shell
2. Valence electrons (valence shell)
3. Atoms with the same number of electrons in their valence shell exhibit similar chemical behavior
• Consider: F and Cl– Both combine with Na 1:1– NaF and NaCl
4. Completed valence shell atoms are unreactive (inert)
5. Orbitals describe the 3-D space occupied (90% of the time) by an electron as it orbits a nucleus.
6. Reactivity of an atom arises from the presence of unpaired electrons in one or more orbitals of an atom’s valence shell
7. Unpaired electrons of atoms interact to complete their valence shells
Elemental Isotopes• Atoms have same number
of protons
• Isotopes have varying numbers of neutrons in their nucleus
• Isotopes behave similarly in chemical reactions despite different masses.
• Carbon (6C) Isotopes– 12C (stable)– 13C (stable)– 14C (radioactive)
• Radioactive isotopes decay spontaneously - giving off particles and energy
• Atomic mass number is actually an average of the atomic masses of all the element’s isotopes
7
Bonding of Atoms
Bonds form when atoms combine with other atoms
Electrons occupy regions of space called orbitals (subshells)Different energy levels (shells) circle the nucleus
Outermost (valence) electrons responsible for bonding•Atoms may lose/gain electrons •Atoms may share electrons
8
Bonding of Atoms: Ions
Ion• An atom that gains or loses electrons to become stable• An electrically charged atom
Cation• A positively charged ion• Formed when an atom loses electrons
Anion• A negatively charged ion• Formed when an atom gainselectrons
11p+
12n0
Sodium atom (Na) Chlorine atom (Cl)
(a) Separate atoms If a sodium atom loses an electron to a chlorine atom, the sodium atom becomes a sodium ion (Na+), and the chlorine atom becomes a chloride ion (Cl–).
17p+
18n0
Ionic CompoundsHighly unequally electronegative atom strips an electron from its partner’s valence shell
NaCl is a compound, not a moleculeFormula is a ratio
10
Covalent Bonds
Formed when atoms share electrons
All organic (carbon) substances are formed by covalent bonds, are molecules
Hydrogen atom +
H
Hydrogen molecule
H2
Hydrogen atom
H
+ + ++
- -
-
-
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11
Structural formulas show how atoms bond and are arranged in various molecules
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
HH
H OO O
CO2H2OO2H2
CO OH
Polar MoleculesMolecule with a slightly negative end and a slightly positive endResults when electrons are not shared equally in covalent bonds
• Water is an important polar molecule
Slightly negative end
Slightly positive ends(a)
Elements and CompoundsElement: Cannot be broken down• Bulk elements – required by the Bulk elements – required by the
body in large amountsbody in large amounts• Trace elements - required by the Trace elements - required by the
body in small amountsbody in small amounts• Ultratrace elements – required by Ultratrace elements – required by
the body in very minute amountsthe body in very minute amounts
Compound• Two or more elements in a fixed Two or more elements in a fixed
ratioratio• Chemical bonds maintain ratioChemical bonds maintain ratio• Example: Sodium Chloride Example: Sodium Chloride
(NaCl)(NaCl)
Compound properties different than elements that form it
13
Molecules and Compounds
Molecule – particle formed when two or more atoms chemically combine
Compound – particle formed when two or more atoms of different elements chemically combine
Molecular formulas – depict the elements present and the number of each atom present in the molecule
H2 C6H12O6 H2O
H
H
H
H
H
H
HH
H
H
O
O
O
O
O
Hydrogen bonds
14
Hydrogen BondsA weak attraction between the positive end of one polar molecule and the negative end of another polar molecule
•Formed between water molecules•Important for protein and nucleic acid structure
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15
Chemical Reactions
Chemical reactions occur when chemical bonds form or break among atoms, ions, or molecules
Reactants are the starting materials of the reaction - the atoms, ions, or molecules
Products are substances formed at the end of the chemical reaction
NaCl ’ Na+ + Cl-
Reactant Products
Chemical Reactions• Do not gain/lose atoms in a reaction
6 CO2 + 6 H2O C6H12O6 + 6 O2
• Most reactions are reversible: products can change back to the reactants
3 H2 + N2 2 NH3
• Chemical equilibrium: forward and reverse reactions occur at the same rate
17
Types of Chemical Reactions
Synthesis Reaction – more complex chemical structure is formed A + B ’ AB
Decomposition Reaction – chemical bonds are broken to forma simpler chemical structure
AB ’ A + B
Exchange Reaction – chemical bonds are broken and new bonds are formed AB + C ’ A + CB
AB + CD ’ AD + CB
18
Acids, Bases, and SaltsCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Ions insolution
Na+
Cl–
Na+
Cl–
Salt crystal
19
Acid and Base Concentration
pH scale - indicates the concentration of hydrogen ions insolution
Neutral – pH 7;indicates equal concentrations of H+
and OH-
Acidic – pH less than7; indicates a greater concentration of H+
Basic or alkaline – pH greater than 7;indicates a greater concentration of OH-
OH– concentration increasesH+ concentration increases
AcidicH+
RelativeAmountsof H+ (red)and OH–
(blue)
BasicOH–
2.0gastricjuice
6.0corn
7.0Distilledwater
8.0Eggwhite
10.5milk ofmagnesia
11.5Householdammonia
pH 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14Basic (alkaline)NeutralAcidic
3.0applejuice
4.2tomatojuice
5.3cabbage
6.6cow’smilk
7.4Humanblood
8.4Sodiumbiocarbonate
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Each pH unit represents a 10 fold increase in hydrogen ion concentration
pH = -log [H+]Power of hydrogen
20
Acids, Bases, and Salts
Electrolytes – substances that release ions in water
Salts –formed by the reaction between an acid & base
NaCl Na+ + Cl-
HCl + NaOH H2O + NaCl
Changes in pH and Buffers
21
Blood pH• Normal blood pH is 7.35 – 7.45• Alkalosis occurs when blood pH rises to 7.5 – 7.8• Acidosis occurs when blood pH drops to 7.0 – 7.3• Homeostatic mechanisms help regulate pH• Buffers are chemicals which act to resist pH changes
Buffers
• Minimize pH changes• Accepts or donates hydrogen ions• Most are a weak acid and its conjugate
base
• H2CO3 HCO3- + H+
WaterHydrogen bonds produce a phenomenon known as cohesion
Water molecules adhere to substances
Water has a greater surface tension than most other liquids
Water and Energy Transfer• Heat is the measure of the kinetic energy due
to molecular motion in a body of matter• Temperature measures the the heat due to the
average kinetic energy• Kinetic energy is transferred from a body with
a higher kinetic energy to a body with a lower kinetic energy
• Temperature is measured using Celsius scale
• Calorie is a measure of heat• Kilocalorie (kcal)
– Unit used in for cellular reactions
Water: The Solvent of Life• Solutions• Solvents• Solutes• Aqueous Solutions• Water forms hydration
shells around dissolved ions of an ionic compound
• Water also surrounds organic compounds if they have ionic and polar regions
Dissociation of Water
H2O H+ + OH-
27
2.3: Chemical Constituents of Cells
Organic v. Inorganic MoleculesOrganic molecules
• Contain C and H• Usually larger than inorganic molecules• Dissolve in water and organic liquids• Carbohydrates, proteins, lipids, and nucleic acids
Inorganic molecules • Generally do not contain C• Usually smaller than organic molecules• Usually dissociate in water, forming ions • Water, oxygen, carbon dioxide, and inorganic salts
28
Inorganic SubstancesWater
• Most abundant compound in living material• Two-thirds of the weight of an adult human• Major component of all body fluids• Medium for most metabolic reactions• Important role in transporting chemicals in the body• Absorbs and transports heat
Oxygen (O2) • Used by organelles to release energy from nutrients in order to drive cell’s metabolic activities• Necessary for survival
29
Inorganic Substances
Carbon dioxide (CO2)• Waste product released during metabolic reactions• Must be removed from the body
Inorganic salts• Abundant in body fluids• Sources of necessary ions (Na+, Cl-, K+, Ca2+, etc.)• Play important roles in metabolism
Chemistry of Living Things
– C,H,O,N = 96%– All biological compounds are based on
hydrocarbon chains• C-C-C-C-C-C• Chains are very long
– 4 Main types of biological compounds• Proteins• Carbohydrates• Lipids• Nucleic Acids
II.Proteins– Composed of amino acid building
blocks• COOH group• NH2 Group
– Protein = Many amino acids hooked together
• Special covalent bond = peptide bond– Links C-N-C
• Only found in proteins• Proteins = polypeptides
Protein
Pleatedstructure
Coiledstructure
Amino acids
N
N
N
NN
HH
HH
H
C
CC
C
O
O
O
CC
C
C
CC
OC
O
NN
H H
C
OC
C
OC
H
NN
H
O
O
C
CC
C
N
N
N
N H
H
H O C
CC
O
O
CC
C
H OC
C
C
N
C
NHO
CC
H OC
C
N
N
N
N H
H
H O C
O
O
CC
C
H OC
H
R
H
R
H
R
H
R
H
R
H
R
H
R
H
R
H
R
H
H
R
H
H
R
H
R
H
R
HHRR
HHRR
CH
CH
32
Four Levels of Protein Structure
(b) Secondary structure—The polypeptide chain of a protein molecule is often either pleated or twisted to form a coil. Dotted lines represent hydrogen bonds.
R groups (see fig. 2.17)are indicated in bold.
(a) Primary structure—Eachoblong shape in thispolypeptide chain representsan amino acid molecule. Thewhole chain represents aportion of a protein molecule.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Three-dimensionalfolding
H H
(c) Tertiary structure—The pleated and coiledpolypeptide chain of aprotein molecule foldsinto a unique three-dimensional structure.
(d) Quaternary structure—Two ormore polypeptide chains may be connected to form a singleprotein molecule.
33
Animation: Protein Denaturation
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Please note that due to differing operating systems, some animations will not appear until the presentation is viewed in Presentation Mode (Slide Show view). You may see blank slides in the “Normal” or “Slide Sorter” views. All animations will appear after viewing in Presentation Mode and playing each animation. Most animations will require the latest version of the Flash Player, which is available at http://get.adobe.com/flashplayer.
C.Functions of proteins
1) Enzymes
2) Muscles
3) Cell Membranes
4) Structure of cells
5) Some Hormones
a) insulin
III.Carbohydrates = sugars and starches– Composed of monosaccharides
(single sugars)• m.s.+m.s. disaccharide + HOH
– Dehydration synthesis
– (m.s.+m.s. polysaccharide+many HOH(polysaccharide = starch)
• Examples of monosaccharides– Glucose– Fructose– Galactose
• Examples of disaccharides– Sucrose– Lactose– Maltose
36
Functions
• Provide energy to cells
• Supply materials to build cell structures
• Water-soluble• Contain C, H, and O• Ratio of H to O close to 2:1 (C6H12O6)• Monosaccharides – glucose, fructose• Disaccharides – sucrose, lactose• Polysaccharides – glycogen, cellulose
37
Carbohydrate shapes
(a) Some glucose molecules (C6H12O6) have a straight chain of carbon atoms.
C
C
C
C
C
C
H
O
H
O
O
O
HH
OH
H
H
H
H O
H
H
H
H
C
H
O
O H
H
OH
O H
H
H H
C
O
H
C
C C
OC
H
(b) More commonly, glucose molecules form a ring structure.
O
(c) This shape symbolizes the ring structure of a glucose molecule.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
38
Lipids
• Soluble in organic solvents; insoluble in water
• Fats (triglycerides)• Used primarily for energy; most common lipid in the body• Contain C, H, and O but less O than carbohydrates (C57H110O6)• Building blocks are 1 glycerol and 3 fatty acids per molecule• Saturated and unsaturated
Glycerolportion
Fatty acidportions
C
O
OH C C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
O
OH C C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
O
OH C C
H
HH
C
H
H
C
H
H
C
H
H
C
H H
H
C
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39
Lipids
• Steroids• Four connected rings of carbon• Widely distributed in the body, various functions• Component of cell membrane• Used to synthesize hormones• Cholesterol
(a) General structure of a steroid
CC
CH2C
H2C C
H
(b) Cholesterol
C
CH CH2
CH2
CH
CH3
CH2
HC
HC
H2
H2
CH2 CHCH2
CH3
CH3
CH2
CH
CH3
HO C
CH3
CH2
CHC
40
Organic SubstancesLipids
• Phospholipids
• Building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per molecule
• Hydrophilic and hydrophobic
• Major component of cell membranes
C
H
C
OH
CH
H
Glycerol portion
(a) A fat molecule
O
O
Fatty acid
Fatty acid
Fatty acid
H
C
H H
HH
C
H
H
N
O
O
Fatty acid
Fatty acid
O
POCH
O–
Phosphate portion
(b) A phospholipid molecule(the unshaded portion may vary)
H
CH
C
H
H
O
(c) Schematic representationof a phospholipid molecule
Water-insoluble (hydrophobic) “tail”
Water-soluble(hydrophilic)“head”
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
V.Nucleic Acids = DNA + RNA• Made of 3 components
– 5-C sugar– Phosphate– Nitrogen Base– Together these make 1 nucleotide– Nucleotides = Building Blocks
• Functions– Carries genetic code/blueprint– Cell fuel (ATP)– Important in cell cycles
42
Nucleic Acids
• Carry genes• Encode amino acid sequences of proteins• Building blocks are nucleotides
• DNA (deoxyribonucleic acid) – double polynucleotide• RNA (ribonucleic acid) – single polynucleotide
S
P B
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43
Nucleic Acids
S
P
S
P
S
P
S
P
S
P
S
P
B
B
B
B
B
B
S
S
S
S
S
S
P
P
P
P
P
P
B
B
B
B
B
B
(b)
S
P
S
P
S
P
S
P
S
P
S
P
B
B
B
B
B
B
(a)
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44
45
Important Points in Chapter 2:Outcomes to be Assessed
2.1: Introduction
Give examples of how the study of living materials requires and understanding of chemistry.
2.2: Structure of Matter
Describe how atomic structure determines how atoms interact.
Describe the relationships among matter, atoms, and molecules.
Explain how molecular and structural formulas symbolize the composition of compounds.
Describe three types of chemical reactions.
Explain what acids, bases, and buffers are.
Define pH.
46
Important Points in Chapter 2:Outcomes to be Assessed Continued
2.3: Chemical Constituents of Cells
List the major groups of inorganic chemicals common in cells.
Describe the general functions of the main classes of organic molecules in cells.