chapter 2chemical basis of life anatomy & physiology i (dr. rothschild)

Chapter 2 Chemical Basis of LifeAnatomy & Physiology I (Dr. Rothschild)

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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

-

-

-

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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

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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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Structural formulas show how atoms bond and are arranged in various molecules

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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

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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

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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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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

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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

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Acids, Bases, and SaltsCopyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Ions insolution

Na+

Cl–

Na+

Cl–

Salt crystal

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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

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Each pH unit represents a 10 fold increase in hydrogen ion concentration

pH = -log [H+]Power of hydrogen

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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

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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-

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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

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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

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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

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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.

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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.

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Animation: Protein Denaturation

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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

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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

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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.

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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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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

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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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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

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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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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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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.

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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.