Chapter 2• Atomic Structure

• Chemical Bonds

• Chemical Reactions

• Carbohydrates – Lipids

• Proteins– Amino Acids– Enzymes

• DNA

Matter

• The “stuff” of the universe

• Anything that has mass and takes up space

• States of matter– Solid – has definite shape and volume– Liquid – has definite volume, changeable shape– Gas – has changeable shape and volume

Energy

• The capacity to do work (put matter into motion)

• Types of energy– Kinetic – energy in action– Potential – energy of position; stored (inactive)

energy

PLAYPLAY Energy Concepts

Forms of Energy• Chemical – stored in the bonds of chemical

substances

• Electrical – results from the movement of charged particles

• Mechanical – directly involved in moving matter

• Radiant or electromagnetic – energy traveling in waves (i.e., visible light, ultraviolet light, and X-rays)

Energy Form Conversions

• Energy is easily converted from one form to another

• During conversion, some energy is “lost” as heat

Composition of Matter

• Elements – unique substances that cannot be broken down by ordinary chemical means

• Atoms – more-or-less identical building blocks for each element

• Atomic symbol – one- or two-letter chemical shorthand for each element

Properties of Elements

• Each element has unique physical and chemical properties– Physical properties – those detected with our

senses– Chemical properties – pertain to the way atoms

interact with one another

Major Elements of the Human Body

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

Lesser and Trace Elements of the Human Body

• Lesser elements make up 3.9% of the body and include:– Calcium (Ca), phosphorus (P), potassium (K),

sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe)

Lesser and Trace Elements of the Human Body

• Trace elements make up less than 0.01% of the body– They are required in minute amounts, and are

found as part of enzymes

Atomic Structure

• The nucleus consists of neutrons and protons– Neutrons – have no charge and a mass of one atomic

mass unit (amu)– Protons – have a positive charge and a mass of

1 amu

• Electrons are found orbiting the nucleus– Electrons – have a negative charge and 1/2000 the

mass of a proton (0 amu)

Models of the Atom

• Planetary Model – electrons move around the nucleus in fixed, circular orbits

• Orbital Model – regions around the nucleus in which electrons are most likely to be found

Identification of Elements

• Atomic number – equal to the number of protons

• Mass number – equal to the mass of the protons and neutrons

• Atomic weight – average of the mass numbers of all isotopes

Identification of Elements

• Isotope – atoms with same number of protons but a different number of neutrons

• Radioisotopes – atoms that undergo spontaneous decay called radioactivity

Identification of Elements: Atomic Structure

Figure 2.2

Identification of Elements: Isotopes of Hydrogen

Figure 2.3

Molecules and Compounds

• Molecule – two or more atoms held together by chemical bonds

• Compound – two or more different kinds of atoms chemically bonded together

Mixtures and Solutions

• Mixtures – two or more components physically intermixed (not chemically bonded)

• Solutions – homogeneous mixtures of components– Solvent – substance present in greatest amount– Solute – substance(s) present in smaller

amounts

Concentration of Solutions

• Percent, or parts per 100 parts

• Molarity, or moles per liter (M)

• A mole of an element or compound is equal to its atomic or molecular weight (sum of atomic weights) in grams

Colloids and Suspensions

• Colloids (emulsions) – heterogeneous mixtures whose solutes do not settle out

• Suspensions – heterogeneous mixtures with visible solutes that tend to settle out

Mixtures Compared with Compounds

• No chemical bonding takes place in mixtures

• Most mixtures can be separated by physical means

• Mixtures can be heterogeneous or homogeneous

• Compounds cannot be separated by physical means

• All compounds are homogeneous

Chemical Bonds

• Electron shells, or energy levels, surround the nucleus of an atom

• Bonds are formed using the electrons in the outermost energy level

• Valence shell – outermost energy level containing chemically active electrons

• Octet rule – except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their valence shell

Chemically Inert Elements

• Inert elements have their outermost energy level fully occupied by electrons

Figure 2.4a

Chemically Reactive Elements

• Reactive elements do not have their outermost energy level fully occupied by electrons

Figure 2.4b

Types of Chemical Bonds

• Ionic

• Covalent

• Hydrogen

Ionic Bonds

• Ions are charged atoms resulting from the gain or loss of electrons

• Anions have gained one or more electrons

• Cations have lost one or more electrons

Formation of an Ionic Bond

• Ionic bonds form between atoms by the transfer of one or more electrons

• Ionic compounds form crystals instead of individual molecules

• Example: NaCl (sodium chloride)

Formation of an Ionic Bond

Figure 2.5a

Formation of an Ionic Bond

Figure 2.5b

Covalent Bonds

• Covalent bonds are formed by the sharing of two or more electrons

• Electron sharing produces molecules

Single Covalent Bonds

Figure 2.7a

Double Covalent Bonds

Figure 2.7b

Triple Covalent Bonds

Figure 2.7c

Polar and Nonpolar Molecules

• Electrons shared equally between atoms produce nonpolar molecules

• Unequal sharing of electrons produces polar molecules

• Atoms with six or seven valence shell electrons are electronegative

• Atoms with one or two valence shell electrons are electropositive

Comparison of Ionic, Polar Covalent, and Nonpolar Covalent

Bonds

Figure 2.9

Hydrogen Bonds

• Too weak to bind atoms together

• Common in dipoles such as water

• Responsible for surface tension in water

• Important as intramolecular bonds, giving the molecule a three-dimensional shape

PLAYPLAY Hydrogen Bonds

Hydrogen Bonds

Figure 2.10a

Chemical Reactions

• Occur when chemical bonds are formed, rearranged, or broken

• Written in symbolic form using chemical equations

• Chemical equations contain:– Number and type of reacting substances, and

products produced– Relative amounts of reactants and products

Examples of Chemical Reactions

Patterns of Chemical Reactions

• Combination reactions: Synthesis reactions which always involve bond formation

A + B AB

Patterns of Chemical Reactions

• Decomposition reactions: Molecules are broken down into smaller molecules

AB A + B

Patterns of Chemical Reactions

• Exchange reactions: Bonds are both made and broken

AB + C AC + B

Oxidation-Reduction (Redox) Reactions

• Reactants losing electrons are electron donors and are oxidized

• Reactants taking up electrons are electron acceptors and become reduced

Energy Flow in Chemical Reactions

• Exergonic reactions – reactions that release energy

• Endergonic reactions – reactions whose products contain more potential energy than did its reactants

Reversibility in Chemical Reactions

• All chemical reactions are theoretically reversible

A + B AB

AB A + B

• If neither a forward nor reverse reaction is dominant, chemical equilibrium is reached

Factors Influencing Rate of Chemical Reactions

• Temperature – chemical reactions proceed quicker at higher temperatures

• Particle size – the smaller the particle the faster the chemical reaction

• Concentration – higher reacting particle concentrations produce faster reactions

Factors Influencing Rate of Chemical Reactions

• Catalysts – increase the rate of a reaction without being chemically changed

• Enzymes – biological catalysts

Biochemistry

• Organic compounds– Contain carbon, are covalently bonded, and are

often large

• Inorganic compounds– Do not contain carbon– Water, salts, and many acids and bases

Properties of Water

• High heat capacity – absorbs and releases large amounts of heat before changing temperature

• High heat of vaporization – changing from a liquid to a gas requires large amounts of heat

• Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport medium

PLAYPLAY InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids

Properties of Water

• Reactivity – is an important part of hydrolysis and dehydration synthesis reactions

• Cushioning – resilient cushion around certain body organs

Salts

• Inorganic compounds

• Contain cations other than H+ and anions other than OH–

• Are electrolytes; they conduct electrical currents

Acids and Bases

• Acids release H+ and are therefore proton donors

HCl H+ + Cl –

• Bases release OH– and are proton acceptorsNaOH Na+ + OH–

Acid-Base Concentration (pH)

• Acidic solutions have higher H+ concentration and therefore a lower pH

• Alkaline solutions have lower H+

concentration and therefore a higher pH

• Neutral solutions have equal H+ and OH– concentrations

Acid-Base Concentration (pH)

• Acidic: pH 0–6.99

• Basic: pH 7.01–14

• Neutral: pH 7.00

Figure 2.13

Buffers

• Systems that resist abrupt and large swings in the pH of body fluids

• Carbonic acid-bicarbonate system– Carbonic acid dissociates, reversibly releasing

bicarbonate ions and protons– The chemical equilibrium between carbonic acid

and bicarbonate resists pH changes in the blood

PLAYPLAY InterActive Physiology®: Fluid, Electrolyte, and Acid/Base Balance: Acid/Base Homeostasis

Organic Compounds

• Molecules unique to living systems contain carbon and hence are organic compounds

• They include:– Carbohydrates– Lipids– Proteins– Nucleic Acids

Carbohydrates

• Contain carbon, hydrogen, and oxygen

• Their major function is to supply a source of cellular food

• Examples:– Monosaccharides or simple sugars

Figure 2.14a

Carbohydrates

• Disaccharides or double sugars

Figure 2.14b

PLAYPLAY Disaccharides

Carbohydrates

• Polysaccharides or polymers of simple sugars

Figure 2.14c

PLAYPLAY Polysaccharides

Lipids• Contain C, H, and O, but the proportion of

oxygen in lipids is less than in carbohydrates

• Examples:– Neutral fats or triglycerides– Phospholipids– Steroids– Eicosanoids

PLAYPLAY Fats

Neutral Fats (Triglycerides)

• Composed of three fatty acids bonded to a glycerol molecule

Figure 2.15a

Representative Lipids Found in the Body

• Neutral fats – found in subcutaneous tissue and around organs

• Phospholipids – chief component of cell membranes

• Steroids – cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones

Other Lipids

• Phospholipids – modified triglycerides with two fatty acid groups and a phosphorus group

Figure 2.15b

Representative Lipids Found in the Body

• Fat-soluble vitamins – vitamins A, E, and K• Eicosanoids – prostaglandins, leukotrienes,

and thromboxanes• Lipoproteins – transport fatty acids and

cholesterol in the bloodstream

Other Lipids• Steroids – flat molecules with four

interlocking hydrocarbon rings

• Eicosanoids – 20-carbon fatty acids found in cell membranes

Figure 2.15c

Amino Acids

• Building blocks of protein, containing an amino group and a carboxyl group

• Amino group NH2

• Carboxyl groups COOH

Amino Acids

Figure 2.16a–c

Amino Acids

Figure 2.16d, e

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Amino acid Amino acid

Dehydrationsynthesis

HydrolysisDipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Amino acid Amino acid

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O

OH OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Amino acid Amino acid

Dehydrationsynthesis

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

OH OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Amino acid Amino acid

Dehydrationsynthesis

Dipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Dipeptide

Peptide bond

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

HydrolysisDipeptide

Peptide bond

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Amino acid Amino acidHydrolysis

Dipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Figure 2.17

Amino acid Amino acid

Dehydrationsynthesis

HydrolysisDipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

Structural Levels of Proteins

• Primary – amino acid sequence

• Secondary – alpha helices or beta pleated sheets

• Tertiary – superimposed folding of secondary structures

• Quaternary – polypeptide chains linked together in a specific manner

PLAYPLAY

PLAYPLAY

Structural Levels of Proteins

Figure 2.18a–c

Structural Levels of Proteins

Figure 2.18b,d,e

Fibrous and Globular Proteins

• Fibrous proteins (a.k.a. structural proteins)– Extended and strand-like proteins – usually

only secondary structure– Rope-like side by side fibers make then great

“building materials” – Insoluble in water– Examples: keratin, elastin, collagen, and certain

contractile fibers of muscle

Fibrous and Globular Proteins

• Globular proteins (a.k.a. functional proteins)– Compact, spherical proteins with tertiary and

quaternary structures– Examples: antibodies, hormones, and enzymes

Protein Denuaturation

• Reversible unfolding of proteins due to drops in pH and/or increased temperature

Figure 2.19a

Protein Denuaturation

• Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes

Figure 2.19b

Molecular Chaperones (Chaperonins)

• Help other proteins to achieve their functional three-dimensional shape

• Maintain folding integrity

• Assist in translocation of proteins and some metal ions (Cu, Fe, Zn) across membranes

• Promote the breakdown of damaged or denatured proteins

Characteristics of Enzymes

• Most are globular proteins that act as biological catalysts – they don’t make reactions happen, they only increase the speed.

• Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion Cu, Fe, B-Vits, etc.)

• Enzymes are chemically specific

Characteristics of Enzymes

• Frequently named for the type of reaction they catalyze (e.g. hydrolases – add water hydolysis)

• Enzyme names usually end in -ase

• Lower activation energy

Characteristics of Enzymes

Figure 2.20

Mechanism of Enzyme Action

• Enzyme binds with substrate

• Product is formed at a lower activation energy

• Product is released

PLAYPLAY How Enzymes Work

Figure 2.21

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

Figure 2.21

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Substrates (S)

H2O

+

Figure 2.21

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Substrates (S)

H2O

+

Figure 2.21

Active siteAmino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

Nucleic Acids

• Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus

• Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group

Nucleic Acids

• Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)

• Two major classes – DNA and RNA

Deoxyribonucleic Acid (DNA)

• Double-stranded helical molecule found in the nucleus of the cell

• Replicates itself before the cell divides, ensuring genetic continuity

• Provides instructions for protein synthesis

Complimentary Bases/Structure of DNA

Figure 2.22a

Structure of DNA

Figure 2.22b

Ribonucleic Acid (RNA)

• Single-stranded molecule found in both the nucleus and the cytoplasm of a cell

• Uses the nitrogenous base uracil instead of thymine

• Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA

• Viral RNA is unique

Adenosine Triphosphate (ATP)

Figure 2.23

Figure 2.24

Solute Solute transported

Contracted smoothmuscle cell

Product made

Relaxed smoothmuscle cell

Reactants

Membraneprotein

P Pi

ATP

PX X

Y

Y

+

(a) Transport work

(b) Mechanical work

(c) Chemical work

Pi

Pi

+ADP

Figure 2.24

Solute

Membraneprotein

P

ATP

(a) Transport work

Figure 2.24

Solute Solute transported

Membraneprotein

P Pi

ATP

(a) Transport work

Pi

+ADP

Figure 2.24

Relaxed smoothmuscle cell

ATP

(b) Mechanical work

Figure 2.24

Contracted smoothmuscle cell

Relaxed smoothmuscle cell

ATP

(b) Mechanical work

Pi

+ADP

Figure 2.24

Reactants

ATP

PX

Y+

(c) Chemical work

Figure 2.24

Product madeReactants

ATP

PX X

Y

Y

+

(c) Chemical work

Pi

Pi

+ADP

Figure 2.24

Solute Solute transported

Contracted smoothmuscle cell

Product made

Relaxed smoothmuscle cell

Reactants

Membraneprotein

P Pi

ATP

PX X

Y

Y

+

(a) Transport work

(b) Mechanical work

(c) Chemical work

Pi

Pi

+ADP