Chapter 2

J.F. Thompson, Ph.D.

Chemistry Comes Alive!

Definitions: Matter and MassMatter

•All living and nonliving things consist of matter matter - anything which occupies space and has mass liquid, solid or gas (the phases which matter takes)

•Mass vs. Weight mass is the actual amount of matter an object contains weight is a measure of the force of gravity on a mass

o mass is same everywhereo weight varies with the position of an object on or above earth

Definitions: EnergyEnergy - the capacity to do work

•Kinds of Energypotential energy - inactive or storedkinetic energy - energy of motion

•Forms of energychemical energy – the making or breaking of chemical

bondselectrical energy – the movement of charged particlesmechanical energy - movement of matter radiant energy – light or other electromagnetic

radiation

•Energy conversion is inefficient, with “waste heat” always lost

Composition of MatterElements and Atoms

•Element a substance which cannot be split into simpler

substances by ordinary chemical reactions composed of specific types of atoms

•112 elements (at least) 92 occur naturally in nature 24 occur naturally in the body most common: H, C, O, N

Composition of Atoms Atomic structure

•Protons, neutrons, electrons protons positively charged neutrons neutral electrons negatively charged

•The same number of protons and electrons are present in an atom – each atom is electrically neutral

•Protons and neutrons are found in the nucleus; electrons orbit the nucleus

Atomic Number The number of protons in the nucleus is the

element’s atomic number

This is the large number on the periodic table

The number of protons in the nucleus makes atoms of one element differ from the atoms of other elements

Hydrogen: 1 proton, helium: 2 protons, carbon: 6 protons, etc.

How Atoms Are CombinedMolecules and Compounds

•Molecule - 2 or more atoms held together by chemical bonds (they may be the same element)

•CompoundMolecules which can be broken down into 2 or more

different elements by chemical means, e.g., H2O

Demonstrates new characteristics of the combined atoms which may be quite different that the characteristics of the individual elements, e.g., H and O are gases at temperatures at which H2O is a liquid or solid

Mixtures Substances composed of two or more components

physically intermixed; they may be in a gas, a liquid or a solid phase.

• Solutions – e.g., salt water and blood plasma Homogeneous with each molecule a separate entity in the mix Mixture of two or more components (types of molecules)

o Solvent – the medium in which the other materials are mixedo Solute – the various other components in the mix

• Colloids – e.g., Jell-O and cell cytoplasm heterogeneous mixtures that appear translucent or milky smaller particles, clumps of similar molecules, which scatter

light the particles will not settle out because of gravity

• Suspensions - blood (red blood cells suspended in plasma) heterogeneous mixture with larger, often visible particles particles will settle out due to gravity if the suspension is not in

motion

Mixtures

Mixtures

Types of Chemical BondsFrom Strongest to Weakest:

•Covalent

•Ionic

•Hydrogen

•van der Walls = hydrophobic

Covalent Bonds Electrons are shared among two or more atoms

Carbon + 4 Hydrogen = Methane• carbon - 4 valence

electrons to share

• hydrogen - 1 valence electron to share

Single, double or triple bonds refer to the number of electrons shared between 2 atoms

Types of Covalent BondsPolar and nonpolar

molecules•If electrons are shared

equally = nonpolar covalent bond

•Carbon dioxide has two nonpolar covalent bonds

•If electrons are shared unequally = polar covalent bond

•Water is a dipole because it has two polar covalent bonds

Ionic Bonds

Electrons can be completely separated and are transferred from one atom to another – forming positive and negative ions

Cations: Electron donors that have a net positive charge

Anions: Electron acceptors that have a net negative charge

Oppositely charged ions attract each other: ionic bonds

Ionic Bonds Example: table salt (sodium chloride)

• Sodium atom has one electron in its outer valence shell it can lose 1 electron for greater stability

• Chlorine has 7 electrons in its outer shell – it needs 1 more for greater stability

• Sodium transfers one electron to chlorine Cl- becomes an anion and Na+ becomes an cation

• Ions are created and they attract each other forming an ionic bond

Compare Covalent and Ionic Bonds

molecular stability

Hydrogen Bonds Hydrogen Bonds

•Weak attractions between different molecules which contain polar covalent bonds

•Covalently bound hydrogen attracts other charged atoms

Water•Forms many H-bonds

•Surface tension

•Very important to water’s properties which support life

Chemical ReactionsThe formation, rearrangement, or breaking of chemical bonds

Energy is transferred in the process; waste heat is lost

Chemical equations - written to describe the chemical reactions involved:

A + B → Creactants product

Synthesis = Anabolic ReactionsAtoms or molecules combine to form larger,

more complex molecules•Always involves some type of chemical bond

formation

•Always involves the input of chemical energy

•A+B C

•Amino acids protein

Decomposition = Catabolic Reactions Larger molecule is broken down into smaller

molecules or constituent atoms•Chemical bonds are broken

•Chemical energy is always released, but that energy may or may notmay or may not be useful for another purpose

•D E + E + E … + E

•Glycogen (animal starch) glucose

Chemical Exchange Reactions Both synthesis and decomposition occur in the

same reaction

•Chemical bonds are made and broken; molecular parts are exchanged

•AB + CD ⇌ AD + CB

•ATP + Glucose ⇌ Glucose-6-phosphate + ADP

Oxidation-Reduction (redox) Reactions• Electrons are exchanged between reactants

•Hydrogen ions often follow the electrons in the reaction

• Reactant losing electron(s) [& H+ ions] Electron Donor Electron Donor OxidizedOxidizedEnergy is releasedDecreased in potential (useful chemical) energy of

the oxidized molecule

• Reactant gaining electron(s) [& H+ ions] Electron Acceptor Electron Acceptor ReducedReduced (its positive charge is reduced)Energy is absorbed Increased in potential (useful chemical) energy of the

reduced molecule

Energy Flow in Chemical Reactions

•ExergonicExergonic Reactions - release energy the products have less energy in their chemical

bonds than the reactants the reaction releases chemical energy, which may may

bebe usable the reaction releases waste heat = = exothermicexothermic

•EndergonicEndergonic Reactions - require energy products have more potential energy in bonds

than reactants the reaction requires energy input = = endothermicendothermicoften coupled to exergonic reactions which

provide the energy to drive the endergonic reaction

Reversibility of Chemical ReactionsAll chemical reactions are theoretically

reversiblereversiblemore difficult when energy is released during reactionenergy must be added back to reverse the reaction

All chemical reactions tend toward an equilibriumequilibrium state

the rates of the forward and reverse reactions are equal the products and reactants are in balanced proportionsa change in energy relationships or a change in the

concentrations of reactants or products will cause a proportionate shift in the other components of the reaction

Factors Influencing Rate of ReactionsMolecular Collisions are required for

chemical reactions to occurThe Probability of collisions is affected

by:TemperatureTemperature - changes in kinetic energy;

hotter particles move fasterParticle sizeParticle size - smaller particles move fasterConcentrationConcentration - collisions are more likely to

occur when more molecules are presentCatalystsCatalysts - bring reactants together more

rapidly or in more favorable orientations for reactions to take place, or both

Inorganic Compoundsusually lack carbon atoms (a few

exceptions, e.g., carbon monoxide and carbon dioxide and carbides)

usually smaller molecules

water (H2O)

gases, e.g., O2, CO2, N2

various ions = electrolytes (derived from dietary minerals and certain salts, acids, and bases)

Water Has Special Properties Due to itsAbility to Form Hydrogen Bonds1. High heat capacity

• Considerable kinetic energy must be added or subtracted to change the temperature of water by a degree

• Contributes to temperature stability for the body

2. High heat of vaporization• The change from liquid to gas phase requires

breaking many hydrogen bonds

• Considerable energy is used to boil (vaporize) water

• Sweating is a similar transition to gas phase that takes heat (energy) away from the body

Water Has Special Properties

3. Polarity/solvent properties – polar covalent bonds

• Water is a good solvent

• Water brings solute molecules into close proximity, making reactions more likely

4. Reactivity • Water participates in many chemical reactions

• Added/removed from molecules in breakdown or synthesis reactions

5. Lubrication and cushioning• SerousSerous and MucousMucous fluids in many body locations

lubricate the movements of various parts

• Cerebrospinal fluid cushions the brain and spinal cord

• Amniotic fluid cushions the fetus

SaltsContain cations and

anions -- neither of which is H+ or OH-

•Examples - NaCl, Ca2CO3

Dissociate (ionize) into component ions when dissolved in water

Ions are called electrolytes

Acids & BasesCompounds which break their ionic bonds

when dissolved in H2O, altering the number of hydrogen ions in the solution•Acids

proton donors (H+ ion donors)dissociate to release hydrogen ion(s) (H+) and

anion(s)HCl, H2CO3 H2SO4, H3PO4

•Basesproton acceptors (H+ ion acceptors)generally dissociate into hydroxyl ion (OH-) and one

or more cationsNaOH, Ca(OH)2, NH3OH (ammonia)

pH Scale Concentration of hydrogen

ions is measured in pH units

pH ranges from 0 to 14•Based on the concentration of

H+ ions = [H+] in solution

•Neutral pH is 7, [H+] = [OH-]

•A 1 pH unit change = a 10x change in [H+]

•Below pH 7, solutions are acidic; have more H+ ions

•Above pH 7, solutions are basic; have more OH- ions

Acid-Base Balance It is very important for internal homeostasis

to keep acids/bases in balance in body fluids

Biochemical reactions are very sensitive to pH

pH maintained at 7.35-7.45

Humans use 3 homeostatic mechanisms to regulate the acid-base balance

1.Buffers

2.Respiratory System

3.Renal System

Acids & Bases

Neutralization• Acids and bases react to form salts

• HCl + NaOH H2O + NaCl

Buffers – resist changes in pH

•Common body buffers: HCO3-, HPO4

-, proteins

•The renal and respiratory systems control pH by regulating buffer concentrations

•H2O + CO2 H2CO3 H+ + HCO3-

the bicarbonate buffer system is especially important

General Properties of Organic Compounds

ALWAYS contain C, H, and generally O

S, N, P and a few other elements maymay be present Carbon can form 4 covalent bonds

Carbon atoms can form chains with other carbons

Polar organic compounds dissolve well in water

Non-polar organic compounds do not dissolve well in water

Covalent bonds in organic compounds may be broken to release useful chemical energy•adenosine triphosphate (ATP) transfers this energy

General Properties of Organic CompoundsOrganic molecules may be quite largeOrganic molecules make good structural

components Simple molecules = monomers are joined

to form macromolecules = polymersFour classes of biologically important

polymers:•Carbohydrates

•Lipids

•Proteins

•Nucleic Acids

CarbohydratesSugars, starch, glycogen, cellulose, chitinClassified by sizeChemical formula = [CH2O]N (multiples of

CH2O)e.g., C6H12O6 = glucose

Carbohydrates have many functionsStructural components of molecules (e.g., DNA,

RNA), cells and tissueso cellulose is the most abundant organic substance on eartho we cannot digest it, but it is an important part of our diet

Broken down for chemical energy production; often ATP formation

Chemical energy is stored as glycogen for future use

MonosaccharidesMonomers = simple sugars = monosaccharidesSingle chain or ring structures

•glucose – the preferred source of energy in the body

•fructose

•galactose

•deoxyribose

•ribose

Disaccharides2 monosaccharides joined together

•dehydration synthesis – a water molecule is removed during bond formation

•hydrolysis - add a water molecule to liberate the monosaccharides

•examples: sucrose, maltose, lactose

Polysaccharides Large, relatively insoluble carbohydrate

polymers

10’s or 100’s of monosaccharides bonded together•glycogen - storage of glucose for energy in humans

in liver cells, skeletal muscle cells and endometrial lining cells

•starch – storage of glucose for energy in plants

•cellulose – structural fiber in plants; “roughage” in our diet

•chitin – structural fiber in some fungi, insects, crustaceans

Lipids = FatsContain carbons, hydrogens, oxygens

(fewer oxygens per carbon)Roughly 18-25% of body weightFewer polar covalent bondsInsoluble in water = hydrophobicDissolve in lipid solvents, e.g., alcohols,

detergents, oilsMajor energy storage compoundsStructural components of cell membranesSome serve as molecular signal

compounds•steroid hormones, prostaglandins, etc.

TriglyceridesStorage form of fats for energyNon-polar, hydrophobicGlycerol head and 3 fatty acid side-chains Saturated fatty acids vs. unsaturated fatty acids

•double bonds in unsaturated fatty acids

•the more unsaturated bonds, the more fluid at room temp.

Note dehydration synthesisNote dehydration synthesis

PhospholipidsModified triglyceride

•2 fatty acids and a phosphate group attached to glycerol

Phosphate group is a polar group•dipole

•amphipathic - has polar and non-polar regions

•can hydrogen bond with water due to phosphate’s polarity

Found in cell membraneshydrophilic head

hydrophobic tail

Other Lipid Compounds Steroids

•4 rings of carbon atoms

•Non-polar

•Fat soluble/hydrophobic

•Cholesterol is a membrane structural component

•Cholesterol-derived steroid hormones

Eicosanoids (Local Hormones)•Prostaglandins,

leukotrienes

•Regulate blood clotting, inflammation, immune reactions, labor, etc.

1 2

3 4

Proteins contain carbon, hydrogen, oxygen, nitrogen, sulfur 12 - 18% of body mass a wide variety of structural and functional roles amino acids are the building blocks of proteins

• 20 different AA's

• each AA has a hydrogen (H), an amino group (NH2), carboxyl group (CO2H), and side group (R)

• some R groups (amino, carboxyl groups) ionize; these buffer body fluids

Peptide Bond Formationamino acids (monomers) combine in a linear

sequence to form a polypeptide (polymer)AA's covalently bonded together by “peptide

bonds” between carboxyl and amino groupsa water molecule is created as well form dipeptides tripeptides polypeptides

Hierarchy of Protein Structure Primary – amino acid sequence

Secondary - due to hydrogen bonds between adjacent amino acids• random coil, α-helix, or ß-pleated

sheet

Tertiary – due to various types of bonds between more distant amino acids• produces a unique 3D shape, for

each protein, and causes a unique function

• fibrous vs. globular shapes

Quaternary - 2 or more polypeptide chains bound together to form a functional whole protein

Protein Denaturation Protein structure is

generally stable

Strong structure/function relationship is dependent on the 3D shape of the protein

High temperatures and strong pH alter proteins

Structural changes reduce or completely stop activity

Structural changes are irreversible at temperature and pH extremes

EnzymesMost have names ending with –aseGlobular proteins that are organic catalysts

•apoenzyme (protein portion)

•cofactors and coenzymes may assist in the enzyme-catalyzed reaction

Enzyme-catazyzed reactions are thousands to millions times more likely than reactions caused by random molecular collisions

Enzymes are highly specific for their substrates and the reactions they catalyze

Enzyme Action – Catalytic Mechanism Activation energy – the

energy needed to trigger a reaction to occur

Enzymes (catalysts) decrease the activation energy required•increase interactions

between substrates

•without increasing temperature or pressure

•properly orient molecules

Enzyme Action and Regulation Three basic steps

1.bind at the active site to form an enzyme-substrate complex

2.cause internal bond rearrangements

3.release the product(s) & repeat

Many regulatory controls• Substrate specificity

• Many cellular regulation systems (feedback controls)

Nucleic AcidsDeoxyribonucleic Acid (DNA) & Ribonucleic acid

(RNA)DNA, RNA made of nucleotides monomers- 3

parts to a nucleotide•nitrogenous bases: adenine, thymine (DNA only),

cytosine, guanine, uracil (RNA only)

•pentose sugar (5 carbon): deoxyribose or ribose

•phosphate group

Nucleic Acids DNA is the Genetic

Material 4 nucleotide monomers

• adenine (A), guanine (G), cytosine (C), thymine (T)

complimentay bases connect the two strands:• A-T, C-G

forms a double helix, i.e., a double stranded coil

RNA carries hereditary information from nuclear DNA to the cytoplasm (inside cells)• uracil (U) replaces T

• single stranded

Adenosine Triphosphate three phosphate

groups, attached to a ribose sugar and adenine (adenosine nucleotide)

ATP ADP + Pi

high-energy phosphate groups are attached by aerobic or anaerobic catabolic reactions

ATP is the major cellular energy transfer compound

high energy bonds

End Chapter 2

Note: You will find additional slides after this “end” slide with additional details of chemistry processes, which you may review on your own.

Mass Number Mass number = total number of protons + neutrons

•Mass number may vary among the atoms of an element because of different numbers of neutrons (isotopes)

•All isotopes of an element have: the same number of protons the same chemical characteristics

•Radioactive isotopes are unstable isotopes which “decay” into other isotopes, even into other types of elements

Identifying Elements Isotopes of an element:

•Have different numbers of neutrons

•Have the same number of protons

•Have the same chemical characteristics

•The mass number indicates the number of protons & neutrons

•Radioactive isotopes are unstable and “decay” into other isotopes, even into other types of elements

The Role of ElectronsElectrons form clouds called

shells •Each shell contains one or

more orbitals

•The first three shells hold 2, 8, and 18 electrons, respectively The outer shell is the valence shell

•Atoms are stable (inert) when the valence shell is filled with electrons

•Atoms are chemically reactive if the valence shell is not full of electrons

Composition of Atoms Electron structure

•Electrons orbit nucleus in shells

•The first three shells hold 2, 8, and 18 electrons, respectively

•Shells contain subshells

•The outer shell is the valence shell

•Atoms are the most stable when the valence shell is filled with electrons

End Chapter 2

Note: The following slides refer you to specific exercises you may access on-line at your textbook publisher’s website, if you wish additional review of the chemistry from CH 2. This same suggested exercises can be found on a page linked from the Exam 1 Review page on Dr. T’s webpages.

Anatomy and Physiology Place Assignment PART I: BASIC CHEMISTRY Definition of Concepts: Matter and Energy (25-26) 

• Animation: Energy Concepts Composition of Matter: Atoms and Elements (27-30) 

• Animation: Atomic Structure How Matter Is Combined: Molecules and Mixtures (30-31) 

Chemical Bonds (31-36)  Chemical Reactions (36-40)  Part II: BIOCHEMISTRY Inorganic Compounds (40-43) 

• InterActive Physiology®: Introduction to Body Fluids Organic Compounds (43-59) 

Animations: Disaccharides | Polysaccharides | FatsArt Labeling: Lipids (fig. 2.15, p. 47)Animations: Structure of Proteins | Primary and Secondary Structure | Tertiary and Quaternary StructureAnimation: How Enzymes WorkArt Labeling: Mechanism of Enzyme Action (fig. 2.21, p. 55)Art Labeling: Structure of DNA (fig. 2.22, p. 56)Memory: Important Molecules Chapter Summary 

Anatomy and Physiology Place

Chapter QuizzesArt Labeling QuizMatching QuizMultiple-Choice Quiz (Level I)Multiple-Choice Quiz (Level II)True-False Quiz

Crossword PuzzlesCrossword Puzzle 2.1Crossword Puzzle 2.2Crossword Puzzle 2.3

Get Ready for A&P ActivitiesYour Starting Point: Pre-Quiz

Atomic Structure 165•Atoms and Isotopes•Build an Atom

Period Table of Elements 171•Periodic Table

Chemical Bonding 177

•Hydrogen BondingNonpolar and Polar Molecules

What Did You Learn? Post Quiz

End Chapter 2