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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