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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