Download Chapter 2: Chemistry Level

Chemistry Comes Alive
Part A
2
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
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)
 96% of body matter
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)
 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
Models of the Atom
Figure 2.1
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
 Isotope – atoms with same number of protons but a
different number of neutrons
 Radioisotopes – atoms that undergo spontaneous
decay called radioactivity
Identification of Elements
Figure 2.2
Identification of Elements
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, or emulsions, are heterogeneous mixtures
whose solutes do not settle out
 Example: Jello and Cytosol
 Suspensions are heterogeneous mixtures with visible
solutes that tend to settle out
 Example: Blood
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 2.6a
Double Covalent Bonds
Figure 2.6b
Triple Covalent Bonds
Figure 2.6c
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 2.8
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
Hydrogen Bonds
Figure 2.9
Chemical Reactions
 Occur when chemical bonds are formed, rearranged,
or broken
 Are 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
 Decomposition reactions: Molecules are broken
down into smaller molecules
AB  A + B
 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
 Therefore, both decomposition and electron
exchange occur.
Energy Flow in Chemical Reactions
 Exergonic reactions – reactions that release energy
 Usually when a bond is broken.
 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
 Catalysts – increase the rate of a reaction without
being chemically changed
 Enzymes – biological catalysts
Chemistry Comes Alive:
Biochemistry
Part B
2
Biochemistry
 Inorganic compounds
 Do not contain carbon
 Water, salts, and many acids and bases
 Organic compounds
 Contain carbon, are covalently bonded, and are
often large
Inorganic: 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
Inorganic: Water
 Reactivity – is an important part of hydrolysis and
dehydration synthesis reactions
 Cushioning – resilient cushion around certain body
organs
Inorganic: Salts
 Inorganic compounds
 Contain cations other than H+ and anions other than
OH–
 Are electrolytes; they conduct electrical currents
Inorganic: Acids and Bases
 Acids release H+ and are therefore proton donors
HCl  H+ + Cl –
 Bases release OH– and are proton acceptors
NaOH  Na+ + OH–
Inorganic: 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
Inorganic: Acid-Base Concentration (pH)
 Acidic: pH 0–6.99
 Basic: pH 7.01–14
 Neutral: pH 7.00
Figure 2.12
Inorganic: 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
Organic Compounds
 Molecules unique to living systems contain carbon
and hence are organic compounds
 They include:
 Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
Organic: Carbohydrates
 Contain carbon, hydrogen, and oxygen
 Their major function is to supply a source of cellular
food
 Examples:
 Monosaccharides or simple sugars
Figure 2.13a
Organic: Carbohydrates
 Disaccharides or double sugars
Figure 2.13b
Organic: Carbohydrates
 Polysaccharides or polymers of simple sugars
Figure 2.13c
Organic: 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
Organic: Neutral Fats (Triglycerides)
 Composed of three fatty acids bonded to a glycerol
molecule
Figure 2.14a
Organic: Other Lipids
 Phospholipids – modified triglycerides with two
fatty acid groups and a phosphorus group
Figure 2.14b
Organic: Other Lipids
 Steroids – flat molecules with four interlocking hydrocarbon rings
 Eicosanoids – 20-carbon fatty acids found in cell membranes
Figure 2.14c
Organic: 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
 Fat-soluble vitamins – vitamins A, E, and K
 Eicosanoids – prostaglandins, leukotriens, and
thromboxanes
 Lipoproteins – transport fatty acids and cholesterol in
the bloodstream
Organic: Amino Acids
 Building blocks of protein, containing an amino
group and a carboxyl group
 Amino acid structure
Organic: Amino Acids
Figure 2.15a-c
Organic: Amino Acids
Figure 2.15d, e
Organic: Protein
 Macromolecules composed of combinations of 20
types of amino acids bound together with peptide
bonds
Figure 2.16
Organic: Structural Levels of Proteins
 Primary – amino acid sequence
 Secondary – alpha helices or beta pleated sheets
Organic: Structural Levels of Proteins
 Tertiary – superimposed folding of secondary
structures
 Quaternary – polypeptide chains linked together in a
specific manner
Organic: Structural Levels of Proteins
Figure 2.17a-c
Organic: Structural Levels of Proteins
Figure 2.17d, e
Organic: Fibrous and Globular Proteins
 Fibrous proteins
 Extended and strandlike proteins
 Examples: keratin, elastin, collagen, and certain
contractile fibers
 Globular proteins
 Compact, spherical proteins with tertiary and
quaternary structures
 Examples: antibodies, hormones, and enzymes
Organic: Protein Denuaturation
 Reversible
unfolding of
proteins due to
drops in pH
and/or increased
temperature
Figure 2.18a
Organic: Protein Denuaturation
 Irreversibly denatured proteins cannot refold and
are formed by extreme pH or temperature changes
Figure 2.18b
Organic: Molecular Chaperones (Chaperonins)
 Help other proteins to achieve their functional threedimensional shape
 Maintain folding integrity
 Assist in translocation of proteins across membranes
 Promote the breakdown of damaged or denatured
proteins
Organic: Characteristics of Enzymes
 Most are globular proteins that act as biological
catalysts
 Holoenzymes consist of an apoenzyme (protein) and
a cofactor (usually an ion)
 Enzymes are chemically specific
 Frequently named for the type of reaction they
catalyze
 Enzyme names usually end in -ase
 Lower activation energy
Organic: Characteristics of Enzymes
Figure 2.19
Organic: Mechanism of Enzyme Action
 Enzyme binds with substrate
 Product is formed at a lower activation energy
 Product is released
Organic: Mechanism of Enzyme Action
Active site
Amino acids
1
Enzyme (E)
Substrates (s)
H20
Enzymesubstrate
complex (E–S)
2
Free enzyme (E)
3
Peptide bond
Internal rearrangements
leading to catalysis
Dipeptide product (P)
Figure 2.20
Organic: 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
 Five nitrogen bases contribute to nucleotide
structure – adenine (A), guanine (G), cytosine (C),
thymine (T), and uracil (U)
 Two major classes – DNA and RNA
Organic: 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
Organic: Structure of DNA
Figure 2.21a
Organic: Structure of DNA
Figure 2.21b
Organic: 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
Organic: Adenosine Triphosphate (ATP)
 Source of immediately usable energy for the cell
 Adenine-containing RNA nucleotide with three
phosphate groups
Organic: Adenosine Triphosphate (ATP)
Figure 2.22
Organic: How ATP Drives Cellular Work
Figure 2.23