chemistry ch 2. the “stuff” of the universe anything that has mass and takes up space states of...
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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
GraphiteGraphite — — layer structure layer structure of carbon of carbon atoms reflects atoms reflects physical physical properties.properties.
A Chemist’s View of A Chemist’s View of WaterWater
H2O (gas, liquid, solid)
MacroscopicMacroscopicMacroscopicMacroscopic
SymbolicSymbolicSymbolicSymbolicParticulateParticulateParticulateParticulate
STATES OF MATTERSTATES OF MATTERSTATES OF MATTERSTATES OF MATTER
______________ — have rigid shape, fixed volume. External — have rigid shape, fixed volume. External shape can reflect the atomic and molecular shape can reflect the atomic and molecular arrangement.arrangement.
– Reasonably well understood.Reasonably well understood.______________ — have no fixed shape and may not fill a — have no fixed shape and may not fill a
container completely. container completely. – Not well understood.Not well understood.
______________ — expand to fill their container. — expand to fill their container. – Good theoretical understanding.Good theoretical understanding.
OTHER STATES OF OTHER STATES OF MATTERMATTEROTHER STATES OF OTHER STATES OF MATTERMATTER
PLASMAPLASMA — an electrically charged gas; — an electrically charged gas; Example: the sun or any other starExample: the sun or any other star
BOSE-EINSTEIN CONDENSATEBOSE-EINSTEIN CONDENSATE — — a condensate that forms near absolute a condensate that forms near absolute zero that has superconductive properties; zero that has superconductive properties; Example: supercooled Rb gasExample: supercooled Rb gas
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)
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
Physical Physical PropertiesProperties
What are some What are some physical properties?physical properties?
colorcolormelting and boiling melting and boiling
pointpointodorodor
Physical ChangesPhysical Changes
– can be observed without changing the identity of the substance
Some Some physical changes physical changes would would bebe
boiling of a liquidboiling of a liquid melting of a solidmelting of a solid dissolving a solid in a liquid to dissolving a solid in a liquid to
give a homogeneous mixture give a homogeneous mixture — a SOLUTION.— a SOLUTION.
A Chemist’s ViewA Chemist’s View
2 H2(g) + O2 (g) --> 2 H2O(g)
MacroscopicMacroscopicMacroscopicMacroscopic
SymbolicSymbolicSymbolicSymbolicParticulateParticulateParticulateParticulate
Chemical Properties and Chemical Properties and Chemical ChangeChemical Change
Chemical change Chemical change or or chemical chemical reactionreaction — transformation of — transformation of one or more atoms or one or more atoms or molecules into one or more molecules into one or more different molecules.different molecules.
•Burning hydrogen (HBurning hydrogen (H22) in ) in oxygen (Ooxygen (O22) gives H) gives H22O.O.
Sure Signs of a Sure Signs of a Chemical ChangeChemical Change
HeatHeatLightLightGas Produced (not Gas Produced (not
from boiling!)from boiling!)Precipitate – a solid Precipitate – a solid
formed by mixing formed by mixing two liquids togethertwo liquids together
Physical vs. Chemical
Examples:
– melting point
– flammable
– density
– magnetic
– tarnishes in air
physical
chemical
physical
physical
chemical
Physical vs. Chemical Examples:
– rusting iron
– dissolving in water
– burning a log
– melting ice
– grinding spices
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
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
Radiotherapy
Rapidly dividing cells are particularly sensitive to damage by radiation. For this reason, some cancerous growths can be controlled or eliminated by irradiating the area containing the growth. External irradiation can be carried out using a gamma beam from a radioactive cobalt-60 source, though in developed countries the much more versatile linear accelerators are now being utilized as a high-energy x-ray source (gamma and x-rays are much the same).
Internal radiotherapy is by administering or planting a small radiation source, usually a gamma or beta emitter, in the target area. Iodine-131 is commonly used to treat thyroid cancer, probably the most successful kind of cancer treatment. It is also used to treat non-malignant thyroid disorders. Iridium-192 implants are used especially in the head and breast. They are produced in wire form and are introduced through a catheter to the target area. After administering the correct dose, the implant wire is removed to shielded storage. This brachytherapy (short-range) procedure gives less overall radiation to the body, is more localized to the target tumor and is cost effective.
Molecules and Compounds
Molecule – two or more atoms held together by chemical bonds
Compound – two or more different kinds of atoms chemically bonded together
The Nature of MatterThe Nature of MatterThe Nature of MatterThe Nature of Matter
Chemists are interested in the nature of matter and Chemists are interested in the nature of matter and how this is related to its atoms and molecules.how this is related to its atoms and molecules.
GoldGold MercuryMercury
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
Types of Mixtures
Variable combination of 2 or more pure substances.
Heterogeneous –visibly separate phases
Homogeneous – Same throughout
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
Suspensions are 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 ElementsInert elements have their outermost energy level fully occupied by electrons
Chemically Reactive ElementsReactive elements do not have their outermost energy level fully occupied by electrons
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)
Covalent Bonds
Covalent bonds are formed by the sharing of two or more electrons
Electron sharing produces molecules
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
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
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
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
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
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
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
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
Carbohydrates
CarbohydratesContain carbon, hydrogen, and oxygenTheir major function is to supply a source of cellular foodExamples:
Monosaccharides or simple sugars
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
Other LipidsPhospholipids – modified triglycerides with two fatty acid groups and a phosphorus group
Other LipidsSteroids – flat molecules with four interlocking hydrocarbon ringsEicosanoids – 20-carbon fatty acids found in cell membranes
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
Amino Acids
Building blocks of protein, containing an amino group and a carboxyl group
Amino acid structure
ProteinMacromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds
Structural Levels of Proteins
Primary – amino acid sequence
Secondary – alpha helices or beta pleated sheets
Structural Levels of Proteins
Tertiary – superimposed folding of secondary structures
Quaternary – polypeptide chains linked together in a specific manner
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
What Are Enzymes?What Are Enzymes?
Most enzymes are Proteins Proteins ((tertiary and quaternary structures)
Act as CatalystCatalyst to accelerates a reaction
Not permanentlyNot permanently changed in the process
EnzymesEnzymes
Are specific for what they will catalyzecatalyze
Are ReusableReusable End in –asease-Sucrase-Sucrase-Lactase-Lactase-Maltase-Maltase
How do enzymes Work?How do enzymes Work?
Enzymes work by weakening weakening bondsbonds which lowers owers activation energy
EnzymesEnzymes
FreeEnergy
Progress of the reaction
Reactants
Products
Free energy of activationFree energy of activation
Without Enzyme
With Enzyme
EnzymeJoinsSubstrate
Enzyme-Substrate ComplexEnzyme-Substrate ComplexThe substancesubstance (reactant) an enzymeenzyme acts on is the substratesubstrate
Induced FitInduced FitA change in the shapeshape of an enzyme’s active siteInduced Induced by the substrate
Protein DenuaturationReversible unfolding of proteins due to drops in pH and/or increased temperature
Protein DenuaturationIrreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes
Factors Affecting Enzyme Factors Affecting Enzyme ActivityActivity
TemperaturepHCofactors & CoenzymesInhibitors
Temperature & pHTemperature & pH
High temperaturesHigh temperatures are the most dangerous reactions & denaturedenature enzymes (Most like normal Body (Most like normal Body temperaturestemperatures)
Most enzymes like near neutral pH (6 to 8)
Denatured (unfolded) by ionic saltsionic salts
Cofactors and CoenzymesCofactors and Coenzymes
Inorganic substancesInorganic substances (zinc, iron) (zinc, iron) and vitaminsvitamins (respectively) are sometimes need for proper enzymatic activityenzymatic activity.
ExampleExample::
IronIron must be present in the quaternary structure of hemoglobinhemoglobin in order for it to pick up oxygenoxygen.
Two examples of Enzyme Two examples of Enzyme InhibitorsInhibitors
a. a. Competitive inhibitorsCompetitive inhibitors:: are chemicals that resembleresemble an enzyme’s enzyme’s normal substratenormal substrate and competecompete with it for the active siteactive site.
EnzymeSubstrate
InhibitorsInhibitors
Noncompetitive inhibitorsNoncompetitive inhibitors::Inhibitors that do not enter thedo not enter the
active siteactive site, but bind tobind to another partanother part of the enzymeenzyme causing the enzymeenzyme to change its change its shapeshape, which in turn alters the alters the active siteactive site.
Enzyme
NoncompetitiveInhibitorSubstrate
Molecular Chaperones (Chaperonins)
Help other proteins to achieve their functional three-dimensional shape
Maintain folding integrity Assist in translocation of proteins across
membranes Promote the breakdown of damaged or
denatured proteins
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
Mechanism of Enzyme Action
Enzyme binds with substrate Product is formed at a lower activation
energy Product is released
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
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
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
Adenosine Triphosphate (ATP)
Source of immediately usable energy for the cell
Adenine-containing RNA nucleotide with three phosphate groups