Chemistry Ch 2. The “stuff” of the universe Anything that has mass and takes up space States of matter – Solid – has definite shape and volume – Liquid.

Chemistry Ch 2

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

Matter And Matter And EnergyEnergy

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

Kinetic and Potential 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)

Forms of Energy

Endergonic and Exergonic Reactions

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

Atoms and Elements

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

Major Elements of the 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)

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

Molecules

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

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

Formation of an Ionic Bond

Covalent Bonds

Covalent bonds are formed by the sharing of two or more electrons

Electron sharing produces molecules

Single Covlent Bonds

Double Covlalent Bonds

Triple Covalent Bonds

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

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

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

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

Surface tension

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

Acids and Bases Video

Acid-Base Concentration (pH)Acidic: pH 0–6.99 Basic: pH 7.01–14Neutral: pH 7.00

pH Scale Video

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

Carbohydrate Video

CarbohydratesDisaccharides or double sugars

CarbohydratesPolysaccharides or polymers of 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

Neutral Fats (Triglycerides)Composed of three fatty acids bonded to a glycerol molecule

Lipids Video

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

Amino Acids

Protein Video

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

Characteristics of Enzymes

Mechanism of Enzyme Action

Enzyme binds with substrate Product is formed at a lower activation

energy Product is released

Mechanism of Enzyme Action

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

Nucleic Acid Video

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

Structure of DNA

Structure of DNA

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

Adenosine Triphosphate (ATP)

How ATP Drives Cellular Work