Chemistry Part 1

Has mass & takes up space States of Matter Has mass & takes up space States of Solid – definite shape & volume Liquid –definite volume, changeable shape Gas – changeable shape & volume

Conversion between forms Conservation of energy Capacity to do work Types of energy Kinetic – motion/action Potential – position; stored energy Forms Chemical – atomic bonds Electrical – movement of charged particles Mechanical – moving matter Radiant – energy traveling in waves Conversion between forms Conservation of energy

Subatomic particles Atoms Elements Atomic symbols Composition of Matter Subatomic particles Electrons (e-) Neutrons Protons Atoms Unique arrangements of subatomic particles Can’t break down chemically Elements Matter of one type of atom Atomic symbols

Properties of Elements Periodic table Elements grouped by properties Unique physical & chemical properties Physical properties –detected by senses Chemical properties –way atoms interact

Elemental Composition of the Human Body Major Constituents O ~ 65% C ~ 18.5% H ~ 9.5% N ~ 3.2 % Remaining ~ 3.8% Ca, P, K, S, Na, Cl, Mg, I, Fe Trace elements Zn, Mn, Cu

Nucleus Electron orbitals Atomic Structure Neutrons no charge mass = 1 atomic mass unit (amu) Protons +1 charge mass = 1 amu Electron orbitals Electrons surround nucleus in energy levels (orbitals) -1 charge mass = 0.0005 amu

Electrons move around the nucleus in fixed, circular orbits Atomic Models 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

Characteristics of Atoms & Elements Atomic number – # protons Atomic mass – # protons + # neutrons Isotope – neutron # can vary different # of neutrons Atomic weight – average mass of all isotopes 11C, 12C, 13C, 14C or 235U, 238U Radioisotopes – atoms that undergo spontaneous decay called radioactivity 131I, 99mTc, 60Co, 14C, or 235U

Subatomic Configuration of Elements Figure 2.2

Isotopes of Elements Figure 2.3

Chemically Inert Elements Inert elements have full outer e- orbitals Full = 8 e- (except for He) Figure 2.4a

Chemically Reactive Elements Reactive elements have unfilled outer orbitals Figure 2.4b

Molecule – ≥ 2 atoms bonded Molecules & Compounds Molecule – ≥ 2 atoms bonded Compound – ≥ 2 different kinds of atoms bonded ALL Compounds Are Molecules BUT All Molecules NOT Compounds

Chemical bonds formed by e- in outer orbitals (valence shell) The Octet rule Atoms interact to have 8 e-s in valence shells (except H only 2 e-s) lose, gain or share Types of Bonds Ionic – loss or gain e-s Covalent – sharing e-s

Example: NaCl (sodium chloride) Ionic Bonds Ions charged atoms Anions - charge = gained e- Cations + charge = lost e- Example: NaCl (sodium chloride)

Formation of an Ionic Bond Ionic compounds form crystal structures

Single bond each atom donates 1 e- Covalent Bonds Sharing e-s fill outer orbitals Single bond each atom donates 1 e-

Double & Triple Covalent Bonds Atoms share 2 or 3 e-s

Electronegative & electropositive atoms form ionic bonds Polar & Nonpolar Bonds Polar bonds Unequal e- sharing Electronegative & electropositive atoms form ionic bonds Atoms w/ 6 -7 valence shell e-s = electronegative Atoms w/ 1-2 valence shell e-s = electropositive Nonpolar bonds Equal sharing of e-s Atoms w/ 3-5 valence e-s form covalent bonds

Comparison of Ionic, Polar Covalent, & Nonpolar Covalent Bonds

Crucial bond for life functions Hydrogen Bonds Crucial bond for life functions Allows reversible interactions between molecules Unequal sharing of H’s e- with N or O Responsible for properties of H2O Bonds between large macromolecules (ie proteins & nucleic acids)

Hydrogen Bonds in H2O Figure 2.9

Properties of Water High heat capacity – absorbs & releases large amounts of heat before changing temperature High heat of vaporization – boiling requires large amounts of heat Polar solvent properties – dissolves ionic substances, forms hydration layers around large charged molecules, & serves as the body’s major transport medium Reactivity – is an important part of hydrolysis & dehydration synthesis reactions

Mixtures & Solutions Mixtures – two or more components physically intermixed but not chemically bonded Solutions – homogeneous mixtures of components Solvent – substance present in greatest amount Solute – substance(s) present in smaller amounts Colloids - heterogeneous mixtures whose solutes do not settle out Suspensions - heterogeneous mixtures with visible solutes that settle out

Concept of Concentration Concentration refers to the amount of a substance in a given volume A critical concept to master

Mass (weight) Review of Metric Units Kg g mg 1Kg = 1000g OR 1g = 0.001Kg 1g = 1000mg OR 1mg = 0.001g 1mg = 1000 mg OR 1 mg = 0.001mg

Volume Review of Metric Units L ml 1 L = 1000ml OR 1 ml = 0.001 L 1 ml = 1000 ml OR 1 ml = 0.001ml Less common units: dL = deciliter 1dL = 100ml OR 1dL = 0.1L

Units of Concentration Percent – parts per hundred PPM – parts per million PPB – parts per billion Molarity – moles per liter Molality – moles particles per kg solvent Mass/volume g/ml (gram per milliliter) mg/ml (milligram per milliliter ) g/ml (microgram per milliliter) Mass/Mass mg/kg body mass g/kg body mass

Molecular Weight, Moles & Molarity The mass of a mole of atoms or molecules Has units of g/mole = atomic weight of an atom in grams 1 mole of C = 12 g OR C is 12g/mole Molecule’s molecular weight = sum of the atomic weights of its atoms 1 mole of H2O = 1g + 1g + 16g = 18 g MW of H2O = 18g/mole

Molecular Weight, Moles & Molarity What’s a mole?? The number of molecules in the gram molecular weight of that molecule MW of C = 12 there are 12g C/mole C there are 6.02 x 1023 C atoms in 12g of C MW of H2O = 18 there are 18g H2O/mole H2O there are 6.02 x 1023 H2O molecules in 18g of H2O Always 6.02 x 1023 This magical number is Avogadro’s Number

Molarity – The Standard of Chemical Concentration Terms Molarity = moles of solute per liter (L) of solvent Abbreviated with M A 5M NaCl solution contains 5 moles of NaCl molecules per liter of solution So 1 L of a 5 M NaCl solution contains 3.01 x 1024 molecules of NaCl 6.02 x 1023 molecules/mole x 5 moles = 3.01 x 1024 What mass of NaCl is in 1 L of a 5 M solution? MW NaCl = 23+35.5 = 58.5g/mole 5 moles x 58.5g/mole = 292.5g NaCl

Chemical formula for glucose is C6H12O6 Calculating Molarity Chemical formula for glucose is C6H12O6 MW = 180 g/mole (6 x 12)+ (12 x 1) + (6 x 18) =180 What is concentration of glucose in a can of coke? 42g of glucose/355ml H2O How many moles of glucose? 42g 180g/mole = 0.233 moles How many liters of coke? 355 ml  1000ml/L = 0.355 L How many moles/liter? 0.233 moles/0.355 L = 0.656 M

Examples using Molarity Ion concentrations in cells & body fluids [Na] = 0.15M outside cells & 0.015M inside cells [K] = 0.005M outside cells & 0.15M inside cells How much more Na is outside than inside? How much more K is inside than outside? Molar is often converted to millimolar (mM) M = moles/L mM = millimoles/L 0.15M = 150mM multiply M by 1000 to convert M to mM

Mass/Volume & Percent Concentration Terms Many molecules in the body are measured in mass/volume Normal glucose = 100mg/dL or 100mg/100ml or 1mg/ml or 1g/L or 0.001g/ml or 0.1g/100ml Cholesterol should be below 200mg/dL or 0.2g/dL or 0.2g/100ml Many substances are described in percentages Percentage is g/100g or g/100ml Blood [glucose] would = 0.1% Blood [cholesterol] would = 0.2%

Forming or breaking chemical bonds Chemical equations show: Chemical Reactions Forming or breaking chemical bonds Chemical equations show: Reactants & products & their relative amounts

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 & broken AB + C  AC + B

Oxidation-Reduction (Redox) Reactions C6H12O6 + 6O2 6CO2 + 6H2O glucose carbon dioxide Reactants losing electrons are electron donors & are oxidized Reactants taking up electrons are electron acceptors & 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

Rates & Reversibility of Chemical Reactions A + B AB Chemical reactions proceed with measurable rates All reactions are theoretically reversible Equilibrium (dynamic) Forward & reverse reactions proceed at same rate

Factors Influencing Rate of Chemical Reactions Temperature higher temperatures increase rates Concentration higher [reactant] increases rates Catalysts Molecules that increase reaction rates Enzymes Biological catalysts with high specificities

Chemistry Comes Alive Part 2

Categories of Molecules Organic molecules Contain C Covalent bonds Produced by living or once living organisms Inorganic molecules Typically do not contain C Include: Water, ammonia, salts, & some acids & bases

Examples: NaCl, KCl, CaCl2, Ca3(PO4)2 Salts Electrolytes conduct electrical currents Examples: NaCl, KCl, CaCl2, Ca3(PO4)2

Acids release H+ Bases release OH– Acids & Bases HCl  H+ + Cl – NaOH  Na+ + OH–

Acid-Base Concentration (pH) pH describes the concentration of H+ in a solution pH = -log[H+] pH scale based on [H+] of H2O H2O  H+ + OHˉ [H+] =1x10-7M & [OHˉ] = 1x10-7M Therefore H2O has a pH = 7 Acidic solutions have [H+] higher than 1x10-7M & therefore a pH < 7 Alkaline solutions have lower [H+] concentrations & therefore a pH > 7

Acid-Base Concentration (pH) Acidic: pH 0–6.99 Neutral: pH 7.00 Basic: pH 7.01–14 Figure 2.12

Solutions of molecules that resist changes in pH Buffers Solutions of molecules that resist changes in pH pH of blood is maintained by carbonic acid-bicarbonate buffering system Carbonic acid dissociates, reversibly releasing bicarbonate ions & protons The chemical equilibrium between carbonic acid & bicarbonate resists pH changes in the blood H2O + CO2 H2CO3 H+ + HCO3ˉ

Unique to living systems - hence organic Organic Molecules Unique to living systems - hence organic Small molecules & macromolecules (biomolecules) Macromolecules are polymers of smaller organic molecules Major biomolecule groups Carbohydrates Lipids Proteins Nucleic Acids

Monosaccharides or simple sugars Carbohydrates Major functions energy source structural support (plants, fungi & bacteria) parts of other macromolecules Monosaccharides or simple sugars

Carbohydrates Disaccharides

Carbohydrates Polysaccharides - polymers of simple sugars Each monosaccharide is a residue Glycogen - energy storage in animals Starch – energy storage in plants Cellulose – support structures in plants Figure 2.13c

Carbohydrates in other Biomolecules Glycoproteins & proteoglycans Proteins containing sugar residues Glycolipids Phospholipids with sugar residues Ribose & Deoxyribose sugars part of nucleotides & nucleic acids

Lipids Representatives Neutral fats – triglycerides - adipose tissue Phospholipids – chief component of cell membranes Steroids – cholesterol, bile salts, vitamin D, hormones Vitamins A, E & K Eicosanoids – prostaglandins

Fatty Acids & Triglycerides

Phospholipids Figure 2.14b

Phospholipids in membranes Phospholipids make up cellular membranes (lipid bilayers)

Steroid Lipids

Used to make prostaglandins Eicosanoids – Used to make prostaglandins

Polymers of amino acids Protein Polymers of amino acids Figure 2.16

Amino Acids Building blocks of protein, containing an amine group, a carboxyl group, & a variable side chain

Structural Levels of Proteins

Structural Levels of Proteins

Structural Levels of Proteins Figure 2.17d, e

Fibrous & Globular Proteins Fibrous proteins Extended & thread-like proteins Examples: keratin, elastin, collagen, myosin, actin Globular proteins Compact, spherical proteins with tertiary & quaternary structures Examples: antibodies, peptide-hormones, & enzymes

Characteristics of Enzymes Proteins that are biological catalysts Chemically specific Usually named for the reaction they catalyze Names often end in suffix -ase

Protein Function - Enzymes Protein & substrate fit together in a specific way due to H-bonds, ionic bonds & non-polar interactions Figure 2.18a

Mechanism of Enzyme Action Active site Substrates 1 Enzyme (E) Substrates (s) Enzyme-substrate complex (E–S) H20 Free enzyme (E) 2 3 Covalent bond Internal rearrangements leading to catalysis Product (P)

Polymers of nucleotides Nucleotide is Nucleic Acids Polymers of nucleotides Nucleotide is N-containing base pentose sugar phosphate group DNA & RNA

Nucleotides – The Bases

Nucleotides – The Sugars for RNA for DNA

Nucleosides – Sugar + Base Deoxyadenosine

Nucleotide – Nucleoside + Phosphates

Nucleic Acids – Polymers of Nucleotides

Complementary base-pairing A-T G-C Structure of DNA Complementary base-pairing A-T G-C Figure 2.21a

Deoxyribonucleic Acid (DNA) Double-stranded helical molecule Constitutes chromosomes in nucleus Replicates ensuring genetic continuity Provides instructions for protein synthesis

Ribonucleic Acid (RNA) Contains the base uracil in place of thymine Made from a DNA template Three major varieties of RNA: mRNA – encodes a protein tRNA – conveys amino acid to ribosome as directed by mRNA rRNA – joins amino acids together to form protein as directed by mRNA

Adenosine Triphosphate (ATP) Source of immediately usable energy for the cell Figure 2.22

How ATP Drives Cellular Work Figure 2.23