1.1 Chemical Fundamentals. Living things are composed of matter. Matter has mass, occupies space. Atoms composed of: Small nucleus Proton (positive.

Unit 1 Metabolic Processes The Chemical Basis of Life

Unit 1 Metabolic ProcessesThe Chemical Basis of Life1.1 Chemical FundamentalsChemical Fundamentals Review Living things are composed of matter. Matter has mass, occupies space.Atoms composed of: Small nucleusProton (positive charge)Neutron (no charge)Surrounded byElectrons (negative charge)

IsotopesAtoms of an element with the same atomic number but a different mass numberNumber of protons ALWAYS stays the sameNumber of neutrons changes which distinguishes isotopes from one anotherBecause they have the same number of electrons, all isotopes of an element have the same chemical properties.a

Nonradioactive carbon-12Nonradioactive carbon-13Radioactive carbon-146 electrons6 protons6 neutrons6 electrons6 protons8 neutrons6 electrons6 protons7 neutronsCarbon - 14Known as a radioisotopenucleus of some isotopes spontaneously breaks apart or decays resulting in the formation of different elementsCarbon-14 spontaneously decays into nitrogen-14Radioisotopes each have a unique property called a half lifeThe time it takes for one half of the neclei sample to decay

Uses of RadioisotopesCarbon datingRadioactive tracers Follow chemicals path through chemical reactions as they move through the cellDiagnosis and treatmentCancer

Why are Electrons so Important? The chemical behaviour of an atom is determined by its electron configuration that is, the distribution of electrons in the atoms electron shells.

The chemical behaviour of an atom depends mostly on the number of electrons in its outermost shell. (= valence electron/shell)

All atoms with incomplete valence shells are chemically reactive and are responsible for the formation of chemical bonds between atoms.

Octet Rule = atoms tend to gain, lose or share electrons so as to have 8 electronsC would like to N would like toO would like toH would like toGain 4 electronsGain 3 electronsGain 2 electronsGain 1 electronLewis Dot DiagramsDiagrams of the elements only showing valence electrons.

Atoms bond to form compounds Compounds are made up of at least 2 different kinds of atoms (e.g., H2O)

Bonds are formed by the sharing or transfer of electrons

2 Types of Chemical BondsIonic BondsCovalent bonds

Ionic Bonds occur when one atom donates or gives up one or more electrons

Ionic Compound ( Na+Cl-) Salt crystalsOpposite charges attract to form ionic bonds

Covalent Bonds involve a sharing of a pair of valence electrons between atoms.Figure. 1.5, p.10

Single covalent bondDouble covalent bondFour single covalent bondsTwo single covalent bonds2 Types of Covalent BondsPolar CovalentNon-polar covalentEqual sharing of electronsUnequal sharing of electronsDetermined by the atoms ELECTRONEGATIVITYE.g. H2O2E.g. H2OElectronegativitythe measure of an atoms attraction for additional electrons

Polar Covalent Bond - unequal sharing of electrons between two atoms with different electronegativity results.

Non-Polar Covalent Bond equal sharing of electrons between two atoms. Electronegativity = Stronger pull of shared electrons

The electronegativity difference (En) is the difference in electronegativity number between two atoms participating in a covalent bond.

Electronegativity Differences

Most Biological compounds contain: Carbon, Oxygen, Hydrogen, and NitrogenOxygen and Nitrogen form polar bonds with atoms of most other elementsCarbon and Hydrogen bonds are generally considered non-polar

Molecular PolarityDepends on Distribution of charges Molecular shape

Symmetrical molecular shapes produce non-polar molecules (whether bonds are polar or not)

Asymmetrical molecular shapes produce polar molecules

Balanced charges produce non-polar molecules

Non-balanced charges produce polar molecules

VSEPRValence shell electron pair repulsion

Electrons repel one another forming the shape of the molecule

Includes both bonded electron pairs and non-bonding electron pairs (lone pairs)

Polar MoleculesAlign themselves to other polar molecules

Soluble in water

Exclude non-polar molecules (oils and fats)Intermolecular Forcesintermolecular forces of attraction exist between molecules

Influence physical properties of a molecule(Solubility, Melting point, Brittleness etc)

Intermolecular forces are known as van der Waals forces. Example of van der Waals ForcesHydrogen BondsStrongest and most biologically significant Crucial to function of cells and cellular processesWeaker when compared with ionic and covalent bondsExample WATERProperties are high heat capacity, high melting point and boiling points, cohesion, adhesion, surface tension

Other van der Waals forcesLondon forces and dipole-dipole Weak forcesProminent in non-polar moleculesSize and shape of molecule influence strength of attraction (gas, liquid at room temperature)Chemical ReactionBreaking and formation of chemical bonds rearranging atoms and ions

4 TypesDehydration HydrolysisNeutralization Redox reactionsDehydrationAlso called condensation reactions

Removal of a OH (hydroxyl group) and a -H (hydrogen) from reactants to form a water molecule

Most common reaction used by cells

Assemble complex carbohydrates and proteinsDehydration Reaction Example

HydrolysisReverse of dehydration reactions

A water molecule is used to split a larger molecule

A hydroxyl group and a hydrogen attach to small sub units

Two products are formedHydrolysis

NeutralizationAcid reacts with a base to form water and a salt

Acid + Base Salt + WaterRedox Electrons are lost from one atom and gained by another

Oxidation is loss of electrons (OIL)

Reduction is gain of electrons (RIG)

Responsible for most energy transfers in cells

Waterhighly polar because of asymmetrical shape and polar covalent bondThe polarity of water molecules results in hydrogen boding

http://www.youtube.com/watch?v=Wnx9thXySGw

Hydrogenbonds++HH++ Like Dissolves LikeIonic compounds dissolve in water because the ions separate

Also includeSmaller polar covalent molecules (eg: sugars, alcohols) can dissolve in water, Small non-polar molecules (eg: O2, CO2) Does not includelarge non-polar molecules (eg: oils, fats)

Like Dissolves LikeHydrophilic water-loving; dissolves in water e.g. polar or ionic molecules, carbohydrates, saltsHydrophobic water-fearing; does not dissolve in water e.g. non-polar molecules, lipids

Autoionization of WaterReaction between 2 water molecules

Results in formation of a hydronium ion (HO) and a hydroxide ion (OH)

In equilibrium

Acids and BasesAcidic environment[HO] ions > [OH] ionsSour taste, conduct electricity, turn blue litmus paper redBasic Environment[HO] ions < [OH] ionsBitter taste, slippery feel, conduct electricity, turn red litmus paper blue pH scale measures the acidity of a solution

Strong and Weak Acids/Basesstrong acids and bases ionize completely when dissolved in waterHCl(aq) (100% H3O+(aq))NaOH(aq) (100% OH-(aq))weak acids and bases ionize only partially when dissolved in waterCH3COOH(aq) (1.3% H3O+(aq))NH3(aq) (10% OH-(aq))

BuffersThe internal pH of most living cells must remain close to pH 7BuffersDonate H+ ions or remove H+ ions to maintain a pH of 7E.g. carbonic acid creates bicarbonate ions (base) and hydrogen ions (acid) (reversible reaction)

CarbonMakes up the base of every organic moleculeForm 4 covalent bonds (single, double, triple)HydrocarbonsLong chains, rings, or branched structure of carbonChains can be linear or branched

CarbonIn Biological Molecules Carbon mostly bonds withHydrogenNitrogenSulfurOxygen

These elements provide biological molecules with different functional properties

Four categoriesCarbohydratesProteinsNucleic AcidsLipids

Functional GroupsFound on all 4 major classifications of biologically important molecules

Small reactive groups that participate in chemical reactions

Usually ionic or strongly polar (helps to initiate chemical reactions)

Form different types of bonding

Carbohydrates (Sugars)Biomolecule consisting of carbon, oxygen, and hydrogen.

General molecular formula (C H O) (CHO)

RolesEnergy source (foods, product of photosynthesis)Structural support Cell

Contain many functional groups

Hydrophilic

MonosaccharidesSimplest type of carbohydrate (Sugar)

Contains a single sugar unit (Eg; glucose, ribose, fructose, glyceraldehyde)

Most Common3 carbon (linear) triose5 carbon pentose ring6 carbon hexose ring

Link together to form disaccharides

Why?Folding into a ring occurs through a reaction between carbonyl group and hydroxy l group GlucoseHexose ringTwo possible arrangements - glucose glucose

Carbon atoms have assigned numbersUsed when discussing structures of sugars

Isomers same molecular formula, different structural formula

Linkages are designated or from the position of the OH group on the 1 carbonDisaccharidesConsist of two monosaccharides ( Eg; maltose, sucrose, lactose)

Joined together by a dehydration synthesis reaction

Glycosidic bond link monosaccharides together

Common linkages (between carbons)1 41 21 31 6Disaccharides

PolysaccharidesComplex carbohydrate, polymer

Chain of hundreds to thousands of monosaccharides (monomers) with many subunits

RolesEnergy storage (glycogen, starch)Structural support (cellulose and chitin)PolysaccharidesAssembled by dehydration reactionGlycosidic linkage

Linear unbranched hydrogen bonds form between molecules

Contain branches side chains of sugar units attach to main chain

Polar

Hydrophilic

Non-soluble in water

Polymerization linkage of identical or various monomers to form long chains

Examples

Amylose soluble component of starch

Glycogen energy storage in animals

Cellulose main component of plant cell walls

Chitin hard exoskeleton of insect and crustaceans LipidsNon-polar

Made up of mostly carbon and hydrogen

Not polymers

Do not dissolve in water

Roles Formation of cell membranes Energy source Hormones Vitamins

5 main categories Fatty acids Fats Phospholipids Steroids Waxes

Fatty AcidsDerivative of most lipids (structural backbone)

Consists ofSingle hydrocarbon chain (14 to 22)Carboxyl functional group at one end (-COOH)Gives the fatty acid its acidic properties

As chain length increases, insolubility in water increases

Fatty AcidsSaturated Max number of hydrogen atoms attached to carbonsSingle bonds throughout the carbon chain

UnsaturatedFormation of double bonds in carbon chainMonounsaturated one double bondPolyunsaturated many double bondsCauses a bent formation in molecule

Fats Consists of 1 to 3 fatty acid chainsGlycerol

Dehydration synthesisHydroxyl group of glycerol and carboxyl group of fatty acid

Can have identical/different fatty acid chains

Hydrophobic

Triglycerides Most well known fatContains 3 fatty acid chainsStored energy Yield more than twice as much energy as carbohydrates

Fats Saturated Long fatty acid chains all have single bonds between carbonsSolid at room temperatureButter, lard

Unsaturated (Cis/Trans)Short fatty acid chains contain double bonds between carbonsLiquid at room temperaturePlants, fish

PhospholipidsConsists of2 fatty acid chains - hydrophobic Glycerol Phosphate group contains a polar unit - hydrophilic

Amphipathic molecule Contains both hydrophobic and hydrophilic regions

PhispholipidsRolesLipid bilayer of cell membranes Hydrophilic end faces toward waterHydrophobic end faces inwardUnsaturated tail makes memebrane more permeable to water and small molecules

SteroidsConsists of Four fused carbon ringSide group

SterolsMost abundant Consists of Single polar OH group Non polar hydrocarbon chain Amphipathic moleculeEg; Cholesterol , Phytosterols

CholesterolFormed in the liver

Structural component of plasma membrane

FunctionMaintain membranesproper membrane permeability/fluidity

Types LDL low density lipoprotein Promote cardiovascular disease HDL high density lipoproteinGood cholesterol removes cholesterol from artery

Sex HormonesControl development of sexual traits and sex cells Eg; testosterone, estrogen, progesterone

Anabolic Steroids

WaxesConsist of Long fatty acid chainsAlcohol molecule or Carbon ring

Hydrophobic

Extremely non-polar

Soft Solids

FunctionsWaterproof coating on various plant and animal partsCutin plants conserve water and fights diseaseBeeswax production of honeycomb

ProteinsPolymer with many subunits

Folded into a 3-D structure PrimarySecondaryTertiary Quaternary

Folding allows protein to function

Structure specifies function of protein

Composed of Amino Acids (monomers)

Formed by dehydration synthesis reaction

Peptide bonds link amino acids together

Amino Acids20 different amino acids8 essential - supplied by diet

Contain:Central carbonAmino group (-NH)Carboxyl group (-COOH)R group

R groups give each amino acids specific characteristicsPolarity, acidity

Amino Acids

ProteinsTypes Structural framework support (Eg; hair, tendon, ligaments)Defensive infection fighters (Eg; antibodies)Signal messenger (Eg; hormones)Carrier transport of materials (Eg; hemoglobin)Recognition and Receptor cellular markers (Eg; major histocompatability complex)Enzyme catalyst (Eg; amylase)Motile movement (Eg; actin and myosin)Peptide BondCovalent bond between -NH group of one amino acid and COOH group of another.

Amino acids are only added to the C-terminal of a growing peptide

PeptideString of 1-49 amino acidsContains no side branchesPolypeptideString of 50 or more amino acids

Peptide Bond Formation

Protein StructurePrimary Structure Linear sequence of amino acids in polypeptide chainChanging one amino acid with change overall structure of protein

Protein Structure Secondary Structure Polypeptides fold or coil into patternsResult of hydrogen bonding-pleated sheetsSide-by-side alignment(Eg; strength of silk)-helix Coil that is held together by hydrogen bonds between every 4th amino acid(Eg; filamentous proteins, transmembrane proteins)

Protein StructureTertiary Structure3-D shape of a proteinIntermolecular reactions of amino acid R groups determines shapeIncludeIonic bondsHydrogen bondsHydrophobic interactions Non-polar side groups cluster when introduced to waterDisulfide bridgesBond formed from two cysteine amino acids (-SH group)Stabilizes proteins shape

Protein Structure Quaternary StructureComposed of 2 or more polypeptidesFunctional proteinsForms subunits Same bonds and forces as tertiary structure

Protein Prosthetic GroupsNon-protein componentsMetal ions (Fe Mg)

Needed for protein to function

Hemoglobin4 polypetide chains each with a heme groups Each group has s single iron ion (Fe) Oxygen binds to heme groups via (Fe)How many molecules of O can hemoglobin carry at one time?

Nucleic AcidsPolynucleotide chains serve as assembly instructions for all proteins in living organisms

2 TypesDNA deoxyribonucleic acidStores hereditary informationRNA Ribonucleic acidHereditary molecule of some virusesInvolved in protein synthesis

Composed of nucleotides

Linked by a phosphodiester bond

NucleotidesConsists ofNitrogenous baseUracil (U), thymine (T), cytosine (C), adenine (A), guanine (G)SugarPhosphate groups

FunctionsTransport chemical energyRegulate and adjust cellular activity

Nitrogenous Bases2 typesPyrimidinesUracil (U), Thymine (T), Cytosine (C)Purines Adenine (A), Guanine (G)

Phosphodiester BondLinks nucleotides togetherPhosphate bridge forms between the 5 carbon of one sugar and the 3 carbon of the next sugar.Forms the backbone of a nucleic acid chainNitrogenous bases project from the backbone

DNAConsists of Deoxyribose sugarPhosphate groupA, T, C, G

Double stranded molecule (Double Helix)Two strands of DNA run antiparallel to each other (opposite direction)5 to 3 5 is the end with the phosphate group3 is where deoxyribose sugar is located

Nitrogenous basesHeld together by hydrogen bondsA pairs with T ( forms double bond)C pairs with G (forms a triple bond) http://i-biology.net/2012/01/15/drew-berrys-animations-of-unseeable-biology-ted-talk/

RNAConsists ofRibose sugarPhosphate group A, U, C, G

Single stranded molecule

Converts information stored in DNA into proteins

Enzymes3-D biological catalystUsually a protein

Used in reactionsSpeeds up a chemical reaction Is not consumed Does not change products of the reactionLowers activation energy of reaction

Eg. Catalase breaks down the build up of hydrogen peroxide in the body

Enzyme Functionhttp://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

http://www.youtube.com/watch?v=hoBhOdQV7vw&list=PLBAC6D002DBAE5224

Binds substrate (reactant or reactants) at the active site (pocket in enzyme)Forms an enzyme-substrate complexEnzyme changes shape to better bind substrateInduced-fit model

Enzyme Cycle

Cofactors and CoenzymesEnzymes require them to function properlyCofactorNon-protein group that binds to an enzymeOften metals (Fe Cu)CoenzymeOrganic Derived from water-soluble vitaminsShuttle molecules from enzyme to anotherEg. NADFactors That Affect Enzyme ActivityEnzyme and substrate concentrationIncreasing enzyme concentration increases rate of reactionIncreasing substrate increases rate of reaction to a point called saturation level

Factors That Affect Enzyme ActivityTemperatureIncreasing temperature increases rate of reaction (collision between enzyme and substrate) 40C or higher Enzyme begins to denature

Factors That Affect Enzyme ActivitypHOptimal enzyme pH is 7 (most)Increasing or decreasing pH from optimal value decreases rate of reactionExceptions pepsin (1.5) trypsin (8)

Enzyme Inhibition (Toxic)http://www.youtube.com/watch?v=PILzvT3spCQ

Bind to an enzyme lowering the rate at which an enzyme catalyzes a reaction

Competitive InhibitionCompetes with normal substrate to bind at the active site of enzymeEg. Penicilin

Noncompetitive InhibitionBinds to enzyme at a location other than the active siteChanges shape of enzyme (substrate cannot bind)Toxic to the cell Eg. Cyanide

Feedback Inhibition (Natural Regulation)Regulates enzyme activity (allosteric regulation) Increases or decreases depending on concentration of productUse allosteric regulatorsBind to enzyme at an allosteric site (not the active site)

Enzyme Application