Ch i t f LifChemistry of Life

BiochemistryChapter 2

y

Chapter 3Chapter 3

Everything in the universe is made up of

MatterMatter is anything that occupies space and has mass.

M th tit f tt bj t hMass: the quantity of matter an object has.

Are mass and weight the same?

ATOMSATOMSThe smallest particle of matter that can existThe smallest particle of matter that can exist

and still have the properties of a particular kind of matterkind of matter.

Atoms are composed of:1 N l t l t f th t1. Nucleus – central part of the atom2. Protons – positively charged particles (+)3. Neutrons – uncharged particles4. Electrons – negatively charged particles (-)

electrons

Electron Energy LevelsElectron Energy LevelsSubdivisions of the electron cloud where electrons are

located. Also called orbitals.7 energy levels known to date• 1st energy level holds a max of 2 electrons• 2nd energy level holds a max of 8 electrons

3rd energy level holds a max of 18 electrons• 3rd energy level holds a max of 18 electrons• 4th energy level holds a max of 32 electrons.

# of protons = # of electrons, atom is electrically neutral.Atomic # = # protons; #N = atomic mass # - Atomic #

IsotopesIsotopes Atoms of the same element that have differentAtoms of the same element that have different

number of neutrons.

ElementsElements

http://www.chemsoc.org/viselements/pages/page3.html

Substances that are made up entirely ofSubstances that are made up entirely of atoms of the same kind and cannot be divided into simpler substances bydivided into simpler substances by ordinary chemical means.

C H N

S b l h th d th d f ti

O P S

Symbol – a shorthand method of representing an element.

How many protons, electrons, and neutrons are found i th f ll i t ?in the following atoms?

Calcium – Iodine –Ca I

protons –

electrons –

t

protons –

electrons –

t

20

20

53

53

74neutrons - neutrons -20 74

Gold –

protons –

electrons

Au

79

79electrons –

neutrons -

79

118

Molecule the smallest part of a substance that has allMolecule – the smallest part of a substance that has all the chemical properties of that substance. Made up of atoms of the same or different kinds of atoms.

Compound – matter made up of 2 or more atoms that are chemically combined from different elements.are chemically combined from different elements.

H O NH O 2NaCl 4H CO HeH2O NH3 O2 2NaCl 4H2 CO2 He

Chemical ReactionsChemical ReactionsOne or more substances change to produce one or g p

more different substances.If the reaction proceeds in only one direction:

reactants: shown on the left side of the equationproducts: shown on the right side

Some chemical reaction can proceed in either direction and a two directional arrow is used:

CO2 + H20 H2CO3

Activation EnergyActivation Energy

The amount of energy needed to start a tireaction.

Oxidation Reduction ReactionsOxidation Reduction Reactions•Also known as redox reactions.

•Reactions in which electrons are transferred between atoms.

2 t2 types:

oxidation reaction: a reactant loses one or more electrons becoming more positive in chargeelectrons becoming more positive in charge.

reduction reaction: reactant gains one or more electrons becoming more negative in charge.electrons becoming more negative in charge.

N + + Cl N ClNa+ + Cl- NaCl

Chemical BondsChemical Bonds

The forces that hold atoms together in a molecule.2 types: a) Ionic

b) Covalent

Ionic BondsIonic BondsThe attraction of positive ions for negativeThe attraction of positive ions for negative

ions.Ion: an element that has lost or gained g

electrons.positive ion: when atom loses electron (cation)p ( )negative ion: when atom gains electron (anion)

Ionic Bond

11P

12N

17P

18N

Na Clanion

+ -

cation anion

Covalent BondCovalent BondThe bond that forms between atoms when they sharey

electrons.

H22

+

H2O

+ +

Types of Chemical ReactionsTypes of Chemical ReactionsSynthesis: 2 or more substances combine, f i th b tforming another substances.

A + B ABA + B AB

Na + Cl NaClNa + Cl NaCl

Decomposition: one substance breaks downDecomposition: one substance breaks down into simpler substances.

AB A + BNaCl Na + Cl2

Single-replacement: one element replaces a similar element in a compound.

AB + C A + CB

C C2HCl + Mg H2 + MgCl2Cl + 2KBr 2KCl + BrCl2 + 2KBr 2KCl + Br2

Double-replacement: the 2 compounds exchange l i l ti t f 2 d

Double -

places in a solution to form 2 new compounds.

Double AB + CD AD + CB

FeS + 2HCl FeCl2 + H2S

HCl + NaOH HOH +NaClHCl + NaOH HOH +NaCl

Balancing Chemical EquationsBalancing Chemical Equations

1. Identify the components of the equation (elements y p q (and/or compounds)

2. Determine the number of atoms for each element.

3. Select an element from one side and balance it with the same element on the other side.

4. Start all over and see if the elements balance with each other.

5. Continue to balance the other elements. Each time a change is made, start all over to determine what is balanced and what is not.

DO’s & DON’TsDO s & DON Ts1. Numbers can ONLY be placed in p

FRONT(coefficient) of the element or compound2. Numbers CANNOT be placed in between elements

t th d f l t dor at the end of an element or compound as a subscript.

3. Subscripts CANNOT be changed.3. Subscripts CANNOT be changed.4. Always express coefficients in lowest whole

number.

H + Cl2 HCl Yes H2O H2 + O2 Yes2 2 2 2

Na + O2 Na2O2 NO2

Practice ExercisePractice Exercise

HgO Hg + O22 2HgO Hg + O22 2

Zn + HCl ZnCl + H2Zn + HCl ZnCl2 + H22

C7H16 + O2 CO2 + H2O11 7 8

• The ability to do work and cause changeThe ability to do work and cause change• Required to make and maintain order

Energy and Matter: States of MatterEnergy and Matter: States of Matter

• All atoms and molecules in a substance are in constant motion.

Solid: maintains a fixed volume and shapeSolid: maintains a fixed volume and shapeLiquid: maintains a fixed volume, but its particles move

more freely than those of a solid; conforms to the y ;shape of any container.

Gas: have little or no attraction to each other and they fill th l f th t i thfill the volume of the container they occupy.

Water and SolutionsWater and Solutions

P l it d ib h ll b diPolarity: describes how equally bonding electrons are shared between atoms.

• Water is a polar compound because of its• Water is a polar compound because of its uneven distribution of charge, even though its total charge is neutral.its total charge is neutral.

• Water’s polar nature allows it to dissolve polar substances. It does not dissolve pnonpolar substances.

Hydrogen BondingHydrogen BondingThe force of attraction between a hydrogen molecule

with a partial positive charge and another atom or molecule with a partial or full negative charge.

• Hydrogen bonds form, break, and reform with great frequencyq y

• Accounts for the unique properties of water:cohesiondh iadhesion

ability to absorb relatively large amounts of energy as heatgy

ability to cool surfaces through evaporationability to dissolve many substancesd it f idensity of ice

Cohesion and AdhesionCohesion: an attractive force that holds molecules of a

single substance together.

Cohesion due to hydrogen bonding between water molecules contributes to the upward movement of water from plant roots to their leaves.p

Surface tension: cohesive forces of water resulting fromSurface tension: cohesive forces of water resulting from hydrogen bonds causing molecules at the surface of water to be pulled downward into the liquid; water acts like it has a thin “skin” on its surfacelike it has a thin “skin” on its surface.

Adhesion: the attractive force between two particles of different substances, such as glass and water moleculesmolecules.

Capillarity: the attraction between molecules that results in the rise of the surface of a liquid when in contact with a solidcontact with a solid.

Temperature Moderation

• Water has a high heat capacity – can absorb or release relatively large amounts of energy in the f f h t ith l li ht h i t tform of heat with only slight changes in temperature.

• Allows organisms to keep cells at an even temperature despite temperature changes in thetemperature despite temperature changes in the environment.

• Evaporative cooling prevents organisms that live on fland from overheating.

Density of Ice

• Solid water is less dense than liquid water.• When water forms solid ice, the angles in the , g

molecules cause ice crystals to have large amounts of open space causing it to have a low density.B di f t d d l k f f th• Bodies of water, ponds and lakes, freeze from the top down. Ice insulates the cold water below the cold air.

SolutionsSolutionsA mixture in which one or more substances are

uniformly distributed in another substance.Solute: substance dissolved in the solvent.Solvent: the substance in which the solute is

dissolved.Concentration: the amount of solute dissolved in aConcentration: the amount of solute dissolved in a

fixed amount of the solution. The more solute dissolved, the greater the concentration of solution.

Saturated solution: one in which no more solute can dissolve.

Aqueous solution: solutions in which water is theAqueous solution: solutions in which water is the solvent

Acids & BasesAcids & Bases

Water dissociates or separates into 2Water dissociates, or separates, into 2 ions:

a positive hydrogen ion (H+)a positive hydrogen ion (H+)a negative hydroxide ion (OH-)

Represented as:pH2O H+ + OH-

AcidAcid

A chemical that produces hydrogen ionsA chemical that produces hydrogen ions in a water solution.

Ex: HCl H2SO4Hydrochloric acid Sulfuric acid

The chemical formulas for acids always begin with H (hydrogen).always begin with H (hydrogen).

BaseBase

A chemical that produces hydroxide ionsA chemical that produces hydroxide ions in a water solution. (The chemical formulas for bases always end in OH )formulas for bases always end in OH.)

Ex: NaOHSodium hydroxideSodium hydroxide

General Formula:General Formula:Acid + Base Salt + Water

HCl + NaOH NaCl + H OHCl + NaOH NaCl + H2O

Scale used for measuring the hydrogen ion g y glevel of a solution.

Ranges from 0 to 14g

Solution w/a pH of 7 is neutral. # of H+ = # of OH-

Solution w/a pH below 7 is acidic. # of H+ > # of OH-

Solution w/a pH above 7 is basic. # of H+ < # of OH-Solution w/a pH above 7 is basic. # of H # of OH7

0 6.9 7.1 14

Substance pHpVinegar

Human Blood2.2

7.4Human BloodBattery AcidAmmonia

1.0

11 0AmmoniaMilk

Pure Water

11.0

6.6

7 0Pure WaterMilk of Magnesia

7.0

10.5

Carbon CompoundsCarbon CompoundsOrganic compounds: compounds made primarily of g p p p y

carbon. Must have a carbon-carbon, carbon-hydrogen bond, or both.

I i d d t t i b ithInorganic compounds: do not contain carbon, with a few exceptions.

H O CCl NH CH COH2O CCl4 NH3 CH4 CO2

Carbon

• Has four electrons in its outermost energy level.gy• Forms four covalent bonds.• Can form straight chains, branched chains, and

rings.

2-methylbutane Glucose

propane

• Can form single, double and triple bonds.

Methane

Propene

EthyneEthyne

Functional GroupsClusters of atoms that influence the characteristics of a

molecule they compose and the chemical reactions the molecules undergo.the molecules undergo.

OH – can make molecule polar; soluble in water (hydrophilic); alcohol – organic compound with a hydroxyl group attached to a carbon atom.

Propanol

COOH – carboxyl group; present in amino acids and carboxylic groups.

Methanoic acidFormic acid

NH2 – amino group; part of the structure of amino acids.

General formula for aminoGeneral formula for amino acids

PO4 – Phosphate group; One of three components of a nucleotide, comprised of a central phosphorous surrounded by four oxygens.

Phosphoric acid

Large Carbon MoleculesLarge Carbon MoleculesMonomers: small, simple carbon molecules., pPolymers: molecule that consists of monomers bonded

together.Macromolecules: large polymers.Condensation reaction: chemical reaction in which two

or more molecules combine to produce anotheror more molecules combine to produce another molecule along with water.

Hydrolysis: process in which complex molecules, such as polymers, are broken down.

CARBON: the most important element to life.

4 basic kinds of carbon-containing molecules:4 basic kinds of carbon containing molecules:Carbohydrates

Lipids

Proteins

Nucleic Acids

Carbohydrates – the body’s main source of energy.

ex: sugars and starchesg3 types:• Monosaccharides – sugars that contain only 7 or

fewer carbons in each molecule. Known as simple sugars.

ex: glucose – produced by green plants duringex: glucose – produced by green plants during photosynthesis. It supplies the energy for a cell’s metabolic activity.

C6H12O6

fructose: found in fruits, honey, & vegetables

C6H12O66 12 6

C6H12O6

Disaccharides: produced when 2 monosaccharides chemically combine; y ;double sugar

ex: sucrose – composed of glucose and p gfructose; table sugar

+ H O+ H2O

C12H22O11C12H22O11

Polysaccharides: large molecules formed whenPolysaccharides: large molecules formed when many monosaccharides bond together.

ex: cellulose – used to make the rigid walls of a new plant cell.

ex: starch: made of many glucose molecules bonded together; produced by plants; an g ; p y p ;important storage compound in plants.

The chief carbohydrate used yby animals for energy storage.

Lipids: large, nonpolar molecules; do not dissolve in water; composed of C,H, & O

Fatty Acids: y• Unbranched carbon chains that make up most lipids.• Has two ends:

the carboxyl end is polar (hydrophilic)the hydro-carbon end is nonpolar (hydrophobic)

S f• Saturated fats: each carbon atom is covalently bonded to four atoms.

• Unsaturated fats: carbon atoms are not bonded toUnsaturated fats: carbon atoms are not bonded to the maximum number of atoms.

Triglycerides:• composed of three fatty acid molecules joined to

l l f l lone molecule of glycerol.• Saturated triglycerides include butter and fats• Unsaturated triglycerides are found in plant seeds;Unsaturated triglycerides are found in plant seeds;

they serve as an energy and carbon source for germinating plants.

Fat that is either stored in body tissues or circulating in the blood.the blood.

Phospholipids: • two fatty acid molecules attached to a molecule oftwo fatty acid molecules attached to a molecule of

glycerol.• Cell membrane is made up of a phospholipid bilayer.Waxes: • long fatty acid chain attaches to a long alcohol

chainchain.• Waterproof• Protective coating in plants and animalsProtective coating in plants and animalsSteroids: • Composed of four fused carbon rings with various

functional groups attached to them.• Many animal hormones are steroids; testosterone

M t t id i h l t l• Most common steroid is cholesterol.

1 g. of fat contains more than 2x as much1 g. of fat contains more than 2x as much chemical energy as 1g. of carbohydrate; fats are better storage compounds.

PROTEINS: form part of the structure of cells; form enzymes.Amino acids: subunits of proteinAmino acids: subunits of protein• contain C,H,N,O (2 a.a. contain S)• 20 different kinds of a a that can be found in20 different kinds of a.a. that can be found in

a protein molecule.• Bond together as peptide bondsBond together as peptide bonds• There are 3 types of bonds

1. Dipeptide: 2 a.a. linked together.2. Tripeptide: 3 a.a. linked together2. Tripeptide: 3 a.a. linked together3. Polypeptide: a long chain of a.a

dipeptide

tripeptidetripeptide

polypeptide

catalysts: compounds that speed up or slows d ti / it lf b i t f thdown a reaction w/o itself being part of the substances reacting.

enzymes: the specialized and highly specific catalysts present in organisms.

ex: amylase – enzyme found in saliva

catalase – catalyzes the decompositioncatalase catalyzes the decomposition of hydrogen peroxide into water and oxygen.

H2O2 H2O + O22 2

Enzymes: large, complex proteins made yby the cell; promote reactions but are not used up in the reaction (catalyst). One enzyme

l l l t th timolecule can complete the same reaction thousands of times in a single minute.

Active site: small part of the enzyme that attaches to the substrate so a specific reaction can take place.p p

Substrate: molecule that fits into an active site to begin a chemical reaction.

f“Enzymes and substrates fit together like a lock and key.”

Nucleic Acids: the hereditary or genetic material for all organisms important in encoding instructions for cell processes. Composed of C,H,N,O,P

2 types of nucleic acids:yp• DNA – deoxyribonucleic acid. Determines the

genetic characteristics of the cell and the gorganism.

• RNA – ribonucleic acid. Required for the synthesis of proteins, including enzymes.

Nucleotides: subunits of both DNA & RNA made up of 3 small molecules linked together:

a phosphate groupa 5-C sugara nitrogen baseg