1

BIOCHEMISTRYBIOCHEMISTRY

The chemical The chemical

basis of lifebasis of life

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ATOMSATOMS Basic unit of matterBasic unit of matter Two regionsTwo regions

NucleusNucleus Electron cloudElectron cloud

Atomic particlesAtomic particles Protons Protons

• Positively charged particles Positively charged particles • Located in the nucleusLocated in the nucleus

Neutrons Neutrons • Neutral particlesNeutral particles• Located in the nucleus & act as the glue thereLocated in the nucleus & act as the glue there

Electrons Electrons • Negatively charged particlesNegatively charged particles• Located in the electron cloudLocated in the electron cloud• These are the particles involved in chemical These are the particles involved in chemical

reactionsreactions

CC66

CarbonCarbon

12.01112.011

Atomic

Atomic

Number

Number

33

ElementsElements Elements Elements

Contain all of the same type of atom Contain all of the same type of atom within the elementwithin the element

Elements of LifeElements of Life• 96% 96% Carbon (C), Hydrogen (H), Oxygen Carbon (C), Hydrogen (H), Oxygen

(O), and Nitrogen (N)(O), and Nitrogen (N)• 3% 3% P, S, Ca, K, Na, Mg, Fe, Cl P, S, Ca, K, Na, Mg, Fe, Cl • 1% 1% other trace elements other trace elements

44

IsotopesIsotopes IsotopesIsotopes

Elements that contain a different Elements that contain a different number of neutronsnumber of neutrons

Radioactive isotopes will breakdown Radioactive isotopes will breakdown at a specific rate and are used in at a specific rate and are used in figuring the age of different things figuring the age of different things (i.e. fossils & rocks)(i.e. fossils & rocks)Nonradioactive carbon-12Nonradioactive carbon-13 Radioactive carbon-

14

6 protons6 protons6 electrons 6 electrons 6 neutrons6 neutrons

6 protons6 protons6 electrons6 electrons8 neutrons8 neutrons

6 protons 6 protons 6 electrons 6 electrons 7 neutrons7 neutrons

All of these are carbon because they have 6 protons. They are just different forms of carbon.

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IonsIons Charged atoms formed when

electrons are gained or lost.Sodium atom (Na)Chlorine atom (Cl)Sodium ion (Na+)Chloride ion (Cl-)

Transferof electron

Protons +11Electrons -11Charge 0

Protons +17Electrons -17Charge 0

Protons +11Electrons -10Charge +1

Protons +17Electrons -18Charge -1

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CompoundsCompounds Elements combine chemically to Elements combine chemically to

form compounds.form compounds. Compounds are held together by Compounds are held together by

chemical bonds which are based chemical bonds which are based upon the individual elements upon the individual elements desire for 8 outer electrons.desire for 8 outer electrons.

In compounds, all atoms are In compounds, all atoms are stable having 8 valence stable having 8 valence electrons.electrons.

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Chemical BondsChemical Bonds Ionic BondsIonic Bonds: :

Elements become compounds by giving and Elements become compounds by giving and taking electrons to have 8 outer electrons. This taking electrons to have 8 outer electrons. This leaves them with a charge. Opposite charges leaves them with a charge. Opposite charges attract…and a bond is formed holding a positive attract…and a bond is formed holding a positive ion to a negative ion. (Occurs inside compounds)ion to a negative ion. (Occurs inside compounds)

Covalent BondsCovalent Bonds: : Elements become compounds by sharing Elements become compounds by sharing

electrons between two atoms. This sharing electrons between two atoms. This sharing leaves them bound together as a compound. leaves them bound together as a compound. (Occurs inside compounds)(Occurs inside compounds)

Hydrogen bondsHydrogen bonds: : Bonds that hold hydrogen-containing molecules Bonds that hold hydrogen-containing molecules

together. This is why water forms beads. together. This is why water forms beads. (Occurs between molecules…outside of (Occurs between molecules…outside of compounds)compounds)

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Water (HWater (H22O)O) Most abundant compound in Most abundant compound in

organismsorganisms Many unique properties that Many unique properties that

make water so versatile & so make water so versatile & so important to lifeimportant to life

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Water (HWater (H22O)O) PolarityPolarity

Unequally shares electrons Unequally shares electrons between hydrogen & oxygen between hydrogen & oxygen atomsatoms

Makes it possible for other Makes it possible for other compounds to dissolve in watercompounds to dissolve in water

Water has hydrogen bondsWater has hydrogen bonds AdhesionAdhesion

• HH22O sticking to other substances O sticking to other substances CohesionCohesion

• HH22O molecules sticking to other HO molecules sticking to other H22O O moleculesmolecules

Surface tensionSurface tension• Measure of how difficult it is to stretch Measure of how difficult it is to stretch

or break the surface of a liquidor break the surface of a liquid Capillary actionCapillary action

• Combination of cohesion & adhesion (used Combination of cohesion & adhesion (used in the uptake of water in plants)in the uptake of water in plants)

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Water (HWater (H22O)O) Solvent abilitiesSolvent abilities

Occur because of its Occur because of its polaritypolarity

Hydrophobic(water-Hydrophobic(water-fearing)fearing)• Non-polar compounds that Non-polar compounds that

are NOT water solubleare NOT water soluble Hydrophillic (water-loving)Hydrophillic (water-loving)

• Polar & Ionic compounds Polar & Ionic compounds that are water solublethat are water soluble

Most biochemical reactions Most biochemical reactions involve solutes dissolved involve solutes dissolved in waterin water

Figure 2.14

Ions in solution

Salt crystal

Cl–

Na+

Cl–

–

– –

–

–Na+

+

+

+

+

1111

pH scale & bufferspH scale & buffers The pH of The pH of

substances substances ranges from 0-14 ranges from 0-14 7 = neutral7 = neutral 0-6.9 = acid0-6.9 = acid 7.1-14 = base7.1-14 = base

BuffersBuffers Prevent sharp, Prevent sharp,

sudden changes sudden changes in pH so that the in pH so that the body can maintain body can maintain homeostasishomeostasis

pH of most fluids pH of most fluids in the body = 6.5-in the body = 6.5-7.57.5

Figure 2.15

pH scale

Acidic solutionAcidic solution

Neutral solution

Basic solutionIn

crea

sin

gly

AC

IDIC

(Hig

her

co

nc

entr

atio

n

of

H+)

Incr

easi

ng

ly B

AS

IC(L

ow

er

con

cen

trat

ion

of

H+)

NEUTRAL[H+] = [OH–]

Lemon juice; gastric juiceGrapefruit juice

Tomato juice

Urine

PURE WATER

Seawater

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Human blood

H+

OH–

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Organic vs. InorganicOrganic vs. Inorganic All compounds can be separated All compounds can be separated

into two groups: into two groups: InorganicInorganic

• Doesn’t contain carbonDoesn’t contain carbon• Non-livingNon-living• Examples: Oxygen gas, metals, rocks, Examples: Oxygen gas, metals, rocks,

water water OrganicOrganic

• Contains carbonContains carbon• Living (or dead)Living (or dead)• Examples: wood, grass, diamonds, Examples: wood, grass, diamonds,

petroleumpetroleum

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PolymerizationPolymerization MonomersMonomers

One unit of a compoundOne unit of a compound PolymersPolymers

Many monomers combine to make Many monomers combine to make a polymera polymer

MacromoleculesMacromolecules Many large molecules combined Many large molecules combined

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Combining monomers to Combining monomers to make polymersmake polymers

Dehydration Dehydration synthesissynthesis Each monomer Each monomer

is added as a is added as a water molecule water molecule is released is released

Energy is Energy is requiredrequired

Anabolic Anabolic processprocess

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Breaking polymers into Breaking polymers into monomersmonomers

Hydrolysis The reverse of

dehydration synthesis

Breaks bonds between monomers by adding water molecules

Energy is released Catabolic process

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CarbohydratesCarbohydrates Made of C, H, & OMade of C, H, & O FunctionsFunctions

Main energy source in organismsMain energy source in organisms Structural component in plantsStructural component in plants

TypesTypes Sugars Sugars

• gives off energy when broken downgives off energy when broken down• Cellulose Cellulose twisted chain of sugars, not digestible by twisted chain of sugars, not digestible by

humanshumans• Chitin Chitin hard cellulose found in the exoskeletons of hard cellulose found in the exoskeletons of

invertebratesinvertebrates• Ex. Sucrose, fructose, glucoseEx. Sucrose, fructose, glucose

Starches Starches • used as a storage molecule for sugarsused as a storage molecule for sugars

• Many athletes eat these before eventsMany athletes eat these before events• Ex. Bread, rice, pasta, cornEx. Bread, rice, pasta, corn

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CarbohydratesCarbohydrates Monosaccharides are single-unit sugars Monosaccharides are single-unit sugars These molecules typically have a formula that is These molecules typically have a formula that is

a multiple of CHa multiple of CH22O O Each molecule contains hydroxyl groups Each molecule contains hydroxyl groups

and a carbonyl groupand a carbonyl group Monosaccharides are the fuels for cellular workMonosaccharides are the fuels for cellular work Monosaccharides can join to form disaccharides, Monosaccharides can join to form disaccharides,

such as sucrose (table sugar) and maltose such as sucrose (table sugar) and maltose (brewing sugar)(brewing sugar)

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Figure 3.7

Starch granules in potato tuber cells

Glucosemonomer

STARCH

GLYCOGEN

CELLULOSE

Glycogen granules in muscle tissue

Cellulose fibrils ina plant cell wallCellulosemolecules

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LipidsLipids Made of C, H, O Made of C, H, O

in the form of glycerol and fatty acid chainsin the form of glycerol and fatty acid chains Commonly called fats, oils, & waxesCommonly called fats, oils, & waxes FunctionsFunctions

Storage of energyStorage of energy Parts of biological membranesParts of biological membranes Water proof coveringsWater proof coverings Chemical messengers (steroids)Chemical messengers (steroids)

Insoluble in waterInsoluble in water Ex. Lard, butter, oil, hormones, steroids Ex. Lard, butter, oil, hormones, steroids

2020

Saturated fats (lard) lack double bondsSaturated fats (lard) lack double bonds They are solid at room temperatureThey are solid at room temperature

Fatty acid

Figure 3.8C

Figure 3.8B

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Nucleic acidsNucleic acids Made of C, H, O, N, & PMade of C, H, O, N, & P Monomers are called Monomers are called

nucleotidesnucleotides Nucleotides are made up Nucleotides are made up

of a 5-carbon sugar, of a 5-carbon sugar, phosphate group and a phosphate group and a nitrogen basenitrogen base

FunctionsFunctions Store hereditary Store hereditary

informationinformation Transmit hereditary Transmit hereditary

informationinformation Two typesTwo types

RNA (ribonucleic acid)RNA (ribonucleic acid) DNA (deoxyribonucleic DNA (deoxyribonucleic

acid)acid)

Phosphate

groupSugar

Figure 3.20A

Nitrogenous

base (A)

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ProteinsProteins Made of C, H, O, & NMade of C, H, O, & N Monomers are amino acidsMonomers are amino acids

There are 20 different amino There are 20 different amino acids that combine in different acids that combine in different ways to make millions of proteinsways to make millions of proteins

The most diverse The most diverse macromoleculesmacromolecules

FunctionsFunctions Control the rates of chemical Control the rates of chemical

reactions (enzymes)reactions (enzymes) Regulate cell processesRegulate cell processes Used to form bone & musclesUsed to form bone & muscles Transport substances into or out Transport substances into or out

of cellsof cells Help fight diseaseHelp fight disease

Aminogroup

Carboxyl (acid)group

Figure 3.12A

2323

Figure 3.15, 16

Amino acid

Hydrogen bond

Pleated sheet

Primarystructure

Secondarystructure

Figure 3.17, 18

Polypeptide(single subunitof transthyretin)

Transthyretin, with fouridentical polypeptide subunits

Tertiarystructure

Quaternarystructure

Alpha helix

2424

EnzymesEnzymesReaction pathwaywithout enzyme Activation energy

without enzyme

Activationenergywith enzyme

Reaction pathwaywith enzyme

Reactants

Products

Special PROTEINSSpecial PROTEINS Act as biological catalystsAct as biological catalysts

CatalystCatalyst• Substance whose job is to speed up the rate of a Substance whose job is to speed up the rate of a

chemical reactionchemical reaction

Act by lowering the activation energy Act by lowering the activation energy of the reactionof the reaction

Are very specific with respect to the Are very specific with respect to the reactions that they will catalyze…reactions that they will catalyze… They will only catalyze one specific They will only catalyze one specific

substance because they actually bind with substance because they actually bind with that substance in a unique waythat substance in a unique way