BIOCHEMISTRYBIOCHEMISTRY

Unit 3Unit 3

ELEMENTSELEMENTS

Can’t be broken downCan’t be broken down

25 essential for humans25 essential for humans

96%- C,H,N,O96%- C,H,N,O

4%-trace- Fe, I4%-trace- Fe, I

ATOMSATOMS Nucleus contains protons and neutronsNucleus contains protons and neutrons Proton (Proton (+ charge)+ charge) Neutron (no charge)Neutron (no charge) Electron Electron ( (-- charge) charge) travel around nucleus travel around nucleus

Atomic weight Atomic weight -- Atomic. number Atomic. number = Neutrons = Neutrons

Atomic weight = # protons +# neutronsAtomic weight = # protons +# neutrons

Each element has different # of protons(atomic Each element has different # of protons(atomic number)number)

ISOTOPESISOTOPES

Atoms of the same element, but with Atoms of the same element, but with different # of neutrons ( different # of neutrons ( different weightsdifferent weights))

Some radioactiveSome radioactiveC dating (C dating (1414C)C)

CompoundsCompounds

Substance composed of 2 or more atomsSubstance composed of 2 or more atomsStay together with bondsStay together with bonds2 types2 types

a. a. CovalentCovalent

b. b. IonicIonic

BONDSBONDS

COVALENTCOVALENT•Share electronsShare electrons•Molecules held together by covalent Molecules held together by covalent bondsbonds•Sometimes unequal sharing(polar molecule)Sometimes unequal sharing(polar molecule)

IONICIONICGain and lose electronsGain and lose electrons

Charged particlesCharged particlesNaNa+ + ClCl--

Cation + chargeCation + charge

Anion- chargeAnion- charge

Chemical ReactionsChemical Reactions

Bonds broken and formed between Bonds broken and formed between compoundscompounds

MetabolismMetabolismReactant + Reactant ProductReactant + Reactant ProductReactants must equal products Reactants must equal products

ex. Mg + 2Cl = MgClex. Mg + 2Cl = MgCl22

Mixture- combination of substances Mixture- combination of substances which retain their own propertieswhich retain their own properties

ex. Sand and sugar (no bonds broken)ex. Sand and sugar (no bonds broken)

Solution- Solution- solute(solid)solute(solid) evenly evenly

distributed in distributed in solvent(liquid)solvent(liquid)

ex. ex. KoolaidKoolaid and and waterwater

GatoradeGatorade andand water water

ACIDS AND BASESACIDS AND BASES

pH- measure of [HpH- measure of [H++]] ionsions

0-1-2-3-4-5-6-0-1-2-3-4-5-6-77--8-9-10-11-12-13-148-9-10-11-12-13-14

acidacid neutralneutral base base

Acid- forms [HAcid- forms [H++] ions ex. HCl- hydrochloric acid] ions ex. HCl- hydrochloric acid

Base- forms [OHBase- forms [OH--] ions ex. KOH- Potassium ] ions ex. KOH- Potassium HydroxideHydroxide

WATERWATER

Most important substanceMost important substance 70-90% of most organisms70-90% of most organisms Unique propertiesUnique properties

Polar moleculePolar molecule Oxygen keeps electrons closer and Oxygen keeps electrons closer and

Hydrogen has electrons farther awayHydrogen has electrons farther away

Causes O to have – chargeCauses O to have – charge

H has + chargeH has + charge

Amazing WaterAmazing Water

Polar molecule- sticks to itself (b/c of charged Polar molecule- sticks to itself (b/c of charged molecule (cohesion and adhesion)molecule (cohesion and adhesion)

Forms H bonds between 2 water moleculesForms H bonds between 2 water molecules Resists temperature change- requires more heat Resists temperature change- requires more heat

to raise 1 g/1°C (High Specific Heat)to raise 1 g/1°C (High Specific Heat) Sticks to itself-Sticks to itself-cohesioncohesion Sticks to other things- Sticks to other things- adhesionadhesion

Expands when it freezes-makes it float, which Expands when it freezes-makes it float, which makes ice’s density <1makes ice’s density <1

Life SubstancesLife Substances

CARBON- organicCARBON- organic C has 4 outer electrons- can make 4 strong C has 4 outer electrons- can make 4 strong

covalent bondscovalent bonds Can form Single,double, triple bondsCan form Single,double, triple bonds Can form chains, branched chains and ringsCan form chains, branched chains and rings Mono-(1), di- (2)Mono-(1), di- (2) Polymer-large molecule made of many small Polymer-large molecule made of many small

molecules(called a monomer)molecules(called a monomer)

CarbonCarbonC-CC-CC=CC=CCC= C= C

PolymerizationWhen several monomers are joined

together to form a polymer. Polymers can have as many as 2-2000 monomers .

Every Carbohydrate, lipid, protein and nucleic acid is a polymer or macromolecule. Each of their monomers are different from the others’ monomers.

Ex- Protein monomer- amino acid

Carbohydrate monomer- monosaccharide

CARBOHYDRATECARBOHYDRATESugars and StarchSugars and Starch

Quick energy compoundQuick energy compoundBiomolecule COHBiomolecule COH2 (simple formula)2 (simple formula)

Monosaccharide- simple sugar- glucoseMonosaccharide- simple sugar- glucoseDisaccharide- 2 sugarsDisaccharide- 2 sugars

glucose +fructose= sucroseglucose +fructose= sucrosePolysaccharide- Starch, Polysaccharide- Starch,

Glycogen( energy storage)Glycogen( energy storage)

CelluloseCellulose

ISOMERISOMER

same formula, same formula, different different structurestructure

glucose and glucose and galactose galactose CC66HH1212OO66

Dehydration synthesis

How are 2 monomers joined together?A water molecule is pulled out from the 2

monomers:

1 gives up an H, the other an OH

Called dehydration synthesis

Polysaccarides

Formed when there is an excess of glucose. Glucose is the body’s raw material needed to make energy. Plants get their glucose through photosynthesis. Animals get theirs through food.

Plants store their excess glucose as starch or cellulose. Cellulose is used to make cell walls. (we can’t digest cellulose)

Animals store their excess glucose as glycogen in the liver and muscle cells

Hydrolysis

When glucose levels are low plants and animals can use their stored glucose but first they must break the polymer up into the monomer glucose.

This requires the reverse reaction of dehydration synthesis. Instead of pulling out a water molecule, a water molecule is added to break the bond.

One monomer will get the H, the other the OH

Hydrolysis

LIPIDSLIPIDS

Fats, oils, waxes, steroidsFats, oils, waxes, steroids Insoluble in water (oil and Water don’t mix)Insoluble in water (oil and Water don’t mix)Made of 4 smaller molecules:a glycerol Made of 4 smaller molecules:a glycerol

molecule and 3 fatty acid molecule and 3 fatty acid chains(chains(Dehydration synthesis)Dehydration synthesis)

NonpolarNonpolarEnergy storage, coatingsEnergy storage, coatings

Monomer lipid has 2 partsMonomer lipid has 2 parts

3 fatty acid chains which are composed of 3 fatty acid chains which are composed of a long chain of carbons with H atoms and a long chain of carbons with H atoms and a carboxyl group (C=OOH) at the end a carboxyl group (C=OOH) at the end which is like an ID tag.which is like an ID tag.

Glycerol molecule which is an organic Glycerol molecule which is an organic alcohol that is attached to the 3FA through alcohol that is attached to the 3FA through a DH synthesis reaction.a DH synthesis reaction.

LIPIDSLIPIDS

3 different kinds of Fatty Acids3 different kinds of Fatty Acids

SaturatedSaturatedUnsaturatedUnsaturatedPolyunsaturatedPolyunsaturated

Saturated FatsSaturated Fats

Fatty acid chain has all single bonded Fatty acid chain has all single bonded carbons. All other bonds have H’s carbons. All other bonds have H’s attachedattached

Unhealthy for us.Unhealthy for us.Since all the bonds are single the Since all the bonds are single the

molecule has little flexibilitymolecule has little flexibilitySat. Fats are solid at room temp.Ex.-ButterSat. Fats are solid at room temp.Ex.-Butter

Unsaturated FatsUnsaturated Fats

Have at least 1 double bondHave at least 1 double bondMore flexibleMore flexibleEx. Margarine- easier to spread than Ex. Margarine- easier to spread than

butter due to the double bondsbutter due to the double bondsBetter for usBetter for us

Polyunsaturated FatsPolyunsaturated Fats

Fatty acid chains have many double bonds.Fatty acid chains have many double bonds.

Liquid at room temp. Ex. –OilLiquid at room temp. Ex. –Oil

Better for us.Better for us.

Over time saturated and unsaturated fats Over time saturated and unsaturated fats can build up on the walls of our arteries can build up on the walls of our arteries and can lead to heart disease.(Plaque)and can lead to heart disease.(Plaque)

Other uses for fatsOther uses for fats

Sterols- special lipids that act as chemical Sterols- special lipids that act as chemical messengers. Ex. Cholesterol.messengers. Ex. Cholesterol.

Phospholipids- found as part of cell Phospholipids- found as part of cell membranes. Regulates passage of membranes. Regulates passage of material in and out of cell. These are material in and out of cell. These are unique because a portion of the molecule unique because a portion of the molecule is hydrophobic(the fatty end) and the other is hydrophobic(the fatty end) and the other is hydrophilic(the phosphate end) is hydrophilic(the phosphate end)

PROTEINSPROTEINS

Large macromoleculesLarge macromoleculesBasic building material for all cell Basic building material for all cell

structuresstructuresProvide structure for tissues and organs to Provide structure for tissues and organs to

carry out metabolismcarry out metabolismContains NContains N Involved in muscle contraction, Involved in muscle contraction,

transporting oxygen, enzymestransporting oxygen, enzymes

AMINO ACIDSAMINO ACIDS

Building block of all proteins(20 AA)Building block of all proteins(20 AA)AA join by making peptide bond- AA join by making peptide bond-

loss of Hloss of H22O H----OHO H----OHMake all thousands of proteinsMake all thousands of proteins

3 parts of Amino Acid3 parts of Amino Acid

Amino group- NH2Amino group- NH2Carboxyl group-COOHCarboxyl group-COOHR group- R groups are different for each of R group- R groups are different for each of

the 20 amino acids.the 20 amino acids.

Amino AcidAmino Acid

The smallest protein is a dipeptide which The smallest protein is a dipeptide which consists of 2 amino acids linked together consists of 2 amino acids linked together by a peptide bond.by a peptide bond.

Polypeptide:long chain of amino acids Polypeptide:long chain of amino acids bonded by peptide bondsbonded by peptide bonds

Peptide bondPeptide bond

Quaternary structureQuaternary structureof Proteinsof Proteins

1- sequence of amino acids1- sequence of amino acids2- bending and coiling2- bending and coiling3-Folds in on itself3-Folds in on itself4-Binds with other proteins4-Binds with other proteins

Uses for proteinsUses for proteins

Construct many parts of the cellConstruct many parts of the cellAs hormones such as insulinAs hormones such as insulinTransport oxygen-hemoglobinTransport oxygen-hemoglobinSpecial proteins called ENZYMES-these Special proteins called ENZYMES-these

speed up reactions in the body so they speed up reactions in the body so they happen quickly.happen quickly.

EnzymesEnzymes

Every chemical reaction must be started or Every chemical reaction must be started or ignited with ACTIVATION ENERGY. ignited with ACTIVATION ENERGY.

In most chemical reactions this AE is in the In most chemical reactions this AE is in the form of heatform of heat

This heat energy moves the reactants This heat energy moves the reactants called SUBSTRATES around causing them called SUBSTRATES around causing them to bump into each other.to bump into each other.

In the body, heat can’t be used as AE In the body, heat can’t be used as AE because it would harm the body.because it would harm the body.

We need a different AE-called ENZYMESWe need a different AE-called ENZYMESEnzymes join with substrates and bring Enzymes join with substrates and bring

them together.them together.This happens at the enzymes active site.This happens at the enzymes active site.Enzymes do their job and then move on to Enzymes do their job and then move on to

next reaction.next reaction.They do not become part of the product.They do not become part of the product.They remain unchanged.They remain unchanged.

Enzymes are Enzymes are SUBSTRATE SPECIFIC:SUBSTRATE SPECIFIC:

there is a specific enzyme for each there is a specific enzyme for each substrate.substrate.

They must fit perfectly like a “lock and key”They must fit perfectly like a “lock and key”

ENZYMESENZYMES

Speed up rxnsSpeed up rxns Depends on temp, Depends on temp,

concentration, pHconcentration, pH Substrate specificSubstrate specific Lock and keyLock and key No change to enzymeNo change to enzyme Most End in Most End in ase ase

(lactase breaks down (lactase breaks down lactose)lactose)

1000’s of reactions every minute1000’s of reactions every minuteEnzymes are needed to start these Enzymes are needed to start these

reactionsreactionsSome disease where individual doesn’t Some disease where individual doesn’t

make a certain enzyme. Can be fatal. make a certain enzyme. Can be fatal. Example ; Tay Sachs-missing enzyme that Example ; Tay Sachs-missing enzyme that breaks down fats in the brain. These fats breaks down fats in the brain. These fats accumulate and cause death by age 5.accumulate and cause death by age 5.

NUCLEIC ACIDSNUCLEIC ACIDS

Building block of DNA and RNA-transmit Building block of DNA and RNA-transmit genetic information.genetic information.

Made of Monomers called nucleotides put Made of Monomers called nucleotides put together in a dehydration synthesis together in a dehydration synthesis reaction.reaction.

3 Parts: Sugar3 Parts: Sugar phosphate phosphate and and basebase

Nucleotide structureNucleotide structure

Phosphate

SugarBase

NucleotideNucleotide

5 carbon sugar5 carbon sugar

DNA has deoxyriboseDNA has deoxyribose

RNA has riboseRNA has ribosePhosphate groupPhosphate groupNitrogenous base(Adenine-Thymine) Nitrogenous base(Adenine-Thymine)

(Guanine –Cytosine)(Guanine –Cytosine)

(Uracil replaces thymine (Uracil replaces thymine in RNA) in RNA)

DNA-double stranded,RNA singleDNA-double stranded,RNA single

RNARNA

RNA- template for making proteinsRNA- template for making proteins