Chapter 3Chapter 3

Molecules of a cellMolecules of a cell

MoleculesMolecules

2 types– Organic– Inorganic

Organic- generally C based

Inorganic- generally non-C based

** Exceptions include CO2, CO, CN, etc

C-H

• Hydrocarbons– Compounds

composed of only C and H Methane, propane,

butane, benzene, etc

• Chain, branch or ring of C– C skeleton

H H

HH

H H

Ethane Propane

HH

H H

H

H

H

H

H

H

Carbon skeletons vary in length.

H

H

H

H

H H

H H

H H

H H

H H

H H

H

H

H

H

H

H H H H

H

H

C

HH H

H H

H H

H

H

H

H H

H

H

H

H

H

H

H H

H

H

Butane Isobutane

Skeletons may be unbranched or branched.

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

CC C

C

C

CH

CC

C

C

CC

Cyclohexane Benzene

Skeletons may be arranged in rings.

C C C C C

C C C C

C

C CC

CCC C CCCH H

H H

HH

H H

Ethane Propane

HH

H H

H

H

H

H

H

H

Carbon skeletons vary in length.

H

H

H

H

H H

H H

H H

H H

H H

H H

H

H

H

H

H

H H H H

H

H

C

HH H

H H

H H

H

H

H

H H

H

H

H

H

H

H

H H

H

H

Butane Isobutane

Skeletons may be unbranched or branched.

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

CC C

C

C

CH

CC

C

C

CC

Cyclohexane Benzene

Skeletons may be arranged in rings.

C C C C C

C C C C

C

C CC

CCC C CCCH H

IsomersIsomers Compounds with the same formula different Compounds with the same formula different

structuresstructures

– Different shapes = unique propertiesDifferent shapes = unique properties

Functional GroupsFunctional Groups• Determine the Determine the

properties of organic properties of organic compoundscompounds

• PolarPolar– O and N exert a O and N exert a

“strong pull” on “strong pull” on shared electronsshared electrons

– HydrophilicHydrophilic

Functional GroupsFunctional Groups

• Hydroxyl- OHHydroxyl- OH

• Carbonyl- C=OCarbonyl- C=O

• Carboxyl- COOHCarboxyl- COOH

• Amino- NHAmino- NH22

• Phosphate- OPOPhosphate- OPO332-2-

• Methyl- CHMethyl- CH33

Biological MoleculesBiological Molecules

4 primary classes4 primary classes1.1. CarbohydratesCarbohydrates

2.2. LipidsLipids

3.3. ProteinsProteins

4.4. Nucleic acidsNucleic acids

These molecules are large (dozens to millions These molecules are large (dozens to millions of C) = macromoleculesof C) = macromolecules

Polymers & MonomersPolymers & Monomers

Cells make large molecules by joining together Cells make large molecules by joining together smaller molecules into chainssmaller molecules into chains– Chains are called Chains are called polymerspolymers– Individual molecules are Individual molecules are monomersmonomers

• Monomers connect into polymersMonomers connect into polymers

***Mono=1***Mono=1

Poly=manyPoly=many

Meros= partMeros= part

Making PolymersMaking Polymers• Cells link monomers to form polymers Cells link monomers to form polymers

via a dehydration reactionvia a dehydration reaction

Dehydration ReactionDehydration Reaction• Removes H-O-HRemoves H-O-H

• For each monomer added, 1 molecule For each monomer added, 1 molecule water is removedwater is removed

• Held via covalent bondsHeld via covalent bonds

**2 monomers are contributing to the H**2 monomers are contributing to the H220 0

moleculemolecule

One monomer looses a hydroxyl One monomer looses a hydroxyl group and the other looses a H atomgroup and the other looses a H atom

Breaking PolymersBreaking Polymers• Cells break polymers into monomers via a Cells break polymers into monomers via a

hydrolysis reactionhydrolysis reaction

Hydrolysis ReactionHydrolysis Reaction

• Breaks covalent bond between monomers Breaks covalent bond between monomers by adding waterby adding water

• A OH- joins to one monomer and a H joins A OH- joins to one monomer and a H joins to an adjacent monomer to an adjacent monomer

• For each monomer removed, 1 molecule For each monomer removed, 1 molecule water is addedwater is added

Sugar!Sugar!

• CarbohydratesCarbohydrates– Monomer is Monomer is

glucose glucose (monosaccharide)(monosaccharide)

– Link two sugars Link two sugars into disaccharideinto disaccharide• Ex: Ex: sucrose (table

sugar) and maltose (brewing sugar)

H

HH H

HH

H

H

H

H

H

H

H

H

H HH

H

H

H

OH OH

OHOHOH

HO

O O

O

OH

OH

OH

CH2OH CH2OH

CH2OH CH2OH

H2O

OH

HO

O

OH O

H

Glucose Glucose

Maltose

O

OH

• Monosaccharides- Monosaccharides- one monomer (glucose)one monomer (glucose)• Disaccharides- Disaccharides- two monomers (sucrose)two monomers (sucrose)• Oligosaccharides-Oligosaccharides- several monomers several monomers• Polysaccharides-Polysaccharides- hundreds of monomers hundreds of monomers

Sugar storageSugar storage• Starch and glycogen: Nutritional Store Starch and glycogen: Nutritional Store

chemical energy chemical energy – Starch in plantsStarch in plants– Glycogen in animalsGlycogen in animals

• Cellulose: StructuralCellulose: Structural– Forms the cell walls of plantsForms the cell walls of plants– Digestible by some animals, but not humansDigestible by some animals, but not humans

• Chitin forms exoskeletons of insects and Chitin forms exoskeletons of insects and crustaceans and cell walls in fungicrustaceans and cell walls in fungi

Sugar StorageSugar StorageStarch granules in potato tuber cells

Glycogen granules in muscle tissue

Cellulose fibrils in a plant cell wall

Glucose monomer

Cellulose molecules

STARCH

GLYCOGEN

CELLULOSE

O O

OOOOOO

O O O

O

OO

OO

OO

OO

OO

OO

O

OO

OO

OO

OO O

OOOOOO

OOOOOO

O

OH

OH

Figure 3.7

LipidsLipids• Not true polymersNot true polymers

– some are formed via some are formed via dehydration reactionsdehydration reactions

• Fats, Steroids, Fats, Steroids, PhospholipidsPhospholipids

• Energy storage, Energy storage, membrane functionmembrane function

• HydrophobicHydrophobic

FatsFats

• Solid and liquid statesSolid and liquid states

• Consist of glycerol Consist of glycerol linked to three fatty linked to three fatty acidsacids– Termed TriacylglycerolTermed Triacylglycerol

– HydrophobicHydrophobic

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

H2O

H H

HH

OHOH OH

H

HO

C O

C C C

Fatty acid

Glycerol

H HH

H H

CH2

O O O

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

CH2

CH2

CH

CH

CH2

CH2

CH2

CH2

CH2

CH2

CH3

C C C OOO

C C C

H

Figure 3.8BFigure 3.8C

Fatty AcidsFatty Acids

• Simple lipids containing 2 partsSimple lipids containing 2 parts– Long hydrocarbon chain (non-polar, Long hydrocarbon chain (non-polar,

hydrophobic)hydrophobic)– Carboxylic acid functional group (polar, Carboxylic acid functional group (polar,

hydrophilic)hydrophilic)

Saturated & UnsaturatedSaturated & Unsaturated

• Double bonding between C prevents H Double bonding between C prevents H from bonding to the C skeletonfrom bonding to the C skeleton– Fatty acids with double bonds are Fatty acids with double bonds are unsaturatedunsaturated– Fatty acids without double bonds are Fatty acids without double bonds are

saturatedsaturated

Saturated/unsaturated refers to whether or Saturated/unsaturated refers to whether or not the C chains contain the maximum not the C chains contain the maximum number of H possiblenumber of H possible

KinkyKinky

• Double bonds Double bonds kink the structurekink the structure

• Kinks reduce Kinks reduce packing densitypacking density

• Lower packing Lower packing density density decreases decreases melting pointmelting point

Saturation and melting pointSaturation and melting point

• Saturated fatty Saturated fatty acids have melting acids have melting points above 25ºCpoints above 25ºC– Liquid at room tempLiquid at room temp

• As number of As number of double bonds double bonds increases, melting increases, melting point decreasespoint decreases– More likely to be More likely to be

solid at room tempsolid at room temp

HydrogenationHydrogenation

• Highly unsaturated fats can be very soft Highly unsaturated fats can be very soft and are hydrogenated (saturated) to make and are hydrogenated (saturated) to make them more butter-like.them more butter-like.

• Addition of hydrogen to C=C double bond.Addition of hydrogen to C=C double bond.• Some of the Some of the ciscis bonds are converted to bonds are converted to

transtrans. .

Trans FatsTrans Fats• Naturally occurring unsaturated fats are Naturally occurring unsaturated fats are cis: cis:

hydrocarbon chain is kinked.hydrocarbon chain is kinked.• TransTrans fats are straight. fats are straight.

Buyer BewareBuyer Beware

• TransTrans fats are straighter than fats are straighter than ciscis fats and the fats and the product is stiffer.product is stiffer.

• TransTrans fats pose a health risk – are not broken fats pose a health risk – are not broken down readily.down readily.

PhospholipidsPhospholipids

• Significant component of cell membranesSignificant component of cell membranes

• Contain a glycerol backbone: Contain a glycerol backbone: – Glycerol with two fatty acidsGlycerol with two fatty acids– Also bonded with P group and another small, Also bonded with P group and another small,

polar grouppolar group

• Amphipathic properties significant for cell Amphipathic properties significant for cell membranesmembranes– Created water resistant membraneCreated water resistant membrane

PhospholipidsPhospholipids

Hydrophilic/HyrdophobicHydrophilic/Hyrdophobic

• Cell membrane is bilayer of Cell membrane is bilayer of phospholipidsphospholipids

• Hydrophilic “head”Hydrophilic “head”

• Hydrophobic “tail”Hydrophobic “tail”

Steroids & WaxesSteroids & Waxes• Steroids Steroids

– C skeletons contain 4 fused ringsC skeletons contain 4 fused rings– Often hormonesOften hormones– Cholesterol is an exampleCholesterol is an example

• Waxes form waterproof coatingWaxes form waterproof coating

HO

CH3

CH3

H3C CH3

CH3

ProteinsProteins• Monomer= Amino AcidsMonomer= Amino Acids

• Unique sequence of AA (20 AA in total)Unique sequence of AA (20 AA in total)

• Link between amino acids in protein is a Link between amino acids in protein is a peptide peptide bondbond

Amino AcidsAmino Acids

• Specific properties based on its structureSpecific properties based on its structure

H

H

N

H

C

CH2

CH

CH3 CH3

C

O

OH

H

H

N C

H

CH2

OH

C

O

OH

H

H

N C

H

C

O

OHCH2

C

OH O

Leucine (Leu) Serine (Ser) Aspartic acid (Asp)

Hydrophobic Hydrophilic

Figure 3.12B

Form determines functionForm determines function• One or more polypeptide chains folded One or more polypeptide chains folded

into a unique shapeinto a unique shape– Unique shape determines the functionUnique shape determines the function

GrooveGroove

Levels of Protein StructureLevels of Protein Structure• PrimaryPrimary

– Unique sequence of AA forming the polypeptide Unique sequence of AA forming the polypeptide chainchain

Levels of Protein Structure

Primary structureGly

Thr

Gly Glu

Ser Lys

Cys

Pro

Leu Met

Val

Lys

Val

Leu Asp Ala Val ArgGly Ser

Pro

Ala

Ile

Asn Val

Ala

Val

HisVal

Amino acids

Phe

Arg

Levels of Protein StructureLevels of Protein Structure• SecondarySecondary

– Conformation of portions of the polypeptide Conformation of portions of the polypeptide chainchain• Conformation- 3-d arrangement of atoms in a

molecule (spatial organization)

• Alpha helix & pleated sheets

Figure 3.14B

Secondary structure

C

N

O C

C

N H

O C

C

H

Hydrogenbond

O C

N H

C

CO

N H

OC

C

N H

C

N

O C

C

N H

OC

C

N H

CO

C

H

N H

CO

HC R

HN

Alpha helix

CN

H

C C

HH

O

N

RC C

O

N

H

O

CC N

H

C C

O

N

H

O

CC N

H

C

O

CN

H

O

CC N

H

C

O

O

C

C

N

H

C C

O

N

H

CC

O

N

H

C

C

O

N

H

CC

O

N

H

CC

O

N

H

CC

O

N

H

C

C

O

H

N

C

Pleated sheet

Amino acids

Levels of Protein StructureLevels of Protein Structure• TertiaryTertiary

– Overall three-Overall three-dimensional dimensional shape of a shape of a polypeptidepolypeptide

– Globular or Globular or fibrousfibrous

Tertiary structure

Polypeptide(single subunitof transthyretin)

Levels of Protein StructureLevels of Protein Structure

• Quaternary structureQuaternary structure– Results from the association of two or more Results from the association of two or more

polypeptide chainspolypeptide chains

Quaternary structure

Transthyretin, withfour identical

polypeptide subunits

Polypeptidechain

Collagen

When shape failsWhen shape fails

• DenaturationDenaturation– Polypeptide chains unravel, unfold and Polypeptide chains unravel, unfold and

disorganizedisorganize– Results from heat, salt concentration, pH, etc. Results from heat, salt concentration, pH, etc.

• Resulting altered shape causes proteins to Resulting altered shape causes proteins to loose their functionloose their function

Functions of ProteinsFunctions of Proteins

EnzymesEnzymesStructuralStructuralContractileContractileDefensiveDefensiveSignalSignalReceptorReceptorTransportTransportStorageStorage**Significant in the plasma membrane**Significant in the plasma membrane

EnzymesEnzymes

• CatalystsCatalysts– Increase rate of chemical reactions in cellsIncrease rate of chemical reactions in cells

Nucleic AcidsNucleic Acids• Monomer= Monomer=

nucleotidesnucleotides– Storage and Storage and

transmission of transmission of genetic genetic informationinformation

– Two types of Two types of nucleic acidsnucleic acids

• DNA and RNADNA and RNA

Sugar

OH

O P O

O

CH2

H

O

H H

OH H

H

N

N

H

N

N H

HHN

Phosphategroup

Nitrogenousbase (A)

DNA & RNADNA & RNA• DNA consists of two DNA consists of two

polynucleotides tpolynucleotides twisted wisted around each other in a around each other in a double helix double helix – Held together by hydrogen Held together by hydrogen

bondingbonding• RNA typically consists of a RNA typically consists of a

single polynucleotide strandsingle polynucleotide strand

C

TA

GC

C G

T A

C G

A T

A

G C

A T

A T

T A

Basepair

T

DNA & RNA

• Five types of nitrogenous Five types of nitrogenous basesbases– Purines and PyrimidinesPurines and Pyrimidines– DNA = A,T,G and CDNA = A,T,G and C– RNA = A,U,G and CRNA = A,U,G and C