CH 3: The Molecules of CH 3: The Molecules of CellsCells

Molecules of LifeMolecules of Life

The molecules of life are all organic The molecules of life are all organic compounds….meaning carbon containingcompounds….meaning carbon containing Carbohydrates: C, H, OCarbohydrates: C, H, O Lipids: C, H, OLipids: C, H, O Proteins: C, H, O, N, SProteins: C, H, O, N, S Nucleic acids: C, H, O, N, PNucleic acids: C, H, O, N, P

Carbon Carbon (3.1)(3.1)

In compounds, C always forms 4 In compounds, C always forms 4 covalent bondscovalent bonds Diagramming C compounds Diagramming C compounds

C to C single bonds can rotate freelyC to C single bonds can rotate freely• Allows C compounds to form ringsAllows C compounds to form rings

C to C double bonds are rigidC to C double bonds are rigid

HydrocarbonsHydrocarbons

Hydrocarbons – compounds Hydrocarbons – compounds containing only C and Hcontaining only C and H Are hydrocarbons polar or nonpolar?Are hydrocarbons polar or nonpolar? Are they hydrophilic or hydrophobic?Are they hydrophilic or hydrophobic?

IsomersIsomers

Isomers – compounds with same formula, Isomers – compounds with same formula, but different arrangement of the atomsbut different arrangement of the atoms Isomers differ in properties and in biological Isomers differ in properties and in biological

activityactivity

Functional GroupsFunctional Groups

Molecules of life are all substituted Molecules of life are all substituted hydrocarbonshydrocarbons (Most) functional groups contain atoms (Most) functional groups contain atoms

other than C and Hother than C and H• Many are polar and change properties of the Many are polar and change properties of the

compoundcompound

Substitute functional group(s) for Substitute functional group(s) for hydrogenshydrogens

Six main functional groupsSix main functional groups are important are important in the chemistry of biological molecules:in the chemistry of biological molecules:

POLAR Functional groupsPOLAR Functional groups Hydroxyl group (OH)Hydroxyl group (OH) Carbonyl group (C=O)Carbonyl group (C=O)

• May be an aldehyde or ketoneMay be an aldehyde or ketone Carboxyl group (COOH) - Acidic Carboxyl group (COOH) - Acidic Amino group (NHAmino group (NH22) - basic) - basic

Phosphate group (OPOPhosphate group (OPO33))

NONPOLAR Functional GroupNONPOLAR Functional Group

• Methyl (CHMethyl (CH33))

Estradiol

Male lion

TestosteroneFemale lion

Functional Groups Impact FunctionFunctional Groups Impact Function Differences in Differences in position and types of functional groupsposition and types of functional groups greatly impact greatly impact

the function of the moleculethe function of the molecule

Classes of Chemical Classes of Chemical Reactions Reactions (3.3)(3.3)

1. Rearrangement1. Rearrangement• Convert one isomer to anotherConvert one isomer to another• Example Example

• Reaction that converts glucose to fructoseReaction that converts glucose to fructose• Reaction is used to make high fructose corn Reaction is used to make high fructose corn

syrupsyrup

Making PolymersMaking Polymers

2. Dehydration* Reaction - 2. Dehydration* Reaction - links molecules links molecules togethertogether

• A covalent bond forms between molecules A covalent bond forms between molecules and water is removedand water is removed

• Reaction by which monomers are joined to form larger Reaction by which monomers are joined to form larger moleculesmolecules

• Examples:Examples:

• *Also called a condensation reaction*Also called a condensation reaction

Breaking PolymersBreaking Polymers

3. Hydrolysis reaction – 3. Hydrolysis reaction – breaks down breaks down larger moleculeslarger molecules

• Water is added to a larger molecule to Water is added to a larger molecule to split off a smaller molecule.split off a smaller molecule.

• Reaction involves breaking a covalent Reaction involves breaking a covalent bond by adding waterbond by adding water• Reverse of a dehydration reactionReverse of a dehydration reaction

Example from lab this weekExample from lab this week

MonomersMonomers Polymer FormedPolymer Formed Monosaccharides Monosaccharides Di & Di &

PolysaccharidesPolysaccharides Fatty acids Fatty acids TriglyceridesTriglycerides Amino acids Amino acids ProteinsProteins Nucleotides Nucleotides Nucleic acids Nucleic acids

SUMMARYSUMMARY Monomers are linked by Monomers are linked by condensation reactions condensation reactions (also (also

called called dehydration reactionsdehydration reactions))• A water molecule is producedA water molecule is produced• A covalent bond is formed between monomer unitsA covalent bond is formed between monomer units

Polymers are broken down to monomers by the reverse Polymers are broken down to monomers by the reverse process, process, hydrolysishydrolysis• A water molecule is brokenA water molecule is broken• A covalent bond is broken between monomer unitsA covalent bond is broken between monomer units

Carbohydrates Carbohydrates (3.4-3.7)(3.4-3.7)

Class of molecules with many Class of molecules with many hydroxyl groups (OH) and one hydroxyl groups (OH) and one carbonyl group (C=O)carbonyl group (C=O)

Consider 3 Classes of CarbohydratesConsider 3 Classes of Carbohydrates MonosaccharidesMonosaccharides Disaccharides Disaccharides

• and other moderate size carbohydratesand other moderate size carbohydrates PolysaccharidesPolysaccharides

MonosaccharidesMonosaccharides

General Formula: CGeneral Formula: CnnHH2n2nOOnn

Typically 3-7 carbons longTypically 3-7 carbons long• Many –OH groups and one carbon is Many –OH groups and one carbon is

attached to an aldehyde or ketone groupattached to an aldehyde or ketone group• Form rings – see pg 37Form rings – see pg 37

Common MonosaccharidesCommon Monosaccharides

Pentose monosaccharidesPentose monosaccharides:: Deoxyribose – Deoxyribose – sugar in DNAsugar in DNA Ribose – Ribose – sugar in RNAsugar in RNA

Hexose MonosaccharidesHexose Monosaccharides: : Glucose all isomers ofGlucose all isomers of Fructose CFructose C66HH1212OO66

GalactoseGalactose

6 C - Hexose Sugars6 C - Hexose Sugars

All isomers of All isomers of CC66HH1212OO66

Glucose - Glucose - • Blood sugarBlood sugar• Primary source of energy for cellsPrimary source of energy for cells

FructoseFructose• ““Fruit” sugarFruit” sugar• Sweetest of all the sugarsSweetest of all the sugars

GalactoseGalactose• Formed when lactose is digestedFormed when lactose is digested

Glucose is an aldehyde sugar

Aldose

Fructose is a ________ sugar

_____ose

DisaccharidesDisaccharides

Formed when 2 monosaccharides are Formed when 2 monosaccharides are joined in a ___________ reaction.joined in a ___________ reaction. One sugar gives up a H and the other a -OHOne sugar gives up a H and the other a -OH

3 Disaccharides to know3 Disaccharides to know Sucrose = glucose - Sucrose = glucose - Lactose = glucose - Lactose = glucose - Maltose = glucose -Maltose = glucose -

Synthesis of MaltoseSynthesis of Maltose

DisaccharidesDisaccharides

Sucrose Sucrose = glucose covalently = glucose covalently bonded to a fructose bonded to a fructose Table sugarTable sugar In the small intestines the enzyme In the small intestines the enzyme

sucrase catalyzes the hydrolysis of the sucrase catalyzes the hydrolysis of the bond between glucose and fructose bond between glucose and fructose • In the lab this bond can be broken by…..?In the lab this bond can be broken by…..?

DisaccharidesDisaccharides

Lactose = glucose-galactoseLactose = glucose-galactose Milk sugarMilk sugar The enzyme The enzyme lactaselactase catalyzes the catalyzes the

hydrolysis of the bond between glucose hydrolysis of the bond between glucose and galactose.and galactose.• Individuals who do not make the enzyme lactase Individuals who do not make the enzyme lactase

are lactose intolerant.are lactose intolerant.

Lactose IntoleranceLactose Intolerance

Populations at greatest risk: Populations at greatest risk: Asian - ~ 90% Asian - ~ 90% African descent - ~ 75%African descent - ~ 75% Hispanic, Native Americans - ~ 75%Hispanic, Native Americans - ~ 75%

Last DisaccharidesLast Disaccharides

Maltose = glucose-glucoseMaltose = glucose-glucose Found in germinating grains, malt Found in germinating grains, malt

productsproducts Formed when starch is hydrolyzed Formed when starch is hydrolyzed

(digested)(digested)

OligosaccharidesOligosaccharides ~20- 30 monosaccharides long~20- 30 monosaccharides long

found on the outside of the plasma found on the outside of the plasma membrane, Often branched, Help cells membrane, Often branched, Help cells recognize each otherrecognize each other

PolysaccharidesPolysaccharides

All polymers of glucoseAll polymers of glucose Differ in:Differ in:

• FunctionFunction• Type of bonding between glucoseType of bonding between glucose• Length of the glucose chainLength of the glucose chain• Frequency of branchingFrequency of branching• Incidence of coilingIncidence of coiling

Major PolysaccharidesMajor Polysaccharides

Glycogen Starch CelluloseGlycogen Starch Cellulose

GlycogenGlycogen

Function – animal storage form of glucoseFunction – animal storage form of glucose Made and stored in:Made and stored in:

LiverLiver• Source of glucose for the entire bodySource of glucose for the entire body

Muscle cells Muscle cells • Source of glucose for muscle cells onlySource of glucose for muscle cells only

GlycogenGlycogen StructureStructure

~ 1 million glucose joined by covalent bonds ~ 1 million glucose joined by covalent bonds called alpha glycosidic bondscalled alpha glycosidic bonds• We have the enzymes needed to hydrolyze the We have the enzymes needed to hydrolyze the

alpha bonds in glycogenalpha bonds in glycogen Highly branchedHighly branched

• Branch every 5-6 glucoseBranch every 5-6 glucose

StarchStarch Function – plant storage form of glucoseFunction – plant storage form of glucose

Structure – ~100, 000 glucose joined by Structure – ~100, 000 glucose joined by covalent bonds called alpha glycosidic covalent bonds called alpha glycosidic bondsbonds• Molecules are either coiled or branched – Molecules are either coiled or branched –

depending on type of starchdepending on type of starch

CelluloseCellulose

Function – structural polysaccharideFunction – structural polysaccharide• Component of cell wallsComponent of cell walls

StructureStructure• Long chains of glucose joined by covalent bonds Long chains of glucose joined by covalent bonds

called called betabeta glycosidic bonds glycosidic bonds• We do not have the enzymes needed to hydrolyze We do not have the enzymes needed to hydrolyze

beta bondsbeta bonds

CelluloseCellulose

StructureStructure Hydrogen bonds link chains to each other to Hydrogen bonds link chains to each other to

form fibersform fibers The fibers then form bundlesThe fibers then form bundles

• See page 39See page 39 The resulting structure is VERY strong. The resulting structure is VERY strong.

CelluloseCellulose

Lipids Lipids (3.8 – 3.10)(3.8 – 3.10)

Water insoluble components of cellsWater insoluble components of cells Primarily hydrocarbon, nonpolar Primarily hydrocarbon, nonpolar

substancessubstances Classes of Lipids:Classes of Lipids:

• Triglycerides (fats) and fatty acidsTriglycerides (fats) and fatty acids• PhospholipidsPhospholipids• SterolsSterols• Waxes (no coverage)Waxes (no coverage)

Triglycerides and Fatty Acids

Triglycerides are made by linking 3 fatty acids to a glycerol molecule

Triglyceride

Fatty AcidsFatty Acids

Fatty Acids Fatty Acids (FA)(FA) Long hydrocarbon chains with a Long hydrocarbon chains with a

carboxylic acid head.carboxylic acid head.• Saturated FA: all carbon to carbon single Saturated FA: all carbon to carbon single

bondsbonds• Unsaturated FA: at least one carbon to Unsaturated FA: at least one carbon to

carbon double bondcarbon double bond

Fatty AcidsFatty Acids

Red = polar head Black = nonpolar tail

Triglycerides: Triglycerides: (TG)(TG)

Function: storage form of energyFunction: storage form of energy Structure: 3 fatty acids covalently Structure: 3 fatty acids covalently

bonded to a glycerol backbonebonded to a glycerol backbone• 3 FA are often different from each other3 FA are often different from each other• FA determine the properties of the TGFA determine the properties of the TG

Mostly unsaturated FA => liquid (oil), healthierMostly unsaturated FA => liquid (oil), healthier Mostly saturated FA => solid, heatlh issuesMostly saturated FA => solid, heatlh issues Trans FA => health issues, formed in Trans FA => health issues, formed in

hydrogenation reactionhydrogenation reaction

TriglycerideTriglyceride

Phospholipids (3.9)Phospholipids (3.9)

Function: major component of Function: major component of plasma membraneplasma membrane Structure: ………….Structure: ………….

SteroidsSteroids

Steroids (sterols)Steroids (sterols) Functions varyFunctions vary Examples of sterols include:Examples of sterols include:

• Hormones – testosterone, estrogenHormones – testosterone, estrogen• Vitamin DVitamin D• CholesterolCholesterol

Structure: 4 linked rings……..Structure: 4 linked rings……..

SteroidsSteroids

Cholesterol

General steroid structure

ProteinsProteins

Functions/examples of proteins:Functions/examples of proteins: EnzymesEnzymes AntibodiesAntibodies HemoglobinHemoglobin InsulinInsulin Component of cell membranesComponent of cell membranes Hair, nails, cartilageHair, nails, cartilage

ProteinsProteins

StructureStructure:: Chain of covalently bonded amino acids Chain of covalently bonded amino acids

(a.a)(a.a) Bond between a.a. called a Bond between a.a. called a peptide peptide

bondbond 20 different amino acids…………..20 different amino acids…………..

Carboxyl (acid)group

Aminogroup

Amino Acid Structure

The structure of the The structure of the R groupR group determines the specific determines the specific properties of each amino acidproperties of each amino acid

Leucine (Leu) Serine (Ser)

Hydrophobic R Group

Aspartic acid (Asp)

Hydrophilic R groups

ProteinsProteins Synthesis of proteins:Synthesis of proteins:

a.a. + a.a a.a. + a.a dipeptide + H dipeptide + H22OO

What type of reaction is this?What type of reaction is this?

ProteinsProteins

Order of the a.a. in a protein determines Order of the a.a. in a protein determines the:the: 3D shape of the protein3D shape of the protein Function of the proteinFunction of the protein

Any change in protein structure may Any change in protein structure may impact the ability of the protein to function.impact the ability of the protein to function. More to come on this.More to come on this.

Describing Protein StructureDescribing Protein Structure

Primary structure: 1Primary structure: 100

Order of amino acids in a proteinOrder of amino acids in a protein

Bonding: peptide bonds between amino Bonding: peptide bonds between amino acidsacids• Peptide bonds are _________ bondsPeptide bonds are _________ bonds

Protein StructureProtein Structure

Example of a Primary structure: Example of a Primary structure:

Methonine-proline-serine-asparagine-tryptophan-leucine-tyrosine-Methonine-proline-serine-asparagine-tryptophan-leucine-tyrosine-

valine-proline-alanine-glycine…….valine-proline-alanine-glycine…….

Secondary Structure: 2Secondary Structure: 200

The polypeptide (protein) chain coils or The polypeptide (protein) chain coils or folds to form:folds to form:• Alpha helix or beta pleated sheetsAlpha helix or beta pleated sheets

Bonding: H bondsBonding: H bonds

Alpha helix Beta-sheet

Tertiary Structure: 3Tertiary Structure: 300

Folding of the secondary structure to Folding of the secondary structure to form domains form domains • order of aa determines how the protein order of aa determines how the protein

foldsfolds• Domain = self-organized, stable, functional Domain = self-organized, stable, functional

unitunit

Describing Protein StructureDescribing Protein Structure

Tertiary Structure Bonding: Tertiary Structure Bonding: • R group interactionsR group interactions

H bondsH bonds Hydrophilic R groups on the outside and Hydrophilic R groups on the outside and

hydrophobic R groups are on the inside hydrophobic R groups are on the inside of the proteinof the protein

Disulfide bonds between S containing Disulfide bonds between S containing a.a.a.a.

Ionic bonds between charged R groupsIonic bonds between charged R groups

Tertiary Structure: 3Tertiary Structure: 300

Tertiary structure descries the overall 3D Tertiary structure descries the overall 3D shape of single polypeptideshape of single polypeptide

Most polypeptides can be described as either:Most polypeptides can be described as either:

GlobularGlobular FFibrousibrous

most enzymes hair, spider silkmost enzymes hair, spider silk

Describing Describing Protein Structure

Quaternary Structure: 4Quaternary Structure: 400

Arrangement of 2 or more protein Arrangement of 2 or more protein chains.chains.

Bonding – same R group interactions as Bonding – same R group interactions as 330 0 structurestructure

Collagen – fibrous protein with 40 structure

Simple Diagram of Levels of Simple Diagram of Levels of Protein StructureProtein Structure

Identify the stabilizing forces at each levelIdentify the stabilizing forces at each level

Protein denaturation - change in the Protein denaturation - change in the 3D structure of a protein3D structure of a protein Changes occur to 2Changes occur to 200 -4 -400 structure structure Causes a loss of protein functionCauses a loss of protein function

Functional protein

Protein isno longerfunctional

Partially denatured proteinsPartially denatured proteins Minor changesMinor changes to active site(s) to active site(s) Can still function but very Can still function but very reduced ratereduced rate

Fully denatured proteinsFully denatured proteins Major changesMajor changes to active site(s) to active site(s) Protein Protein cannot cannot function at allfunction at all

Denaturing AgentsDenaturing Agents

pH changes pH changes - changes ionic interactions - changes ionic interactions between charged amino acids between charged amino acids

Salt concentration increased- Salt concentration increased- interferes interferes with ionic bonds between charged aawith ionic bonds between charged aa

Higher temperatures Higher temperatures – break hydrogen – break hydrogen bondsbonds

Heavy metals Heavy metals - break S-S bonds between - break S-S bonds between cysteinescysteines

Nucleotides & Nucleic AcidsNucleotides & Nucleic Acids Nucleotides - Nucleotides - General compositionGeneral composition

5 Carbon sugar5 Carbon sugar 1 or more phosphate groups1 or more phosphate groups Nitrogenous baseNitrogenous base

NucleotidesNucleotides

Examples of nucleotides:Examples of nucleotides: ATP - ATP - major energy carrier in cells major energy carrier in cells

NADH/NADNADH/NAD+ + - - Coenzyme that transports HCoenzyme that transports H+ +

and electrons and electrons

Nucleic AcidsNucleic Acids

Nucleic AcidsNucleic Acids Long chain(s) of covalently bonded Long chain(s) of covalently bonded

nucleotidesnucleotides 2 types of nucleic acids:2 types of nucleic acids:

• RNA – single stranded, shorterRNA – single stranded, shorter

• DNA – double stranded, very longDNA – double stranded, very long

DNA DNA RNA RNA

Nucleic Acids - RNANucleic Acids - RNA

RNA – RNA – ribonucleic acidribonucleic acid 1 strand of covalently bonded nucleotides1 strand of covalently bonded nucleotides

Composition of RNA nucleotides:Composition of RNA nucleotides: RiboseRibose PhosphatePhosphate 1 of 4 possible nitrogenous bases1 of 4 possible nitrogenous bases

• AdenineAdenine• GuanineGuanine• UracilUracil• CytosineCytosine

Nucleic Acids - DNANucleic Acids - DNA

DNA – deoxyribonulceic acidDNA – deoxyribonulceic acid 2 strands of covalently bonded nucleotides2 strands of covalently bonded nucleotides

DNA nucleotides:DNA nucleotides: DeoxyriboseDeoxyribose PhosphatePhosphate 1 of 4 Nitrogenous bases1 of 4 Nitrogenous bases

• AdenineAdenine• GuanineGuanine• ThymineThymine• CytosineCytosine

Nucleic AcidsNucleic Acids DNA – deoxyribonucleic acidDNA – deoxyribonucleic acid

Double strandedDouble stranded

• Hydrogen bonds between bases join Hydrogen bonds between bases join the two strandsthe two strands

DNADNA