Chapter 2: The Molecules of Chapter 2: The Molecules of CellsCells

TOPIC OUTLINETOPIC OUTLINE

► ThermodynamicsThermodynamics First LawFirst Law Second LawSecond Law Steady State vs Equilibrium Steady State vs Equilibrium

► ChemistryChemistry Atoms and moleculesAtoms and molecules Chemical ReactionsChemical Reactions WaterWater Acids and BasesAcids and Bases Biological MoleculesBiological Molecules

DefinitionsDefinitions►EnergyEnergy

PotentialPotential KineticKinetic ChemicalChemical Matter and energy are interconvertible.Matter and energy are interconvertible.

►WorkWork►spontaneous change vs non-spontaneous change vs non-

spontaneous changespontaneous change►Do characteristics of life require work?Do characteristics of life require work?

Types of Energy in Biological Systems• Kinetic energy - energy of motion, work done

• Potential energy - stored energy, can be released to do work

• Archer draws bowstring back - used kinetic energy

• Tension now in bowstring represents potential energy

• Release of bowstring converts potential energy to kinetic energy

Energy (cont’d)Energy (cont’d)

ThermodynamicsThermodynamics► a a system:system:

Some portion of the universe that you wish to studySome portion of the universe that you wish to study

► The The surroundings:surroundings:The adjacent part of the universe The adjacent part of the universe

outside the system, i.e. everything but outside the system, i.e. everything but the systemthe systemChanges in a system are associated with the Changes in a system are associated with the

transfer of energytransfer of energy

Natural systems tend toward states of minimum Natural systems tend toward states of minimum energyenergy

1st Law of 1st Law of ThermodynamicsThermodynamics

Total Energy in Universe is Constant energy cannot be created or destroyed Energy can be converted from one

form to another The pathway of conversion is irrelevant,

the energy change between identical initial and final states is equal

When it comes to energy-You can’t get ahead!

2nd Law of 2nd Law of Thermodynamics-You can’t Thermodynamics-You can’t

break even, either!break even, either!► No conversion is 100% efficient. ► Total useful energy in a closed system

decreases as conversions occur. ► Closed systems go from complex to simple.► Entropy

Measure of Disorder Closed systems tend to their highest state of

disorder Entropy of the universe increases with every

conversion

2nd Law of 2nd Law of ThermodynamicsThermodynamics

Randomness is spontaneous in a closed system

• Beaker on left has different colored marbles separated from each other

• Highly ordered system

• Low entropy

Examples of Entropy

low entropy high entropy

• Beaker on right has different colored marbles scattered amongst each other

• Highly disordered system

• High entropy Other examples?

SUMMARY-SUMMARY-THERMODYNAMICSTHERMODYNAMICS

►First LawFirst Law: Energy cannot be : Energy cannot be created or destroyed, but it can be created or destroyed, but it can be changed from one form to changed from one form to another.another.

►Second LawSecond Law: Energy cannot be : Energy cannot be changed from one form to another changed from one form to another without loss of usable energywithout loss of usable energy

GRADIENTS—A CASE STUDYGRADIENTS—A CASE STUDY

►What is a gradient?What is a gradient?►TypesTypes

PressurePressure TemperatureTemperature ChemicalChemical

►What does the 2What does the 2ndnd Law say about Law say about gradients?gradients?

Equilibriums--Closed systems go Equilibriums--Closed systems go to equilibriumto equilibrium

Universe-200 Universe-200 atomsatoms

Hydrogen—182Hydrogen—182

Helium---18Helium---18

All others<1/2All others<1/2

Human 200 atomsHuman 200 atomsHydrogen---126Hydrogen---126Oxygen---51Oxygen---51Carbon—19Carbon—19Nitrogen—3Nitrogen—3All others---1All others---1

What happens if you achieve equilibrium?

Equilibrium vs Steady StateEquilibrium vs Steady State

►Living things go from simple to Living things go from simple to complex. Evolution goes from simple complex. Evolution goes from simple to complex. How? Are biological to complex. How? Are biological systems not subject to the 2systems not subject to the 2ndnd Law? Law?

Basic ChemistryBasic ChemistryMatterMatter

Elements.Elements.

AtomsAtoms

CompoundsCompounds

MoleculesMolecules

Model of an AtomModel of an Atom

Model of an AtomModel of an Atom

Periodic Table of ElementsPeriodic Table of Elements

Atomic symbolAtomic symbol

Atomic numberAtomic number

Atomic mass (weight).Atomic mass (weight).

ATOMS

CHEMICAL REACTIONSCHEMICAL REACTIONS

►Electron shellsElectron shells►Valence (outer) Valence (outer)

shellshell►Octet ruleOctet rule►Ionic bondsIonic bonds►Covalent bondsCovalent bonds

Atoms will ‘strive’ to fill their Atoms will ‘strive’ to fill their outer (valence) orbitalsouter (valence) orbitals

► If an atom has 1 valence If an atom has 1 valence e-, it’s ‘happy’ to give it e-, it’s ‘happy’ to give it away away

► Example: SodiumExample: Sodium

1 valence e-

Atoms will ‘strive’ to fill their Atoms will ‘strive’ to fill their outer (valence) orbitalsouter (valence) orbitals

AND…If an atom has 7 valence e-, it’s ‘happy’ to pick up oneEx. Chlorine

7 valence e-

Ionic BondsIonic Bonds

Ions can have important biological Ions can have important biological functions.functions.

Covalent BondingCovalent Bonding

Carbon (C) 4

CC H

Hydrogen (H) 1

CCH

H

H

H

Methane CH4

Each pair of electronsrepresents the formationof a covalent bond.

Aside from single covalent bonds, Aside from single covalent bonds, double, or triple covalent bonds double, or triple covalent bonds can form.can form.

ReviewReview

► Ionic bonds occur when e- are shared Ionic bonds occur when e- are shared in a +/- arrangementin a +/- arrangement

►Covalent bonds exist when one atom Covalent bonds exist when one atom shares 1 or more e- with another shares 1 or more e- with another atom. atom.

►One covalent bond means 2 e- are One covalent bond means 2 e- are involved. involved. Always involves a pair of e- Always involves a pair of e-

Oxidation/ReductionOxidation/Reduction

►Oxidation----loss of electronOxidation----loss of electron►Reduction----Gain of electron Reduction----Gain of electron ►Examples?Examples?

►Water is the most abundant molecule Water is the most abundant molecule in living things.in living things.

►Water has special traits that make it Water has special traits that make it important to life.important to life.

Water and LifeWater and Life

Water molecules: 2-H covalently Water molecules: 2-H covalently bonded to 1-O. Covalent=shared bonded to 1-O. Covalent=shared ee--. But is sharing equal?. But is sharing equal?

Chemistry of WaterChemistry of Water

Amazing stuff!!!Should not be a liquid at room temp…Highly Polar molecule.

WATERWATER►Hydrogen bondsHydrogen bonds

►Polarity Polarity

Hydrogen BondingHydrogen Bonding

Positively charged hydrogen end

Negatively charged oxygen end Hydrogen Bonds

Covalent bonds between hydrogen and oxygen

Characteristics of water:Characteristics of water: 1.1. liquid at room temperatureliquid at room temperature

2.2. universal solvent for polar moleculesuniversal solvent for polar molecules

3.3. water molecules are cohesivewater molecules are cohesive

4.4. water molecules are adhesivewater molecules are adhesive

5.5. temperature of water changes slowlytemperature of water changes slowly

6.6. absorbs heat upon vaporizationabsorbs heat upon vaporization

7.7. releases heat upon freezingreleases heat upon freezing

8.8. frozen water is less densefrozen water is less dense

Water as a Water as a Solvent –Solvent –

How it How it WorksWorks

Dissociation of Water Dissociation of Water MoleculesMolecules

Water dissociates and releases hydrogen Water dissociates and releases hydrogen ions (Hions (H++) and hydroxide ions (OH) and hydroxide ions (OH--).).

ACIDS AND BASESACIDS AND BASES►AcidsAcids - release hydrogen - release hydrogen

ions (Hions (H++) in solution.) in solution. HCl HCl H H++ + Cl + Cl--

►BasesBases - take up hydrogen - take up hydrogen ions (Hions (H++) or give off ) or give off hydroxide ions (OHhydroxide ions (OH--) in ) in solution.solution. NaOH NaOH Na Na++ + OH + OH--

pH—a Measure of pH—a Measure of AcidityAcidity

If ph<7, acid

If pH>7, base

7=neutral

►Buffers Buffers --substances that --substances that help to resist change in help to resist change in pH.pH.

►Why important?Why important?

Water—Final NotesWater—Final Notes►Hydrophilic--polarHydrophilic--polar►Hydrophobic– non-polarHydrophobic– non-polar►Amphipathic---contain Amphipathic---contain hydrophilic hydrophilic andand hydrophobic partshydrophobic parts

Organic molecules are found in Organic molecules are found in living things.living things.

The chemistry of carbon accounts The chemistry of carbon accounts for the chemistry of organic for the chemistry of organic molecules.molecules.

Macromolecules (Polymers)Macromolecules (Polymers)

Organic Molecules—carbon Organic Molecules—carbon basedbased

Organic MoleculesOrganic Molecules

monomer

polymer

Macromolecules Macromolecules (polymers) and (polymers) and

monomers.monomers.

PolymerPolymer MonomerMonomer

carbohydrate carbohydrate monosaccharidesmonosaccharides

protein amino acidprotein amino acid

nucleic acid nucleotidenucleic acid nucleotide

Dehydration Synthesis or Dehydration Synthesis or Condensation ReactionsCondensation Reactions

vsvsHydrolysisHydrolysis

A BOH H+ + H—O—H or H2O

A B

covalent bonds

If the reaction is carried out multiple times you create a polymer!

+ H2O molecules

Condensation

Hydrolysis

Dehydration (condensation) builds. Hydrolysis breaks down.

What do they do?What do they do?

StructureStructure

Act as Act as enzymesenzymes to speed reactions to speed reactions

Serve as carriersServe as carriers

Act as antibodiesAct as antibodies

Transporters and channelsTransporters and channels

ProteinsProteins

Proteins --polymers of Proteins --polymers of amino acidsamino acids..

Peptide BondsPeptide Bonds

Proteins--Levels of Organization.Proteins--Levels of Organization.

TERTIARY (3º) STRUCTURE—3DTERTIARY (3º) STRUCTURE—3D► 1º structure and 1º structure and

environmentenvironment► Factors—R-groupsFactors—R-groups

Hydrogen bondingHydrogen bonding Hydrophobic Hydrophobic

interactionsinteractions Ionic (salt) bridgesIonic (salt) bridges Disulfide bondsDisulfide bonds

► Native vs DenaturedNative vs Denatured► REMEMBER: A

PROTEIN’S FUNCTION IS A RESULT OF ITS FORM!!

►Catalyst?Catalyst? Speeds up reactionSpeeds up reaction

►ProteinsProteins

The Model:The Model:

Enzymes—Biological Enzymes—Biological CatalystsCatalysts

E+S ES E+P

E=Enzyme

S=Substrate

P=Product

Classes of EnzymesClasses of Enzymes

1. Oxidoreductases1. Oxidoreductases

2. Transferases2. Transferases

3. Hydrolases3. Hydrolases

4. Lyases4. Lyases

5. Isomerases5. Isomerases

6. Ligases6. Ligases

Enzymes Lower Energy of Enzymes Lower Energy of ActivationActivation

EA barrier

Reactants

1 Products 2

En

zym

eFigure 5.5A

Enzymes-- lower the energy Enzymes-- lower the energy barrierbarrier

Enzyme-Substrate Enzyme-Substrate ComplexesComplexes

►Every reaction in a cell requires a Every reaction in a cell requires a specific enzyme.specific enzyme.

►Enzymes are named for their Enzymes are named for their substrates:substrates:

►SubstrateSubstrate EnzymeEnzyme►Lipid LipaseLipid Lipase►Urea UreaseUrea Urease►Maltose MaltaseMaltose Maltase►Ribonucleic acid RibonucleaseRibonucleic acid Ribonuclease

ACTIVE SITEACTIVE SITE►Where does Where does

enzyme bind enzyme bind to substrate?to substrate?

►How does How does enzyme enzyme recognize its recognize its substrate?substrate?

Induced Fit Induced Fit ModelModel

Induced fit modelInduced fit model

Enzymatic reactionEnzymatic reaction

Cell ChemistryCell Chemistry►Enzymes—involved in almost Enzymes—involved in almost

all chemical reactions.all chemical reactions.►Anabolism—The building Anabolism—The building

reactions. EX. Protein synthesisreactions. EX. Protein synthesis►Catabolism—The breakdown Catabolism—The breakdown

reactions. EX. Protein digestionreactions. EX. Protein digestion►Metabolism—sum of all Metabolism—sum of all

reactionsreactions

Factors Affecting Enzymatic Factors Affecting Enzymatic SpeedSpeed

►REMEMBER—FORM FOLLOWS REMEMBER—FORM FOLLOWS FUNCTION!!!FUNCTION!!!

►FactorsFactors Substrate concentration-to a pointSubstrate concentration-to a point EnvironmentEnvironment

►TemperatureTemperature►pHpH►Salt concentrationSalt concentration

►ANYTHING THAT AFFECTS FORM ANYTHING THAT AFFECTS FORM AFFECTS FUNCTION!!!AFFECTS FUNCTION!!!

Temperature OptimumTemperature OptimumpH OptimumpH Optimum

INHIBITION MODELSINHIBITION MODELS

► Inhibition----reduced activityInhibition----reduced activity►CompetitiveCompetitive

E + S+ I E + S+ I ↔ ES + EI ↔E + P or I or P↔ ES + EI ↔E + P or I or P22

►Non-competitive (allosteric) Non-competitive (allosteric) E + S +I E + S +I ↔ no or reduced ES ↔E + no ↔ no or reduced ES ↔E + no

product or reduced productproduct or reduced product

EX. Feedback InhibitionEX. Feedback Inhibition

Feedback InhibitionFeedback Inhibition►Non-competitive (allosteric) inhibitionNon-competitive (allosteric) inhibition

Allosteric site vs Active siteAllosteric site vs Active site

Feedback Inhibition 2Feedback Inhibition 2

Feedback Inhibition 3Feedback Inhibition 3

PROBLEMPROBLEM

ETHANOLETHANOL

ETHYLENE GLYCOL ETHYLENE GLYCOL

Enzyme CofactorsEnzyme Cofactors►CofactorsCofactors ---may be necessary for ---may be necessary for

some enzymes to carry out their some enzymes to carry out their functions. Two types:functions. Two types: Metal ions. EX copper (CuMetal ions. EX copper (Cu+2+2) or ) or

iron (Feiron (Fe+2+2) ) CoenzymesCoenzymes Organic molecules, Organic molecules,

must be present for other must be present for other enzymes to function. EX enzymes to function. EX vitaminsvitamins

Levels of Protein Structure—Levels of Protein Structure—Quaternary (4º) StructureQuaternary (4º) Structure

Multiple chains: Multiple chains: interactions of interactions of more than one more than one polypeptide chain polypeptide chain to form the to form the complete, complete, functional protein. functional protein. Ex. Hemoglobin Ex. Hemoglobin and antibodiesand antibodies

• Generally, C:H:O in a 1:2:1 ratio Generally, C:H:O in a 1:2:1 ratio (CH(CH22O)O)nn

• FunctionsFunctions• quick energy and short-term energy quick energy and short-term energy

storage.storage. EX glycogen, starch EX glycogen, starch• Structure. EX. CelluloseStructure. EX. Cellulose

• Polymer=polysaccharides EX. StarchPolymer=polysaccharides EX. Starch• Monomers= monosaccharides EX. Monomers= monosaccharides EX.

glucoseglucose

CarbohydratesCarbohydrates

NOMENCLATURENOMENCLATURE

►Based on number of carbonsBased on number of carbons►3C==triose3C==triose►4C==tetrose4C==tetrose►5C==pentose, etc5C==pentose, etc

Structure of GlucoseStructure of Glucose

DisaccharidesDisaccharides

Polymerization of Polymerization of CarbohydratesCarbohydrates

POLYSACCHARIDESPOLYSACCHARIDES

STARCH

GLYCOGEN

CELLULOSE

LIPIDSLIPIDS►NON-POLAR BIOLOGICAL MOLECULESNON-POLAR BIOLOGICAL MOLECULES►FUNCTIONSFUNCTIONS

Energy storageEnergy storage: Fats and oils.: Fats and oils. WaterproofingWaterproofing: Waxes and oils: Waxes and oils InsulationInsulation: Fat layers (blubber): Fat layers (blubber) CushioningCushioning: Fat layers (soles of your : Fat layers (soles of your

feet)feet) Regulating metabolismRegulating metabolism: Steroids: Steroids Component of cell membranesComponent of cell membranes: :

PhospholipidsPhospholipids

Lipid structure (Triglyceride)Lipid structure (Triglyceride)

► Glycerol Glycerol backbonebackbone

►Fatty acid tailsFatty acid tails►Fats vs oilsFats vs oils

X3

Triglyceride formationTriglyceride formation

H

H-C—OH

H-C—OH

H-C—OH

H

GLYCEROL

O H H H H H HO-C-C-C-C-C-C-H H H H H H O H H H H H HO-C-C-C-C-C-C-H H H H H H O H H H H H HO-C-C-C-C-C-C-H H H H H H

FATTY ACIDS

H

H-C—O

H-C—O

H-C—O

H

O H H H H H -C-C-C-C-C-C-H H H H H H

O H H H H H -C-C-C-C-C-C-H H H H H H O H H H H H -C-C-C-C-C-C-H H H H H H

+ H20

+ 3 H20TRIGLYCERIDE

What type of reaction forms a triglyceride? Dehydration Synthesis

+ H20

+ H20

Saturated vs. Unsaturated Saturated vs. Unsaturated FatsFats

Saturated vs. Unsaturated Saturated vs. Unsaturated FatsFats

Fatty Acids: cis vs. Fatty Acids: cis vs. transtrans

-linolenic acid

Trans -linolenic acid

PhospholipidsPhospholipids

The major structural component of cell membranes

Phospholipid BehaviorPhospholipid Behavior

PhospholipidsPhospholipids

Soaps and EmulsifiersSoaps and Emulsifiers

Steroids-Hormones Steroids-Hormones and Structureand Structure

Nucleic AcidsNucleic Acids

►Polymers: DNA and RNAPolymers: DNA and RNA►Monomers: nucleotidesMonomers: nucleotides►FunctionsFunctions

Information storage and Information storage and transmissiontransmission

ATP is energy currency of cellATP is energy currency of cell

Nucleotide StructureNucleotide Structure

DNA vs RNADNA vs RNA

The Double Helix of DNA-The Double Helix of DNA-Complementary base pairingComplementary base pairing

The Central Dogma

Transcription---

Translation---

Replication---

RNA

Protein

DNA

duplication of DNA using DNA as the template

synthesis of RNA using DNA as the template

synthesis of proteins using RNA as the template

ATGAGTAACGCGTACTCATTGCGC

ATGAGTAACGCGTACTCATTGCGC

ATGAGTAACGCGTACTCATTGCGC

+

AUGAGUAACGCG

MetSerAsnAla

mRNA-message

Protein--end product

DNA-gene

Mutation-DNA Mutation-DNA ChangeChange

Adenosine Triphosphate-ATPAdenosine Triphosphate-ATP

Adenosine triphosphate (ATP) is the energy currency of cells

ReviewReview►ThermodynamicsThermodynamics►Basic ChemistryBasic Chemistry

AtomsAtoms IsotopesIsotopes Molecules and CompoundsMolecules and Compounds

►Chemical BondingChemical Bonding Ionic and CovalentIonic and Covalent HydrogenHydrogen

►Properties of WaterProperties of Water►Acids and Bases, pHAcids and Bases, pH

Review 2Review 2►3 Reactions3 Reactions

Oxidation/reductionOxidation/reduction Dehydration (condensation)Dehydration (condensation) HydrolysisHydrolysis

►Organic vs InorganicOrganic vs Inorganic►MacromoleculesMacromolecules

Proteins Proteins CarbohydratesCarbohydrates LipidsLipids Nucleic AcidsNucleic Acids