Chapter 2: The Molecules Chapter 2: The Molecules of Cells of Cells
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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
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