chapter 3 molecules of a cell. quiz 1 answer the questions that you got wronganswer the questions...
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Chapter 3Chapter 3
Molecules of a cellMolecules of a cell
Quiz 1Quiz 1
• Answer the questions that you got Answer the questions that you got wrongwrong
1.1.Correct answerCorrect answer
2.2.Why that is the correct answerWhy that is the correct answer
3.3.Get back half the points you missedGet back half the points you missed
*** Q 3 and Q 4*** Q 3 and Q 4
HypothesesHypotheses
• Tentative, testable statement that Tentative, testable statement that proposes a possible outcome/explanation proposes a possible outcome/explanation to an event to an event
TESTABLE!!!!TESTABLE!!!!
A tentative relationship is stated, not just A tentative relationship is stated, not just a prediction.a prediction.
Predictions are not necessarily testablePredictions are not necessarily testable
Prediction vs HypothesisPrediction vs Hypothesis
• Predictions “guess” what will happenPredictions “guess” what will happen• Hypothesis presents a relationship, Hypothesis presents a relationship,
which explains what will happenwhich explains what will happen
• ***Hypotheses do not draw conclusions***Hypotheses do not draw conclusions– Ex: Squirrels are different colors at Ex: Squirrels are different colors at
different locations due to diet differences different locations due to diet differences because this lets them blend into their because this lets them blend into their surroundings. surroundings.
Language of a hypothesisLanguage of a hypothesis
• Contain the dependent and Contain the dependent and independent variablesindependent variables– If If leaf color leaf color change is change is relatedrelated to to
temperaturetemperature , , thenthen exposing plants to exposing plants to low temperatures will result in changes low temperatures will result in changes in leaf color.in leaf color.
• If the reader cannot figure out what If the reader cannot figure out what you are testing, it is not a hypothesisyou are testing, it is not a hypothesis
• Can be in “If- Then” format, but it Can be in “If- Then” format, but it does not have to bedoes not have to be
HypothesesHypotheses• The coral snake’s bright color pattern serves to The coral snake’s bright color pattern serves to
warn off potential predators.warn off potential predators.• The king snake suffers less predation because it The king snake suffers less predation because it
mimics or looks like the coral snake.mimics or looks like the coral snake.• The protection that king snakes receive by The protection that king snakes receive by
mimicking coral snake will depend on the presence mimicking coral snake will depend on the presence of coral snakes.of coral snakes.
• Rotting meat produces fliesRotting meat produces flies• The markings on the winds of flies increase survival The markings on the winds of flies increase survival
of flies by causing spiders to fleeof flies by causing spiders to flee• If fermentation rate is related to temperature, then If fermentation rate is related to temperature, then
increasing the temperature will increase gas increasing the temperature will increase gas productionproduction
BondsBonds
TypeType e-e- links?links?overall overall chargecharge
IonicIonic taken/receivedtaken/received atomsatoms pos/negpos/neg
CovalentCovalent sharedshared atomsatoms neutralneutral
polarpolar sharedshared atomsatoms partialpartial
non-non-polarpolar sharedshared atomsatoms neutralneutral
HydrogenHydrogen sharedshared moleculesmolecules neutralneutral
MoleculesMolecules
2 types2 types– OrganicOrganic– InorganicInorganic
Organic- generally C based Organic- generally C based
Inorganic- generally non-C basedInorganic- generally non-C based
** Exceptions include CO** Exceptions include CO22, CO, CN, , CO, CN, etcetc
C-HC-H
• HydrocarbonsHydrocarbons– Compounds Compounds
composed of only composed of only C and HC and H Methane, Methane,
propane, butane, propane, butane, benzene, etcbenzene, etc
• Chain, branch or Chain, branch or ring of Cring of C– C skeletonC 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
Ex: 16 isomers of CEx: 16 isomers of C66HH1212OO44, but only one, d- Glucose, , but only one, d- Glucose, is used in metabolismis used in metabolism
Functional GroupsFunctional Groups• Determine the Determine the
properties of properties of organic 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= These molecules are large= macromoleculesmacromolecules
Polymers & MonomersPolymers & Monomers
• Cells make large molecules by joining Cells make large molecules by joining together smaller molecules into chainstogether smaller 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 Cells link monomers to form polymers via a dehydration polymers via a dehydration reactionreactionH
OH H
OH
H OH
Unlinked monomer
Dehydration reaction
Longer polymer
Short polymer
OH H
H OH
Unlinked monomer
Dehydration reaction
Short polymer
H2O
Dehydration ReactionDehydration Reaction
• Removes waterRemoves water– Unlinked monomers have a hydroxyl group (-Unlinked monomers have a hydroxyl group (-
OH) at one end & a hydrogen (-H) at the otherOH) at one end & a hydrogen (-H) at the other
• 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
Dehydration ReactionDehydration ReactionH
OH H
OH
H OH
Unlinked monomer
Dehydration reaction
Longer polymer
Short polymer
OH H
H OH
Unlinked monomer
Dehydration reaction
Short polymer
H2O
Breaking PolymersBreaking Polymers• Cells break polymers into monomers Cells break polymers into monomers
via a hydrolysis reactionvia a hydrolysis reaction
H
H2O
OH
H OHOH H
Hydrolysis
Hydrolysis ReactionHydrolysis Reaction
• Breaks covalent bond between Breaks covalent bond between monomers by adding watermonomers by adding water
• A OH- joins to one monomer and a H A OH- joins to one monomer and a H joins to an adjacent monomerjoins to an adjacent monomer
• For each monomer removed, 1 For each monomer removed, 1 molecule water is addedmolecule water is added
Hydrolysis ReactionHydrolysis Reaction
H
H2O
OH
H OH
OH H
Hydrolysis
EnzymesEnzymes
• CatalystsCatalysts• Macromolecules that increase rate Macromolecules that increase rate
of chemical reactions in cellsof chemical reactions in cells• Typically proteinsTypically proteins
Sugar!Sugar!• Carbohydrates are Carbohydrates are
polymers called polymers called saccharidessaccharides
• Monosaccharides Monosaccharides contain contain one monomer (glucose)one monomer (glucose)
• DisaccharidesDisaccharides contain contain two monomers (sucrose)two monomers (sucrose)
• Oligosaccharides Oligosaccharides contain contain several monomersseveral monomers
• PolysaccharidesPolysaccharides contain contain hundreds of monomershundreds of monomers
DisaccharidesDisaccharides• Cells link two single sugars to form Cells link two single sugars to form
disaccharidesdisaccharides– Monosaccharides can join to form Monosaccharides can join to form
disaccharides using dehydration reactionsdisaccharides using dehydration reactions• Such as sucrose (table sugar) and maltose Such as sucrose (table sugar) and maltose
(brewing sugar)(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
Sugar storageSugar storage
• Starch and glycogen store Starch and glycogen store polysaccharides polysaccharides – Starch in plantsStarch in plants– Glycogen in animalsGlycogen in animals
• Cellulose forms the cell walls of plantsCellulose forms 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 Not true
polymers, polymers, although some are although some are formed via formed via dehydration dehydration reactionsreactions
• HydrophobicHydrophobic• Energy storageEnergy storage• Solid and liquid Solid and liquid
statesstates
FatsFats
• TriglyceridesTriglycerides• Energy storageEnergy storage
• Consist of Consist of glycerol linked glycerol linked to three fatty to three fatty acidsacids
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)– Carboxylic acid functional group (polar)Carboxylic acid functional group (polar)
Polar and nonpolar character in one Polar and nonpolar character in one molecule: which wins?molecule: which wins?
Hydrocarbon chain Hydrocarbon chain dominatesdominates
• Length of hydrocarbon chain means Length of hydrocarbon chain means that nonpolar character dominatesthat nonpolar character dominates– Fatty acids dissolve in nonpolar Fatty acids dissolve in nonpolar
solventssolvents
Saturated vs UnsaturatedSaturated vs 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 Saturated/unsaturated refers to whether or not the C chains contain the or not the C chains contain the maximum number of H possiblemaximum number of H possible
KinkyKinky
• Double bonds Double bonds kink the kink the structurestructure
• Kinks reduce Kinks reduce packing packing densitydensity
• Lower packing Lower packing density density decreases decreases melting pointmelting point
Saturation and melting Saturation and melting pointpoint
• Saturated fatty Saturated fatty acids have melting acids have melting points above 25ºCpoints above 25ºC– Liquid at room Liquid at room
temptemp
• 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 Highly unsaturated fats can be very soft and are hydrogenated soft and are hydrogenated (saturated) to make them more (saturated) to make them more butter-like.butter-like.
• Addition of hydrogen to C=C double Addition of hydrogen to C=C double bond.bond.
• Some of the Some of the ciscis bonds are converted bonds are converted to 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 fats and the product is stiffer.the product is stiffer.
• TransTrans fats pose a health risk – are not fats pose a health risk – are not broken down readily.broken down readily.
PhospholipidsPhospholipids
• Significant component of cell Significant component of cell membranesmembranes
• Contain a glycerol backbone: Contain a glycerol backbone: – Two fatty acidsTwo fatty acids– One phosphate group and small organic One phosphate group and small organic
moleculemolecule
• Hydrophilic and Hydrophobic portionHydrophilic and Hydrophobic portion– 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
• Polymer constructed from amino acid Polymer constructed from amino acid monomersmonomers
• Amino acids contain:Amino acids contain:– -NH-NH22..
– -COOH.-COOH.– R groups (R varies from one amino acid R groups (R varies from one amino acid
to another).to another).
• Link between amino acids in protein Link between amino acids in protein is a is a peptide peptide bondbond
ProteinsProteins
Functions of ProteinsFunctions of Proteins
• Multiple functionsMultiple functions– EnzymesEnzymes– StructuralStructural– ContractileContractile– DefensiveDefensive– SignalSignal– ReceptorReceptor– TransportTransport– StorageStorage
Building ProteinsBuilding Proteins
• Built from amino acids (AA)Built from amino acids (AA)– 20 AA20 AA
• Amino acids form chain with R Amino acids form chain with R groups from side chainsgroups from side chains– R group determines protein varietyR group determines protein variety
Amino AcidsAmino Acids
• Specific properties based on its Specific properties based on its structurestructure
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
Amino AcidsAmino Acids
• Cells link AA together via Cells link AA together via dehydration synthesisdehydration synthesis– Bonds broken via hydrolysisBonds broken via hydrolysis
• Bonds between monomers are Bonds between monomers are peptide bondspeptide bonds– 2 bonded AA= dipeptide2 bonded AA= dipeptide– > 2 bonded AA= polypeptide> 2 bonded AA= polypeptide
H
H
N C C
O
OH H
HN+ C
H
R
C
O
OHH2O
H
H
N C C N C C
R H R OH
O
Peptidebond
DipeptideAmino acid
Dehydrationreaction
Amino group
H
R
Amino acid
Carboxyl group
H O H
Form determines Form determines functionfunction
• A protein consists of one or more A protein consists of one or more polypeptide chains folded into a polypeptide chains folded into a unique shapeunique shape– Unique shape of protein determines the Unique shape of protein determines the
functionfunction
GrooveGroove
Levels of Protein Levels of Protein StructureStructure
• PrimaryPrimary– Unique sequence of AA forming the Unique sequence of AA forming the
polypeptide chainpolypeptide chainLevels 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 Levels of Protein StructureStructure
• SecondarySecondary– Coiling or folding of the chain, Coiling or folding of the chain,
stabilized by H bondingstabilized by H bonding•Alpha helix & pleated sheetsAlpha 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 Levels of Protein StructureStructure
• TertiaryTertiary– Overall three-Overall three-
dimensional dimensional shape of a shape of a polypeptidepolypeptide
– Globular or Globular or fibrousfibrous
– Interactions Interactions between R between R groupsgroups
Tertiary structure
Polypeptide(single subunitof transthyretin)
Levels of Protein Levels of Protein StructureStructure
• Quaternary structureQuaternary structure– Results from the association of two or Results from the association of two or
more polypeptide chainsmore polypeptide chains
Quaternary structure
Transthyretin, withfour identical
polypeptide subunits
Polypeptidechain
Collagen
When shape failsWhen shape fails
• DenaturationDenaturation– Polypeptide chains unravelPolypeptide chains unravel– Results from heat, salt concentration, Results from heat, salt concentration,
pH, etc. pH, etc.
• Resulting altered shape causes Resulting altered shape causes proteins to loose their functionproteins to loose their function
Nucleic AcidsNucleic Acids• Information-Information-
rich polymers rich polymers of nucleotidesof nucleotides– Nucleic acids Nucleic acids
such as DNA such as DNA and RNA serve and RNA serve as the as the blueprints for blueprints for proteins and proteins and thus control thus control the life of a cellthe life of a cell
– The monomers The monomers of nucleic acids of nucleic acids are nucleotidesare nucleotides
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 polynucleotides – Twisted around each other in a Twisted around each other in a
double helix double helix – Held together by hydrogen Held together by hydrogen
bondingbonding• RNA consists of a single RNA consists of a single
polynucleotide strandpolynucleotide strand• There are five types of There are five types of
nitrogenous basesnitrogenous bases– DNA has A,T,G and CDNA has A,T,G and C– RNA has A,U,G and CRNA has A,U,G and C
C
TA
GC
C G
T A
C G
A T
A
G C
A T
A T
T A
Basepair
T