chapter 3 molecules of a cell. molecules 2 types –organic –inorganic organic- generally c based...
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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