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Biological Molecules
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Chapter 3
Biological Biological MoleculesMolecules
Chapter 3 2 Why Is Carbon So Important?Why Is Carbon So Important?
Organic vs. Inorganic in ChemistryOrganic vs. Inorganic in Chemistry• OrganicOrganic refers to molecules containing a refers to molecules containing a
carbon skeletoncarbon skeleton• InorganicInorganic refers to carbon dioxide and all refers to carbon dioxide and all
molecules without carbonmolecules without carbon
Chapter 3 3 Why Is Carbon So Important?Why Is Carbon So Important?
Carbon atoms are versatile and can Carbon atoms are versatile and can form up to four bonds (single, double, form up to four bonds (single, double, or triple) in rings and chainsor triple) in rings and chains
Bonds are very high in energy Bonds are very high in energy (strongest substance on Earth = pure (strongest substance on Earth = pure carbon = …?)carbon = …?)
Functional groups in organic molecules Functional groups in organic molecules confer chemical reactivity and other confer chemical reactivity and other characteristics…characteristics…
Chapter 3 4
HydroxylHydroxyl
HydrogenHydrogen
Example Groups, IExample Groups, I
HHHH
OHOHOHOH
• Polar / Nonpolar• Dehyd. Synth /
Hydrolysis• Almost all
biochemicals
• Polar / Nonpolar• Dehyd. Synth /
Hydrolysis• Almost all
biochemicals
• Polar• Dehyd. Synth /
Hydrolysis• Sugars
• Polar• Dehyd. Synth /
Hydrolysis• Sugars
Chapter 3 5
Amine Amine or Aminoor Amino
Carboxyl Carboxyl (Carboxylic (Carboxylic
acid)acid)
Example Groups, IIExample Groups, II• Polar & acidic
• Peptide bonds
• Fats; amino acids
• Polar & acidic
• Peptide bonds
• Fats; amino acids
• Polar & basic
• Peptide bonds
• Amino acids; proteins
• Polar & basic
• Peptide bonds
• Amino acids; proteins
COOHCOOHCOOHCOOH
NHNH22NHNH22
Chapter 3 6
MethylMethyl
PhosphatePhosphate
ExampleExampleGroups, IIIGroups, III
• Acidic & polar• Energetic bonds;
Links nucleotides• DNA; ATP;
Phospholipids
• Acidic & polar• Energetic bonds;
Links nucleotides• DNA; ATP;
Phospholipids
• Nonpolar
• Hydrophobic
• Many, especially lipids
• Nonpolar
• Hydrophobic
• Many, especially lipids
HH22POPO44HH22POPO44
CHCH44CHCH44
Chapter 3 7
Joining Monomers TogetherJoining Monomers TogetherBuilds bigger moleculesBuilds bigger molecules
H from one joins OH from anotherH from one joins OH from another
Forms water (condensation) – the molecule Forms water (condensation) – the molecule loses water “DEHYDRATION”loses water “DEHYDRATION”
Loose bonds of remaining molecules joinLoose bonds of remaining molecules join
““SYNTHESIS” of SYNTHESIS” of starchstarch
Chapter 3 8
Splitting Polymers ApartSplitting Polymers Apart
Opposite of condensationOpposite of condensation
"Splitting (lysis) with water (hydro-)""Splitting (lysis) with water (hydro-)"
Molecule broken in twoMolecule broken in two
Water is split (Water is split (“HYDROLYSIS”“HYDROLYSIS”))
––HH++ goes to one; –OH goes to one; –OH-- goes to other goes to other
DigestionDigestion
Chapter 3 9
Dehydration / HydrolysisDehydration / Hydrolysis
Dehydration SynthesisDehydration Synthesis
HydrolysisHydrolysis
Chapter 3 10
MonosaccharidesMonosaccharides
““Mono-” means “one”Mono-” means “one”
Simple sugars — glucose, fructoseSimple sugars — glucose, fructose
Usually with 5 or 6 carbonsUsually with 5 or 6 carbons• 5-carbon sugars are pentoses5-carbon sugars are pentoses• 6-carbon sugars are hexoses6-carbon sugars are hexoses• etc.etc.
Soluble in waterSoluble in water
Taste sweetTaste sweet
OOHOCHHOCH22 HH
OHOH
HHHOHO
HOHO
HH HH
CHCH22OHOH
HH
HOHO
HHOHOH
HH
HOHO
HH
OHOH
HH
OODeoxyriboseDeoxyribose
GalactoseGalactose
1. Carbohydrates1. Carbohydrates
Chapter 3 11
OligosaccharidesOligosaccharides
““Oligo-” means “few”Oligo-” means “few”Few monosaccharides joined togetherFew monosaccharides joined togetherSucrose is Sucrose is disaccharidedisaccharide of of glucoseglucose & & fructosefructose
Often combined with other moleculesOften combined with other moleculesSometimes used for cell I.D.Sometimes used for cell I.D.
HOHOHH
CHCH22OHOH
HH
HOHO
HHOHOH
HH
HOHO
HH HHOOOO
HOCHHOCH22 HH
CHCH22OHOH
HHHOHO
HH HOHOOO
CHCH22OHOH
HH
HOHO
HHOHOH
HH
HOHO
HH
OHOH
HHOO
GlucoseGlucose
OOHOCHHOCH22 HH
CHCH22OHOH
HHHOHO
HOHOHH HOHO
FructoseFructose Sucrose & WaterSucrose & Water++
++
1. Carbohydrates1. Carbohydrates
Chapter 3 12
Polymerization of glucose to form starchOH
O
OCH2OH
OHO
OCH2OH
OHOO
CH2OH
OHOOCH 2
OH
OHO
OCH 2OH
OHO
OCH2OH
OHO
O
CH2OH
OH O
O
CH2 OH
Plant Starch (Amylose)Plant Starch (Amylose)
Actually formsActually formsa spirala spiral
OHO
OCH2OH
OHO
OCH2OH
OHO
OCH2OH
GlucoseGlucose
1. Carbohydrates1. Carbohydrates
Chapter 3 13
OHO
CH2OH
OHO
CH2OH
OHO
CH2OH
OHO
CH2
OH
CH2OH
OHO
CH2OH
OHO
O O O O
OOOCH2OH
StarchStarch1. Carbohydrates1. Carbohydrates
Chapter 3 14
CelluloseCellulose
OH
OOCH2OH
HO
OO
CH2OH OH
OOCH2OH
HO
OO
CH2OH OH
OOCH2OH
OH
OOCH2OH
HO
OO
CH2OH OH
OOCH2OH
HO
OO
CH2OH OH
OOCH2OH
OH
OOCH2OH
HO
OO
CH2OH OH
OOCH2OH
HO
OO
CH2OH OH
OOCH2OH
Chapter 3 15
Cellulose Structure & FunctionCellulose Structure & Function1. Carbohydrates1. Carbohydrates
Chapter 3 16
ChitinChitinLike cellulose, but with nitrogenLike cellulose, but with nitrogenArthropods’ exoskeletons, fungal cell wallsArthropods’ exoskeletons, fungal cell wallsStrong, very resistant to digestionStrong, very resistant to digestion
N HCOCH3
N HCO
CH3
OOCH2OH
OO
CH2OH
OOCH2OH
OO
CH2OH
OOCH2OH
N HCOCH3
N HCO
CH3
N HCOCH3
1. Carbohydrates1. Carbohydrates
Chapter 3 17
ChitinChitin1. Carbohydrates1. Carbohydrates
Chapter 3 18
Lipids - 2nd of 4 Classes Lipids - 2nd of 4 Classes of Organic Compoundsof Organic Compounds
Slippery-oilsSlippery-oils
Nonpolar; mostly C & H, little bit of ONonpolar; mostly C & H, little bit of O
Heterogeneous groupHeterogeneous group
• Other classes more homogeneousOther classes more homogeneous
• Unified by insolubility in waterUnified by insolubility in water
Fatty-acidFatty-acid types: Oils & waxes types: Oils & waxes
Nonfatty-acid types: Nonfatty-acid types: steroidssteroids
Chapter 3 19
Fat MoleculesFat Molecules
TriglyceridesTriglycerides from beef, vegetable oils from beef, vegetable oils
Three fatty acids and a Three fatty acids and a glycerolglycerol
• Glycerol has 3 carbonsGlycerol has 3 carbons
• Each with an –OH groupEach with an –OH group
Each fatty acid has a COOHEach fatty acid has a COOH
These condense to form triglyceride and These condense to form triglyceride and HH22OO
2. Lipids2. Lipids
Chapter 3 20
Fatty AcidsFatty Acids
Determines properties of fatDetermines properties of fat
Hydrocarbon chain with a COOHHydrocarbon chain with a COOH
Most fats = 3 FAs + glycerolMost fats = 3 FAs + glycerol
• Glycerol: 3-carbon alcoholGlycerol: 3-carbon alcohol
• 3 OHs attract the COOH of FAs3 OHs attract the COOH of FAs
2. Lipids2. Lipids
Chapter 3 21
Components of TriglyceridesComponents of Triglycerides
Chapter 3 22
H HC
H
C
H
OH
C
H
OHOH
C OCCC
HHH
HHH
HCC
HHH
HHH
H
CC O C O
CCC
HHH
HHH
H
TriglycerideTriglyceride
TriglycerideTriglyceride(Fat) Formation(Fat) Formation
C
OH
C
CC
OHHH
HHH
H
Add 3FattyAcids
Add 3FattyAcids
GlycerolGlycerol
HOH HOH HOH
3 Waters
C
OH
C
CC
OHHH
HHH
H
C
OH
C
CC
OHHH
HHH
H
OC
H
C
H
C
H
O OH H
RemoveTheseWaters
RemoveTheseWaters
C OCCC
HHH
HHH
HCC
HHH
HHH
H
CC O C O
CCC
HHH
HHH
H
Chapter 3 23
Fatty Acid TypesFatty Acid Types
SaturatedSaturated - No C=C - No C=C double bondsdouble bonds
animal fat, solid @ animal fat, solid @
room temp, “bad” fatsroom temp, “bad” fats
UnsaturatedUnsaturated - One or more - One or more
C=C double bondsC=C double bondsplants & fish, liquidsplants & fish, liquidsoils, “good” fatsoils, “good” fats
2. Lipids2. Lipids
Chapter 3 24
PhospholipidsPhospholipids
PhospholipidsPhospholipids - mostly in - mostly in cell membranescell membranes
1 glycerol, 2 FAs, & 1 polar phosphate 1 glycerol, 2 FAs, & 1 polar phosphate groupgroup
• Like a triglyceride...Like a triglyceride...
• 1 FA swapped for polar, phosphate group1 FA swapped for polar, phosphate group
Soap-like propertiesSoap-like properties
Likes to get between polar and nonpolar Likes to get between polar and nonpolar materialsmaterials
2. Lipids2. Lipids
Chapter 3 25
PhospholipidsPhospholipids
PolarPolarHeadHead GlycerolGlycerol Fatty Acid TailsFatty Acid Tails
HydrophobicHydrophobicHydrophilicHydrophilic
2. Lipids2. Lipids
Chapter 3 26
Complex ring formsComplex ring forms
Some hormonesSome hormones
CholesterolCholesterol
• Natural substanceNatural substance
• Found in membranesFound in membranes
• Gives membranes natural flexibilityGives membranes natural flexibility
SteroidsSteroids2. Lipids2. Lipids
Chapter 3 27
SteroidsSteroids
Cholesterol Estradiol
Testosterone
2. Lipids2. Lipids
Chapter 3 28
Proteins - 3Proteins - 3rdrd of 4 Classes of 4 Classes of Organic Compoundsof Organic Compounds
ProteinsProteins are amino acid polymers are amino acid polymers
Many roles in the cell…Many roles in the cell…
• EnzymesEnzymes
• HormonesHormones
• Structure (muscle, hair, nails)Structure (muscle, hair, nails)
• Cell membrane pumps and channelsCell membrane pumps and channels
Chapter 3 29
Amino AcidsAmino Acids
Small molecules — 20 kinds Small molecules — 20 kinds
• 1 amino group1 amino group
• 1 carboxyl group1 carboxyl group
• 1 "R" group1 "R" group
Joined by peptide bonds to form Joined by peptide bonds to form polypeptidepolypeptide
Different sequence makes different proteinDifferent sequence makes different protein
3. Proteins3. Proteins
Chapter 3 30
Generic AminoGeneric AminoAcid: 20 Different “R” GroupsAcid: 20 Different “R” Groups
AmineAmineGroup Group
The “R” GroupThe “R” GroupPlaceholderPlaceholder
Carboxylic AcidCarboxylic AcidGroupGroup
““Alpha”Alpha”CarbonCarbon
RR
Chapter 3 31
Amino Acids:Amino Acids:Glutamic Acid StructureGlutamic Acid Structure
Glutamic AcidGlutamic Acid“R” Group“R” Group
AmineAmineGroup Group
Carboxylic AcidCarboxylic Acid Group Group
““Alpha”Alpha”CarbonCarbon
Chapter 3 32
Amino Acids: Leucine StructureAmino Acids: Leucine Structure
Leucine “R”Leucine “R” Group Group
AmineAmineGroup Group
Carboxylic AcidCarboxylic Acid Group Group
3. Proteins3. Proteins
Chapter 3 33
Amino Acids: Cysteine StructureAmino Acids: Cysteine Structure
Cysteine “R”Cysteine “R” Group Group
AmineAmineGroup Group
Carboxylic AcidCarboxylic Acid Group Group
3. Proteins3. Proteins
Chapter 3 34
Structural ProteinsStructural Proteins
HairHair
HornHorn
SpiderwebSpiderweb
3. Proteins3. Proteins
Chapter 3 35
Peptide BondPeptide Bond Formation Formation
By Condensation between COOH & NH2
PhenylalaninePhenylalanine LeucineLeucine
3. Proteins3. Proteins
Chapter 3 36
Peptide Bond:Peptide Bond:Phenylalanine-Leucine DipeptidePhenylalanine-Leucine Dipeptide
WaterWaterWaterWater
The Peptide BondThe Peptide BondThe Peptide BondThe Peptide Bond
Chapter 3 37
Levels of Protein StructureLevels of Protein Structure
Like describing a knot by starting with the Like describing a knot by starting with the strands of the ropestrands of the rope
• PrimaryPrimary: The amino acid sequence: The amino acid sequence
• SecondarySecondary: Coiling or folding: Coiling or folding
• TertiaryTertiary: folding, kinking, twisting entire structure: folding, kinking, twisting entire structure
• QuaternaryQuaternary: Two or more chains together: Two or more chains together
3. Proteins3. Proteins
Chapter 3 38
Illustration ofIllustration ofProtein StructureProtein Structure
PrimaryPrimary(Sequence)(Sequence)
PrimaryPrimary(Sequence)(Sequence)
SecondarySecondary(Coiling)(Coiling)
SecondarySecondary(Coiling)(Coiling)
TertiaryTertiary(Bending)(Bending)TertiaryTertiary
(Bending)(Bending)
QuaternaryQuaternary(Layering)(Layering)
QuaternaryQuaternary(Layering)(Layering)
Chapter 3 39
Pleated SheetsPleated Sheets““Right-side up” AAsRight-side up” AAs
““Flipped” AAsFlipped” AAsHydrogenHydrogen
BondsBonds
3. Proteins3. Proteins
Chapter 3 40
Nucleic Acids: 4Nucleic Acids: 4thth Class Class of Organic Compoundof Organic Compound
Nucleic acidsNucleic acids are are nucleotidenucleotide polymers polymers
Genetics & cell controlGenetics & cell control
DNADNA: Genes: Genes
RNARNA: Manages protein synthesis: Manages protein synthesis
Chapter 3 41
NucleotidesNucleotides
5-carbon sugar, a PO5-carbon sugar, a PO33, and a nitrogenous , and a nitrogenous basebase
Not only serve to make RNA & DNANot only serve to make RNA & DNA
Some are energy carriers (Some are energy carriers (ATPATP, NAD), NAD)
Some are chemical messengers (Some are chemical messengers (cAMPcAMP))
4. Nucleic Acids4. Nucleic Acids
Chapter 3 42
Nucleotide Structure: 3 PartsNucleotide Structure: 3 Parts
NitrogenousNitrogenousBase (1 of 5)Base (1 of 5)
CHCH22CHCH22
HHHH
DeoxyriboseDeoxyriboseoror
RiboseRibose
OOOO
HHHH
OHOHOHOH HHHH
HHHHHHHH
OH
HO P O
O
Pentose SugarPentose Sugar
Phosphate GroupPhosphate Group
NNNNHCHCHCHC
NNNN CCCC
CCCC
CCCC
CHCHCHCH
NNNN
NNNN
NHNH22NHNH22
4. Nucleic Acids4. Nucleic Acids
Chapter 3 43
Nucleic Acid MoleculeNucleic Acid MoleculeNucleotides can be joined Nucleotides can be joined together into a chaintogether into a chain
Result is a nucleic acidResult is a nucleic acid
Nucleotide polymerNucleotide polymer
DNA, RNADNA, RNA
Connected by “sugar-Connected by “sugar-phosphate” backbonephosphate” backbone
4. Nucleic Acids4. Nucleic Acids
Chapter 3 44
Cyclic AMP:Cyclic AMP:(Adenosine Monophosphate)(Adenosine Monophosphate)
CHCH22CHCH22
HHHH
RiboseOOOO
HHHH
OOOO OHOHOHOH
HHHHHHHH
OH
O
O P
NNNNHCHCHCHC
NNNN CCCC
CCCC
CCCC
CHCHCHCH
NNNN
NNNN
NHNH22NHNH22
Used for intracellularUsed for intracellularcommunicationcommunicationUsed for intracellularUsed for intracellularcommunicationcommunication
Chapter 3 45
ATP: (Adenosine Triphosphate)ATP: (Adenosine Triphosphate)
CHCH22CHCH22
HHHH
DeoxyriboseDeoxyriboseoror
RiboseRibose
OOOO
HHHH
OHOHOHOH HHHH
HHHHHHHH
OH
P O
O
OPOPHO
OH
O
OH
O
NNNNHCHCHCHC
NNNN CCCC
CCCC
CCCC
CHCHCHCH
NNNN
NNNN
NHNH22NHNH22Used for energy transferUsed for energy transferfrom one molecule to anotherfrom one molecule to anotherUsed for energy transferUsed for energy transferfrom one molecule to anotherfrom one molecule to another
4. Nucleic Acids4. Nucleic Acids
Chapter 3 46
Coenzyme StructureCoenzyme Structure
CHCH22CHCH22
HHHH
DeoxyriboseDeoxyriboseoror
RiboseRibose
OOOO
HHHH
OHOHOHOH HHHH
HHHHHHHH
OH
HO P O
O
NNNNHCHCHCHC
NNNN CCCC
CCCC
CCCC
CHCHCHCH
NNNN
NNNN
NHNH22NHNH22
4. Nucleic Acids4. Nucleic Acids
Chapter 3
The EndThe End
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