Ap Bio Ch3 PowerPoint

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++

++


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


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


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


Carboxylic AcidCarboxylic Acid Group Group

““Alpha”Alpha”CarbonCarbon

Chapter 3 32

Amino Acids: Leucine StructureAmino Acids: Leucine Structure

Leucine “R”Leucine “R” Group Group




Chapter 3 33

Amino Acids: Cysteine StructureAmino Acids: Cysteine Structure

Cysteine “R”Cysteine “R” Group Group




Chapter 3 34

Structural ProteinsStructural Proteins

HairHair

HornHorn

SpiderwebSpiderweb


Chapter 3 35

Peptide BondPeptide Bond Formation Formation

By Condensation between COOH & NH2

PhenylalaninePhenylalanine LeucineLeucine


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


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


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


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


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


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


Chapter 3 46

Coenzyme StructureCoenzyme Structure

CHCH22CHCH22

HHHH


RiboseRibose

OOOO

HHHH

OHOHOHOH HHHH

HHHHHHHH

OH

HO P O

O

NNNNHCHCHCHC

NNNN CCCC

CCCC

CCCC

CHCHCHCH

NNNN

NNNN

NHNH22NHNH22


Chapter 3

The EndThe End

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Ap Bio Ch3 PowerPoint