Organic Molecules of Life

Organic Molecules of LifeOrganic Molecules of Life

Organic molecules :Organic molecules :

are compounds created by are compounds created by living organismsliving organisms

contain the elements contain the elements carbon and hydrogencarbon and hydrogen

Carbon atoms:Carbon atoms: need four electrons to fill their need four electrons to fill their

outer electron shell outer electron shell

Must form four bonds with Must form four bonds with other elements. other elements.

These are covalent bonds.These are covalent bonds.

Most often bond with Most often bond with Hydrogen, Oxygen, Nitrogen, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur, and other Phosphorus, Sulfur, and other

Carbon atomsCarbon atoms

6 P

6 N

These can include:These can include: Single bonds Single bonds

(one electron shared)(one electron shared)

Double bonds Double bonds (two electrons shared)(two electrons shared)

Or triple bonds Or triple bonds (three electrons shared)(three electrons shared)

Carbon Atoms:Carbon Atoms:

These chains can be:

Can bond with other atoms of carbon to form long chains

Straight

Branched

Rings

IsomersIsomers

Molecules with the Molecules with the same formulasame formula

Atoms are arranged Atoms are arranged differentlydifferently

Carbons are Carbons are branched in various branched in various waysways

Functional groups:Functional groups: Are special groups of atoms that Are special groups of atoms that

stay together and act as a single stay together and act as a single unit unit

can bond with the carbon chains can bond with the carbon chains determine how the entire determine how the entire

molecule will react. molecule will react.

The functional groups The functional groups you need to know are:you need to know are:

Hydroxyl GroupHydroxyl Group

•one oxygen and one hydrogen

• usually written as

-OH

Oxygen

Hydrogen

Carboxyl GroupCarboxyl Group one carbon with a one carbon with a

double bond to an double bond to an oxygen AND a single oxygen AND a single bond to a hydroxyl bond to a hydroxyl group group

usually written as usually written as COOH or COOH or

O=C–OHO=C–OHCreates an organic Creates an organic

acid (carboxylic)acid (carboxylic)

Carbon

Oxygen

Oxygen

Hydrogen

Amino GroupAmino Group

one nitrogen one nitrogen bonded to two bonded to two hydrogenhydrogen

usually written usually written as NHas NH22 or or

H–N–HH–N–H

Nitrogen

Hydrogen

Hydrogen

Phosphate Group:Phosphate Group:

One phosphorus bonded to two hydroxyl One phosphorus bonded to two hydroxyl groups, and two other oxygens (one has a groups, and two other oxygens (one has a double bond)double bond)

Usually written as –P orUsually written as –P or OHOH

O P OO P O

OHOH

Phosphorus

Biological Biological molecules molecules

can be can be made up of made up of thousands thousands of atomsof atoms

These large molecules These large molecules are built from basic are built from basic

units called units called

monomersmonomers..

One monomer

The monomers are linked The monomers are linked together to form the large together to form the large

molecules called molecules called

polymers.polymers.

Polymer – chain of repeating monomer units

Making and Breaking Polymer Making and Breaking Polymer BondsBonds

When two monomers are put together to form larger molecules, a water molecule is created.

Monomers

Polymer

This process is called:This process is called:

(Dehydration means to lose water (Dehydration means to lose water

Synthesis means to build or put Synthesis means to build or put things together)things together)

Dehydration Synthesis.Dehydration Synthesis.

When polymers are broken apart, it is done by adding a water molecule.

This is called

Hydrolysis

(hydro- for water, -lysis for breaking apart)

Types of Organic MoleculesTypes of Organic Molecules

There are four categories of organic There are four categories of organic molecules in organisms:molecules in organisms:

CarbohydratesCarbohydrates

LipidsLipids

ProteinsProteins

Nucleic acidsNucleic acids

CarbohydratesCarbohydrates

What are Carbohydrates?What are Carbohydrates?

Organic compoundsOrganic compoundsCommonly called starches and Commonly called starches and

sugarssugarsUsed as:Used as:

An energy sourceAn energy sourceEnergy storageEnergy storageCellular structures Cellular structures

Chemical CompositionChemical CompositionContains only three elements:Contains only three elements:

CarbonCarbonHydrogenHydrogenOxygenOxygen

Ratio of hydrogen to oxygen is 2:1Ratio of hydrogen to oxygen is 2:1 (just like water)(just like water)

Example: CExample: C66HH1212OO66

Basic Unit is called a saccharideBasic Unit is called a saccharide

Types of CarbohydratesTypes of Carbohydrates

MonosaccharidesMonosaccharidesSimple, single (mono-) sugar unitSimple, single (mono-) sugar unitBuilding block of all other Building block of all other

carbohydrates carbohydrates Name usually ends in –oseName usually ends in –oseUsed as energy sourceUsed as energy source

Examples of MonosaccharidesExamples of Monosaccharides Glucose – blood sugarGlucose – blood sugar Fructose – fruit sugarFructose – fruit sugar Galactose – one monomer in lactose (milk)Galactose – one monomer in lactose (milk)

Isomers of CIsomers of C6HH12OO6

Examples of MonosaccharidesExamples of Monosaccharides

Ribose and Deoxyribose Ribose and Deoxyribose 5 - Carbon sugars in RNA and DNA5 - Carbon sugars in RNA and DNA

Types of CarbohydratesTypes of CarbohydratesDisaccharidesDisaccharides

Double sugar units Double sugar units synthesized from synthesized from monosaccharidesmonosaccharides

All are isomers of All are isomers of CC12HH22OO11

Formed by Formed by dehydration dehydration synthesis (requires synthesis (requires enzymes)enzymes)

OH

OH

H

OH

H

OHH

OH

H

OH

H

HOH

OH

H

OH

H

OHH

OH

H

OH

H

H

OH

OH

H

O

H

OHH

OH

H

OH

H

HOH H

OH

H

OHH

OH

H

OH

H

H

H

O

H

Examples of DisaccharidesExamples of Disaccharides

Sucrose – table sugarSucrose – table sugar Glucose + FructoseGlucose + Fructose

Maltose – seed sugar Maltose – seed sugar Glucose + GlucoseGlucose + Glucose

Lactose – milk sugarLactose – milk sugar Glucose + GalactoseGlucose + Galactose

Types of CarbohydratesTypes of Carbohydrates

PolysaccharidesPolysaccharidesLarge, complex chains of many (poly-) Large, complex chains of many (poly-)

repeating sugar unitsrepeating sugar unitsPolymersPolymersBonded together by dehydration synthesisBonded together by dehydration synthesisUsed by living things as a sugar storage or for Used by living things as a sugar storage or for

structuresstructures

Examples of PolysaccharidesExamples of Polysaccharides Amylose – plant starch Amylose – plant starch

Used as sugar storage in seeds, roots, stemsUsed as sugar storage in seeds, roots, stems Glycogen – animal starchGlycogen – animal starch

Used as sugar storage by humans in the liverUsed as sugar storage by humans in the liver CelluloseCellulose

Very tough polymer Very tough polymer Used as a main component of cell wallsUsed as a main component of cell walls Indigestible by humansIndigestible by humans

ChitinChitin Very tough polymerVery tough polymer Used in exoskeletons (crab shells, insects)Used in exoskeletons (crab shells, insects)

Digesting PolysaccharidesDigesting Polysaccharides

Broken apart by Broken apart by hydrolysis with the hydrolysis with the help of enzymeshelp of enzymes

OH

OH

H

O

H

OHH

OH

H

OH

H

HOH H

OH

H

OHH

OH

H

OH

H

H

OH

OH

H

OH

H

OHH

OH

H

OH

H

H

OH

OH

H

OH

H

OHH

OH

H

OH

H

H

H

O

H

LipidsLipids

What are Lipids?What are Lipids? Three elements: Carbon Hydrogen OxygenThree elements: Carbon Hydrogen Oxygen Ratio of H:O much greater than 2:1Ratio of H:O much greater than 2:1

Example: Oleic acid CExample: Oleic acid C18HH34OO3

Insoluble in waterInsoluble in water Greasy, slippery textureGreasy, slippery texture Three main groups:Three main groups:

Fats oils and waxesFats oils and waxes At room temperature: Liquid – oils/Solid – fats and waxesAt room temperature: Liquid – oils/Solid – fats and waxes

PhospholipidsPhospholipids SteroidsSteroids

What are the Functions of Lipids?What are the Functions of Lipids?

Fats, Oils and Waxes:Fats, Oils and Waxes:

Long term energy storageLong term energy storage More than twice as much energy stored than More than twice as much energy stored than

carbohydrates carbohydrates fats- 9 Calories/gram; carbohydrates- 4 Cal/gfats- 9 Calories/gram; carbohydrates- 4 Cal/g

In plants: stored in and around seeds In plants: stored in and around seeds Peanut oil, corn oil, olive oilPeanut oil, corn oil, olive oil

In animals: stored under the skin and around In animals: stored under the skin and around internal organsinternal organs Used as insulation and shock absorberUsed as insulation and shock absorber

What are the Functions of Lipids?What are the Functions of Lipids?

Phospholipids Phospholipids Structural Part of Cell membranesStructural Part of Cell membranes

SteroidsSteroidsPart of cell membranes, transport of lipids, Part of cell membranes, transport of lipids,

regulate body functions (hormones) regulate body functions (hormones)

Chemical Composition Chemical Composition Fats Oils, Waxes Fats Oils, Waxes

One or more fatty acids One or more fatty acids attached to a Glycerol attached to a Glycerol backbone backbone Fatty Acids: Long chains Fatty Acids: Long chains

of carbon with a carboxyl of carbon with a carboxyl group at the endgroup at the end

Glycerol: CGlycerol: C3HH8OO3

Formed by dehydration Formed by dehydration synthesissynthesis

NOT a polymerNOT a polymer

GlycerolFatty Acid

Lipid

Glycerol

Formation of a Triglyceride:Formation of a Triglyceride:

Types of FatsTypes of Fats SaturatedSaturated

All carbons of the fatty acid have single bondsAll carbons of the fatty acid have single bonds All carbons are “filled” with hydrogenAll carbons are “filled” with hydrogen Solid at room temperatureSolid at room temperature Associated with heart disease riskAssociated with heart disease risk Examples: Bacon grease, butterExamples: Bacon grease, butter

Types of FatsTypes of Fats UnsaturatedUnsaturated

Carbons share one or more double or triple bonds Carbons share one or more double or triple bonds with other carbonswith other carbons

Monounsaturated – only one double bondMonounsaturated – only one double bond Polyunsaturated – many double or triple bondsPolyunsaturated – many double or triple bonds

Liquid at room temperatureLiquid at room temperature Examples: corn oil, olive oilExamples: corn oil, olive oil

PhospholipidsPhospholipids Phosphate Phosphate

group replaces group replaces fatty acid on fatty acid on one endone end

Used as the Used as the main main component of component of cellular cellular membranesmembranes

Steroids: Four Fused RingsSteroids: Four Fused Rings

lipids with four fused hydrocarbon rings

Includes: Cholesterol - found in animal

cell membranes Testosterone, estrogen,

progesterone - sex hormones Vitamin D

An anabolic steroid is a synthetic testosterone.

ProteinsProteins

Protein FunctionsProtein Functions

Structural partsStructural parts cell membrane, muscles, hair, nails, pigmentscell membrane, muscles, hair, nails, pigments

RegulatorsRegulators Hormones, enzymesHormones, enzymes

CarriersCarriersTransport materials in, out and around cellsTransport materials in, out and around cells

IdentificationIdentification Allow cells to recognize each other Allow cells to recognize each other Immune system antibodiesImmune system antibodies

Composition of ProteinsComposition of Proteins

Elements: Elements: carbon, hydrogen, oxygen and NITROGENcarbon, hydrogen, oxygen and NITROGEN

Very large, complexVery large, complexHemoglobin: CHemoglobin: C30323032HH48164816OO872872NN780780SS88FeFe44

Monomers (building blocks) are amino Monomers (building blocks) are amino acidsacids20 common amino acids20 common amino acids

9 are essential 11 are non essential9 are essential 11 are non essential

Amino AcidsAmino Acids

The R group is different for

each of the twenty amino

acids

Peptide BondsPeptide Bonds•Chains of amino acids are called peptides

•Amino acids are joined by dehydration synthesis

•This occurs between the carboxyl end of one amino acid and the amino end of another amino acid.

•The resulting bond is called a Peptide bond

Primary StructurePrimary Structure

The sequence of The sequence of amino acids in a amino acids in a protein is called the protein is called the Primary StructurePrimary Structure

The sequence is The sequence is unique for each unique for each protein and is protein and is determined by the determined by the DNADNA

Secondary StructureSecondary Structure

Hydrogen bonds are Hydrogen bonds are formed between the formed between the chains of amino acids chains of amino acids causing different causing different shapes.shapes.

Secondary StructureSecondary StructureTwo shapes are common – Two shapes are common –

a helix and a sheet. a helix and a sheet.

Sheet and Helix

Tertiary StructureTertiary Structure The 3-D The 3-D

arrangement of the arrangement of the molecule caused molecule caused by weak bonds by weak bonds between the R between the R groupsgroups

The most important The most important structure format structure format

Determines the Determines the function of the function of the proteinprotein

Quaternary StructureQuaternary Structure More than one protein More than one protein

molecule can molecule can combine to create a combine to create a macromoleculemacromolecule

This is the quaternary This is the quaternary structure of the structure of the proteinprotein

This creates either This creates either globular (hemoglobin) globular (hemoglobin) or fibrous (collagen) or fibrous (collagen) proteinsproteins

Nucleic AcidsNucleic Acids

Nucleic Acids are:Nucleic Acids are:The largest molecules in living thingsThe largest molecules in living thingsThe DNA of humans has about 6 billion The DNA of humans has about 6 billion

monomersmonomersSome reptiles have 20 times more unitsSome reptiles have 20 times more unitsThe largest DNA known is a flower with 5 The largest DNA known is a flower with 5

trillion unitstrillion units

The two most important The two most important Nucleic Acids:Nucleic Acids:

DNA (deoxyribonucleic DNA (deoxyribonucleic acid)acid)

RNA (ribonucleic acid)RNA (ribonucleic acid)

Functions of Nucleic AcidsFunctions of Nucleic AcidsDNADNA

make up chromosomes and their genes that make up chromosomes and their genes that carry hereditary information carry hereditary information

found in the nucleus, mitochondria and found in the nucleus, mitochondria and chloroplasts (plants)chloroplasts (plants)

RNARNA functions in the synthesis of proteins for the cellfunctions in the synthesis of proteins for the cell found in cell parts: nucleoli, ribosomes, and found in cell parts: nucleoli, ribosomes, and

throughout the cytoplasm throughout the cytoplasm

General Structure of General Structure of Nucleic AcidsNucleic Acids

Polymers, with many repeating units Polymers, with many repeating units called nucleotidescalled nucleotides

Nucleotides have three subunits:Nucleotides have three subunits:a five carbon sugara five carbon sugara phosphate groupa phosphate groupa nitrogenous basea nitrogenous base

(a base that contains nitrogen)(a base that contains nitrogen)

Phosphate group

Five Carbon Sugar

Nitrogenous Base

Structure of DNAStructure of DNA

The sugar backbone is deoxyriboseThe sugar backbone is deoxyribose

Structure of DNAStructure of DNA

The base can be one of four: The base can be one of four: AdenineAdenine GuanineGuanine ThymineThymine CytosineCytosine

Structure of DNAStructure of DNA

The bases pair upThe bases pair up – –

A (adenine) always pairs with T A (adenine) always pairs with T (thymine)(thymine)

G (guanine) always pairs with C G (guanine) always pairs with C (cytosine)(cytosine)

Structure of DNAStructure of DNA

Structure of DNAStructure of DNA

Two polymer Two polymer chains of chains of nucleotides are nucleotides are connected by connected by weak hydrogen weak hydrogen bonds and are bonds and are twisted into a twisted into a double helixdouble helix

Structure of DNAStructure of DNA

Sequence of nitrogenous bases Sequence of nitrogenous bases codes for specific amino acids codes for specific amino acids

Amino acid sequence Amino acid sequence determines the protein made in determines the protein made in the cell and the cellular activitythe cell and the cellular activity

Relationship Between Proteins and Relationship Between Proteins and Nucleic AcidsNucleic Acids

Structure of RNAStructure of RNA Ribose is its sugar backboneRibose is its sugar backbone

Structure of RNAStructure of RNAThe base can be one of four:The base can be one of four: AdenineAdenine GuanineGuanine CytosineCytosine UracilUracil

Thymine is replaced by UracilThymine is replaced by Uracil

Structure of RNAStructure of RNA Only a single polymer chain is Only a single polymer chain is

created in RNA, but strands of RNA created in RNA, but strands of RNA have complex, folded structures that have complex, folded structures that compliment their function.compliment their function.

EnzymesEnzymes

What are Enzymes?What are Enzymes?

Large, Complex ProteinsLarge, Complex ProteinsFunction as Organic CatalystsFunction as Organic Catalysts

Allow reactions to occur at lower Allow reactions to occur at lower temperatures ( 37° C)temperatures ( 37° C)

Used temporarilyUsed temporarilyUnchanged by the reactionUnchanged by the reactionCan be reusedCan be reusedSpecific to one reactionSpecific to one reaction

What are Enzymes?What are Enzymes?

Bind to reactants called substratesBind to reactants called substratesEnzyme names usually end in –ase and Enzyme names usually end in –ase and

can be named for their substrate:can be named for their substrate:Protease – proteinsProtease – proteinsLipase – lipidsLipase – lipidsMaltase – maltoseMaltase – maltoseATPase – ATPATPase – ATPAcetylcholinesterase - acetylcholineAcetylcholinesterase - acetylcholine

How Do Enzymes Work?How Do Enzymes Work?

Reduces energy needed to begin reaction Reduces energy needed to begin reaction (Activation energy)(Activation energy)

Ene

rgy

Time

Ene

rgy

Time

Without catalyst With catalyst

Activation Energy

How Do Enzymes Work?How Do Enzymes Work?

Lock and Key ModelLock and Key Model

Enzyme Enzyme Enzyme

Substrate

Active Site

Products

Substrate attaches to enzyme at active site

Enzyme Substrate Complex Formed

Reaction takes place and products are released

How Do Enzymes Work?How Do Enzymes Work?

Induced Fit ModelInduced Fit Model

Substrate attaches to active site

Enzyme changes shape to match substrate –

Stressed molecule may help to weaken bonds

Enzyme resumes original shape after product formed

Enzyme EnzymeEnzyme

SubstrateEnzyme substrate complex formed

Product

How Do Enzymes Work?How Do Enzymes Work?

Coenzymes sometimes neededCoenzymes sometimes neededNon proteins – minerals, vitaminsNon proteins – minerals, vitaminsSmaller moleculesSmaller moleculesPart of the enzyme structure or Part of the enzyme structure or

work along side the enzymework along side the enzyme

Enzyme and substrate do not match

Coenzyme fills in needed shape

Coenzyme

Denaturation:Denaturation:

If the shape changes, the enzyme cannot function properly

Factors Affecting EnzymesFactors Affecting Enzymes TemperatureTemperature

Enzyme activity Enzyme activity increases with increases with temperaturetemperature

Optimum temperature Optimum temperature for each enzymefor each enzyme

Higher temperatures Higher temperatures denature (change the denature (change the shape) of the enzyme’s shape) of the enzyme’s active siteactive site

Rate of reaction Rate of reaction decreases quickly after decreases quickly after optimum temperatureoptimum temperature

10 20 30 40 50

Optimum temperature

Factors Affecting EnzymesFactors Affecting Enzymes pHpH

Enzymes are pH dependentEnzymes are pH dependent Some work at low pH (acid) Some work at low pH (acid)

Some at high pH (basic)Some at high pH (basic) Surrounding solutions will Surrounding solutions will

activate or deactivate enzyme by activate or deactivate enzyme by changing the shape of the active changing the shape of the active site site

Extremely high or low pH values Extremely high or low pH values generally result in complete loss generally result in complete loss of activity for most enzymes of activity for most enzymes

pH for Optimum Activity EnzymeEnzyme pH OptimumpH Optimum

Lipase (pancreas)Lipase (pancreas) 8.08.0

Lipase (stomach)Lipase (stomach) 4.0 - 5.04.0 - 5.0

Lipase (castor oil)Lipase (castor oil) 4.74.7

PepsinPepsin 1.5 - 1.61.5 - 1.6

TrypsinTrypsin 7.8 - 8.77.8 - 8.7

UreaseUrease 7.07.0

InvertaseInvertase 4.54.5

MaltaseMaltase 6.1 - 6.86.1 - 6.8

Amylase Amylase (pancreas)(pancreas) 6.7 - 7.06.7 - 7.0

Amylase (malt)Amylase (malt) 4.6 - 5.24.6 - 5.2

CatalaseCatalase 7.07.0

Factors Affecting EnzymesFactors Affecting EnzymesConcentration:Concentration:

Increasing amount of enzyme: Increasing amount of enzyme: rate increases then levels offrate increases then levels offsubstrate levels fall and reduces efficiencysubstrate levels fall and reduces efficiency

Increasing amount of substrate: Increasing amount of substrate: rate increases then levels off rate increases then levels off enzyme is saturated and no additional reactions enzyme is saturated and no additional reactions

can occur can occur

Presence of InhibitorsPresence of InhibitorsBind to enzyme and change shape or Bind to enzyme and change shape or

compete with the substratecompete with the substrate