Chapter 3Chapter 3

Molecules of LifeMolecules of Life

ObjectivesObjectives

Understand how small organic molecules can be Understand how small organic molecules can be assembled into large macromolecules by assembled into large macromolecules by condensation. Understand how large condensation. Understand how large macromolecules can be broken into subunits by macromolecules can be broken into subunits by hydrolysis.hydrolysis.

Learn the functional groups presented and know Learn the functional groups presented and know the properties they confer when attached to the properties they confer when attached to other moleculesother molecules

ObjectivesObjectives Know the general structure of a Know the general structure of a

monosaccharide, a fatty acid, an amino acid, monosaccharide, a fatty acid, an amino acid, and a nucleotide.and a nucleotide.

Know the macromolecules into which these Know the macromolecules into which these essential building blocks can be assembled by essential building blocks can be assembled by condensation, or the smaller molecules they can condensation, or the smaller molecules they can be broken down into by hydrolysis.be broken down into by hydrolysis.

Know where these carbon compounds tend to Know where these carbon compounds tend to be located in cells or organelles and the be located in cells or organelles and the activities in which they participate.activities in which they participate.

There may be a thousand billion tons of frozen methane There may be a thousand billion tons of frozen methane hydrate on the seafloor. These ice crystals are unstable.hydrate on the seafloor. These ice crystals are unstable.

View the picture of the world’s largest reservoir of View the picture of the world’s largest reservoir of natural gas (pg. 32)natural gas (pg. 32)

Methane is one of the greenhouse gases and a Methane is one of the greenhouse gases and a contributing factor to global warming.contributing factor to global warming.

Should we try to harvest more as a source of energy?Should we try to harvest more as a source of energy?

Science or the Supernatural?Science or the Supernatural?

Fig. 3-1b, p.32

Consider MethaneConsider Methane

Methane (CHMethane (CH44) a “lifeless” hydrocarbon, ) a “lifeless” hydrocarbon, is present in vast methane hydrate is present in vast methane hydrate deposits beneath the ocean floordeposits beneath the ocean floor

Methane hydrate disintegration can be Methane hydrate disintegration can be explosive, causing a chain reaction that explosive, causing a chain reaction that depletes oxygendepletes oxygen

Evidence points to such an event Evidence points to such an event ending the Permian period 250 million ending the Permian period 250 million years agoyears ago

3.1 Organic Compounds3.1 Organic Compounds

The molecules of life are organic The molecules of life are organic compounds. They are composed of at compounds. They are composed of at least one hydrogen and other elements least one hydrogen and other elements that are covalently bonded to carbon.that are covalently bonded to carbon.

Hydrocarbons – composed of only Hydrocarbons – composed of only hydrogen atoms covalently bonded to hydrogen atoms covalently bonded to carbon.carbon. Example -Gasoline and fossil fuelsExample -Gasoline and fossil fuels

Organic CompoundsOrganic Compounds

Only living cells can synthesize organic Only living cells can synthesize organic compounds – carbohydrates, lipids, compounds – carbohydrates, lipids, proteins, and nucleic acidsproteins, and nucleic acids

Each organic compound is characterized Each organic compound is characterized by one of more functional groupsby one of more functional groups Particular atoms or cluster of atoms covalently Particular atoms or cluster of atoms covalently

bonded to carbonbonded to carbon

Carbon’s Bonding Behavior Carbon’s Bonding Behavior

Outer shell of carbon Outer shell of carbon has 4 electrons; can has 4 electrons; can hold 8hold 8

Each carbon atom Each carbon atom can form covalent can form covalent bonds with up to four bonds with up to four atomsatoms

Bonding ArrangementsBonding Arrangements

Carbon atoms can Carbon atoms can form chains or ringsform chains or rings

Other atoms project Other atoms project from the carbon from the carbon backbonebackbone

structural formulafor methane

ball-and-stick model – depicts bonding of atoms

space-filling model – convey a molecules

size and surfaces

p.34b

Ways to represent Organic Ways to represent Organic CompoundsCompounds

Representing larger moleculesRepresenting larger molecules

Larger molecules are best visualized using Larger molecules are best visualized using ribbon models, such as those generated ribbon models, such as those generated by computer programs, and even more by computer programs, and even more complex computer models that show local complex computer models that show local differences in electric charge across differences in electric charge across molecular surfaces.molecular surfaces.

See page 35 of text.See page 35 of text.

3.2 How cells build organic 3.2 How cells build organic compounds.compounds.

There are four families of building blocks, There are four families of building blocks, made of small compounds:made of small compounds: Simple sugarsSimple sugars Fatty acidsFatty acids Amino acidsAmino acids NucleotidesNucleotides

Many kinds of molecules in each family contain Many kinds of molecules in each family contain 2 to 36 carbon atoms, at most.2 to 36 carbon atoms, at most.

Monomers & PolymersMonomers & Polymers

Monomers – are individual subunitsMonomers – are individual subunits

Polymers – 3 to millions of monomers Polymers – 3 to millions of monomers bound together. When they are broken bound together. When they are broken apart, the released monomers are used as apart, the released monomers are used as energy or may be used as free molecules.energy or may be used as free molecules.

Functional GroupsFunctional Groups

Atoms or clusters of atoms that are Atoms or clusters of atoms that are covalently bonded to carbon backbonecovalently bonded to carbon backbone

These groups give organic compounds These groups give organic compounds their different propertiestheir different properties

Each has a specific chemical and physical Each has a specific chemical and physical properties that are consistent from one properties that are consistent from one molecule to the next.molecule to the next.

Examples of Functional GroupsExamples of Functional Groups

Hydroxyl group Hydroxyl group - OH - OH

Amino groupAmino group - NH- NH33++

Carboxyl groupCarboxyl group - COOH- COOH

Phosphate groupPhosphate group - PO- PO33--

Sulfhydryl groupSulfhydryl group - SH- SH

Common Common Functional Functional Groups in Groups in Biological Biological Molecules,Molecules,

see pg. 36see pg. 36

Fig. 3-4, p.36

Estrogen and testosterone are hormones responsible for observable Estrogen and testosterone are hormones responsible for observable differences in traits between male and female wood ducksdifferences in traits between male and female wood ducks

Differences in position of functional groups attached to ring structure (pg. Differences in position of functional groups attached to ring structure (pg. 36)36)

Functional Groups in HormonesFunctional Groups in Hormones

An Estrogen Testosterone

Five categories of ReactionsFive categories of Reactions

Functional group transferFunctional group transfer- one molecules gives - one molecules gives an entire functional group to a different moleculean entire functional group to a different molecule

Electron transferElectron transfer – an electron is donated to – an electron is donated to another moleculeanother molecule

RearrangementRearrangement – juggling of internal bonds – juggling of internal bonds converts the compound into anotherconverts the compound into another

CondensationCondensation – covalent bonds join two – covalent bonds join two molecules into a larger moleculemolecules into a larger molecule

CleavageCleavage – a molecule splits into two smaller – a molecule splits into two smaller onesones

Condensation ReactionsCondensation Reactions

Form polymers from subunits Form polymers from subunits

Enzymes remove -OH from one molecule, Enzymes remove -OH from one molecule, HH++ from another, form bond between two from another, form bond between two moleculesmolecules

Discarded atoms can join to form waterDiscarded atoms can join to form water See page 38.See page 38.

HydrolysisHydrolysis

A type of cleavage reactionA type of cleavage reaction Breaks polymers into smaller unitsBreaks polymers into smaller units Enzymes split molecules into two or more Enzymes split molecules into two or more

partsparts An -OH group and an HAn -OH group and an H++ atom derived atom derived

from water are attached at exposed sitesfrom water are attached at exposed sites See page 38See page 38

3.3 Carbohydrates3.3 Carbohydrates The most plentiful biological molecules in The most plentiful biological molecules in

nature are the carbohydrates nature are the carbohydrates

Monosaccharide's - (simple sugars)Monosaccharide's - (simple sugars)

Oligosaccharides - (short-chain Oligosaccharides - (short-chain carbohydrates – 3 or more monomers)carbohydrates – 3 or more monomers)

Polysaccharides - (complex carbohydrates) Polysaccharides - (complex carbohydrates)

Monosaccharides Monosaccharides

Simplest carbohydrates – one sugar unitSimplest carbohydrates – one sugar unit Most are sweet tasting, water soluble, have at Most are sweet tasting, water soluble, have at

least two –OH groups and one aldehyde or least two –OH groups and one aldehyde or ketone group.ketone group.

Most have 5- or 6-carbon backbone:Most have 5- or 6-carbon backbone:

Glucose (6 C)Glucose (6 C) - is used by cells as instant - is used by cells as instant energy.energy. Fructose (6 C)Fructose (6 C)

Ribose (5 C)Ribose (5 C) Deoxyribose (5 C)Deoxyribose (5 C)

MonosaccharidesMonosaccharides

Other important molecules derived from Other important molecules derived from sugar monomers include glycerol and sugar monomers include glycerol and Vitamin C.Vitamin C.

Glycerol – an alcohol with three –OH Glycerol – an alcohol with three –OH groups. It forms the backbone of groups. It forms the backbone of triglycerides. Ctriglycerides. C33HH88OO33

DisaccharidesDisaccharides Type of oligosaccharide Type of oligosaccharide

– short chain of 2 or – short chain of 2 or more sugar monomersmore sugar monomers

Composed of two Composed of two monosaccharide's monosaccharide's covalently bonded covalently bonded

Formed by condensation Formed by condensation reactionreaction

+ H2O

glucose fructose

sucrose

Fig. 3-7b, p.38

DisaccharidesDisaccharides

Sucrose – the most plentiful sugar in Sucrose – the most plentiful sugar in nature. Also know an table sugar.nature. Also know an table sugar.

Composed of glucose & fructoseComposed of glucose & fructose Harvested from sugar caneHarvested from sugar cane Lactose – sugar present in milkLactose – sugar present in milk Composed of glucose & galactose.Composed of glucose & galactose.

PolysaccharidesPolysaccharides

Straight or branched chains of many sugar Straight or branched chains of many sugar monomersmonomers

Most common ones are composed entirely Most common ones are composed entirely of glucoseof glucose CelluloseCellulose Starch (such as amylose)Starch (such as amylose) GlycogenGlycogen ChitinChitin

Cellulose & StarchCellulose & Starch

Differ in bonding patterns between Differ in bonding patterns between monomers (see page 38)monomers (see page 38)

CelluloseCellulose - tough, indigestible, fiber-like - tough, indigestible, fiber-like structural material in plantsstructural material in plants

StarchStarch – a storage form of energy, – a storage form of energy, arranged as unbranched coiled chains, arranged as unbranched coiled chains, easily hydrolyzed to glucose units.easily hydrolyzed to glucose units.

GlycogenGlycogen

Highly branched chainHighly branched chain

Used by animals to store energy Used by animals to store energy in muscle and liver cells.in muscle and liver cells.

When blood sugar decreases, When blood sugar decreases, liver cells degrade glycogen, and liver cells degrade glycogen, and release glucoserelease glucose

Fig. 3-9, p.38

ChitinChitin

A specialized polysaccharide A specialized polysaccharide Nitrogen-containing groups attached to Nitrogen-containing groups attached to

glucose monomersglucose monomers Structural material for hard parts (body Structural material for hard parts (body

coverings or exoskeletons) of coverings or exoskeletons) of invertebrates (ticks, crabs, insects, and invertebrates (ticks, crabs, insects, and spiders), cell walls of many fungispiders), cell walls of many fungi

Lipids are nonpolar hydrocarbonsLipids are nonpolar hydrocarbons Lipids are used as energy reservoirs, and Lipids are used as energy reservoirs, and

structural and signaling molecules.structural and signaling molecules. Tend to be insoluble in water Tend to be insoluble in water Most include fatty acidsMost include fatty acids

FatsFats PhospholipidsPhospholipids WaxesWaxes Cholesterol and other Sterols Cholesterol and other Sterols

3.4 Lipids3.4 Lipids

FatsFats

Fats are lipids with Fats are lipids with

one, two or three one, two or three

fatty acid(s) attached fatty acid(s) attached

to glycerolto glycerol

Triglycerides are Triglycerides are

most commonmost common

Fig. 3-12, p.40

Fatty AcidsFatty Acids

A fatty acid is a long unbranched hydrocarbon A fatty acid is a long unbranched hydrocarbon

with a Carboxyl group (-COOH) at one endwith a Carboxyl group (-COOH) at one end

Carbon backbone (up to 36 C atoms)Carbon backbone (up to 36 C atoms) Saturated - Single bonds between carbons in Saturated - Single bonds between carbons in

their tails and are solids at room temperature.their tails and are solids at room temperature. Unsaturated - One or more double bonds in Unsaturated - One or more double bonds in

their tails and are liquids (oils) at room temp.their tails and are liquids (oils) at room temp.

TriglyceridesTriglycerides

These lipids have three fatty acid tails These lipids have three fatty acid tails attached to a molecules of glycerol.attached to a molecules of glycerol.

They are the body’s most abundant and They are the body’s most abundant and richest source of energy and insulation.richest source of energy and insulation.

Examples are butter, lard, and oilsExamples are butter, lard, and oils They yield twice as much energy as They yield twice as much energy as

carbohydrates.carbohydrates.

PhospholipidsPhospholipids

Composed of a glycerol Composed of a glycerol backbone, two fatty acids, a backbone, two fatty acids, a phosphate group, and a small phosphate group, and a small hydrophilic group.hydrophilic group.

They are important components They are important components of cell membranes. (Bilayer) see of cell membranes. (Bilayer) see page 41.page 41.

WaxesWaxes

Long-chain fatty acids linked to long chain Long-chain fatty acids linked to long chain

alcohols or carbon ringsalcohols or carbon rings

Waxes are firm and repel water.Waxes are firm and repel water.

Important in water-proofing.Important in water-proofing.

Examples are bee honeycombs, and Examples are bee honeycombs, and

animal coverings (birds feathers)animal coverings (birds feathers)

Sterols and DerivativesSterols and Derivatives Rigid backbone of four Rigid backbone of four

fused-together carbon rings, fused-together carbon rings, no fatty acids.no fatty acids.

Found in cell membranes of Found in cell membranes of all eukaryotes and animals all eukaryotes and animals as Cholesterol.as Cholesterol.

Cholesterol – can be Cholesterol – can be modified to form sex modified to form sex hormones, bile salts, and hormones, bile salts, and Vitamin DVitamin D

Fig. 3-14, p.41

3.5 Proteins 3.5 Proteins

Proteins function as: Proteins function as: enzymesenzymes in cell movements in cell movements storage and transport agentsstorage and transport agents hormoneshormones anti-disease agentsanti-disease agents structural material throughout the bodystructural material throughout the body

Amino AcidsAmino Acids

They are small organic molecules with an They are small organic molecules with an amino group, an acid group (carboxyl amino group, an acid group (carboxyl group), a hydrogen atom, and an “R” group), a hydrogen atom, and an “R” group.group.

The 20 different “R” groups determine the The 20 different “R” groups determine the 20 naturally-occurring amino acids20 naturally-occurring amino acids

Amino Acid StructureAmino Acid Structure

aminogroup

carboxylgroup

R group

Protein SynthesisProtein Synthesis

Protein is a chain of amino acids linked Protein is a chain of amino acids linked

by peptide bondsby peptide bonds

Peptide bond (COHN)Peptide bond (COHN) Type of covalent bondType of covalent bond

Links amino group of one amino acid with Links amino group of one amino acid with

carboxyl group of nextcarboxyl group of next

Forms through condensation reactionForms through condensation reaction

Fig. 3-15b, p.42

Primary StructurePrimary Structure

Sequence of amino acidsSequence of amino acids

Unique for each proteinUnique for each protein

Two linked amino acids = dipeptideTwo linked amino acids = dipeptide

Three or more = polypeptideThree or more = polypeptide

Backbone of polypeptide has N atoms:Backbone of polypeptide has N atoms:

-N-C-C-N-C-C-N-C-C-N--N-C-C-N-C-C-N-C-C-N-

one peptide group

Protein Shapes Protein Shapes

Fibrous proteinsFibrous proteins

Polypeptide chains arranged as strands or Polypeptide chains arranged as strands or

sheetssheets

Globular proteins Globular proteins

Polypeptide chains folded into compact, Polypeptide chains folded into compact,

rounded shapes rounded shapes

Primary structure is defined as the chain of Primary structure is defined as the chain of amino acids each linked together is a definite amino acids each linked together is a definite sequence.sequence.

Primary structure influences shape in two Primary structure influences shape in two main ways:main ways: Allows hydrogen bonds to form between Allows hydrogen bonds to form between

different amino acids along length of chaindifferent amino acids along length of chain Puts R groups in positions that allow them Puts R groups in positions that allow them

to interactto interact

Primary StructurePrimary Structure & Protein Shape & Protein Shape

Secondary StructureSecondary Structure

This is the helical coil, spiral staircase, or This is the helical coil, spiral staircase, or sheetlike loops and folds arrangement into sheetlike loops and folds arrangement into which the polypeptide chain is formed.which the polypeptide chain is formed.

This is due to the interaction of hydrogen This is due to the interaction of hydrogen bonds, which join the side groups of the bonds, which join the side groups of the amino acids.amino acids.

Examples of Secondary Examples of Secondary StructureStructure

Tertiary StructureTertiary Structure

This is a result of This is a result of

interactions interactions

among R groups.among R groups.

This produces a This produces a

complex 3D complex 3D

shape.shape.

heme group

coiled and twisted polypeptide chain of one globin molecule

Quaternary StructureQuaternary Structure

Some proteins Some proteins

are made up of are made up of

more than one more than one

polypeptide polypeptide

chainchain

Hemoglobin

Polypeptides with Attached Polypeptides with Attached Organic CompoundsOrganic Compounds

Lipoproteins – bind and transport lipidsLipoproteins – bind and transport lipids Proteins combined with cholesterol, Proteins combined with cholesterol,

triglycerides, phospholipidstriglycerides, phospholipids

Glycoproteins –found on the cell surfaceGlycoproteins –found on the cell surface

Proteins combined with oligosaccharidesProteins combined with oligosaccharides

3.6 Why is Protein Structure So 3.6 Why is Protein Structure So Important?Important?

Just one wrong amino acidJust one wrong amino acid Hemoglobin is a highly organized protein Hemoglobin is a highly organized protein

consisting of four polypeptides, each with a consisting of four polypeptides, each with a heme group that can bind an oxygen heme group that can bind an oxygen molecule.molecule.

In a normal beta polypeptide chain the sixth In a normal beta polypeptide chain the sixth amino acid is glutamate, but a mutation amino acid is glutamate, but a mutation sometimes substitutes a valine.sometimes substitutes a valine.

This may lead to Sickle –Cell Anemia This may lead to Sickle –Cell Anemia

c Glutamate has an overall negative charge; valine has no net charge. The difference gives rise to a water-repellant, sticky patch on HbS molecules. They stick together because of that patch, forming rod-shaped clumps that distort normally rounded red blood cells into sickle shapes. (A sickle is a farm tool that has a crescent-shaped blade.)

sickle cell

normal cell

Fig. 3-18c, p.45

Clumping of cells in bloodstream

Circulatory problems, damage to brain, lungs, heart, skeletal muscles, gut, and kidneys

Heart failure, paralysis, pneumonia, rheumatism, gut pain, kidney failure

Spleen concentrates sickle cells

Spleen enlargement

Immune system compromised

Rapid destruction of sickle cells

Anemia, causing weakness, fatigue, impaired development, heart chamber dilation

Impaired brain function, heart failure Fig. 3-18d, p.45

Denaturation of ProteinsDenaturation of Proteins

Disruption of three-dimensional shapeDisruption of three-dimensional shape Breakage of weak bondsBreakage of weak bonds Causes of denaturation:Causes of denaturation:

Shifts in pH Shifts in pH High temperatureHigh temperature

Destroying protein shape disrupts Destroying protein shape disrupts normal functionnormal function

Nucleotides are composed of:Nucleotides are composed of:

Sugar- 5 carbonSugar- 5 carbon Ribose or deoxyriboseRibose or deoxyribose

At least one phosphate groupAt least one phosphate group

Nitrogen containing BaseNitrogen containing Base Single or double ring structureSingle or double ring structure

3.7 Nucleotide Structure3.7 Nucleotide Structure

Nucleotide FunctionsNucleotide Functions

Energy carriers for cellular Energy carriers for cellular metabolism (ATP)metabolism (ATP)

Coenzymes – transport hydrogen Coenzymes – transport hydrogen atoms and electrons (NAD+, FAD)atoms and electrons (NAD+, FAD)

Chemical messengers within and Chemical messengers within and between cells (cAMP)between cells (cAMP)

Building blocks for nucleic acidsBuilding blocks for nucleic acids

ATP - A Nucleotide that ATP - A Nucleotide that provides energyprovides energy

three phosphate groups

sugar

base

Nucleic AcidsNucleic Acids

In nucleic acids, a covalent bond forms In nucleic acids, a covalent bond forms between the sugar of one nucleotide and between the sugar of one nucleotide and the phosphate group of the next.the phosphate group of the next.

DNA is double stranded, genetic DNA is double stranded, genetic messages are encoded it its base messages are encoded it its base sequences: adenine, guanine, cytosine, sequences: adenine, guanine, cytosine, and thymine.and thymine.

RNA is single stranded, protein synthesis.RNA is single stranded, protein synthesis.

Single ring and double ring structure.Single ring and double ring structure. Sugar-phosphate backboneSugar-phosphate backbone

NucleotidesNucleotides

AdenineCytosine

Bonding Between Bases in Nucleic Bonding Between Bases in Nucleic AcidsAcids

THYMINE(T)

base with asingle-ringstructure

CYTOSINE(C)

base with asingle-ringstructure

Fig. 3-20, p.46

DNA vs. RNADNA vs. RNA

DNADNA

Double-stranded Double-stranded Consists of four types of Consists of four types of

nucleotidesnucleotides A bound to TA bound to T C bound to GC bound to G Heritable informationHeritable information

RNARNA

Single – strandedSingle – stranded Consist of four types of Consist of four types of

nucleotidesnucleotides A bound to U (uracil)A bound to U (uracil) C bound to GC bound to G Protein synthesisProtein synthesis