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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
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