atoms, molecules and macromolecules building complex molecules that comprise living things prof....
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Atoms, Molecules Atoms, Molecules and Macromolecules and Macromolecules
Building Complex Molecules Building Complex Molecules That Comprise Living ThingsThat Comprise Living Things
Prof. Mary ColavitoProf. Mary Colavito& Dr. John Shepanski& Dr. John Shepanski
Comparison of Terms Comparison of Terms
ElementElement Substance that cannot be broken down Substance that cannot be broken down to another substance with different to another substance with different propertiesproperties
AtomAtom Smallest unit that has characteristic Smallest unit that has characteristic properties of the elementproperties of the element
MoleculeMolecule Two or more atoms joined by chemical Two or more atoms joined by chemical bondsbonds
MacromoleculeMacromolecule Large polymer made of monomer unitsLarge polymer made of monomer units
Composition Composition of an Atom of an Atom
• NucleusNucleus
Proton = positively charged particle (+)Proton = positively charged particle (+)
Neutron = uncharged particle (n or Neutron = uncharged particle (n or ++))
Number of protons + Number of neutrons = Atomic massNumber of protons + Number of neutrons = Atomic mass
Number of protons = Atomic numberNumber of protons = Atomic number
CC121266
•Electrons = negatively charged particlesElectrons = negatively charged particles
Number of electrons = Number of protons Number of electrons = Number of protons
Each electron circles the nucleus in an orbitEach electron circles the nucleus in an orbitrepresenting a specific energy level.representing a specific energy level.
4Chapter 2ƒ2-1
Atomic ModelsAtomic Models
Hydrogen (H)Hydrogen (H) Helium (He)Helium (He)NucleusNucleus
ElectronElectronShellShell
5Chapter 2ƒ2-2
Different Kinds of AtomsDifferent Kinds of Atoms
HeliumHelium
Max 2eMax 2e--Max 2eMax 2e--
CarbonCarbon
+7p+7p++
+4p+4p++
+2p+2p++
InnermostInnermostelectron shellelectron shell
+4e+4e--
+4n+4n±±
+2n+2n±±
+2e+2e--
OxygenOxygenMax 8eMax 8e--Max 8eMax 8e--
+7e+7e--
+8n+8n±±
PhosphorusPhosphorus
+5p+5p++
+5e+5e--
+4n+4n±±
CalciumCalcium
22ee--
22nn 22pp++6e6e--
66nn 6p 6p++
8e8e--
88nn 8p 8p++15e15e--
1616nn 15p 15p++20e20e--
2020nn 20p 20p++
http://www.sciencegeek.net/tables/lbltable.pdf
Electron Energy LevelsElectron Energy Levels
Energy Energy LevelLevel
Capacity for Capacity for ElectronsElectrons
11 22
22 88
33 18 (8*)18 (8*)*In forming molecules, atoms combine to fill their outer *In forming molecules, atoms combine to fill their outer ((valencevalence) energy levels. When 8 valence orbitals are ) energy levels. When 8 valence orbitals are filled, remaining, unused slots available in inner levels filled, remaining, unused slots available in inner levels are filled before a new valence shell is added.are filled before a new valence shell is added.
Chemical BondsChemical Bonds
BondBond CharacteristicsCharacteristics
IonicIonic One atom loses an electron, One atom loses an electron, another gains an electronanother gains an electron
CovalentCovalent Atoms share electronsAtoms share electrons
Polar Polar
CovalentCovalent
Electrons are shared Electrons are shared unequallyunequally
HydrogenHydrogen Covalently-bound hydrogen is Covalently-bound hydrogen is attracted to another atomattracted to another atom
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±±++±±++±±++ ±±++±±++±±
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Ionic Bonding in NaClIonic Bonding in NaCl
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±±++±±++±±++ ±±++±±++±±
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SodiumSodium#electrons=11#electrons=11
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±±++±±++±±++ ±±++±±++±±
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ChlorineChlorine#electrons=17#electrons=17
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Sodium ion Sodium ion #electrons=10#electrons=10
ChlorineChlorine#electrons=18#electrons=18
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ElectronElectronCompletelyCompletelyTransferredTransferred
NegativeNegativechargecharge
PositivePositivechargecharge
Ionic Bonding in NaClIonic Bonding in NaCl
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++
NaNa++
NaNa++
NaNa++ NaNa++ NaNa++ NaNa++
• Ion: charged atom Ion: charged atom with unequal with unequal numbers of protons numbers of protons and electrons.and electrons.
• Ions of opposite Ions of opposite charges attract.charges attract.
• Sodium ions nestle Sodium ions nestle between chlorine between chlorine ions.ions.
• Perfectly cubical Perfectly cubical crystals form.crystals form.
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
ClCl-- ClCl-- ClCl-- ClCl--
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++ NaNa++ NaNa++
NaNa++
NaNa++
NaNa++
NaNa++ NaNa++ NaNa++ NaNa++
Covalent BondingCovalent BondingOxygen AtomOxygen Atom Oxygen AtomOxygen Atom
Oxygen Molecule (O2)
In Water, Polar Covalent Bonds In Water, Polar Covalent Bonds Join Oxygen and Hydrogen Join Oxygen and Hydrogen
Hydrogen Bonds Join Water MoleculesHydrogen Bonds Join Water Molecules
OO
OO
HH
HH
HHHH+
+
+
–
–
+
+
HydrogenHydrogenBondsBonds
Water molecules Water molecules are dipoles—the are dipoles—the hydrogen side is hydrogen side is more positive; more positive; the oxygen side the oxygen side is more negativeis more negative
Hydrogen bonds Hydrogen bonds form between O form between O of one water of one water molecule and H molecule and H of another of another
Due to hydrogen bonding, ionic and Due to hydrogen bonding, ionic and polar substances dissolve in waterpolar substances dissolve in water
Organic Molecules Organic Molecules Contain CarbonContain Carbon
HydrophobicHydrophobic Not attracted to waterNot attracted to water& non-polar substances& non-polar substances
HydrophilicHydrophilic Attracted to water,Attracted to water,polar and ionic substancespolar and ionic substances
Each carbon atom can make fourEach carbon atom can make fourcovalent bonds with other types of covalent bonds with other types of atoms or additional carbons.atoms or additional carbons.
Macromolecules: Polymers Macromolecules: Polymers Made of Repeating MonomersMade of Repeating Monomers
MacromoleculeMacromolecule Monomer UnitMonomer Unit
CarbohydratesCarbohydrates SugarsSugars
LipidsLipids Fatty acidsFatty acids
ProteinsProteins Amino acidsAmino acids
Nucleic AcidsNucleic Acids NucleotidesNucleotides
Synthesis and Breakdown of Synthesis and Breakdown of Macromolecules Macromolecules
Condensation Condensation SynthesisSynthesis
Removal of water to add Removal of water to add monomer unitsmonomer units
HydrolysisHydrolysis Addition of OH and H Addition of OH and H groups of water to break groups of water to break a bond between a bond between monomersmonomers
Dehydration Synthesis / HydrolysisDehydration Synthesis / Hydrolysis
Dehydration SynthesisDehydration Synthesis
HydrolysisHydrolysis
Carbohydrates: StructureCarbohydrates: Structure
• SimpleSimple– Monosaccharides= one sugar unitMonosaccharides= one sugar unit
Glucose = blood sugarGlucose = blood sugarAll cells use glucose for energyAll cells use glucose for energy
Carbohydrates: StructureCarbohydrates: Structure
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++
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• SimpleSimple– Disaccharides = two sugar unitsDisaccharides = two sugar units
– Examples: sucrose, lactose, maltoseExamples: sucrose, lactose, maltose
Carbohydrates: StructureCarbohydrates: Structure
• ComplexComplex– Polysaccharides= many sugar unitsPolysaccharides= many sugar units
• Starch -- storage in plantsStarch -- storage in plants• Glycogen -- storage in animalsGlycogen -- storage in animals• Cellulose -- plant cell walls, indigestibleCellulose -- plant cell walls, indigestible
Carbohydrates: Structure• Complex
– Polysaccharides= many sugar units
found in plant cell walls
energy storage in animals
energy storage in plants
Carbohydrates: FunctionsCarbohydrates: Functions
• Energy sourceEnergy source
• Structural component Structural component
• Cell-cell communication Cell-cell communication
Lipids: StructureLipids: Structure
PolarPolarHeadHead GlycerolGlycerol Fatty Acid TailsFatty Acid Tails
HydrophobicHydrophobicHydrophilicHydrophilic
• Phospholipid—Phospholipid—component of cell membranescomponent of cell membranes
Lipids: StructureLipids: Structure• Types of Fatty Acids Types of Fatty Acids
– Saturated – 2H per internal carbonSaturated – 2H per internal carbon
– Unsaturated -- <2H per internal carbon Unsaturated -- <2H per internal carbon one or more double bondsone or more double bonds• Monounsaturated – one double bondMonounsaturated – one double bond
• Polyunsaturated – more than one double bond Polyunsaturated – more than one double bond
Which Is a Source of Unsaturated Fatty Acids?Which Is a Source of Unsaturated Fatty Acids?
Linseed OilLinseed OilBeef Fat Beef Fat
Lipids: FunctionsLipids: Functions• Concentrated energy sourceConcentrated energy source• Structural components of cell membranesStructural components of cell membranes
– Phospholipids Phospholipids – Cholesterol Cholesterol
• CommunicationCommunication– Steroid HormonesSteroid Hormones
• MetabolismMetabolism– Fat-soluble vitaminsFat-soluble vitamins
• InsulationInsulation• Protection from waterProtection from water
– Waxes Waxes
Cholesterol
Phospholipids
Per 23 chromosomes
Now estimated at 30,000
genes
DNADNA
RNARNA
ProteinProtein
Information Flow From DNAInformation Flow From DNA
transcriptiontranscription
translationtranslation
replicationreplication(before cell (before cell duplicates)duplicates)
(ongoing parts of (ongoing parts of cell metabolism)cell metabolism)
Gene: sequence of DNA that codes
for a protein
DNA and RNA StructureDNA and RNA Structure DNADNA RNARNA
Primary Primary StructureStructure
Chain of Chain of nucleotidesnucleotides
Chain of Chain of nucleotidesnucleotides
Secondary Secondary StructureStructure
Double Double helixhelix
Single Single folded chainfolded chain
Nucleotide = Nucleotide = phosphate + sugar + nitrogen-containing basephosphate + sugar + nitrogen-containing base
DNA ReplicationDNA Replication
•DNA chains separateDNA chains separate
•Each chain is used Each chain is used as a pattern to as a pattern to produce a new chain produce a new chain
•Each new DNA helix Each new DNA helix contains one “old” contains one “old” and one “new” chain and one “new” chain
Transcription = Production of RNA UsingTranscription = Production of RNA Using DNA as a Template DNA as a Template
•DNA chains separateDNA chains separate
•ONE DNA chain is used ONE DNA chain is used as a pattern to produce as a pattern to produce an RNA chain an RNA chain
•RNA chain is releasedRNA chain is released and the DNA chains and the DNA chains reform the double-helix reform the double-helix
In DNA In RNA A U T A G C C G
Transcription Transcription Protein Synthesis Protein Synthesis
• Messenger RNAMessenger RNAContains the code words for Contains the code words for the sequence of amino acids the sequence of amino acids in a specific proteinin a specific protein
CODON = group of three CODON = group of three nucleotides acting as a code nucleotides acting as a code word for a protein amino acidword for a protein amino acid
• At sub-cellular structures At sub-cellular structures called ribosomes, RNA code called ribosomes, RNA code is used to guide the assembly is used to guide the assembly of proteinsof proteins
Four Levels of Protein StructureFour Levels of Protein Structure
PrimaryPrimary(Sequence)(Sequence)
PrimaryPrimary(Sequence)(Sequence)
SecondarySecondary(Coiling by (Coiling by
Hydrogen Bonding)Hydrogen Bonding)
SecondarySecondary(Coiling by (Coiling by
Hydrogen Bonding)Hydrogen Bonding)
TertiaryTertiary(Folding by (Folding by
R-group R-group interactions)interactions)
TertiaryTertiary(Folding by (Folding by
R-group R-group interactions)interactions)
QuaternaryQuaternary(Two or more chains (Two or more chains
associating)associating)
QuaternaryQuaternary(Two or more chains (Two or more chains
associating)associating)
Proteins: StructureProteins: Structure
AminoAminoGroup Group
The “R” GroupThe “R” GroupDiffers for Each Amino AcidDiffers for Each Amino Acid
Carboxylic AcidCarboxylic AcidGroupGroup
CentralCentralCarbonCarbon
RR
• Primary structure = chain of amino acidsPrimary structure = chain of amino acids– Amino acids have common featuresAmino acids have common features
Proteins: StructureProteins: Structure Forming the Protein ChainForming the Protein Chain
Dehydration Synthesis between COOH & NH2
PhenylalaninePhenylalanine LeucineLeucine
Secondary structuregoverned by hydrogen bonds
Tertiary structure governed byattraction/repulsion of R-groups
Four Levels of Protein StructureFour Levels of Protein Structure
• Quaternary Structure:Quaternary Structure:
Association of two or more protein Association of two or more protein chains chains
eg. eg. HemoglobinHemoglobin is composed is composed of 4 protein chains of 4 protein chains
2 are called alpha 2 are called alpha hemoglobin hemoglobin
2 are called beta 2 are called beta hemoglobin hemoglobin
CellCellMembraneMembrane
The CellThe Cell
Tissues & OrgansTissues & Organs
Lung TissueLung Tissue
NeuronsNeurons
The BrainThe Brain
The MostComplex AssemblyOf MatterOf WhichWe Know