Atoms, Molecules and Macromolecules Building Complex Molecules That Comprise Living Things Prof. Mary Colavito & Dr. John Shepanski.

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

±±++

––

±±++±±++±±++ ±±++±±++±±

++±±++

––

––

–– ––––

––

±±++

––

––

––

±±++

––

±±++±±++±±++ ±±++±±++±±

++±±++

––

––

–– ––––

––

±±++

––

––

––––

––

––

––

––––

––

Ionic Bonding in NaClIonic Bonding in NaCl

±±++

––

±±++±±++±±++ ±±++±±++±±

++±±++

––

––

–– ––––

––

±±++

––

––

––

––

SodiumSodium#electrons=11#electrons=11

±±++

––

±±++±±++±±++ ±±++±±++±±

++±±++

––

––

–– ––––

––

±±++

––

––

––––

––

––

––

––––

––

ChlorineChlorine#electrons=17#electrons=17

––

––

Sodium ion Sodium ion #electrons=10#electrons=10

ChlorineChlorine#electrons=18#electrons=18

––

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++

++

• 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