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Transcript of Lecture 3: Chemistry of Life Goals: 1. Sprint through General Chemistry 2. Whisper past Organic...
Lecture 3: Lecture 3: ChemistryChemistry of Life of Life
Lecture 3: Chemistry of LifeLecture 3: Chemistry of LifeGoals:
1. Sprint through General Chemistry2. Whisper past Organic Chemistry3. Approach Biochemistry cautiously4. Apply chemistry overview and relate biological
chemistry to this course and your life in general
http://pearl1.lanl.gov/periodic/default.htmhttp://www.chemsoc.org/viselements/pages/pertable_fla.htm
Key Terms: Key Terms: Charge, proton, neutron, electron, radioisotope, tracer, chemical bonds a)ionic, b)covalent, c)hydrogen, atom, molecule, pH scale, buffer, basic, acidic, hydrophobic, hydrophillic, acidosis, alkalosis, solute, polar, non-polar.
ElementsElements• Fundamental forms of matter
• Can’t be broken apart by normal means
• 92 occur naturally on Earth
Less than 12 occur on the exam
Most Common Elements in Most Common Elements in Living OrganismsLiving Organisms
C H O NC H O N
CarbonCarbon
HydrogenHydrogen
OxygenOxygen
NitrogenNitrogen
What Are Atoms?What Are Atoms?
• Smallest particles that retain properties
of an element
• Made up of subatomic particles:
– Protons (+)
– Electrons (-)
– Neutrons (no charge)
Fig. 2.3, p. 22
HYDROGEN HELIUM
electron
proton
neutron
Hydrogen and Helium AtomsHydrogen and Helium Atoms
Atomic NumberAtomic Number
• Number of protons
• All atoms of the same element have the same atomic number
• Atomic number of hydrogen = 1
• Atomic number of carbon = 6
Mass NumberMass Number
Number of protonsNumber of protons++
Number of neutronsNumber of neutrons
Isotopes vary in mass numberIsotopes vary in mass number
(not atomic number or they would be something else)
Atomic MassAtomic Mass
IsotopesIsotopes• Atoms of an element
with different numbers of neutrons (different mass numbers)
• Carbon 12 has 6 protons, 6 neutrons
• Carbon 14 has 6 protons, 8 neutrons
RadioisotopesRadioisotopes• Have an unstable
nucleus that emits energy and particles
• Radioactive decay transforms radioisotope into a different element
• Decay occurs at a fixed rate
Radioisotopes as TracersRadioisotopes as Tracers• Example: Tracer Drug Study
– How long does a drug stay in the patient?– Determine dose guidelines
• Compound synthesized with a radioisotope
• Emissions from the tracer can be detected with special devices– Track levels in the blood, urine and feces
• Following movement of tracers is useful in many areas of biology
High SensitivityHigh Sensitivity
Very Low DoseVery Low Dose
Other Uses of RadioisotopesOther Uses of Radioisotopes• Drive artificial pacemakers• Biomedical Imaging
– Thyroid and bone scans
• Radiation therapyEmissions from some radioisotopes can destroy cells. Some radioisotopes are used to kill small cancers.
What Determines Whether What Determines Whether Atoms Will Interact?Atoms Will Interact?
The most general of The most general of General ChemistryGeneral Chemistry
ElectronsElectrons
• Carry a negative charge
• Repel one another
• Are attracted to protons in the nucleus
• Move in orbitals - volumes of space that surround the nucleus
Z
X
When all p orbitals are full
y
Electron OrbitalsElectron Orbitals
• Orbitals can hold up to two electrons
• Atoms differ in the number of occupied orbitals
• Orbitals closest to nucleus are lower energy and are filled first
Shell ModelShell Model
• First shell
– Lowest energy
– Holds 1 orbital with up to 2
electrons
• Second shell
– 4 orbitals hold up to 8
electrons
CALCIUM20p+ , 20e-
Electron VacanciesElectron Vacancies
• Unfilled shells make atoms likely to react
• Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells
CARBON6p+ , 6e-
NITROGEN7p+ , 7e-
HYDROGEN1p+ , 1e-
Chemical Bonds, Molecules, Chemical Bonds, Molecules,
& Compounds& Compounds• Bond is union between electron
structures of atoms
• Atoms bond to form molecules
• Molecules may contain atoms of only one element - O2
• Molecules of compounds contain more than one element - H2O
Only a few atoms, even fewerOnly a few atoms, even fewer Chemical BondsChemical Bonds
Ionic bondsIonic bondsBetween metallic and non metallic atomsEasily dissolved by water
CovalentCovalentShare at least one pair of electronsPolar and non-polar bondsTight (high energy) bond
Hydrogen bondsHydrogen bondsA hydrogen between atomsNot so tight (low energy) bond: 1/10th covalent
1. Ionic Bonding1. Ionic Bonding
• One atom loses electrons, becomes positively charged ion
• Another atom gains these electrons, becomes negatively charged ion
• Charge difference attracts the two ions to each other
Ion FormationIon Formation
• Atom has equal number of Atom has equal number of electrons and protons - no net electrons and protons - no net chargecharge
• Atom loses electron(s), becomes Atom loses electron(s), becomes positively charged ionpositively charged ion
• Atom gains electron(s), becomes Atom gains electron(s), becomes negatively charged ionnegatively charged ion
Formation of NaClFormation of NaCl
• Sodium atom (Na) Sodium atom (Na) – Outer shell has one electronOuter shell has one electron
• Chlorine atom (Cl) Chlorine atom (Cl) – Outer shell has seven electronsOuter shell has seven electrons
• Na transfers electron to Cl forming NaNa transfers electron to Cl forming Na++ and Cland Cl--
• Ions remain together as NaClIons remain together as NaCl
7mm
SODIUMATOM11 p+
11 e-
SODIUMION
11 p+
10 e-
electron transfer
CHLORINEATOM17 p+
17 e-
CHLORINEION
17 p+
18 e-
Fig. 2.10a, p. 26
Formation of NaClFormation of NaCl
2. Covalent Bonding2. Covalent Bonding
Atoms share a pair or pairs of electrons to fill outermost shell
•Single covalent bond
H2 Single bond
•Double covalent bond
O2 Double bond
•Triple covalent bond
N2 Triple bond
Two Flavors of Two Flavors of Covalent BondsCovalent Bonds
Non-polarNon-polar Covalent Covalent• Atoms share electrons
equally• Nuclei of atoms have
same number of protons
• Example: Hydrogen gas (H-H)
PolarPolar Covalent Covalent• Number of protons in
nuclei of participating atoms is NOT equal
• Molecule held together by polar covalent bonds has no NET charge
• Electrons spend more time near nucleus with most protons– Example: Water – Electrons more attracted
to O nucleus than to H nuclei
+
Polar Covalent BondsPolar Covalent Bonds
O
H H
slight negative charge at this end
slight positive charge at this end
molecule hasno net charge( + and - balanceeach other)
KEEP YOUR EYE ON THE ELECTRONS
Hydrogen BondingHydrogen Bonding
A bond by Hydrogen between two atoms
• Important for O and N
• Lets two electronegative atoms interact– The H gives one a net + and the other one that
is still – is attracted to it.
• The H proton becomes “naked” because its electron gets pulled away.
Hydrogen bond figure
- -
- + -
Like Charge Atoms Repel Each Other
Opposite Charge Atoms Attract Each Other
KEEP YOUR EYE ON THE ELECTRONS
Hydrogen BondHydrogen Bond Covalent BondCovalent Bond
onelargemolecule
anotherlargemolecule
a largemoleculetwistedbackonitself
Examples of Hydrogen BondsExamples of Hydrogen Bonds
Properties of WaterProperties of Water
•PolarityPolarity
•Temperature-StabilizingTemperature-Stabilizing
•CohesiveCohesive
•SolventSolvent
Water Is a Polar Water Is a Polar Covalent MoleculeCovalent Molecule
• Molecule has no net Molecule has no net chargecharge
• Oxygen end has a Oxygen end has a slight negative slight negative chargecharge
• Hydrogen end has a Hydrogen end has a slight positive chargeslight positive charge
O
H H
O
H
HO
H
H
+ _
++
+
_
+
+
Liquid WaterLiquid Water
Hydrophilic & HydrophobicHydrophilic & HydrophobicSubstancesSubstances
• Hydrophilic substances– Polar– Hydrogen bond with water – Example: sugar
• Hydrophobic substances– Non-polar– Repelled by water– Example: oil
Temperature-Stabilizing Temperature-Stabilizing EffectsEffects
• Water absorbs a lot more heat than other liquids, such as oil, before its temperature rises.
• Why? • Heat is Vibration!
– Molecules with lots of vibrational energy feel hot.
• Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules
Evaporation of WaterEvaporation of Water
• Large energy input can cause individual molecules of water to break free into air
• As molecules break free, they carry away some energy (lower temperature)
• Evaporative water loss is used by mammals to lower body temperature
Why Ice FloatsWhy Ice Floats
• In ice, hydrogen bonds lock molecules in a lattice
• Water molecules in lattice are spaced farther apart then those in liquid water
• Ice is less dense than water
Water CohesionWater Cohesion• Hydrogen bonding holds
molecules in liquid water together
• Creates surface tension
• Allows water to move as continuous column upward through stems of plants
Water Is a Good SolventWater Is a Good Solvent
• Ions and polar molecules dissolve easily in water
• When solute dissolves, water molecules cluster around its ions or molecules and keep them separated
Fig. 2.16, p. 29
Na+
Cl–
– –
––
––
–
––
– –
+ ++
+
+
+
+
+
+
+
+
++ +
+
+
+
+
Water as a solvent:Water as a solvent:Spheres of HydrationSpheres of Hydration
Water• Solvent- polarSolvent- polar
– Keeps ions in Keeps ions in solutionsolution
– Doesn’t dissolve Doesn’t dissolve membranesmembranes
• Heat managementHeat management– Loosing heatLoosing heat– Holding heatHolding heat– Density ChangesDensity Changes
If it wasn’t ugly enough already: If it wasn’t ugly enough already:
Hydrogen Ions: HHydrogen Ions: H++
• Unbound protons
• Have important biological effects
• Form when water ionizes
The pH ScaleThe pH Scale
• Measures H+ concentration of fluid• Change of 1 on scale means 10X
change in H+ concentration
Highest H+ Lowest H+
0---------------------7-------------------14Acidic Neutral Basic
Examples of pHExamples of pHPure water is neutral with pH of 7.0
Acidic
Basic
(Alkaline))
Acids & BasesAcids & Bases
• Acids
– Donate H+ when dissolved in water
– Acidic solutions have pH < 7
• Bases
– Accept H+ when dissolved in water
– Acidic solutions have pH > 7
BuffersBuffersMinimize shifts in pH
• When blood pH rises, carbonic acid dissociates to form bicarbonate and H+
H2C03 -----> HC03- + H+
• When blood pH drops, bicarbonate binds H+ to form carbonic acid
HC03- + H+ -----> H2C03
Acidosis- too much COAcidosis- too much CO22 in blood in blood
Alkalosis- blood pH too lowAlkalosis- blood pH too low
Carbonic Acid-Bicarbonate Buffer SystemCarbonic Acid-Bicarbonate Buffer System
Lecture 2: Chemistry of LifeLecture 2: Chemistry of LifePart 2Part 2
Feeling a little burnt out?Feeling a little burnt out?
Demonstration of Chemical Bonds
Tests: 1. Water as a solvent 1. Water as a solvent 2. Bond strength2. Bond strength
Predictions:Covalent bondsCovalent bondsIonic bondsIonic bondsHydrogen bondsHydrogen bondsHydrophilic interactionsHydrophilic interactionsHydrophobic interactionsHydrophobic interactions
Hydrogen Bonds Aliphatic Resin, PVA and Elmer
Why does glue work?1. Mechanical component2. Chemical component
Process1. Infiltrate wood fibers2. Allow tight contact3. Remove water (solvent)
Demonstration of Hydrogen bond strength
Hydrogen Bonds Aliphatic Resin, PVA and Elmer
• Bond Strength:– 3,500 pounds per square inch
• Hydrogen bonds form between the wood and glue as the water leaves
• Conclusion:
Organic CompoundsOrganic Compounds
• Hydrogen and other elementsHydrogen and other elementscovalently bonded to carboncovalently bonded to carbon
• Major Classes of Biological MoleculesMajor Classes of Biological Molecules– CarbohydratesCarbohydrates– LipidsLipids– ProteinsProteins– Nucleic Acids Nucleic Acids
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 can Each carbon atom can form covalent bonds form covalent bonds with up to with up to fourfour atoms atoms
Bonding ArrangementsBonding Arrangements
• Carbon atoms can form chains or rings
• Other atoms project from the carbon backbone
Functional GroupsFunctional Groups
• Atoms or clusters of atoms that are Atoms or clusters of atoms that are covalently bonded to carbon covalently bonded to carbon backbonebackbone
• Give organic compounds their Give organic compounds their different propertiesdifferent properties
Examples of Functional Examples of Functional GroupsGroups
Hydroxyl group - OH Alcohol
Amino group - NH3+ Dead things
Carboxyl group - COOH Acids
Sulfhydryl group - SH Internal bonds
Phosphate group - PO3- On and off switch
Types of ReactionsTypes of Reactions
Functional group transfer
Electron transfer
Rearrangement
Condensation
Cleavage
x Hydrolysis
Condensation ReactionsCondensation Reactions
• Form polymers from subunits
• Enzymes remove -OH from one molecule, H from another, form bond between two molecules
• Discarded atoms can join to form water
-ie. Water condenses on the inside of my window when the air conditioner is on full blast
Or..
Water forms ….
CondensationCondensation
HydrolysisHydrolysis
• A type of cleavage reaction
• Breaks polymers into smaller units
• Enzymes split molecules into two or more parts
• An OH group and an H atom derived from water are attached at exposed sites
HYDROLYSISHYDROLYSIS
CarbohydratesCarbohydrates
Monosaccharides(simple sugars)
Oligosaccharides(short-chain carbohydrates)
Polysaccharides(complex carbohydrates)
MonoMonosaccharidessaccharides
• Simplest carbohydrates
• Most are sweet tasting, water soluble
• Most have 5- or 6-carbon backbone
Glucose (6 C) Fructose (6 C)
Ribose (5 C) Deoxyribose (5 C)
Two MonosaccharidesTwo Monosaccharides
glucose fructose
DiDisaccharidessaccharides
• Type of oligosaccharide
• Two monosaccharides covalently bonded
• Formed by condensation reaction
+ H2O
glucose fructose
sucrose
PolysaccharidesPolysaccharides
• Straight or branched chains of many sugar monomers
• Most common are composed entirely of glucose– Cellulose
– Starch (such as amylose)
– Glycogen
Cellulose & StarchCellulose & Starch
• Differ in bonding patterns between monomers (type of linkage)
• Cellulose - tough, indigestible, structural material in plants
• Starch - easily digested, storage form in plants
Cellulose and StarchCellulose and Starch
Changes in bonds result in:-different interactions-different structures-different physical properties
GlycogenGlycogen
• Sugar storage form in animals
• Large stores in muscle and liver cells
• When blood sugar decreases, liver cells degrade glycogen, release glucose
ChitinChitin• Polysaccharide • Nitrogen-containing groups attached to
glucose monomers• Found in insects, worms, and fungi (not
humans)• Structural material for hard parts of
invertebrates, cell walls of many fungi
• Most include fatty acids– Fats– Phospholipids– Waxes
• Sterols and their derivatives have no fatty acids
• Tend to be insoluble in water
LipidsLipids
Fatty AcidsFatty Acids
• Carboxyl group (-COOH) at one end
• Carbon backbone (up to 36 C atoms)
– Saturated - Single bonds between carbons
– Unsaturated - One or more double bonds
Three Fatty AcidsThree Fatty Acids
stearic acid oleic acid linolenic acid
LardLard FlaxFlaxOliveOlive
FatsFats
• Fatty acid(s)
attached to
glycerol
• Triglycerides
are most
common
PhospholipidsPhospholipids
• Main components of cell
membranes
Sterols and DerivativesSterols and Derivatives
• No fatty acids
• Rigid backbone of
four fused-together
carbon rings
• Cholesterol - most
common type in
animals
WaxesWaxes• Long-chain fatty acids linked
to long chain alcohols or
carbon rings
• Firm consistency, repel water
• Important in water-proofing
• Size matters
•Omega-6 fatty acids are the predominant polyunsaturated fatty acids (PUFAs) in the Western diet.
•The omega-6 and omega-3 fatty acids are metabolically distinct and have opposing physiologic functions.
•The increased omega-6/omega-3 ratio in Western diets most likely contributes to an increased incidence of heart disease and inflammatory disorders.
•Omega-3 PUFAs suppress cell mediated immune responses and reduce inflammation
Omega-3
Omega-6
PolyunsaturatedPolyunsaturated Fatty Acids Fatty Acids
•Bioactive Lipids•Made in all cells•Short range signaling•Eicosanoids?
•Prostaglandins•Inflammation and Pain Perception•Kidney Function•Bone Development•Reproductive Process
•Commercially Important•$4 BILLION/ Year spend on drugs to inhibit prostaglandin synthesis•Vioxx, Celebrex, Ibuprofen, Asprin
Lipids in Cell Signaling
PGE2
Amino Acid Structure
aminogroup
carboxylgroup
R group
Properties of Amino Acids
• Determined by the “R group”
• Amino acids may be:
– Non-polar
– Uncharged, polar
– Positively charged, polar
– Negatively charged, polar
Protein Synthesis
• Protein is a chain of amino acids
linked by peptide bonds
• Peptide bond
– Type of covalent bond
– Links amino group of one amino acid
with carboxyl group of next
– Forms through condensation reaction
Forming Peptide Bonds
Primary Structure
• Sequence of amino acids
• Unique for each protein
• Two linked amino acids = dipeptide
• Three or more = polypeptide
• Backbone of polypeptide has N atoms:
-N-C-C-N-C-C-N-C-C-N-
Protein ShapesProtein Shapes
• Fibrous proteins
– Polypeptide chains arranged as strands or
sheets
• Globular proteins
– Polypeptide chains folded into compact,
rounded shapes
Protein StructureProtein Structure
• Primary- just the sequence (1D)
• Secondary- interactions on the chain (2D)
• Tertiary- interactions between parts of the
chain the chain. (3D)
• Quaternary- interactions with other chains
• Primary structure influences shape in two main ways:– Allows hydrogen bonds to form
between different amino acids along length of chain
– Puts R groups in positions that allow them to interact
Primary StructurePrimary Structure & Protein Shape & Protein Shape
Secondary StructureSecondary Structure
• Hydrogen bonds form between different parts of polypeptide chain
• These bonds give rise to coiled or extended pattern
• Helix or pleated sheet
Examples of Secondary Examples of Secondary StructureStructure
-helix-helix
-sheet-sheet
Tertiary StructureTertiary Structure
Folding as a result
of interactions
between R groups
heme group
coiled and twisted polypeptide chain of one globin molecule
Quaternary StructureQuaternary Structure
Some proteins
are made up of
more than one
polypeptide
chain
Hemoglobin
Polypeptides With Attached Polypeptides With Attached Organic CompoundsOrganic Compounds
Nothing new, just more combinations
• Lipoproteins
– Proteins combined with cholesterol, triglycerides,
phospholipids
• Glycoproteins
– Proteins combined with oligosaccharides
DenaturationDenaturation
• Disruption of three-dimensional shape
• Breakage of weak bonds
• Causes of denaturation:– pH
– Temperature
• Destroying protein shape disrupts function
A Permanent WaveA Permanent Wave
hair wrapped around cuticles
differentbridges form
bridgesbroken
hair’scuticle
keratinmacrofibril
one hair cell microfibril (threechains coiled into one strand)
coiled keratinpolypeptidechain
• Sugar
– Ribose or deoxyribose
• At least one phosphate group
• Base
– Nitrogen-containing
– Single or double ring structure
Nucleotide StructureNucleotide Structure
Nucleotide FunctionsNucleotide Functions
• Energy carriers
• Coenzymes
• Chemical messengers
• Building blocks for
nucleic acids
Careful: Nucleotide isn’t just DNA or RNACareful: Nucleotide isn’t just DNA or RNA
ATP - A Nucleotide
three phosphate groups
sugar
base
• Composed of nucleotides
• Single- or double-stranded
• Sugar-phosphate backbone
Nucleic AcidsAdenineCytosine
DNA
• Double-stranded • Consists of four
types of nucleotides
• A bound to T• C bound to G
RNA
• Usually single strands
• Four types of nucleotides
• Unlike DNA, contains the base uracil in place of thymine
• Three types are key players in protein synthesis
• Normal metabolic products of one
species that can harm or kill a different
species
• Natural pesticides
– Compounds from tobacco
– Compounds from chrysanthemum
Natural Toxins
Synthetic Toxins
atrazine DDTmalathion
Negative Effects of Pesticides
• May be toxic to predators that help fight pests
• May be active for weeks to years
• Can be accidentally inhaled, ingested, or absorbed by humans
• Can cause rashes, headaches, allergic reactions
Producers Capture Carbon
Using photosynthesis, plants and other producers turn carbon dioxide and
water into carbon-based compounds
Atmospheric Carbon Dioxide
• Researchers have studied concentration of CO2 in air since the 1950s
• Concentration shifts with season– Declines in spring and summer when
producers take up CO2 for photosynthesis
CO2 and Global Warming
• Seasonal swings in CO2 increasing
• Spring decline starting earlier
• Temperatures in lower atmosphere increasing
• Warming may be promoting increased photosynthesis
Humans and Global Warming
• Fossil fuels are rich in carbon
• Use of fossil fuels releases CO2 into atmosphere
• Increased CO2 may contribute to global warming
Chemical Benefits and Costs
• Understanding of chemistry provides fertilizers, medicines, etc.
• Chemical pollutants damage ecosystems
Bioremediation
Use of living organisms to withdraw harmful substances
from the environment
Thyroid ScanThyroid Scan
• Measures health of thyroid by detecting radioactive iodine taken up by thyroid gland
normal thyroid enlarged cancerous