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Transcript of Lecture 3: Chemistry of Life Goals: 1. Sprint through General Chemistry 2. Whisper past Organic...
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Lecture 3: Lecture 3: ChemistryChemistry of Life of Life
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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.
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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
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Most Common Elements in Most Common Elements in Living OrganismsLiving Organisms
C H O NC H O N
CarbonCarbon
HydrogenHydrogen
OxygenOxygen
NitrogenNitrogen
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What Are Atoms?What Are Atoms?
• Smallest particles that retain properties
of an element
• Made up of subatomic particles:
– Protons (+)
– Electrons (-)
– Neutrons (no charge)
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Fig. 2.3, p. 22
HYDROGEN HELIUM
electron
proton
neutron
Hydrogen and Helium AtomsHydrogen and Helium Atoms
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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
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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)
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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
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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
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High SensitivityHigh Sensitivity
Very Low DoseVery Low Dose
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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.
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What Determines Whether What Determines Whether Atoms Will Interact?Atoms Will Interact?
The most general of The most general of General ChemistryGeneral Chemistry
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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
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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
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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-
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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-
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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
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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
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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
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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
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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
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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
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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
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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
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+
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
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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.
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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
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onelargemolecule
anotherlargemolecule
a largemoleculetwistedbackonitself
Examples of Hydrogen BondsExamples of Hydrogen Bonds
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Properties of WaterProperties of Water
•PolarityPolarity
•Temperature-StabilizingTemperature-Stabilizing
•CohesiveCohesive
•SolventSolvent
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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
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O
H
HO
H
H
+ _
++
+
_
+
+
Liquid WaterLiquid Water
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Hydrophilic & HydrophobicHydrophilic & HydrophobicSubstancesSubstances
• Hydrophilic substances– Polar– Hydrogen bond with water – Example: sugar
• Hydrophobic substances– Non-polar– Repelled by water– Example: oil
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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
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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
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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
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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
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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
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Fig. 2.16, p. 29
Na+
Cl–
– –
––
––
–
––
– –
+ ++
+
+
+
+
+
+
+
+
++ +
+
+
+
+
Water as a solvent:Water as a solvent:Spheres of HydrationSpheres of Hydration
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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
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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
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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
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Examples of pHExamples of pHPure water is neutral with pH of 7.0
Acidic
Basic
(Alkaline))
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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
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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
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Lecture 2: Chemistry of LifeLecture 2: Chemistry of LifePart 2Part 2
Feeling a little burnt out?Feeling a little burnt out?
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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
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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
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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:
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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
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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
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Bonding ArrangementsBonding Arrangements
• Carbon atoms can form chains or rings
• Other atoms project from the carbon backbone
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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
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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
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Types of ReactionsTypes of Reactions
Functional group transfer
Electron transfer
Rearrangement
Condensation
Cleavage
x Hydrolysis
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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
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-ie. Water condenses on the inside of my window when the air conditioner is on full blast
Or..
Water forms ….
CondensationCondensation
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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
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HYDROLYSISHYDROLYSIS
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CarbohydratesCarbohydrates
Monosaccharides(simple sugars)
Oligosaccharides(short-chain carbohydrates)
Polysaccharides(complex carbohydrates)
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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)
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Two MonosaccharidesTwo Monosaccharides
glucose fructose
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DiDisaccharidessaccharides
• Type of oligosaccharide
• Two monosaccharides covalently bonded
• Formed by condensation reaction
+ H2O
glucose fructose
sucrose
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PolysaccharidesPolysaccharides
• Straight or branched chains of many sugar monomers
• Most common are composed entirely of glucose– Cellulose
– Starch (such as amylose)
– Glycogen
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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
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Cellulose and StarchCellulose and Starch
Changes in bonds result in:-different interactions-different structures-different physical properties
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GlycogenGlycogen
• Sugar storage form in animals
• Large stores in muscle and liver cells
• When blood sugar decreases, liver cells degrade glycogen, release glucose
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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
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• Most include fatty acids– Fats– Phospholipids– Waxes
• Sterols and their derivatives have no fatty acids
• Tend to be insoluble in water
LipidsLipids
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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
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Three Fatty AcidsThree Fatty Acids
stearic acid oleic acid linolenic acid
LardLard FlaxFlaxOliveOlive
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FatsFats
• Fatty acid(s)
attached to
glycerol
• Triglycerides
are most
common
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PhospholipidsPhospholipids
• Main components of cell
membranes
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Sterols and DerivativesSterols and Derivatives
• No fatty acids
• Rigid backbone of
four fused-together
carbon rings
• Cholesterol - most
common type in
animals
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WaxesWaxes• Long-chain fatty acids linked
to long chain alcohols or
carbon rings
• Firm consistency, repel water
• Important in water-proofing
• Size matters
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•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
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•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
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Amino Acid Structure
aminogroup
carboxylgroup
R group
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Properties of Amino Acids
• Determined by the “R group”
• Amino acids may be:
– Non-polar
– Uncharged, polar
– Positively charged, polar
– Negatively charged, polar
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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
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Forming Peptide Bonds
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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-
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Protein ShapesProtein Shapes
• Fibrous proteins
– Polypeptide chains arranged as strands or
sheets
• Globular proteins
– Polypeptide chains folded into compact,
rounded shapes
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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
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• 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
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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
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Examples of Secondary Examples of Secondary StructureStructure
-helix-helix
-sheet-sheet
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Tertiary StructureTertiary Structure
Folding as a result
of interactions
between R groups
heme group
coiled and twisted polypeptide chain of one globin molecule
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Quaternary StructureQuaternary Structure
Some proteins
are made up of
more than one
polypeptide
chain
Hemoglobin
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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
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DenaturationDenaturation
• Disruption of three-dimensional shape
• Breakage of weak bonds
• Causes of denaturation:– pH
– Temperature
• Destroying protein shape disrupts function
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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
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• Sugar
– Ribose or deoxyribose
• At least one phosphate group
• Base
– Nitrogen-containing
– Single or double ring structure
Nucleotide StructureNucleotide Structure
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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
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ATP - A Nucleotide
three phosphate groups
sugar
base
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• Composed of nucleotides
• Single- or double-stranded
• Sugar-phosphate backbone
Nucleic AcidsAdenineCytosine
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DNA
• Double-stranded • Consists of four
types of nucleotides
• A bound to T• C bound to G
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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
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• Normal metabolic products of one
species that can harm or kill a different
species
• Natural pesticides
– Compounds from tobacco
– Compounds from chrysanthemum
Natural Toxins
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Synthetic Toxins
atrazine DDTmalathion
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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
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Producers Capture Carbon
Using photosynthesis, plants and other producers turn carbon dioxide and
water into carbon-based compounds
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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
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CO2 and Global Warming
• Seasonal swings in CO2 increasing
• Spring decline starting earlier
• Temperatures in lower atmosphere increasing
• Warming may be promoting increased photosynthesis
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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
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Chemical Benefits and Costs
• Understanding of chemistry provides fertilizers, medicines, etc.
• Chemical pollutants damage ecosystems
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Bioremediation
Use of living organisms to withdraw harmful substances
from the environment
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Thyroid ScanThyroid Scan
• Measures health of thyroid by detecting radioactive iodine taken up by thyroid gland
normal thyroid enlarged cancerous