AP Biology Chemistry of Carbon Chapter 4 Building Blocks of Life
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Chemistry of Carbon
Chapter 4
Building Blocks of Life
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Why study Carbon?
All of life is built on carbon Cells
~72% H2O ~25% carbon compounds
carbohydrates lipids proteins nucleic acids
~3% salts Na, Cl, K…
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Organic chemistry is the study of carbon compounds
Organic chemistry is the study of carbon compounds
Organic compounds- compounds containing Carbon, and usually hydrogen Ex. CH4- Methane Synthesized abiotically in early Earth Exception- CO2 (inorganic)
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Macromolecules Smaller organic molecules join together to
form larger molecules Macromolecules
4 major classes of macromolecules:carbohydrates
lipids
proteins
nucleic acids
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Carbons forms diverse molecules by bonding to four other Atoms
4 valence electrons- valence of 4 Bonding partners: C,H, O, N
Forms covalent bonds May be single or double Tetravalent
Tetra= 4
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Tetrahedral Forms tetrahydrons- Occurs when Carbon forms 4
single bonds with other atoms (arrangement of orbitals) known as a tetrahedral shape Ex. Methane (CH4) Ethane (C2H6)
Ethene (ethylene)- 2 Carbon atoms joined by a double bond Forms a flat molecule- Carbons are in same plane
Shape of molecule determines function
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Properties of Carbon
C atoms are versatile building blocks Bonding properties 4 stable covalent bonds Accounts for diversity of biological molecules
HHC
H
H
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Studies of Organic Compounds
Vitalism- belief in life outside physical and chemical laws No longer accepted
Freidrich Wohler- 1828 ; German chemist attempted to make an “inorganic” salt (Ammonia cyanate) by mixing ammonia ions (NH4+) and cyanate ions (CNO-) Made urea- organic compound found in urine
Hermann Kolbe- Wohler’s student made acetic acid from inorganic compounds
Abiotic synthesis of organic compounds from early life’s elements- Stanley Miller’s experiment (1953)
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Carbon Skeleton Variation Length
Ethane, Propane
Branching- straight or branched Butane
Double Bonds Butene
Rings Benzene
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Hydrocarbons (HC) Organic compounds consisting of only C & H
Ex. Ethane, Butene, Benzene, Methane Stable Not prevalent in organisms
Except lipids- hydrocarbon tails Gas at room temp Prevalent in fossil fuels
Ex. Petroleum, gasoline
Hydrophobic (Non polar) Store large amounts of energy
Ex. Fats in mammals stored in Adipose tissue
methane(simplest HC)
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Complex molecules assembled like TinkerToys
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Isomers Molecules with same molecular formula but
different structures (shapes) different chemical properties different biological functions
6 carbons
6 carbons
6 carbons
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3 Types of Isomers Structural- different covalent partners
May be differ in location of double bonds Geometric- same covalent partners, different spatial
arrangement Difference in shape- affects biological activity
Enantiomers- Mirror images of each other Middle Carbon- Asymmetric Carbon Ex. Ball & stick models Important for pharmaceuticals
Asthma and pain medications
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3 Types of isomers
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Form affects function Structural differences create important
functional significance amino acid alanine
L-alanine used in proteins but not D-alanine
medicines L-version active but not D-version
sometimes withtragic results…
stereoisomersstereoisomers
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Figure 4.7 The pharmacological importance of enantiomers
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Form affects function Thalidomide
prescribed to pregnant women in 50s & 60s reduced morning sickness, but… stereoisomer caused severe birth defects
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Functional groups Parts of organic molecules that are involved
in chemical reactions give organic molecules distinctive properties
hydroxyl amino
carbonyl sulfhydryl
carboxyl phosphate
Affect reactivity makes hydrocarbons hydrophilic increase solubility in water
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Viva la difference! Basic structure of male & female
hormones is identical identical carbon skeleton attachment of different functional groups interact with different targets in the body
different effects
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Carbonyl C=O
O double bonded to C if C=O at end molecule = aldehyde
if C=O in middle of molecule = ketone
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Figure 5.3 The structure and classification of some monosaccharides
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Hydroxyl –OH
organic compounds with OH = alcohols names typically end in -ol
Ethanol Hydroxyl
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Amino -NH2
N attached to 2 H compounds with NH2 = amines
amino acids
NH2 acts as base
ammonia picks up H+ from solution
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Sulfhydryl –SH
S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins
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Phosphate –PO4
P bound to 4 O
connects to C through an O
lots of O = lots of negative chargehighly reactive
transfers energy between organic molecules ATP, GTP, etc.
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Carboxyl –COOH
C double bonded to O & single bonded to OH group compounds with COOH = acids
fatty acidsamino acids
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ATP
Adenosine Triphosphate (ATP)- cells main energy souce Organic compound attached to 3 Phosphate groups
Adenosine Dihosphate (ADP)- A Phosphate may split off in H2O
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H2O
HO
HO H
H HHO
Polymers Long molecules built by linking repeating
building blocks in a chain monomers
building blocks repeated small units
covalent bonds
Dehydration synthesisDehydration synthesis
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Building & Breaking Polymers Building polymers from
monomer
Synthesis= building
Monomer+ Monomer Polymer
Dehydration= water loss
Breaking down polymers into
monomers
Hydro= water
Lysis= Break down
Polymer Monomers
HydrolysisHydrolysis
Dehydration synthesisDehydration synthesis
Condensation reactionCondensation reaction
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H2O
HO
HO H
H HHO
How to build a polymer Synthesis
joins monomers by “taking” H2O out one monomer donates OH–
other monomer donates H+ together these form H2O
requires energy & enzymes
enzymeDehydration synthesisDehydration synthesis
Condensation reactionCondensation reaction
You gotta be open to“bonding!
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Dehydration SynthesisDehydration Synthesis
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H2O
HO H
HO H HO H
How to break down a polymer
Digestion use H2O to breakdown polymers
reverse of dehydration synthesis cleave off one monomer at a time
H2O is split into H+ and OH–
H+ & OH– attach to ends
requires enzymes releases energy
Breaking upis hard to do!
HydrolysisHydrolysis
DigestionDigestion
enzyme
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AP Biology 2007-2008
Any Questions??
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Vitalism
"Vitalism—the insistence that there is some big, mysterious extra ingredient in all living things—turns out to have been not a deep insight but a failure of imagination." --Daniel Dennett
Vitalism is the metaphysical doctrine that living organisms possess a non-physical inner force or energy that gives them the property of life.
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Vitalists believe that the laws of physics and chemistry alone cannot explain life functions and processes. Vitalism is opposed to mechanistic materialism and its thesis that life emerges from a complex combination of organic matter.
The vitalistic principle goes by many names: chi or qi (China) prana (India and therapeutic touch), ki (Japan);
American advocates much prefer the term energy. Many kinds of alternative therapies or energy medicines are based upon a belief that health is determined by the flow of this alleged energy.
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For examples, see acupuncture, Ayurvedic medicine, therapeutic touch, reiki, and qigong.
Energy medicine is a placebo, leading many advocates to mistake the effects of classical conditioning, expectation of relief that leads to reduction of anxiety and stress, and beliefs about the effectiveness of the medicine as effects of mythical energy.