AP Biology Chemistry of Carbon Chapter 4 Building Blocks of Life

AP Biology Why study Carbon?  All of life is built on carbon  Cells  ~72% H 2 O  ~25% carbon compounds  carbohydrates  lipids  proteins  nucleic acids  ~3% salts  Na, Cl, K…

AP Biology 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)

AP Biology Macromolecules  Smaller organic molecules join together to form larger molecules  Macromolecules 4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids

AP Biology 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

AP Biology 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

AP Biology Properties of Carbon  C atoms are versatile building blocks  Bonding properties  4 stable covalent bonds  Accounts for diversity of biological molecules HH C H H

AP Biology Studies of Organic Compounds  Vitalism- belief in life outside physical and chemical laws  No longer accepted  Freidrich Wohler ; 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)

AP Biology Carbon Skeleton Variation  Length  Ethane, Propane  Branching- straight or branched  Butane  Double Bonds  Butene  Rings  Benzene

AP Biology

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)

AP Biology Complex molecules assembled like TinkerToys

AP Biology Isomers  Molecules with same molecular formula but different structures (shapes)  different chemical properties  different biological functions 6 carbons

AP Biology 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

AP Biology 3 Types of isomers

AP Biology 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 with tragic results… stereoisomers

AP Biology Figure 4.7 The pharmacological importance of enantiomers

AP Biology Form affects function  Thalidomide  prescribed to pregnant women in 50s & 60s  reduced morning sickness, but…  stereoisomer caused severe birth defects

AP Biology 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

AP Biology 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

AP Biology Carbonyl  C=O  O double bonded to C  if C=O at end molecule = aldehyde  if C=O in middle of molecule = ketone

AP Biology Figure 5.3 The structure and classification of some monosaccharides

AP Biology Hydroxyl  –OH  organic compounds with OH = alcohols  names typically end in -ol  Ethanol  Hydroxyl

AP Biology Amino  -NH 2  N attached to 2 H  compounds with NH 2 = amines  amino acids  NH 2 acts as base  ammonia picks up H + from solution

AP Biology Sulfhydryl  –SH  S bonded to H  compounds with SH = thiols  SH groups stabilize the structure of proteins

AP Biology Phosphate  –PO 4  P bound to 4 O  connects to C through an O  lots of O = lots of negative charge  highly reactive  transfers energy between organic molecules  ATP, GTP, etc.

AP Biology Carboxyl  –COOH  C double bonded to O & single bonded to OH group  compounds with COOH = acids  fatty acids  amino acids

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AP Biology 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

AP Biology H2OH2O HO H HH Polymers  Long molecules built by linking repeating building blocks in a chain  monomers  building blocks  repeated small units  covalent bonds Dehydration synthesis

AP Biology 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 Hydrolysis Dehydration synthesis Condensation reaction

AP Biology H2OH2O HO H HH How to build a polymer  Synthesis  joins monomers by “taking” H 2 O out  one monomer donates OH –  other monomer donates H +  together these form H 2 O  requires energy & enzymes enzyme Dehydration synthesis Condensation reaction You gotta be open to “bonding!

AP Biology 33 Dehydration Synthesis

AP Biology H2OH2O HOH H H How to break down a polymer  Digestion  use H 2 O to breakdown polymers  reverse of dehydration synthesis  cleave off one monomer at a time  H 2 O is split into H + and OH –  H + & OH – attach to ends  requires enzymes  releases energy Breaking up is hard to do! Hydrolysis Digestion enzyme

AP Biology 35

AP Biology Any Questions??

AP Biology 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 DennettDaniel Dennett  Vitalism is the metaphysical doctrine that living organisms possess a non-physical inner force or energy that gives them the property of life.

AP Biology  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.mechanistic materialism  The vitalistic principle goes by many names: chi or qi (China) prana (India and therapeutic touch), ki (Japan);chi or qipranatherapeutic touchki  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.energy

AP Biology  For examples, see acupuncture, Ayurvedic medicine, therapeutic touch, reiki, and qigong.acupuncture Ayurvedic medicinetherapeutic touch reikiqigong  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.placebo classical conditioning