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% H2O ~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

HHC

H

H

AP Biology

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)

AP Biology

Carbon Skeleton Variation Length

Ethane, Propane

Branching- straight or branched Butane

Double Bonds Butene

Rings Benzene

AP Biology

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

6 carbons

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 withtragic results…

stereoisomersstereoisomers

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 -NH2

N attached to 2 H compounds with NH2 = amines

amino acids

NH2 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 –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.

AP Biology

Carboxyl –COOH

C double bonded to O & single bonded to OH group compounds with COOH = acids

fatty acidsamino acids

AP Biology28

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

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

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

HydrolysisHydrolysis

Dehydration synthesisDehydration synthesis

Condensation reactionCondensation reaction

AP Biology

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!

AP Biology33

Dehydration SynthesisDehydration Synthesis

AP Biology

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

AP Biology35

AP Biology 2007-2008

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 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.

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.

AP Biology

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.