AP Biology

Chemistry of Carbon:

Building Blocks of Life

AP Biology

What properties make carbon the basis of all life?

AP Biology

Why study Carbon?§ All of life is built on carbon § Cells

u ~72% H2O u ~25% carbon compounds

§ carbohydrates§ lipids§ proteins § nucleic acids

u ~3% salts § Na, Cl, K…

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It was thought that organic compounds could only be produced in living organisms:

Jons Jacob Berzelius “living things work by some mysterious “vital force”, a hypothesis called vitalism. He was the first to make a distinction between organic compounds

using coffee, tea & proteins, thought to arise in only living organisms, and inorganic

compounds were found in the nonliving world. He proposed that compounds could be

distinguished by whether they are made by living organisms or not.

1810

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Pioneers of organic chemistry helped shift the mainstream of biological thought from vitalism to mechanism:§ Mechanism is the view that physical and chemical laws

govern all natural phenomena.§ Vitalism was disproved when chemists were able to

synthesize organic compounds

1828 - Friedrich Wohler accidentally made urea (organic compund), from inorganic salts (ammonium cyanate).

AP Biology

Two proposals of natural phenomenon:

A. Vitalist view (1800’s) - some "vital force" beyond chemical & physical laws explains life phenomena. Not true science!* Based on “pseudo-science”.

B. Mechanist view (1900’s - current) - all life phenomena are ultimately describable in terms of chemical & physical laws.Living organisms are complex machines. * Most predominant in 21st century.* Based on observation & experimentation.

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Organic Molecules and the Origin of Life on Earth:§ Stanley Miller’s classic experiment showed the abiotic

synthesis of organic compounds§ Experiments support the idea that abiotic synthesis of

organic compounds, perhaps near volcanoes, could have been a stage in the origin of life

Prebiotic-chemistry experiments and biosynthesis pathways provide abundant counterevidence to the vitalistic hypothesis

AP Biology

“Atmosphere”

Water vapor

Cooled “rain”containing

organicmolecules

Sample forchemical analysis

Coldwater

Condenser

Electrode

CH4

NH3 H2

H2O“sea

”

Can organic molecules form under conditions estimated to simulate

those on the early Earth?

Some of Stanley Miller’s original vials from his 1958 experiment

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Chemistry of Life:§ Organic chemistry is the study of

carbon compounds§ C atoms are versatile building blocks

u bonding propertiesu 4 stable covalent bonds

HH C

H

H

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Complex molecules assembled like TinkerToys

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Hydrocarbons:§ Combinations of C & H

unon-polar§ not soluble in H2O§ hydrophobic

ustableuvery little attraction

between molecules§ a gas at room temperature

methane(simplest HC)

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Hydrocarbons can grow:

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Isomers:§ Molecules with same molecular formula but different

structures (shapes); geometry/bond angles u different chemical propertiesu different biological functions1. Structural isomers have different covalent

arrangements of their atoms2. Cis-trans isomers have the same covalent

bonds but differ in spatial arrangements3. Enantiomers are isomers that are mirror

images of each other.

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(a) Structural isomers

(b) Cis-trans isomers

Pentane

cis isomer: The two Xs areon the same side.

2-methyl butane

trans isomer: The two Xs areon opposite sides.

(c) Enantiomers

L isomer D isomer

CO2HCO2H

H

CH3 CH3

HNH2NH2

C C

AP Biology

What type of isomers are shown below?

6 carbons 6 carbons

A. Structural isomers

B. Cis-trans isomers

C. Enantiomers

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§ Enantiomers are important in the pharmaceutical industry.

§ Two enantiomers of a drug may have different effects.

§ Usually only one isomer is biologically active.§ Differing effects of enantiomers demonstrate that

organisms are sensitive to even subtle variations in molecules.

§ Enantiomers differ because of the tetrahedralnonsuperimposable arrangement of four different atoms or groups of atoms around an asymmetric carbon. Note: Because of the tetrahedral shape of the covalent bonds

formed by carbon, the four different atoms or groups can occur in two non-superimposable arrangements.

AP Biology

Drug Effects EffectiveEnantiomer

IneffectiveEnantiomer

Ibuprofen

Albuterol

Reducesinflammation

and pain

Relaxes bronchial(airway) muscles,improving airflow

in asthmapatients

S-Ibuprofen

R-AIbuterol S-AIbuterol

R-Ibuprofen

AP Biology

Parkinson’s: A Neurological Disorder – hyposecretion (¯) of dopamine; causes jerky body movements. An inhibition of the motor drive. Usually treated w/ drugs that enhance dopamine’s effect.

One million Americans have Parkinson's disease, including three out of every 100 people over the age of 60

In 1918, an epidemic of sleeping sickness caused an unusual rigid paralysis in some survivors, similar to symptoms of advanced Parkinson’s disease. Years later, L-dopa, a chemical used to treat Parkinson’s, was given to some of these patients. L-dopa was remarkably effective at eliminating the paralysis, at least temporarily. However, its enantiomer, D-dopa, was subsequently shown to have no effect at all, as is the case for Parkinson’s disease. Discuss how the effectiveness of one enantiomer and not the other illustrates the theme of structure and function.

AP Biology

Form affects function:§ Structural differences create

important functional significanceuamino acid alanine§ L-alanine used in proteins§ but not D-alanine

uMedicine, eg. Parkinson’s§ L-version active§ but not D-version

§ L-dopa is effective because its structure allows it to interact with a receptor molecule in the brain.

§ D-dopa is ineffective because it does not fit the receptor.

§ sometimes withtragic results…

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Form affects function:§ Thalidomide

u prescribed to pregnant women in 50s & 60s u reduced morning sickness, but…u enantiomers caused severe birth defects

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Diversity of molecules:§ Substitute other atoms or groups

around the carbonu ethane vs. ethanol

§ H replaced by an hydroxyl group (–OH)§ nonpolar vs. polar§ gas vs. liquid§ biological effects!

ethane (C2H6)

ethanol (C2H5OH)

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Viva la difference!§ Basic structure of male & female hormones is

identicalu identical carbon skeletonu attachment of different functional groupsu interact with different targets in the body

§ different effects

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Functional groups:§ Parts of organic molecules that are involved

in chemical reactionsu give organic molecules distinctive properties

n hydroxyl n aminon carbonyl n sulfhydryln carboxyl n phosphate

§ Affect reactivityu makes hydrocarbons hydrophilicu increase solubility in water

✔

✔

✔

✔

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Hydroxyl§ –OH

u organic compounds with OH = alcoholsu names typically end in -ol

§ ethanol

✔

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Carbonyl – found in sugars

§ C=O u O double bonded to C

§ if C=O at end molecule = aldehyde§ if C=O in middle of molecule = ketone

✔

✔

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Carboxyl § –COOH

u C double bonded to O & single bonded to OH group

u -COOH acts as an acid(proton donor)§ compounds with COOH = acids

w fatty acidswamino acids

✔

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Amino§ -NH2

u N attached to 2 H§ compounds with NH2 = amines

wamino acids§ NH2 acts as base (proton acceptor)

wammonia picks up H+ from solution

✔

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Sulfhydryl –SH

u S bonded to H§ compounds with SH = thiols§ SH groups stabilize the structure of proteins

✔

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Phosphate § –PO4

u P bound to 4 O§ connects to C through an O§ lots of O = lots of negative charge

whighly reactive

§ transfers energy between organic molecules wATP, GTP, etc.

✔

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ATP: An Important Source of Energy for Cellular Processes

§ An important organic phosphate is adenosine triphosphate (ATP).

§ ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups.

§ ATP stores the potential to react with water, a reaction that releases energy to be used by the cell.

Reactswith H2O

Inorganicphosphate

ADP

EnergyAdenosine Adenosine

ATP

P P P P PP i

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Macromolecules

The Building Blocksof Life

AP Biology

The Chemical Elements of Life: A Review

§ The versatility of carbon makes possible the great diversity of organic molecules.

§ Variation at the molecular level lies at the foundation of all biological diversity.

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Macromolecules:§ Smaller organic molecules join together

to form larger moleculesu macromolecules

§ 4 major classes of macromolecules:u carbohydratesu lipidsu proteinsu nucleic acids

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H2O

HO

HO H

H HHO

Polymers:§ Long molecules built by linking repeating

building blocks in a chain u monomers

§ building blocks§ repeated small units

u covalent bonds

Dehydration synthesis

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H2O

HO

HO H

H HHO

How to build a polymer:§ Synthesis

u joins monomers by “taking” H2O out§ one monomer donates OH–

§ other monomer donates H+

§ together these form H2Ou requires energy & enzymes

enzymeDehydration synthesisCondensation reaction

You gottabe open to“bonding!

AP Biology

How many molecules of water are released in order to synthesize a polymer that is 4 monomers long?

(a) Dehydration reaction: synthesizing a polymer

1 2 3

1 2 3 4

Dehydration removes a watermolecule, forming a new bond.

Short polymer Unlinked monomer

H2O

Longer polymer

H2O

AP Biology

H2O

HO H

HO H HO H

How to break down a polymer:§ Digestion

u use H2O to breakdown polymers § reverse of dehydration synthesis§ cleave off one monomer at a time§ H2O is split into H+ and OH–

w H+ & OH– attach to ends

u requires enzymesu releases energy

Breaking upis hard to do!

HydrolysisDigestion

enzyme

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1 2 3 4

H2O

(b) Hydrolysis: breaking down a polymer

Hydrolysis adds a watermolecule, breaking a bond.

1 2 3

How many molecules of water are needed to completely hydrolyze a polymer that is 4 monomers long?

AP Biology 2007-2008

Any Questions??