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…
AP Biology
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
AP Biology
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.
AP Biology
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
AP Biology
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
AP Biology
Complex molecules assembled like TinkerToys
AP Biology
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)
AP Biology
Hydrocarbons can grow:
AP Biology
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.
AP Biology
(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
AP Biology
§ 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…
AP Biology
Form affects function:§ Thalidomide
u prescribed to pregnant women in 50s & 60s u reduced morning sickness, but…u enantiomers caused severe birth defects
AP Biology
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)
AP Biology
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
AP Biology
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
✔
✔
✔
✔
AP Biology
Hydroxyl§ –OH
u organic compounds with OH = alcoholsu names typically end in -ol
§ ethanol
✔
AP Biology
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
✔
✔
AP Biology
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
✔
AP Biology
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
✔
AP Biology
Sulfhydryl –SH
u S bonded to H§ compounds with SH = thiols§ SH groups stabilize the structure of proteins
✔
AP Biology
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.
✔
AP Biology
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
AP Biology
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.
AP Biology
Macromolecules:§ Smaller organic molecules join together
to form larger moleculesu macromolecules
§ 4 major classes of macromolecules:u carbohydratesu lipidsu proteinsu nucleic acids
AP Biology
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
AP Biology
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
AP Biology
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??