Chapter 4:
Chemistry of Carbon
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

AP Biology
~3% salts
 Na, Cl, K…
Life from inorganic molecules?
A testable hypothesis
 Conditions on early Earth
Reducing atmosphere
 water vapor (H2O), CO2, N2, H2, NH3, CH4,
H2S
 lots of available H & its electron
 no free oxygen

 Energy source

AP Biology
lightning, UV radiation,
volcanic
Electrodes discharge
sparks
(lightning simulation)
Origin of Organic Molecules

1953
Miller & Urey
test hypothesis
Water vapor
 formed organic
compounds from
inorganic
compounds
NH3
Mixture of gases
("primitive
atmosphere")
 amino acids
 adenine
AP Biology
CH4
H2
Condenser
Water
Heated water
("ocean")
Condensed
liquid with
complex,
organic
molecules
Chemistry of Life
 Organic chemistry is the study of
carbon compounds
 C atoms are versatile building blocks
bonding properties
 4 stable covalent bonds

H
H
C
H
AP Biology
H
fat molecule
Hydrocarbons
 Combinations of C & H

non-polar. hydrophobic
 not soluble in H2O
 Can form diverse carbon skeletons

AP Biology
stable
Structural isomers
Isomers
 Molecules with same molecular formula
but different structures (shapes)
different chemical properties
 different biological functions
 FIND THE STRUCTURL ISOMERS

AP Biology
Enantiomers: mirror image isomers
Form affects function
 Structural differences create important
functional significance

medicines
 L-version active
 L-Dopa active in treating
Parkinson’s disease
 but not D-version
 Biologically inactive

sometimes with
tragic results…
AP Biology
Form affects function
 Thalidomide
prescribed to pregnant women in 50s & 60s
 It was a mix of two enantiomers
 One reduced morning sickness, but…
the other enantiomer caused severe birth
defects

AP Biology
Isomers?
Geometric Isomers
NOT
ISOMERS
=
No. Recall that single bonds can rotate.
ISOMERS
≠
Trans
Cis
Yes, they are isomers since double/triple bonds cannot rotate.
AP Biology
Functional groups
 Parts of organic molecules that are
involved in chemical reactions

give organic molecules distinctive
properties
hydroxyl
 carbonyl
 carboxyl

amino
 sulfhydryl
 phosphate

 Affect reactivity
makes hydrocarbons hydrophilic
 increase solubility in water

AP Biology
Viva la difference!
 Basic structure of male & female
hormones is identical



AP Biology
identical carbon skeleton
attachment of different functional groups
interact with different targets in the body
 different effects
Hydroxyl
 –OH

organic compounds with OH = alcohols
 Polar, attracts water, dissolves organic
compounds like sugar

names typically end in –ol
 ethanol
AP Biology
Carbonyl
 C=O

O double bonded to C
 Found in carbohydrates
 if C=O at end molecule = aldehyde
 glucose, galactose, ribose
 if C=O in middle of molecule = ketone
 fructose
AP Biology
May
be structural isomers
Carboxyl
 –COOH

C double bonded to O & single bonded
to OH group
 compounds with COOH = acids
 fatty acids
 amino acids
AP Biology
Amino
 -NH2

N attached to 2 H
 compounds with NH2 = amines
 amino acids
 NH2 acts as base
 picks up H+ from solution
AP Biology
Sulfhydryl
 –SH

S bonded to H
 compounds with SH = thiols
 SH groups stabilize the structure of proteins
 Two SH groups can form a disulfide bridge
 Ex: Cystine (amino acid)
AP Biology
Phosphate
 –PO4

P bound to 4 O
 lots of O = lots of negative charge
 highly reactive
 transfers energy between organic molecules
 ATP, GTP
AP Biology
ATP
 An important source of energy for
cellular processes

Adenosine triphosphate
 An example of an organic phosphate
molecule
 Primary energy transferring molecule
AP Biology
How does ATP store energy?
ATP
O– O– O –
–O P –O
O– P O–
O– P –O
O
O O
 Each negative PO4 more difficult to add

a lot of stored energy in each bond
 most energy stored in 3rd Pi
 3rd Pi is hardest group to keep bonded to molecule
 Bonding of negative Pi groups is unstable


spring-loaded
Pi groups “pop” off easily & release energy
AP Biology
Instability of its P bonds makes ATP an excellent energy donor
How does ATP transfer energy?
O– O – O –
–O P –O– P –O
O– P O–
O O
O
O–
–O P O– + energy
O
Pi = inorganic phosphate ion
 ATP  ADP (adenosine diphosphate)

releases energy
 ∆G = -7.3 kcal/mole
 Fuel other reactions
 Allows our cells and bodies to do work
 Biosynthesis: build other molecules
 Contract muscles, protein pumps
AP Biology