The

Chemistry of Life
Chemistry is the foundation of Biology
 Everything is made of matter
 Matter is made of atoms
 About 25 elements are essential
for life
 Four elements make up 96%
of living matter:
 carbon (C)

 hydrogen (H)

 oxygen (O)

 nitrogen (N)
 Four elements make up
most of remaining 4%:
 phosphorus (P)

 calcium (Ca)

 sulfur (S)

 potassium (K)
 Energy levels
 Are represented by electron shells
Third energy level (shell)

Second energy level (shell) Energy

absorbed

First energy level (shell)

Energy
lost
Atomic
nucleus

(b) An electron can move from one level to another only if the energy
it gains or loses is exactly equal to the difference in energy between
the two levels. Arrows indicate some of the step-wise changes in
Figure 2.7B potential energy that are possible.
  The periodic table of the elements
 Shows the electron distribution for all the elements

Hydrogen 2 Atomic number Helium

He 2He
1H 4.00 Element symbol
Atomic mass
First Electron-shell
shell diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 3B 6C 7N 8O 9F 10Ne

Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar

Third
shell

Figure 2.8
 Each electron shell
 Consists of a specific number of orbitals

Electron orbitals.
Each orbital holds
up to two electrons. x Y

Z
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.

(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
Figure 2.9 2 electrons) 8 electrons)
 Formation of a covalent bond Hydrogen atoms (2 H)

In each hydrogen
1 atom, the single electron
is held in its orbital by + +
its attraction to the
proton in the nucleus.

When two hydrogen

2
atoms approach each
other, the electron of
each atom is also + +
attracted to the proton
in the other nucleus.

The two electrons

3 become shared in a
covalent bond, + +
forming an H2
molecule. Hydrogen
molecule (H2)
Figure 2.10
  Single and double covalent bonds

Name Electron- Structural Space-

(molecular shell formula filling
formula) diagram model

(a)
Hydrogen (H2).
Two hydrogen H H
atoms can form a
single bond.

(b) Oxygen (O2).

Two oxygen atoms
share two pairs of O O
electrons to form
a double bond.
 Covalent bonding in compounds

Name Electron- Structural Space-

(molecular shell formula filling
formula) diagram model

(c) Water (H2O).

Two hydrogen
atoms and one O H
oxygen atom are
joined by covalent H
bonds to produce a
molecule of water.
Methane (CH4).
(d) Four hydrogen
atoms can satisfy
H
the valence of
one carbon H C H
atom, forming
methane. H
Figure 2.11 C, D
  In a polar covalent bond
 The atoms have differing electronegativities
 Share the electrons unequally

Because oxygen (O) is more electronegative than hydrogen (H),

shared electrons are pulled more toward oxygen.

d–

This results in a
partial negative
charge on the
oxygen and a
partial positive
O charge on
the hydrogens.

Figure 2.12 H H
d+ d+
H2O
 An ionic bond
 Is an attraction between anions and cations
1 The lone valence electron of a sodium
atom is transferred to join the 7 valence
electrons of a chlorine atom.
2 Each resulting ion has a completed
valence shell. An ionic bond can form
between the oppositely charged ions.

+ –

Na Cl Na Cl

Na+ Cl–
Sodium on Chloride ion
Na Cl
(a cation) (an anion)
Figure 2.13 Sodium atom Chlorine atom
(an uncharged (an uncharged
atom) atom)
Sodium chloride (NaCl)
  A hydrogen bond
 Forms when a hydrogen atom covalently bonded to one electronegative
atom is also attracted to another electronegative atom

d– d+

Water H
(H2O) O A hydrogen
bond results
from the
H attraction
between the
d+ partial positive
charge on the
d– hydrogen atom
of water and
Ammonia the partial
(NH3) N negative charge
on the nitrogen
H H atom of
d+ H d+ ammonia.

Figure 2.15
d+
 Van der Waals interactions
 Occur when transiently positive and negative regions of molecules attract
each other
  In a covalent bond
 The s and p orbitals may hybridize, creating specific molecular shapes

Three p orbitals Four hybrid orbitals

Z

s orbital X

Y
Tetrahedron

(a) Hybridization of orbitals. The single s and three p orbitals

of a valence shell involved in covalent bonding combine to
form four teardrop-shaped hybrid orbitals. These orbitals
extend to the four corners of an imaginary tetrahedron
Figure 2.16 (a) (outlined in pink).
 Space-filling Ball-and-stick Hybrid-orbital model
model model (with ball-and-stick
model superimposed)
Unbonded
Electron pair

O O

H H H H
104.5°
Water (H2O)

H H

C C
H H H H

Methane (CH4) H H

(b) Molecular shape models. Three models representing molecular shape are shown for
two examples; water and methane. The positions of the hybrid orbital determine the
Figure 2.16 (b) shapes of the molecules
 Carbon Nitrogen
Hydrogen Sulfur
Oxygen
Natural
endorphin
Morphine

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

Natural
endorphin Morphine

Brain cell Endorphin

receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
Figure 2.17 recognize and can bind to both endorphin and morphine.
 Chemical reactions
 Convert reactants to products

2 H2 + O2 2 H2O

Reactants Reaction Product

 Properties of Water

 Three-quarters of the Earth’s surface is submerged in water

 The abundance of water is the main reason the Earth is habitable

Figure 3.1
 Why are we studying water?

All life occurs in water

 inside & outside the cell
98% Liquid Metabolism –
2% Vapor/ice all chemical
on earth reactions that
occur in a
living organism
 Allows them to form hydrogen bonds with each
other
 Contributes to the various properties water exhibits
 H2O molecules form H-bonds with each other
 Special properties of water
1.cohesion & adhesion
 surface tension, capillary action
2.good solvent
 many molecules dissolve in H2O
 hydrophilic vs. hydrophobic
3.lower density as a solid
 ice floats!
4.high specific heat
 water stores heat
5.high heat of vaporization
 heats & cools slowly
 Cohesion
 H bonding between H2O molecules
 water is “sticky”
 surface tension
 drinking straw

 Adhesion
 H bonding between H2O & other substances
 capillary action
 meniscus
 water climbs up paper towel or cloth
HOW DOES H2O GET TO TOP OF TREES?
Transpiration is built on cohesion & adhesion
 Polarity makes H2O a good solvent
 polar H2O molecules surround + & – ions
 solvents dissolve solutes creating solutions
What dissolves in water?
 Hydrophilic
 substances have attraction to
H2O:polar

What doesn’t dissolve in water?

 Hydrophobic
 substances that don’t
have an attraction to H2O
non-polar

fat (triglycerol)
  The hydrogen bonds in ice
 Are more “ordered” than in liquid water, making ice less dense

Hydrogen
bond
Ice Liquid water
Hydrogen bonds are stable Hydrogen bonds
constantly break and re-form
Oceans & lakes don’t freeze solid
surface ice insulates water below allowing life to survive the winter
4. SPECIFIC HEAT
 Is the amount of heat that must be absorbed or lost for 1
gram of that substance to change its temperature by 1ºC

 H2O resists changes in temperature

 high specific heat
 takes a lot to heat it up
 takes a lot to cool it down
 Heat is absorbed when hydrogen bonds break
 Heat is released when hydrogen bonds form

 H2O moderates temperatures on Earth

 Evaporative cooling

Organisms rely on heat of

vaporization to remove body heat
IONIZATION OF WATER & PH
 Water ionizes
 H+ splits off from H2O, leaving OH–
 if [H+] = [-OH], water is neutral
 if [H+] > [-OH], water is acidic
 if [H+] < [-OH], water is basic
 pH scale
 how acid or basic solution is
 1  7  14

H2O  H+ + OH–
 H+ Ion Examples of Solutions
Concentration pH
100 0 Hydrochloric acid
10–1 1
10–2 2 Stomach acid, Lemon juice
tenfold change 10–3 3 Vinegar, cola, beer
in H+ ions 10–4 4 Tomatoes
10–5 5 Black coffee, Rainwater
pH1  pH2 Urine, Saliva
10–6 6
10-1  10-2 Pure water, Blood
10 times less H+ 10–7 7
10–8 8 Seawater
pH8  pH7 10–9 9 Baking soda
10-8  10-7 10–10 10 Great Salt Lake
10 times more H+
10–11 11 Household ammonia
pH10  pH8 10–12 12 Household bleach
10-10  10-8 10–13 13 Oven cleaner
100 times more H+
10–14 14 Sodium hydroxide
 pH of cells must be kept ~7
 pH affects shape of molecules
 shape of molecules affect function
 pH affects cellular function

 Control pH by buffers (Are substances that minimize changes in

the concentrations of hydrogen and hydroxide ions in a solution)
 reservoir of H+
9
 donate H+ when [H+] falls
8
 absorb H+ when [H+] rises 7
6
Buffering
5
pH
range
4
3
2
1
0
0 1 2 3 4 5
Amount of base added
 Overview: Carbon—The Backbone of Biological
Molecules
 All living organisms
 Are made up of chemicals based mostly on the
element carbon

Figure 4.1
 The concept of vitalism
 Is the idea that organic compounds arise only within living
organisms
 Was disproved when chemists synthesized the compounds in the
laboratory
In 1953, Stanley Miller simulated what were thought to be environmental
EXPERIMENT conditions on the lifeless, primordial Earth. As shown in this recreation,
Miller used electrical discharges (simulated lightning) to trigger reactions
in a primitive “atmosphere” of H2O, H2, NH3 (ammonia), and CH4
(methane)—some of the gases released by volcanoes.

A variety of organic compounds that play key roles in living cells were
RESULTS synthesized in Miller’s apparatus.
Organic compounds may have been synthesized abiotically on the
CONCLUSION early Earth, setting the stage for the origin of life. (We will explore
Figure 4.2 this hypothesis in more detail in Chapter 26.)
  The bonding versatility of carbon
 Allows it to form many diverse molecules, including carbon skeletons

Name and Molecular Structural Ball-and- Space-Filling

Comments Formula Formula Stick Model Model

H
(a) Methane CH4 H C H
H

H H
(b) Ethane C2H
H C C H
6
H H

(c) Ethene H H
C2H4 C C
igure 4.3 A-C (ethylene) H H
 Carbon chains
 Form the skeletons of most organic molecules
 Vary in length and shape
H H H H H
(a) Length H C C H H C C C H
H H H H H
Ethane Propane
H
H C H
H H H H H H
(b) Branching H C C C C H H C C C H
H H H H H H H
Butane 2-methylpropane
(commonly called isobutane)
H H H H H H H H
(c) Double bonds H
C C C C H H C C C C H
H H H H
1-Butene 2-Butene
H H H
H C H H
(d) Rings H C C H C C H
H C H C
H C H C C
C

Figure 4.5 A-D Cyclohexane Benzene

 Hydrocarbons
 Are found in many of a cell’s organic molecules

Fat droplets (stained red)

100 µm
Figure 4.6 A, B (a) A fat molecule (b) Mammalian adipose cells
 Three types of isomers are

H
H C H
H C H
H H H H H H H
(a) Structural isomers H C C C C C H H C C C H
H H H H H H H H

X X H X
(b) Geometric isomers C C C C
H H X H

CO2H CO2H

(c) Enantiomers H
C
NH2 NH2
C
H
CH3 CH3
 Enantiomers
 Are important in the pharmaceutical industry

L-Dopa D-Dopa
(effective against (biologically
Figure 4.8 Parkinson’s disease) inactive)
  Give organic molecules distinctive chemical properties

OH
CH3
Estradiol

HO

Female lion

OH
CH3

CH3

O
Testosterone

Figure 4.9 Male lion

 Six functional groups are important in the chemistry of life
• Hydroxyl
• Carbonyl
• Carboxyl
• Amino
• Sulfhydryl
• Phosphate

 Some important functional groups of organic compounds

Contd…