BIOLOGY FOR AP® COURSES

Chapter 2 THE CHEMICAL FOUNDATION OF LIFE

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ATOMS ARE THE BUILDING
BLOCKS OF MOLECULES

• Life is composed of matter

• Matter:
• occupies space
• has mass

• Elements are unique forms of matter

1. Specific chemical properties
2. Specific physical properties
ELEMENTS AND THE LIVING WORLD

• Elements cannot be broken down into smaller substances

• Each element is designated by a chemical symbol (one or
two letters)
• Sulfur = S
• Calcium = Ca

• Four most common elements of living organisms

• Carbon C
• Oxygen = O
• Hydrogen = H
• Nitrogen = N
ELEMENTS AND THE LIVING WORLD

Comparing the elements of living

organisms to the non-living world

Element Life Atmosphere Earth’s Crust

(Humans)

Oxygen (O) 65% 21% 46%

Carbon (C) 18% trace trace

Hydrogen (H) 10% trace 0.1%

Nitrogen (N) 3% 78% trace

 ATOMS ARE THE BUILDING
BLOCKS OF ELEMENTS
Atom – smallest unit of matter that retains all
chemical properties of an element

Atoms contains two regions

1. Nucleus – center of the atom and contains
protons and neutrons
2. Outermost region – holds electrons in orbit
around the nucleus

Protons, neutrons, and electrons are referred to

as sub-atomic particles
KEY PROPERTIES OF SUB-ATOMIC PARTICLES
Charge Mass (amu) Location

Proton +1 1 nucleus

Neutron 0 1 nucleus

Electron -1 0 orbitals
 THE ARRANGEMENT OF SUB-ATOMIC PARTICLES IN
AN ATOM
Example of an atom
from the element
Helium (He)

Simplified depiction of how sub-atomic particles are

arranged within an atom.
 WHAT’S THE DIFFERENCE BETWEEN
ATOMIC NUMBER AND ATOMIC MASS?

Atoms of each element have a standard number of protons

and electrons
• Atomic Number is the number of protons
• Each element has a distinct atomic number

• Atomic Mass is the mass of the atom, roughly equal to

number of protons and neutrons
• The number of neutrons can vary in an element
• Elements with different number of neutrons are isotopes
• Electrons don’t need to be included in calculation of atomic mass
• Atomic mass is expressed in atomic mass units (amu)

• We can calculate the number of neutrons in an element by

subtracting the atomic number from the atomic mass
FIGURE 2.3 ATOMIC MASS VS. ATOMIC NUMBER

Carbon has an atomic number of six, and two stable

isotopes with mass numbers of twelve and thirteen,
respectively. Carbon-12’s atomic mass is approx. 12.11.
 ISOTOPES
Forms of an element with different numbers of
neutrons, and thus different mass numbers
Example:
1
H has 0 neutrons
2
H has 1 neutron
3
H has 2 neutrons
ISOTOPE SIMULATION

https://phet.colorado.edu/sims/html/isotopes-and-atomic-mass/latest/i
sotopes-and-atomic-mass_en.html
 ISOTOPES CAN BE USED AS A RESEARCH TOOL

Radioisotopes – isotopes that

emit neutrons, protons, and
electrons

Radiometric dating takes

advantage of this natural
phenomenon

Example: Over time Carbon-14

decays to Nitrogen-14.
Researchers can compare
Carbon-14 in atmosphere to
carbon-14 in fossils remains and
estimate fossil age

The age of carbon-containing remains less than about 50,000 years old, such as this
pygmy mammoth, can be determined using carbon dating.
For older objects, scientists analyze the presence of isotopes of uranium (which decays
to lead), potassium, or rubidium.
PERIODIC TABLE

The periodic table shows the atomic mass and atomic number of each element. The
atomic number appears above the symbol for the element and the approximate atomic
mass appears below it.
ELECTRON SHELLS AND THE BOHR MODEL

• Atoms with neutral charge

• Number of protons = number of electrons
• Number of electrons = atomic number

Bohr model – early model with protons in nucleus and

electrons in circular orbits at specific distance from
nucleus

Orbits: electron shells or energy levels

• An electron normally exists in the lowest available
energy shell (closest to the nucleus)
• Electrons fill orbitals closest to nucleus first, then those
further away in order (i.e. 1n fills first, then 2n, then 3n,
etc
FIGURE 2.7 – ELECTRONS FILLING THEIR SHELLS

Outer shell: Valence shell

• The most stable configuration occurs when the valence shell is filled
• The elements in group 18 of this diagram have full valence shells
FIGURE 2.7 – ELECTRONS FILLING THEIR SHELLS

When the first two outer shells are filled each will have eight electrons (octet rule)
• Group 1 elements (H, Li, NA) could achieve stability by losing an outer electron
• Group 17 elements could achieve stability by gaining one additional electron
WHAT ABOUT ELECTRON ORBITALS?

• Bohr models are incomplete

• Electrons are not in planet-like orbits
• Electron orbitals – complex shapes that
describe how electrons are spatially distributed
around the nucleus
• Quantum mechanics allows us to predict where
an electron might be at any given time
• This predicted area is known as the orbital
FIGURE 2.8 SUBSHELLS HAVE UNIQUE SHAPES

Within each Bohr model shell are subshells

Each subshell (s,p,d,f) has a specified number of orbitals containing
electrons
The s subshell is spherical and has one orbital
The p subshell is dumbbell shaped and has three orbitals
ORBITALS: ELECTRON CONFIGURATION OF SCANDIUM

https://youtu.be/sMt5Dcex0kg
ELECTRONS DETERMINE
HOW ATOMS INTERACT

Chemical reactions are changes in

distribution of electrons between atoms
CHEMICAL REACTIONS

• Reactants – substances used at

beginning of reaction
• Products – substances formed at the end
of the reaction

2H2O2 2H2O + O2
Reactants Products
 CHEMICAL REACTION CAN BE
REVERSIBLE OR IRREVERSIBLE

2H2O2 2H2O + O2
Irreversible reaction: proceeds in one
direction until all the reactants are used up

HCO3- + H+ H2CO3
Reversible reaction: Reactants are converted
to products but some product can be
converted back to reactant
HOW DO ATOMS BOND TO FORM MOLECULES?

Chemical bond: the attractive force that links

atoms together to form molecules
2.9 COVALENT BONDS – ELECTRONS ARE SHARED

Two or more atoms may bond with each other to form a

molecule.
When two hydrogens and an oxygen share electrons via
covalent bonds, a water molecule is formed.
MORE THAN ONE SET OF
ELECTRONS CAN BE SHARED

The oxygen atoms in an O2 molecule are joined by a

double bond.
IONIC BONDS – ATOMS GIVE UP OR GAIN ELECTRONS

In the formation of an ionic compound, metals lose

electrons and nonmetals gain electrons to achieve an
octet.
POLAR BONDS–COVALENT BONDS IN WHICH THERE IS UNEQUAL
SHARING OF THE ELECTRONS

Polar Covalent Bonds

Electrons are unequally shared by
the atoms and attracted more to one
nucleus than the other

Water is a great example

Oxygen has higher
electronegativity than hydrogen
This means it wants the electrons
more than than hydrogen does
NON-POLAR BONDS–COVALENT BONDS IN WHICH THERE IS EQUAL
SHARING OF THE ELECTRONS

Non-Polar Covalent Bonds

Electrons are equally shared
by the atoms
Methane (CH4) is a great
example
Carbon shares electrons with
four hydrogens equally

Why is carbon dioxide a Both bond type and

nonpolar molecule even though molecular shape determine
the oxygen-carbon bond is a whether a molecule is polar or
polar covalent bond? nonpolar
AN EXAMPLE OF MIXING A POLAR COMPOUND WITH A NONPOLAR
COMPOUND

Oil and water do not mix. As this macro image of oil and water shows, oil does
not dissolve in water but forms droplets instead. This is due to it being a
nonpolar compound. (credit: Gautam Dogra).
 HYDROGEN BONDS AND
VANDER WAALS INTERACTIONS

• Ionic and Covalent bonds – require energy to break

Weaker bonds
Hydrogen bonds – interaction between the δ+ of hydrogen
and the δ- of a more electronegative atom on another
molecule – often occurs between water molecules

Van der Waals interactions – weak attractions or

interactions between two or more molecules (in close
proximity) due to changes in electron density
 WATER – ESSENTIAL TO LIFE
• Water makes up 60-70% of
human body

• Most critical molecule for life

on earth

• Why?
1. It is a polar molecule
2. It can form hydrogen
bonds From: http://www.freefoto.com/preview/15-24-1/Stream-of-
running-water
 HYDROGEN BONDS – THE KEY TO WATER
H has a δ+ and O has δ-
• The chemical bonds between
hydrogen and oxygen in water
are polar colvalent bonds

• Oxygen pulls the shared electron

closer—slightly negative charge

• Hydrogen has slightly positive

charge

from: http://cnx.org/content/col11496/1.6
• Hydrogen of one water molecule
forms a weak hydrogen bond
with the oxygen of an adjacent
water molecule
 HYDROGEN BONDS ARE KEY
TO THREE STATES OF WATER

Three states of water

• Liquid water – hydrogen bonds are
constantly made, broken and remade
• Gas - water is heated the increased kinetic
energy of water causes hydrogen bonds to
break and water molecules escape into air
as gas
• Solid water – temperature is lowered and
a crystalline structure is maintained
THE POWER OF HYDROGEN BONDS

Hydrogen bonding makes ice less dense than liquid water. The (a) lattice structure of ice
makes it less dense than the freely flowing molecules of liquid water, enabling it to (b)
float on water. (credit a: modification of work by Jane Whitney, image created using
Visual Molecular Dynamics (VMD) software [1]; credit b: modification of work by Carlos
Ponte)
See video of Ice Lattice: http://www.janewhitney.com/ice_movie_resources.html
 ADDITIONAL IMPORTANT
PROPERTIES OF WATER
Heat capacity – Specific heat capacity
refers to the amount of heat one gram of a
substance must absorb in order to raise its
temperature one degree Celsius

So what does this mean?

It takes a long time for water to heat up and
a long time for it to cool down!
 ADDITIONAL IMPORTANT
PROPERTIES OF WATER

Heat of Vaporization – The amount of

energy required to change one gram of a
liquid substance to gas

Water has a high heat of vaporization

WATERS SOLVENT PROPERTIES

Ions and polar molecules can dissolve in

water

Water is the solvent

The compounds dissolved or mixed in with

the water are the solute
WATER CAN FORM HYDROGEN BONDS WITH OTHER POLAR
MOLECULES AND IONS

Dissociation of NaCl in water

Atoms break off from

molecules and form ions

When table salt (NaCl) is mixed in water, spheres of

hydration are formed around the ions.
 COHESION IN WATER

Cohesion
Water molecules at the
liquid-gas interface
stick together due to
hydrogen bonding

https://bealbio.wikispaces.com/Period+2+Chem+ch+3
COHESION ALLOWS FOR DEVELOPMENT OF SURFACE TENSION

Surface Tension: capacity of a

substance to withstand being
ruptured when placed under
tension or stress

The weight of the needle is pulling the surface downward; at the same time, the surface
tension is pulling it up, suspending it on the surface of the water and keeping it from
sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker)
WATER EXHIBITS UNIQUE PROPERTIES
Capillary action in a glass tube is caused
by the adhesive forces exerted by the
internal surface of the glass exceeding
the cohesive forces between the water
molecules themselves. (credit:
modification of work by Pearson-Scott
Foresman, donated to the Wikimedia
Foundation)

Adhesion – An attraction between water

molecules and other molecules

Water moves up tube because the

molecules of water are attracted to the
charged surface of the glass tube
THE COHESIVE PROPERTY OF WATER CAN BE OBSERVED IN THE
NATURAL WORLD

Water’s cohesive and adhesive properties allow this water strider (Gerris sp.) to stay
afloat. (credit: Tim Vickers)
PH, BUFFERS, ACIDS AND BASES

The pH of a solution indicates acidity or alkalinity

Small percentage of water molecules dissociate (ionize) into
equal number of hydrogen ions (H+) and hydroxide ions (OH-)

H2O(I) H+ (aq) + OH- (aq)

Concentration of H+ ions in pure water = 1 X 10-7 moles/liter

Concentration of OH- ions in pure water = 1 X 10-7 moles/liter

Solutions with high H+ concentration are acidic

Solutions with high OH- concentration are alkaline (basic)
The pH of a solution indicates its acidity
or alkalinity

H2O(I)↔H+(aq)+OH−(aq)

pH is related to concentration of H+ ions

in the solution

pH is the negative of the base 10

logarithm of the [H+]

The log10 of 1 X 10-7 is -7, and the negative

of that number is 7

Neutral solution has a pH of 7

Acidic solutions have pH<7

Basic solutions have pH > 7

Buffers play a key role in maintaining the
internal solutions of an organism at near
neutral pH

FIGURE 2.20
This diagram shows the body’s buffering of blood pH
levels. The blue arrows show the process of raising pH as
more CO2 is made. The purple arrows indicate the reverse
process: the lowering of pH as more bicarbonate is
created.
CARBON

By the end of this section, you will be able to:

1. Explain why carbon is important for life
2. Describe the role of functional groups in
biological molecules
CARBON IS AN ESSENTIAL ATOM OF LIFE

• Carbon – key component of macromolecules

(proteins, carbohydrate, lipids and nucleic acids)

• Carbon is unique
• It can form covalent bonds with up to four
different atoms
• This allows it to serve as the “backbone” for
the macromolecules
• Each carbon has four electrons in the outer
shell
• It forms four covalent bonds to “fill” the outer
shell
• This allows it to achieve the “octet rule”
 HYDROCARBONS

Hydrocarbons = carbon + hydrogen (e.g. methane)

Covent bonds between atoms in hydrocarbons store energy

This energy is released when these molecules are burned

The energy released from these

hydrocarbons heats our homes
and powers our cars
 Methane – binds to four
hydrogens to satisfy the
octet rule

Methane has a tetrahedral geometry, with each of the four

hydrogen atoms spaced 109.5° apart.
HYDROCARBON CHAINS
AKA ALIPHATIC HYDROCARBONS

carbon forms single bonds with other atoms - shape is tetrahedral.

two carbon atoms form a double bond - shape is planar, or flat.
Single bonds, like those found in ethane, are able to rotate.
Double bonds, like those found in ethene cannot rotate, so the atoms
on either side are locked in place.
HYDROCARBON RINGS
AKA AROMATIC HYDROCARBONS
FIGURE 2.23

Carbon can form five-and six membered rings (closed chain)

Single or double bonds may connect the carbons in the ring
Nitrogen may be substituted for carbon

Benzene is a particularly important hydrocarbon ring – used in some

amino acids, cholesterol and its derivatives.
ISOMERS

Isomers - molecules that have

the same chemical formula but
differ in placement/arrangement
of atoms or types of bonds
between atoms

1. Structural isomers - have a

different covalent
arrangement of atoms.
2. Geometric isomers - have a
different arrangement of
atoms around a double bond
3. Enantiomers - molecules
that share chemical formula
and bonds but differ in 3D
placement of atoms; mirror
images
 TRANS VS. CIS MOLECULES

Trans configuration
Carbons are on
opposite sides of
Some long chain hydrocarbons can double bond
have one or more double bonds

Fatty acids with double bond are

unsaturated
Cis configuration
Carbons on same
Fatty acids with no side of double bond
double bonds are saturated

These space-filling models show a cis (oleic acid) and a trans (eliadic
acid) fatty acid. Notice the bend in the molecule cause by the cis
configuration.
A CLOSER LOOK AT ENANTIOMERS

D-alanine and L-alanine are examples of enantiomers or mirror

images

You cannot superimpose these two structures on each other

Only the L-forms of amino acids are used to make proteins

FUNCTIONAL GROUPS

Functional Groups – groups of

atoms within a molecule that
confer consistent specific
properties to these molecules

Each of the four types of

macromolecules has its own set
of characteristic functional
groups

Functional groups often interact

with other functional groups via
hydrogen bonds
Study this table to become
familiar with some of the more
important functional groups
HYDROGEN BONDS BETWEEN FUNCTIONAL
GROUPS HELPS STABILIZE BIOLOGICAL MOLECULES AND ALLOWS THEM TO PERFORM THEIR BIOLOGICAL
FUNCTION

Hydrogen bonds - connect two strands of DNA together to

create the double-helix structure
DNA structure is vital for DNA function!