Chemsitry of Life

Chp 2-4

Living Organisms
Living organisms are Composed of Elements,

Molecules and Matter

Organisms have proteins that differ across species
1. Hemoglobin vs Hemocyanin as oxygen-

transporting proteins
1. Very similar
2. Iron binds Oxygen Hemoglobin
3. Copper binds Oxygen Hemocyanin

2. Macroscopic properties of organisms differ

because elements making up the related

molecules differ
1. Organisms are composed of molecules elements

The study of atoms, elements, molecules, and

matter is the realm of chemistry

. basic concepts of chemistry is essential for

understanding how biological processes work

Elements and Atoms

Element A pure substance that cannot

be broken down into simpler substances

by chemical means
1. Carbon, Gold, Phosphorus. Helium,

Oxygen etc
2. Substance is made up of only one KIND of
atom

Atom Smallest amount of an element

that has the chemical and physical

properties of that element
1. Two or more atoms linked together by a

covalent bond is called a Molecule

a. Each molecule of the oxygen we
breathe is composed of 2 atoms of
elemental oxygen linked covalently .

Compound contains 2 or more different

elements combined in a fixed ratio

1.

Water 2 atoms of hydrogen and one

atom of
oxygen (H2O)

Elements and Atoms

Compound molecule that contains 2 or more different

elements combined in a fixed ratio

NOTE: Will have different characteristics form those of its

elements

Elements and Atoms

Living organisms have 4 essential elements necessary for an

organisms survival
1.
2.
3.
4.

Oxygen
Carbon
Hydrogen
Nitrogen

makes up 96% of all

matter found in
organisms

All organisms require different amounts of

each element
1. Humans require 25 total elements in

different quantities
2. Trace element element needed in tiny quantities.

Iodine.. Normal function of thyroid

Elements and Atoms

All atoms differ from one another, but they all have

the same characteristics (3 sub-atomic particles)

1. Protons + charged particles in the nucleus of an

atom
2. Neutrons neutral particles in the nucleus
3. Electrons neg. charged particles surrounding the
nucleus

Electron Shells and Clouds (most of the space of an atom)

1. Simple models show rings of electrons orbiting around
the nucleus representing energy levels (atomic shells)
good way to visualize the atomic structure and

electrons

2. In reality, electrons are in constant motion within an

area surrounding the nucleus, known as an electron

cloud
3. Because electrons are constantly in motion and have
very little mass, the electron clouds, and thus atoms,
are mostly made of empty space

Most
of
the
mass

Elements and Atoms

An atomic model of any element atom can be

drawn using information from the periodic table

1. As a general rule, the number
of protons and the number of
electrons is equal
2. Atomic number tells you the
number of protons (this
number does not change for
each element; ID number of
the element)
3. Atomic mass is the AVERAGE
mass of an element and all of
its isotopes
1. Mass of an atom = neutrons
and protons
2. You already know the number
of protons from the atomic
number
3. mass number protons =

Electron shells

Elements and Atoms

1. Electrons occupy specific zones around the nucleus (shells)

2. Only a set number electrons in each shell (each shell representing a stable

energy level)*
a) 1st shell (closest to nucleus) = 2 electrons
b) 2nd and third shell = 8 electrons each
c) Electrons must fill a lower shell before it can occupy a higher shell

3. Valence electrons are located in the outermost shell of an atom

(most reactive) in the valence shell .. Determines stability and

reactivity of atom

Calcium
Protons =
20
Neutrons 20
=
20
Electrons
=
2
Valence

Elements and Atoms

Valence Shells determines an elements stability and reactivity

1. When the shell is full (complete number electrons), the element is stable and

not likely to react with another atom (like noble gases that have a full outer
shell and do not react)
2. The closer the element is on the periodic table to a noble gas, the more reactive
(ex Hydrogen vs Oxygen)

Elements and Atoms

Sharing of Valence Electrons

1. Reactivity depends on whether the valence shell is full

Highly
Reactive

Reactive

(two
removed from a noble
gas)

Stabl
e

Stabl
e

Stabl
e

Atomic Isotopes

Remember that the atomic number does not change for each
element
(Carbon always has an atomic number of 6)
1. But some elements have different mass numbers.. Such as
Carbon which can have a mass of 12, 13, or 14. What is
changing if the mass number is changing?
2. Isotopes atoms with same number of protons but different
number of neutrons (can be stable or unstable (radioactive
and undergo decay)
3. Nomenclature: The mass number of isotopes is usually
written after the element name ex: carbon-12; carbon-14,
uranium-235
4. Carbon-14 how many Protons? Neutrons? Electrons?

Chemical Bonds

Chemical bonds hold compounds together and form due to attractions

between atoms
1. attractions can result from atoms sharing valence electrons in the
outer shell (strong covalent bond)
1. Single covalent bond forms between two atoms that share one pair of

electrons
example: methane, ammonia, water
2. Double covalent bond forms from sharing two pairs of electrons

Chemical Bonds

Other types of covalent bonds

Electronegativity describes an atoms attraction for an electron
1. Nonpolar covalent bonds electrons are shared equally between
atoms
a) Example: bonds forming from atoms of the same element are always non-

polar (O2, I2, N2)

2. Polar covalent bonds When one atom has greater attraction

(electronegativity) for the electrons in the bond as compared to the

other atom
1. Forms a partial negative charge over the atom who has greater

electronegativity (electron cloud closer to its nucleus)

2. Forms a partial positive charge over the atom having lower electronegativity
(electron cloud further away from nucleus)

Chemical Bonds

Chemical bonds hold compounds together and form due to attractions

between atoms
1.

Covalent bonds
a) Single and Double
b) Polar and Non-polar

2. Hydrogen bonds weak bonds that

bring together two or more polar

covalent compounds (one of which
has a hydrogen atom) NOT DUE TO
SHARING OF ELECTRONS
a) Oxygen end of a water molecule (net

negative charge) is attracted to the

partial positive charge of the
hydrogen on the other water
molecule
b) Weak Hydrogen bonds impart many
of the unique properties of water
(well see in the next class)

3. van der Waals interactions non-

polar covalent compounds are

held loosely together by these

Chemical Bonds

Chemical bonds hold compounds together and form due to attractions

between atoms
Covalent bonds
a) Single and Double
b) Polar and Non-polar
2. Hydrogen Bonds
3. van der Waals Interactions
1.

4. Ionic bonds strong bond that forms between oppositely charged

ions
1. A very strong electronegative atom can steal one electron from a very weak

electronegative atom forming ions

a) Net negative charge results on atom that receives the electron = anion
b) Net positive charge results on atom that loses the electron = cation
2. Interactions between anions and cations form strong ionic bonds resulting in an
ionic compound
Forms a bond
not due to
a) Ionic compounds are also called salts

sharing of
electrons but
due to charges

Chemical Reactions

Occur when bonds are made or broken changing the composition of the
substance
1. chemical reactions can move forward and backward

Reactant A + Reactant B
2 H atoms + O atom

Water

When the rate of the forward

reaction equals the rate of the
reverse reaction, the reaction has
reached chemical equilibrium.
(condensation from gas to

Water

(evaporation from liquid to gas)

Product

liquid)

2 H atoms + O atom

Chemical Reactions

Occur when bonds are made or broken changing the composition of the
substance
1. chemical reactions can move forward and backward
a) Forward Photosynthesis
b) Reverse Cellular Respiration

1
ATP

Respiration

Photosynthe
sis

Organic Chemistry
Organic Compound most carbon-containing

compounds are organic and most have a

carbon-hydrogen bond (REMEMBER)
Carbon
1. Its chemical properties makes it uniquely

suited as basis for all life

2. Has four valence electrons, allowing for
single and double covalent bonds
3. Great variety of molecules that can form with
carbon

Organic Chemistry
Organic compounds not only vary

in the types of atoms they

contain, but also in
a) the length of the carbon chain
b) the position of branches in the

chain
c) the position of double bonds in
the chain
d) and whether or not the ends of
the carbon chain are linked to
form carbon rings

Ring-shaped hydrocarbons can

themselves vary based on the
position of single and double
bonds (e.g., cyclohexane versus
benzene).

Organic Chemistry
Unique binding properties allow complex

structures to form around the carbon

atom
Isomers compounds with the same

number of atoms of the same element

but configured in different structures
Receptors and enzymes recognize

specific isomers
a) many life processes depend on the
presence for one isomer over
another

Types of isomers
1) Structural C and H atoms arranged

differently
2) Cis contain identical groups on same
side of inflexible double bond
3) Trans contain identical group on

Organic Chemistry
Within organic molecules are

functional groups that are the atoms

typically involved in reactions.
The common functional groups are

hydroxyl, carbonyl, carboxyl, amino,

sulfhydryl, and phosphate.
"R" represents the rest of the molecule

bonded to the functional group.

Organic Chemistry
Polymer a long molecule

composed of many similar (or

identical) building blocks
(monomers) linked by covalent
bonds
1. Carbohydrates
2. Proteins
3. Nucleic acids