Matter & Energy:

Matter & Energy:
The Structure of Matter & Chemical Bonds

EVPP 110 Lecture
GMU
Dr. Largen

Sections

Atoms & molecules
Properties of Water
Rearrangements of Atoms

Atoms and Molecules

Atoms & Molecules -
Biological function starts at chemical level

reductionist approach

scientific approach

whole best understood by studying parts

Atoms & Molecules -
Biological function starts at the chemical level

to understand chemical structure and function
start small

structures at each level are combined into each higher level

note the hierarchical aspect of this idea

matter in all living things
made up of chemicals
structure and function

interrelated at every level

example
certain atoms come together to form complex molecule chlorophyll
many chlorophyll molecules are located in organelles called chloroplasts
many chloroplasts are located in cells of photosynthetic tissues in structures (organs) such as leaves of plants

Figure 2.1 The hierarchy of biological order from atom to organism (Biology, 6th Ed., Campbell & Reece)

Atoms & Molecules -
Life requires about 25 chemical elements

life is composed of matter
matter is composed of chemical elements

Matter

mass – amount of a substance

weight – force gravity exerts on substance

Matter

gas

liquid

solid

chemical element
substance which cannot be broken down into any other substance

each element consists of one type of atom

naturally occurring elements

92 naturally occurring

man-made elements

additional 12 - 17 man-made elements

distribution of elements (non-living vs. living)
in crust of earth (non-living)

9 elements constitute ~99% (by mass) of earth’s crust

distribution of elements (non-living vs. living)
in living organisms

of 92 naturally occurring elements
~ 25 are essential to life

14 of which are found in organisms in any more than trace (>0.01%) amounts
trace elements

of 25 elements essential to life
11 are found in > than trace amounts

4 make up ~96% of human body

C

H

O

N

7 make up remaining ~4% of human body
Ca, P, K, S, Na, Cl,Mg

Table 2.1 Naturally Occurring Elements in the Human Body (Biology, 6th Ed., Campbell & Reece)

Each element has a symbol

examples
gold (Au) - from Latin word aurum

oxygen (O) - from English word oxygen

Elements combine to form molecules and compounds

element

molecule

compound

element
can’t be broken down

atoms with same atomic number

molecule

group of atoms of same type held together

example

molecule of oxygen (O₂)

compound
molecule containing atoms of 2 or more elements combined in a fixed ratio
example

water
H₂O

more common than pure elements

example., table salt (NaCl)
in living organisms

contain at least 3 or 4 different elements
mainly C, H, O, N

Figure 2.2 The emergent properties of a compound (Biology, 6th Ed., Campbell & Reece)

described by combination of symbols and numerals

chemical formula (or molecular formula)

structural formula

chemical formula or molecular formula

consists of chemical symbols and numbers

example

chemical formula for water is H₂O

structural formula
shows arrangement of atoms

example

structural formula for water is H-O-H

Each element consists of one kind of atom

"atom" from Greek word meaning "indivisible"

atom is smallest unit of matter

atoms
composed of many types of subatomic particles

nucleus contains

protons

neutrons

electrons orbit nucleus
others particles

discussed primarily by physicists

Atoms consist of protons, neutrons and electrons

protons (p)

type of charge =
where found =
relative mass =

neutrons (n)

type of charge =
where found =
relative mass =

electrons (e)

type of charge =

relative mass =

where found =

Electron orbitals can be
various shapes

electrons orbit nucleus

Electron orbitals

arrangement of electrons in their orbits

is key to chemical behavior of atom

will return to this point shortly
All atoms of a particular element
have same unique number of protons

known as the element’s

atomic number

number of protons in atom’s nucleus
top number in box for element in periodic table

atom’s atomic mass (also called atomic weight or mass number)

equal to sum of masses of atom’s protons & neutrons

measured in daltons

bottom number in box for element in periodic table

isotopes

atoms of same element that vary in neutron number and atomic mass

isotopes of carbon

carbon ¹²C
carbon ¹³C
carbon ¹⁴C

Isotopes can be

stable

nuclei remain permanently intact

unstable (or radioactive)

nuclei decays spontaneously, giving off particles and energy

Isotopes can be

unstable (or radioactive)

nucleus tends to break up into elements with lower atomic numbers
emits significant amount of energy, called radioactive decay

radioactive isotopes

Radioactive isotopes can be
harmful to life

Radioactive isotopes can have
beneficial uses

Electrons
orbit nucleus of atom
arrangement in orbits is key to chemical behavior of atom
vary in amount of energy they possess

farther nucleus, greater its energy

electrons are far from nucleus
analogy:
result

electrons in atom occur only at certain energy levels
called electron shells (or electron energy levels)
atoms may have 1, 2 or more electron shells

first four electron energy shells

covers most biologically significant elements
first, innermost energy shell

can accommodate only 2 electrons

second, third, fourth energy shells

can each accommodate 8 electrons

atom has # of electron shells needed accommodate its number of electrons

atom with 6 electrons (C) has 2 shells
2 electrons in innermost shell
4 electrons in outermost shell
atom with 11 electrons (Na) has 3
2 electrons in innermost shell
8 electrons in second shell
1 electron in outermost shell

Energy
required to keep electrons in their orbits

electrons have potential energy of position
more potential energy in outermost shells than in innermost shells

number of electrons in outermost shell
determines chemical properties of element

partially full outer shells = reactive
full outer shells = unreactive (inert)

example
hydrogen (H) is highly reactive

one shell, only one electrons

example
helium (He) is highly unreactive (inert)

one shell, two electrons

How does a chemical reaction enable an atom to fill its outer electron shell?
2 atoms w/incomplete outer shells react

each atom gives up or acquires electrons

results in atoms being held together by chemical bonds

strong chemical bonds

ionic bonds

covalent bonds

nonpolar covalent bonds

polar covalent bonds

weak chemical bonds

hydrogen bonds

electron transfer between 2 atoms moves 1 unit of negative charge from one atom to other
original atom now has +1

recipient atom now has charge of -1

ions
atoms in which number of electrons does not equal number of protons

carry a net electrical charge (+ or - )

types of ions

cations
anions

cation
atom with net positive charge (+)

example:

sodium (Na) atom losses an electron, becomes sodium ion, or cation (Na⁺), with charge of +1

Anion

atom with net negative charge (-)

example

chlorine (Cl) atom, gains one electron, becomes chlorine ion, or anion (Cl^-), with charge of -1

two ions with opposite charge attract each other
attraction called an ionic bond

resulting compound is electrically neutral

ionic bond
results from transfer of electron from one atom to another atom

resulting in two ions
cation
anion

oppositely charged ions are attracted to each

resulting compound is electrically neutral

covalent bond
occurs when two atoms share one or more pairs of outer shell electrons

results in both atoms having a full outer electron shell

why is a covalent bond so stable?
resulting molecule (compound)

has no net electrical charge

outer shells are full
no free electrons to form bonds

More than one covalent bond can form between two atoms
single covalent bond
double covalent bond
triple covalent bond

single covalent bond

one pair of electrons shared by two atoms
represented by

example, H - H

least strong of covalent bonds

double covalent bond

two pairs of electrons shared by two atoms

represented by
example, O=O

stronger than single covalent bond

triple covalent bond

three pairs of electrons shared by two atoms

represented by
example, N = N

strongest covalent bonds

covalent bond energy
forming bond requires input of energy

energy is stored in bond

breaking bond results in release of energy

released energy becomes available to do work

Covalent bonds, polar versus non-polar

Atoms in a covalently bonded molecule
in tug-of-war for shared electrons

electronegativity

measure of attraction (affinity) for shared electrons in covalent bond

stronger electronegativity = stronger pull on shared electron

Because of concept of electronegativity,

covalent bonds can be divided into two categories

nonpolar covalent bonds

polar covalent bonds

nonpolar covalent bond
covalent bond between atoms with similar electronegativity
result, electrons are shared equally between two atoms
examples

O₂
H₂
CH₄(methane)

polar covalent bond
a covalent bond between atoms that differ in electronegativity

atom with greater electonegativity pulls shared electrons closer

results in bond has two dissimilar ends

"poles", with partial + and partial - charges

resulting molecules are said to be "polar"
example = H₂ O

hydrogen bonds

result when polar molecules interact with one another
partial – charge of one molecule is attracted to the partial + charge of another molecule
in the case of water:

oxygen is very electronegative

The End