Chapter 2

CONCEPT OF MATTER AND ENERGY

Matter- is anything that occupies space (volume) and has mass

Weight- is a measure of gravity pulling on mass (SI, N)

Mass – measure of the amount of matter that an object contains (SI, Kg)

Chemistry – studies the nature of matter. The composition and the structure of matter

Matter- can be in the form of solid, liquid, gaseous state

Solid – bones, teeth, those that has a definite shape volume

Liquids – have a definite volume, but they conform to the shape of their container, body liquids, (blood
plasma and interstitial fluid

Gases – have neither a shape nor volume, e.g the air we breath is a mixture of gases.

Physical Change – do not alter the basic nature of a substance: melting, foods being cut into smaller
pieces.

Chemical Change – it alters the composition of substance – often substantially. Example: fermenting
grapes to make wine, and digestion of foods.

Energy – the ability to do work or to put matter into motion.

- has no mass and does not take up space.

- Measured by its effects on matters

Kinetic Energy – moving object, is displayed in the constant movement of the tiniest particles of matter
(atoms) , and larger objects (bouncing ball)

Potential Energy – energy is inactive or stored in batteries.

* ** All forms of energy exhibit both kinetic and potential capacities.

***Matter is the substance; while the energy is the mover of the substance.

FORMS OF ENERGY

1. Chemical Energy – stored in the bonds of chemical substances. When the bonds are broken
stored energy is unleashed and becomes energy in action.
- The chemical energy from the foods we eat fuels all the body activities
2. Electrical Energy – results from the movement of charged particles.
- Electrical current is generated in the body when charged particles (IONS) move across the
cell membrane.
- Nerve Impulses - the electrical currents use by Nervous system to transmit message from
one part of the body to another.
3. Mechanical Energy – energy that’s directly involved in moving matter, Example: Pedal a bicycle.
4. Radiant Energy – travels in waves, it is the energy of the electromagnetic spectrum, includes X
rays, infrared radiation (heat energy), visible light, radio, UV waves. Example: Light energy that
stimulates the retinas of the eyes – important in vision, UV waves caused sunburn, but also
stimulates bodies to make Vitamin D.

ENERGY FORMS CONVERSIONS

Chemical energy from food is trapped in the bonds of high energy (ATP) → transformed into Electrical
energy of a nerve impulses/mechanical energy of contracting muscles.

- (not all conversion is efficient, those energy that are excess and unusable becomes heat or
thermal energy – this makes us a warm blooded animal, our body temperature increases.
COMPOSITION OF MATTER

Elements – unique substances that cannot be broken down into simpler substances by ordinary chemical
methods

- 118 elements = 92 occur in nature, the rest are made artificially in accelerator devices.
- Periodic table
o Carbon, Hydrogen, Oxygen, and Nitrogen – CHON – make up about 96.1% of the
weight of the human body.
 CHON- Most abundant element found in the human body

Bulk elements – required by the body large amounts

lesser elements – required by the body in small amounts

trace elements – required by the body in a very minute amount.

Atoms – building blocks of elements, ONE element is composed of very similar particles,

- Element is unique, the atoms are similar inside 1 element but the atom of each elements
differ from those other elements.
- Atomic Symbol – a chemical shorthand for each element instead of writing it as a full name
of element.
- Atoms – (Greek word) incapable of being divided

Atomic Structure

Subatomic particles – atom is cluster of more even smaller components; includes protons, neutrons,
and electrons

*an atom loses the unique properties of its element when it is split into its component particles.

*the electrical charge of a particle is measure of its ability to attract or repel other charged particles. (+
to + or  to ) repel each other; particles with opposite charges (+ to ) attract each other.

* Neutral particles are neither attracted to nor repelled by charge particles

Sub atomic Particles

- All atoms are electrically neutral

- Number of Protons = (equals) Numbers of Electrons in an atom (balanced)

- Positive and Negative charges then cancel the effect of each other.
- IONS – atoms that have gained or lost electrons

Planetary model

 Portrays the atom as a miniature solar system

 Protons and neutrons are in the nucleus
 Electrons are in orbitals
 The planetary model is simple and easy to understand and use

Orbital model

More modern
Predicts chemical behavior of atoms
Electrons are depicted by an electron cloud, a haze of negative charge, outside the nucleus
*Electrons determine an atom’s chemical behavior

Identifying Elements

What determines the unique properties of each elements?

- Atoms of different element are composed of different number of protons, neutrons and
electrons., unique.

Hydrogen – smallest and simplest atom, has one proton, one electron, and no neutrons

Helium – two protons, two neutrons, and two orbiting electrons

Lithium – three protons, four neutrons, and three electrons

*increasing up add one proton and one electron at each step, Neutrons light atoms tend to have equal
numbers of protons and neutrons, while in larger atoms outnumber protons.

Atomic Number – equal to the number of protons its atoms contains, atomic number of each element is
unique. Indirectly tells the number of electrons in an atom

Atomic Mass Number – sum of the masses of all the protons and neutrons contained in an atom’s
nucleus

*The mass number is written as a superscript to the left of the atomic symbol.
Atomic Weight and Isotopes

Atomic weight = atomic mass or mass number of its most abundant isotopes.
- Close to mass number of most abundant isotope
- Atomic weight reflects natural isotope variation
-

Isotopes

- All elements exhibit two or more structural variation

- Have the same number of protons and electrons
- Vary in the number of neutrons
- Isotopes of an element have the same atomic number but different atomic masses

Radioisotopes

- Heavy isotope of certain atoms is unstable

 - Tend to release energy in order to become more stable
- Used in a minute amounts to tag biological molecules so that they can be followed, or traced
through the body
- Valuable tools for medical diagnosis and treatment

Radioactivity – process of spontaneous atomic decay

- All types of radioactive decay involved ejection of particles of alpha or beta particles or
electromagnetic energy (gamma rays)
- Alpha – least penetrating
- Gamma radiation - has the most

Molecules and Compounds

Molecules – two or more atoms of the same elements combined chemically.

Example of a chemical reaction resulting in a molecule:

H (atom)  H (atom)  H2 (molecule) [chemical equation]

 The reactants are the atoms on the left

 The product is the molecule on the right represented by a molecular formula/molecular

hydrogen

Compounds – two or more different atoms bind together to form a molecule

Example of a chemical reaction resulting in a compound:

1. 4H + C  CH4 (methane)
2. Na (Silvery metal) + Cl (poisonous gas)  Sodium Chloride (NaCl) table salt

Chemical Bonds and Chemical Reactions

Chemical Reactions – chemical reactions occur when atoms combine with or dissociate from other
atoms

- Atoms are united by chemical bonds

- Atoms dissociate from other atoms when chemical bonds are broken

Bonds Formation

Chemical Bond – is not an actual physical structure. Am energy relationship that involves interaction
between the electrons of reacting atoms.

Role of Electrons

Electron Shells or Energy levels – orbits, maximum number of electron shells in any atom known so far is
seven, numbered 1 to 7 from the nucleus outward.

- Electrons occupy energy levels called electron shells (levels)

- Electrons closest to the nucleus are most strongly attracted to its positive charge, farther
away are less securely held.
o The more distant electrons are most likely to interact with other atoms. Electron shell
furthest from the nucleus will also the first come into contact to reacting or bonding.
- Each shell has distinct properties
- The number of electrons has an upper limit
- Shells closest to the nucleus fill first
Valence Shell – outermost shell

Valence Electrons – electrons that is in the valence shell

*Bonding behavior involves only interactions between electrons in the outermost (valence) shell

*Atoms with full valence electrons do not form bonds

Inert – Atoms are completely stable and the outermost (valence) shell has 8 complete electrons and is
chemically inactive

• How to fill the atom’s shells:

• Shell 1 can hold a maximum of 2 electrons

• Shell 2 can hold a maximum of 8 electrons

• Shell 3 can hold a maximum of 18 electrons

• Rule of eights – key to chemical reactivity

• Atoms are considered stable when their outermost orbital has 8 electrons

• The exception to this rule of eights is shell 1, which can hold only 2 electrons

Reactive Elements

 Outermost valence shell is incomplete or less than 8 electrons

 Atoms will gain, lose, or share electrons to complete their outermost orbitals

• Atoms reach a stable state

• Bond formation produces a stable valence shell

Types of Chemical Bonds

1. Ionic bonds

 Form when electrons are completely transferred from one atom to another

 Allow atoms to achieve stability through the transfer of electrons

• Ions- Result from the loss or gain of electrons

• Anions have negative charge due to gain of electron(s), less protons, indicated
by a minus sign e.g (Cl-) – Chloride Ion

• Cations have positive charge due to loss of electron(s), more protons,

represented by their atomic symbol plus sign e.g (H+) – Hydrogen Ion

 Tend to stay close together because opposite charges attract

Formation of Ionic Bond

2. Covalent bonds

 Electron do not have to become completely lost or gained for atoms to become stable
 Atoms become stable through shared valence electrons (Covalent molecules)
 Electrons are shared in pairs
 Single covalent bonds share one pair of electrons
 Double covalent bonds share two pairs of electrons
Covalent Bonds
• Covalent bonds are either nonpolar or polar
1. Nonpolar covalent molecules
• Electrons are shared equally between the atoms of the molecule
• Electrically neutral as a molecule
• Example: carbon dioxide

Molecular models illustrating the three-dimensional structure of carbon dioxide

2. Polar
• Electrons are not shared equally between the atoms of the molecule
• Molecule has a positive and negative side (2 charged), or pole
• Example: water
• Orient themselves toward other polar molecules or charged particles (ions,
proteins, and others)
Molecular models illustrating the three-dimensional structure of water

Hydrogen Bonds

 Extremely weak chemical bonds

 Hydrogen is attracted to the negative portion of a polar molecule
 Results in unequal distribution of hydrogen molecules
 Provides attraction between molecules, e.g. hydrogen atom bound to one “electron-hungry” nitrogen
or oxygen then forms a bridge between them
 Responsible for the surface tension of water
 Important for forming intramolecular bonds, as in protein structure
• They help to bind different parts of the same molecule together into a special three-
dimensional shape

Hydrogen bonding between polar water molecules

Patterns of Chemical Reactions

• Synthesis reaction (A  B  AB)

• Atoms or molecules combine
• Energy is absorbed for bond formation
• Underlies all anabolic activities in the body
• important for growth and for repair of worn out damaged tissue. E.g. AA →
Proteins
• Decomposition reaction (AB  A  B) – synthesis reaction reverse
• Molecule is broken down
• Chemical energy is released
• Underlies all catabolic activities in the body
• Ex: digestion of foods into building blocks
• Breakdown of glycogen to release glucose

• Exchange reaction (AB  C  AC  B and AB  CD  AD  CB)

• Involves both synthesis and decomposition reactions as

bonds are both made and broken

• (during) Switch is made between molecule parts (changing

partners), and different molecules are made

Reversible Reaction

• Most chemical reactions are reversible

• Reversibility is indicated by a double arrow

• When arrows differ in length, the longer arrow indicates the more rapid reaction or
major direction of progress
Biochemistry: The Chemical Composition of Living Matter

• Inorganic compounds
• Lack carbon
• Tend to be small, simple molecules
• Include water, salts, and some acids and bases
• Organic compounds
• Contain carbon
• All are large, covalently bonded molecules
• Include carbohydrates, lipids, proteins, and nucleic acids

Important Inorganic Compounds

1. Water

• Most abundant inorganic compound in the body

• Vital properties

a) High heat capacity

b) Polarity/solvent properties

c) Chemical reactivity

d) Cushioning

a) High heat capacity: water absorbs and releases a large amount of heat before it changes
temperature
Prevents sudden changes in body temperature
Otherwise: intense sun exposure, chilling winter winds, or internal events (such as vigorous
muscle activity) that liberate large amounts of heat.
b. Polarity/solvent properties: water is often called the “universal solvent”
• Solvents are liquids or gases that dissolve smaller amounts of solutes
• Solutes are solids, liquids, or gases that are dissolved or suspended by solvents
• Solution mixtures forms when solutes are very tiny; Suspension when solute particles
are fairly large.
• Colloid forms when solutes of intermediate size form a translucent mixture
c. Chemical reactivity
Water is an important reactant in some chemical reactions
Reactions that require water are known as hydrolysis reactions
Example: water helps digest food or break down biological molecules
d. Cushioning
Water serves a protective function
Examples: cerebrospinal fluid protects the brain from physical trauma, and amniotic fluid
protects a developing fetus
2.