Chapter 2: The Chemical

Level of Organization

Matter
Matter anything that has weight and
takes up space.
Includes solids, liquids, and gases

All matter is composed of elements.

There are 112 known elements
Ex. Iron, copper, silver, aluminum, carbon,
hydrogen, oxygen

Matter and Living Organisms

Living organisms require about 20
elements.
Of these, oxygen, carbon, hydrogen
and nitrogen make up more than 95%
of the human body.

Atoms

Elements are composed of

tiny particles called atoms.
Atoms are the smallest
complete units of elements.
Atoms vary in size, weight,
and the ways they interact
with each other.

Nucleus

Protons (+) and neutrons

(neutral) are found on the
atoms nucleus, while electrons
(-) circle the nucleus.
Atomic number - # of protons
Atoms with the same atomic number belong to the same
element, and thus have the same inherent properties.

Atoms

Atomic Weight
Mass refers to the amount of a substance.
Weight refers to the force exerted on a
substance by gravity.
Atomic mass of an atom refers to the sum of
the masses of protons and neutrons.
1 Proton
1 Neutron
1 Electron 1/1840 of that size - negligible

Isotopes

Isotopes - Atoms of an element that possess

a different number of neutrons. Have the
same atomic # b/c # of protons stays the
same
Radioactive isotopes - Spontaneously decay into
elements of lower atomic number.
emit energy and/or subatomic particles
Half-life refers to the amount of time necessary to decay
half the atoms of a given sample.

Electrons
Atoms with the same
number of protons as
electrons are electrically
neutral.
Ions - Atoms in which the
number of protons and
electrons differ.
Cation - Contains more
protons than electrons, and
carries a positive charge.
Anion - Contains fewer
protons than electrons, and
carries a negative charge.

Electrons and Atomic Behavior

Orbital refers to the area around a nucleus

where an electron is most likely found.
Chemical behavior of an atom is determined by
the number and arrangement of its orbitals.
Electrons are attracted to the positively charged
nucleus, thus it takes energy to hold electrons in place.
potential energy of position

Atomic Energy Levels (Orbitals)

Electrons can absorb energy and release energy

8e

8e

2e

Elements?
Electrons of various atoms

Electrons and Atomic Behavior

During some chemical reactions, electrons
are transferred between atoms, while still
retaining their energy of position.
Oxidation - loss of an electron
Reduction - gain of an electron

Kinds of Atoms
~112 Known elements
Ninety-two naturally occurring
Periodic table arranged by grouping atoms based
on valence electrons (electrons in the outer energy
levels).
Russian chemist Dmitri Mendeleev in 1869.
Octet rule
Most atoms important to life can contain no more
than 8 electrons
Inert atoms have outer level filled.
Reactive atoms do not have outer level filled.

Periodic Table of the Elements

Elements in the Human Body

Table 21

Chemical Bonds
A molecule refers to a group of atoms held
together by energy in a stable association. O2
Compound is composed of two or more
different types of atoms bond together. NaCl
Atoms in a molecule are joined by chemical
bonds.

Chemical Bonds
Ionic bonds are
formed
because ions of
opposite
charge attract
one another.
table salt
Sodium Na+
Chlorine Cl-

 Covalent bonds
are formed when
two or more
atoms share pairs
of valence
electrons.
Strength depends
on number of
shared electrons.
Share one = single
bond, share two =
double bond =
share three =
triple bond

Hydrogen Bonding
In a water molecule, both the oxygen and
hydrogen atoms attract the shared
electrons in the covalent bond
(electronegativity).
Oxygen atom is more electronegative than the
hydrogen atoms.

Chemical Reactions
A chemical reaction occurs during the
formation or breaking of chemical bonds.
Chemical reactions can be influenced by:
temperature
concentration of reactants and products
catalysts

Energy

Energy - the power to do work

Work - a change in mass or distance

Energy exists in 2 forms

Kinetic energy - energy of motion
Potential energy - stored energy
Chemical energy - potential energy stored in
chemical bonds. ATP
Electrical energy movement of charged particles
Mechanical energy moving matter
Radiant energy electromagnetic (energy in waves)

Break Down, Build Up

Decomposition reaction (catabolism):
AB A + B
Synthesis reaction (anabolism):
A + B ->AB
Exchange reaction (reversible):
AB A + B

Water In, Water Out

Hydrolysis:
ABCDE + H2O ABCH + HODE

Dehydration synthesis (condensation):

ABCH + HODE ABCDE + H2O

Energy In, Energy Out

Exergonic reactions:
produce more energy than they use

Endergonic reactions:
use more energy than they produce

What is the difference between

organic and inorganic compounds?
Organic and Inorganic Molecules
Organic:
molecules based on carbon and hydrogen

Inorganic:
molecules not based on carbon and hydrogen

Nutrients:

Essential Molecules

essential molecules obtained from food

Metabolites:
molecules made or broken down in the body

Why is water so important to life?

Properties of Water

Solubility:

waters ability to dissolve a solute in a solvent to

make a solution

Reactivity:
most body chemistry uses or occurs in water

High heat capacity:

waters ability to absorb and retain heat

Lubrication:
to moisten and reduce friction

KEY CONCEPT
Most of our body weight is water 2/3
Water is the key structural and functional
component of cells and their control
mechanisms, the nucleic acids

Aqueous Solutions

Polar water molecules form hydration spheres

around ions and small polar molecules to keep
them in solution

Figure 28

Electrolytes
Inorganic ions which conduct electricity in
solution
Electrolyte imbalance seriously disturbs vital
body functions

Molecules and Water

Hydrophilic:

hydro = water, philos = loving

reacts with water

Hydrophobic:
phobos = fear
does not react with water

Solutions
Concentration:
the amount of solute in a solvent (mol/L, mg/mL)

What is pH and why do we need buffers?

pH:
the concentration of hydrogen ions (H+) in a
solution

Neutral pH:
a balance of H+ and OH
pure water = 7.0

Acids and Bases

Acid (acidic): pH lower than 7.0

high H+ concentration,
low OH concentration

Base (basic): pH higher than 7.0

low H+ concentration,
high OH concentration

pH Scale
Has an inverse
relationship with H+
concentration:
more H+ ions mean
lower pH, less H+
ions mean higher pH

pH of body fluids measures free H+ ions in solution

Excess H+ ions (low pH):
damages cells and tissues
alters proteins
interferes with normal physiological functions

Excess OH ions (high pH) also cause problems, but

rarely
Figure 29

 Acidosis:

Acid and Alkaline

excess H+ in body fluid (low pH)

Alkalosis:
excess OH in body fluid (high pH)

Salts:

Controlling pH

positive or negative ions in solution

contain no H+ or OH (NaCl)

Buffers:
weak acid/salt compounds
neutralizes either strong acid or strong
base

What kinds of organic compounds are

there, and how do they work?

Functional Groups
Molecular groups which allow molecules to
interact with other molecules

Carbohydrate Functions

Monosaccharides: simple sugars with 3 to 7

carbon atoms (glucose)
Disaccharides: 2 simple sugars condensed by
dehydration synthesis (sucrose)
Polysaccharides: Chains of many simple sugars
(glycogen)
Carbohydrates are quick energy sources and
components of membranes
Table 25

Lipids

Mainly hydrophobic molecules such as fats,

oils, and waxes
Made mostly of carbon and hydrogen atoms
Lipids have many functions, including
membrane structure and energy storage

Classes of Lipids

 Fatty acids may be:

saturated with hydrogen (no
covalent bonds)
unsaturated (1 or more double
bonds)

Types of Eicosanoids
Leukotrienes: active in immune system
Prostaglandins: local hormones, short-chain fatty
acids

 Glycerides: are the fatty

acids attached to a
glycerol molecule
Triglyceride: are the 3 fattyacid tails, fat storage
molecule

Steroids

Cholesterol: component of
cell membranes
Estrogens and
testosterone: sex hormones
Corticosteroids and
calcitrol: metabolic
regulation
Bile salts: derived from
steroids

Figure 215

 Phospholipids and Glycolipids

Have hydrophilic heads and hydrophobic tails
Are structural lipids, components of cell
membranes

Protein Structure

Proteins are the most abundant and important

organic molecules
Basic elements: carbon (C), hydrogen (H), oxygen
(O), and nitrogen (N)
Basic building blocks: 20 amino acids

Protein Functions

7 major protein functions:

support: structural proteins

movement: contractile proteins
transport: transport proteins
buffering: regulation of pH
metabolic regulation: enzymes
coordination and control: hormones
defense: antibodies

Amino Acid Structure

1.
2.
3.
4.

central carbon
hydrogen
amino group (NH2)
carboxylic acid
group (COOH)
5. variable side chain
or R group

Peptide Bond

A dehydration
synthesis between:
the amino group of 1
amino acid
and the carboxylic
acid group of
another amino acid
producing a peptide

Primary Structure
Polypeptide: a long chain of amino acids

Secondary Structure

Hydrogen bonds form spirals or pleats

Figure 220a

Tertiary Structure

Secondary structure folds

into a unique shape

Quaternary
Structure
Final protein shape:
several tertiary
structures together
Figure 220c

Shape and Function

Protein function is based on shape
Shape is based on sequence of amino acids
Denaturation: loss of shape and function due to heat
or pH

Protein Shapes
Fibrous proteins: structural sheets or strands
Globular proteins: soluble spheres with active
functions

Enzymes

Enzymes are catalysts:

proteins that lower the activation energy of a chemical
reaction
are not changed or used up in the reaction
How Enzymes Work
Substrates: reactants in enzymatic reactions
Active site: a location on an enzyme that fits a particular
substrate

How do enzymes control metabolism?

Activation Energy

Chemical reactions in cells cannot start without help

Activation energy gets a reaction started
Materials in Reactions
Reactants:
materials going into a
reaction
Products:
materials coming out of a
reaction
Enzymes:
proteins that lower the
activation energy of a
reaction

Enzyme Helpers

Cofactor:
an ion or molecule that binds to an enzyme before
substrates can bind
Coenzyme:
nonprotein organic cofactors (vitamins)
Isozymes:
2 enzymes that can catalyze the same reaction

Enzyme Characteristics

Specificity:
one enzyme catalyzes one reaction
Saturation limits:
an enzymes maximum work rate
Regulation:
the ability to turn off and on

Nucleic Acids
Large organic molecules, found in the nucleus, which
store and process information at the molecular level
DNA and RNA

Deoxyribonucleic Acid (DNA)

Determines inherited characteristics

Directs protein synthesis
Controls enzyme production
Controls metabolism

Ribonucleic Acid (RNA)

Codes intermediate steps in protein synthesis

The Bases

Complementary Bases

Complementary base pairs:

purines pair with pyrimidines:

DNA: adenine (A) and thymine (T) and cytosine
(C) and guanine (G)
RNA: uracil (U) replaces thymine (T)

Nucleotides

Are the building

blocks of DNA
Have 3 molecular
parts:
sugar
(deoxyribose)
phosphate group
nitrogenous base
(A, G, T, C)

High Energy Compounds - ADP and ATP

adenosine
diphosphate (ADP):
2 phosphate groups

adenosine
triphosphate (ATP):
3 phosphate groups

Phosphorylation
Adding a phosphate group to ADP with a high-energy
bond to form the high-energy compound ATP
ATPase: the enzyme that catalyzes phophorylation