Chapter 3
Chemistry of Life
Vocabulary
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Atom
Element
Valence electron
Compound
Molecule
Ion
Cohesion
Adhesion
Solution
Acid
Base
pH
Buffer
Carbohydrate
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Lipid
Protein
Amino acid
Nucleic acid
Nucleotide
DNA
RNA
ATP
Energy
Reactant
Product
Activation energy
Enzyme
Active site
substrate
Standard 2: Students know and
understand common properties, forms,
and changes in matter and energy.
• Benchmark 2.1: Elements can be
organized by their physical and chemical
properties.
• Benchmark 2.2: The spatial configuration
of atoms and the structure of the atoms in
a molecule determine the chemical
properties of the substance.
• Benchmark 2.4: Word and chemical
equations are used to relate observed
changes in matter to its composition and
structure.
Matter and Its
Combinations
• All matter is made up of
atoms—the smallest
unit of matter.
• Protons (+ charge) and
neutrons (no charge)
are in the center.
• Electrons ( - charge)
are outside of the
nucleus in an electron
cloud.
• Click here!
Periodic Table
• The periodic table organizes the
elements into rows with increasing
atomic number and columns of
groups/families that have the same
number of outer shell electrons.
Energy Levels
• Electrons travel around
the nucleus at different
energy levels. The farther
away from the nucleus an
electron is, the more
energy it has because it’s
farther away from the pull
of the positively charged
protons.
Atom Song
(3:28)
• The first energy level
closest to the nucleus
can hold up to 2
electrons.
• 2nd level: up to 8
electrons.
• 3rd level: 18 e• 4th level: 32 e-
Elements
(2:05)
Elements (
• Elements are substances composed of
only one kind of atom.
• The number of neutrons in any given
element are the same except in isotopes.
• Isotopes have different numbers of
neutrons and thus different masses than
the most common form of any given
element. Examples: C-12 and C-14 are
isotopes of carbon. One has a mass of
12 amu and the other a mass of 14 amu
because it has more neutrons.
Elements vs. Compounds
(3:47)
• Elements
• Compounds
• Carbon: C
• Methane: CH4
• Hydrogen: H
• Hydrogen molecule: H2
• Oxygen: O
• Oxygen molecule: O2
• Nitrogen: N
• Nitrogen molecule: N2
• Phosphorous: P
• Phosphate ion: PO4 3-
Covalent vs Ionic
bonding
• When atoms combine
chemically by sharing
electrons, they have
formed a covalent bond.
Covalently bonded atoms
are called molecules.
• Ions are atoms that have
given up or taken
electrons. Compounds
that are formed by ions
(2:12) are called ionic
compounds. (17:38)
Water Water
everywhere!
• Water is a polar
molecule.
• It is held together
by covalent bonds.
• Because water is
polar, it dissolves
other polar
substances.
• Water is cohesive in
that the molecules
attract one another
like water beading on
a freshly waxed car.
• This is because of the
hydrogen bonds
between water
molecules.
• Water molecules
stick to other polar
substances due to
adhesion, which is
the attraction
between particles
of different
substances.
Chemical equations
• Chemical equations use formulas to
describe chemical changes that take
place. Numbers of atoms before the
reaction and after the reaction must be
the same.
• Reactants  Products
• Hydrogen + Oxygen produces water
• H2 + O2  H2O (unbalanced equation)
• Balanced, this equation is:
• 2H2 + O2  2H2O
Balance these
equations:
• Zn + HCl  ZnCl2 + H2
• Mg(OH)2 + HCl  MgCl2 + H2O
• NaClO3  NaCl + O2
• CH4 + O2  CO2 + H2O
Solutions
• Solutions are homogeneous
mixtures that are the same
throughout, although they can have
varying amounts of dissolved
substances in them.
• So, why do some things dissolve in
water and others don’t?
• Potassium permanganate
dissolution demo 1. (click here)
• Demo 2 (click here)
(1:00)
(1:00)
Acids and Bases
Introduction to Acids/Bases (2:04)
pH Scale (2:42)
pH in the Chemistry of Nature (3:19)
Acids donate H+ to solutions and lower
the pH below 7.
Bases donate OH- to solutions and
raise the pH above 7
pH Scale
pH and Buffers
• pH is a measure of how acidic or basic a
solution is. It is a measurement of
hydronium ion (H3O+) concentration.
Each one-point increase in pH represents
a 10-fold decrease in H3O+ concentration.
Each one point decrease represents a 10fold increase in H3O+ concentration.
• The pH in living things must be stable.
• Buffers are substances that react to
prevent pH changes in a solution. An
important buffer in living things is the
bicarbonate ion, HCO3-- .
Carbon Compounds
• Carbon compounds
– Structure
– Isomers
• Carbohydrates
– Monosaccharides, Disaccharides and
Polysaccharides
• Lipids
– Structure
• Proteins
– Structure
• Nucleic Acids
– Condensation Reactions
– Hydrolysis
Carbon Compounds
• Living organisms as well as
substances like fossil fuels
are made up of carbon
compounds. Carbon has 4
valence electrons that can
form single, double and triple
bonds.
• Living organisms are made
up of organic compounds.
Isomers
• Isomers are molecules that
have identical formulas but
different structural
arrangements.
• Both of the molecules →
have the formula C6H14 but
have different structures.
• These different shapes do
not constitute different
compounds. To get a
different compound the
bonding pattern of the
atoms would have to
change.
Branched chain isomers (4:36)
Carbohydrates
• Carbohydrates are organic
compounds made up of 1 part
carbon to 2 parts hydrogen and 1
part oxygen, or a 1:2:1 ratio.
• Glucose, galactose and fructose are
examples of simple sugars called
monosaccharides.
• Intro to carbohydrates
(2:00)
Structures of simple
sugars
• Two simple sugars can bond together to
form disaccharides. Sucrose (table sugar),
is made up of glucose and fructose bonded
together.
• glucose + glucose = maltose (malt sugar)
• glucose + galactose = lactose (milk sugar)
• Monosaccharides and disaccharides (click here)
•
(2:16)
Complex Carbohydrates:
Polysaccharides ( click)
(4:32)
• Polysaccharides are
formed from long chains
of monosaccharides in
a dehydration reaction
where water is removed
to form the bond.
• An example is glycogen
which is made up of
glucose. The body can
store the glycogen and
then convert it back to
glucose when needed.
• Others include cellulose
and starch.
Glycogen
Other kinds of carbohydrates
• Chitin and cellulose
are two complex
carbohydrates that
provide support.
• Chitin is found in the
shells of crustaceans
and insects.
• Cellulose is found in
plants.
• Starches are long
chains of glucose
stored in plants.
Fats, Lipids and Fatty
Acids
• Fats and oils belong to
a class of organic
compounds called
lipids.
• Are fats good?
(3:07)
• Lipids and cholesterol (1:12)
• Fatty Acids
(2:45)
Cholesterol
• Cholesterol is a soft,
waxy substance
found among the
lipids (fats) in the
bloodstream and in
all your body's cells.
It's an important part
of a healthy body
because it's used to
form cell membranes,
some hormones and
is needed for other
functions.
LDL and HDL
• About one-third to one• Cholesterol is carried
fourth of blood
through the body by
cholesterol is carried
lipoproteins.
by HDL. Medical experts
• Low-density lipoprotein is
think HDL tends to carry
the major cholesterol
cholesterol away from
carrier in the blood. If too
the arteries and back to
much LDL cholesterol
the liver, where it's
circulates in the blood, it
passed from the body.
can slowly build up in the
Some experts believe
walls of the arteries
HDL removes excess
feeding the heart and
cholesterol from plaques
brain.
and thus slows their
growth.
Steroids
• Steroids are a type of
lipid that has four
interlocking rings.
• Examples of steroids
are cholesterol,
estrogen and
testosterone.
• Anabolic steroids are
synthetic male sex
hormone testosterone.
Water Barriers
• An important
component of a cell
membrane is made of
phospholipids.
• The outer layers are
polar and attracted to
water while the inner
layers are fatty acids
and repel water. The
inner layers are
hydrophobic.
• Some plant stems
and leaves have a
waxy coating that
helps prevent
water evaporation
near the surface.
Proteins and Amino
Acids
(2:30)
• What is protein?
(3:05)
• Proteins are built
from chains of amino
acids. They have a
central carbon atom
bonded to a carboxyl
group, a hydrogen
atom and an amino
group.
• The bonds that form
proteins are called
peptide bonds. (2: 23)
Protein structure
Nucleic Acids
DNA Molecule
• Molecules that
control an
organism’s basic
appearance and
behavior are
called nucleic
acids.
• These include
deoxyribonucleic
acid (DNA) and
ribonucleic acid
(RNA).
DNA structure
• A five carbon sugar
called deoxyribose
(Labeled S)
• A phosphate group (a
phosphorous atom
surrounded by four
oxygen
atoms.) (Labeled P)
• And one of four
nitrogen-containing
molecules called
nucleotides .
(Labeled A, T, C, or
G)
RNA and DNA
Energy Carriers
• Adenosine
triphosphate, or ATP
is a nucleotide that
has three phosphate
groups.
• Energy is released in
a reaction that breaks
off the 3rd phosphate
group. It’s the main
energy source for cell
processes.
Condensation Reaction
• Maltose is a large
disaccharide
formed from the
condensation
(water producing)
reaction between
two glucose
molecules.
• Amino acids from
the foods you eat
form proteins with
this type of
reaction.
Two glucose molecules react
to form maltose and water
Hydrolysis
• Hydrolysis (2:10)
occurs when the
addition of a water
molecule breaks
up a larger
molecule into
smaller molecules.
• A dipeptide +
water can yield
two amino acids
such as glycine
and alanine.
Formation of glucose and fructose
by adding a water molecule to sucrose
ENERGY!!!
• Potential and
Kinetic Energy
(2:07)
• Law of
Conservation of
Energy
(4:35)
Potential and Kinetic Energy
Activation energy/Enzymes
• Activation energy is the
smallest amount of
• Enzymes are proteins
energy it takes to start
that lower the
a chemical reaction.
activation energy
• Different reactions
needed for chemical
require different
reactions in cells.
amounts of energy.
They are a catalyst.
Heat is a common form
of energy used to start
a chemical reaction,
but is not practical
when looking at
biochemical reactions
because too much heat
↑
would kill cells.
I am an enzyme, click on me! (1:37)
Enzymes/Substrates
• Enzymes are reusable and each has a
unique shape that determines its
chemical function.
• Substrates work with enzymes in
chemical reactions.
• Most enzymes are named by adding the
suffix –ase to the name of the substrate
reaction the enzyme controls. ie: the
enzyme that guides the conversion of
maltose to glucose is called maltase.
Substrates/Coenzymes
• Substrates attach themselves to enzymes, which
change shape slightly which lowers the activation
energy needed because the active site of the
enzyme will only fit together with a certain part of
the substrate.
• Coenzymes sometimes made from vitamin
molecules, are reusable, and needed in small
amounts. They are enzymes’ little helpers by
helping substrates bind or transferring atoms from
one substrate to another..
• Because enzymes
reduce the amount
of energy it takes
to start a reaction,
a series of
enzymes can
carry out reactions
that eventually
turn sugars into
HYDROLYSIS OF
energy that is
ADENOSINE TRIPHOSPHATE
(Cells make and consume 10,000,000
stored in ATP
ATP molecules per second.)
molecules.
Micro Elements
(next 9 slides)
• Iron (Fe) Contained in hemoglobin and
myoglobin which are required for oxygen
transport.
• Anemia results from a lack of Fe.
• Enlarged liver, diabetes and cardiac
failure can be caused by too much iron.
• Hemochromatosis is a genetic disease
that causes excess iron absorption which
can adversely affect the heart, cause
cancer or liver disease.
• Potassium (K) is a major electrolyte
of blood and extracellular fluid.
Maintains pH and osmotic balance.
• Chlorine (Cl) Major electrolyte of the
blood and intracellular/extracellular
fluid. Maintains pH and osmotic
balance.
• Sulfur(S) Part of essential amino
acids. Contained in vitamins,
thiamin and biotin. Part of
glutathione
and required for
detoxification.
• Copper (Cu) regulates Fe transport
and release from storage.
• Too much copper can cause liver
disease and is associated with the
genetic disorder, Wilson’s disease,
where excess copper affects the
brain, eyes and kidneys.
• Manganese (Mn) Needed for bone
formation and reproduction. Too
much causes poor Fe absorption.
Iodine: Produces thyroxine which
controls metabolic rate and
prevents goiter.
• Zinc (Zn)
• Selenium (Se)
important for
Deficiency esults
reproduction,
in oxidative
required for DNA
membrane
binding which
damage. In
regulate a variety
humans it causes
of activities. An
heart damage,
excess can cause
known as
anemia or reduced
Keshan’s Disease.
bone formation.
• Fluorine (F) Tooth
development and
protection.
• Strengthens
enamel to prevent
decay.
• Cobalt (Co) An
excess may cause
cardiac failure.
Macro elements—essential for
proteins and enzyme activity
• Calcium: Ca
Structure of bones
and teeth
• Phosphorous: P
• Structure of bones
and teeth,
required for ATP
production.
• Magnesium (Mg)
Bone structure,
too little results in
muscle spasms
and can lead to
Ca deficiency.
• Sodium (Na)
Major electrolyte
of blood and
extracellular fluid.
Maintains pH and
osmotic balance.
• Molybdenum (Mo) An
excess can cause
diarrhea and growth
reduction.
• Chromium (Cr) Helps
regulate sugar levels.
Deficiency may cause
hyperglycemia
(elevated blood
sugar) and
glucosuria. (sugar in
urine)