2.1 Basic Chemistry
Matter is anything that takes up space and has
mass.
All matter, living or nonliving, is made up of
elements.
2.1 Basic Chemistry
Elements are substances that cannot be
broken down to simpler substances with
different properties.
Elements that make up the Earth’s
crust and its organisms.
Elements that make up 95%
of living organisms (by weight)
–C
–H
–N
–O
–P
–S
Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
• Atom: The smallest part of an element that
displays the properties of the element.
• Atoms are made up of subatomic particles.
Subatomic Particles
• Protons (positively charged)
• Neutrons (uncharged)
• Electrons (negatively charged)
Helium
Atomic Symbol
Atomic
Mass
12
Atomic
Number
6
C
Carbon
Atomic Symbol
Atomic Mass =
Number of Protons +
Number of Neutrons
Atomic Number = The Number of Protons
in the Nucleus
The Periodic Table, See pg.A8 for more complete
table
Isotopes
12
13
C C C
6
6
14
*
6
*radioactive
Atoms of the same element with
a differing numbers of neutrons
Radiation
• As radioactive isotopes decay, energy is
released in the form of subatomic particles
(radiation).
• Alpha, Beta, Gamma rays – each with different
energy (both dangerous and useful)
• Cobalt 60 irradiation for sterilization of
plastics, potasium 40, etc.
Some Uses of Low Levels of
Radiation
Some Uses of High Levels of
Radiation
Electrons
• If an atom is electrically neutral, the number
of protons (positively charged) is equal to the
number of electrons (negatively charged).
Energy Levels (electron shells)
• The first shell (closest to the nucleus) can
contain two electrons
Energy Levels (electron shells)
• The first shell (closest to the nucleus) can
contain two electrons
• Each additional shell can contain eight
electrons
Energy Levels (electron shells)
• The first shell (closest to the nucleus) can
contain two electrons
• Each additional shell can contain eight
electrons
• Each lower shell is filled with electrons before
the next higher level contains any electrons.
Periodic Table (Revisited)
Vertical columns indicate
number of electrons
in outermost shell
Horizontal
periods
indicate
total number
of electron
shells
1
I
VIII
1
2
H
III
IV
V
VI
VII
4
5
6
7
8
9
4.003
10
Li
Be
B
C
N
O
F
Ne
6.941
11
9.012
12
10.81
13
12.01
14
14.01
15
16.00
16
19.00
17
20.18
18
Si
P
S
28.09
22
30.97
23
32.07
24
1.008
3
2
3
Na Mg Al
22.99
19
4
He
II
K
39.10
24.31
20
26.98
21
Cl Ar
35.45
25
39.95
26
Ca Ga Ge As Se Br Kr
40.08
69.72
72.59
74.92
78.96
79.90
83.60
Electrons
• Atoms can give up, accept, or share electrons
to have eight electrons in the outer shell.
• Remember: Gain electron – gain negativity
• Lose electron – lose balancing negative and
thus Positive
• Share electrons (pairs) – tightly binds atoms
with no net charge
2.2 Elements and Compounds
• Molecules form when two or more atoms
•
•
•
•
bond together (example: O2)
Definition: simplest unit of a compound
Other examples Carbon Dioxide ______
Water ______ Methane _____
Glucose __________
2.2 Elements and Compounds
• Molecules form when two or more atoms
bond together (example: O2)
• Compounds form when two or more
different elements bond together
(example: H2O)
2.2 Elements and Compounds
• Molecules form when two or more atoms
bond together (example: O2)
• Compounds form when two or more different
elements bond together (H2O)
• When a chemical reaction occurs, energy may
be given off or absorbed.
Ionic Bonding
• Ions are charged particles that form when
electrons are transferred from one atom to
another. Atoms that gain or lose electrons are
called: Ions
• Positive ions are Cations (positive charge,
resulting from loss of electron)
• Negative ions are Anions (negative charge,
resulting from gain of electron)
Ionic Bonding
• Ions are charged particles that form when
electrons are transferred from one atom to
another.
• Ionic compounds are held together by an
attraction between oppositely charged ions
called an ionic bond.
Ionic Bonding
Covalent Bonding
• In covalent bonds, atoms share electrons
allowing each atom to have a completed outer
shell. These are relatively “strong”
representing stored Potential energy.
• Please remember: covalent bonds are shared
“pairs” of electrons; each atom is acquiring a
more stable outer electron configuration
Covalent Bonding
• A covalent bond
• A double covalent bond
Shape of Molecules
Shape of Molecules
• Shape is very important. Later you will see
that shape in complex molecules like sugars,
proteins, nucleic acids determines their
particular function.
Nonpolar covalent bonds
• If the sharing between
two atoms is fairly
equal, the covalent
bond is described as
nonpolar.
Polar Covalent Bonds
If the sharing between two atoms is unequal,
the covalent bond is described as polar.
Hydrogen Bonding
• A hydrogen bond occurs
between a slightly
positive hydrogen atom
of one molecule and a
slightly negative atom
of another molecule, or
between atoms of the
same molecule.
Hydrogen Bonding
• Hydrogen bonds are very important in the
final active shape-structure of key
biomolecules like proteins
• Hydrogen bonds in water give it very
important unique qualities that make life
possible on Earth.
2.3 Chemistry of Water
Properties of Water
• Water has a high heat capacity.
– A calorie is the amount of heat energy needed to
raise the temperature of 1g of water 1°C.
– It only takes about 0.5 calories to raise the
temperature of most other covalently bonded
liquids 10C.
Properties of Water
Properties of Water
• Water has a
high heat of
vaporization.
A good coolant as it
evaporates off of our
skin.
Properties of Water
• Water is a solvent.
• The universal
solvent; it dissolves
more different kinds
of subtstances than
any other solvent.
• Most of a cell is
water.
Properties of Water
• Water molecules are cohesive and adhesive.
– Water molecules cling together because of
hydrogen bonding (cohesion).
– Water’s positive and negative poles allow it to
adhere to polar surfaces (adhesion).
Properties of Water
• Water molecules are cohesive and adhesive.
– Water molecules cling together because of
hydrogen bonding (cohesion).
– Water’s positive and negative poles allow it to
adhere to polar surfaces (adhesion).
– So: Water is an excellent transport system, both
outside and within living organisms.
Properties of Water
• Water has a high surface tension
– This allows some insects to walk on the surface of
a pond or lake.
Properties of Water
• Frozen water is less
dense than liquid water.
• Water that is frozen is
going to “float”.
• Fish in mountain lakes
appreciate that.
Acids and Bases
• Certain chemicals that are dissolved in water
are called acids or bases. So a solution of
water and these materials are called:
– Acidic
– Basic (alkaline)
– Neutral
Acids and Bases
• When water ionizes, it releases an equal number of
hydrogen ions (H+) and hydroxide ions (OH-).
Acids and Bases
• Acidic Solutions
– Acids are substances that dissociate in water,
releasing hydrogen ions (H+).
Acids and Bases
• Acidic Solutions
– Acids are substances that dissociate in water,
releasing hydrogen ions (H+).
– An example:
HCl
H+ + Cl-
Every molecule dissociates when dissolved in water
Hydrochloric acid is thus a strong acid.
Acids and Bases
• Basic Solutions (Low H+ Concentrations)
• Examples: Sodium Hydroxide, Ammonium
Hydroxide
Acids and Bases
• Basic Solutions
– Bases are substances that dissociate in water,
releasing hydroxide ions (OH-) or take up hydrogen
ions (H+).
Acids and Bases
• Basic Solutions
– Bases are substances that dissociate in water,
releasing hydroxide ions (OH-) or take up hydrogen
ions (H+).
– An example:
NaOH
Na+ + OH-
Acids and Bases
• The pH Scale
– Ranges from 0 - 14
– A pH below 7 is acidic [H+] > [OH-]
Acids and Bases
• The pH Scale
– Ranges from 0 - 14
– A pH below 7 is acidic [H+] > [OH-]
– A pH above 7 is alkaline
[OH-] > [H+]
Acids and Bases
• The pH Scale
– Ranges from 0 - 14
– A pH below 7 is acidic [H+] > [OH-]
– A pH above 7 is alkaline
[OH-] > [H+]
– A pH of 7 is neutral
[H+] = [OH-]
The pH Scale
Acids and Bases
• The pH Scale
– Each unit change in pH represents a change of 10X
Buffers and pH
• A buffer is a chemical(s) that keep pH within
normal limits.
• In our bodies, buffers help maintain
“homeostasis” by regulating the acidityalakalinity of fluids, tissues, even cells
Buffers and pH
• A buffer is a chemical(s) that keep pH within
normal limits.
• Bicarbonate ions (HCO3-) and carbonic acid
(H2CO3) found in human blood buffers the pH
to 7.4 (helps prevent acidosis and alkalosis)
Buffers and pH
If hydrogen ions (H+) are added to the blood, this reaction occurs:
H+ + HCO3-
H2CO3
If hydroxide ions (OH-) are added to the blood, this reaction occurs:
OH- + H2CO3
HCO3- + H2O
2.4 Organic Molecules
• Always contain:
– Carbon (C) and Hydrogen (H)
– A carbon atom may share electrons with another carbon atom
2.4 Organic Molecules
• Always contain:
– Carbon (C) and Hydrogen (H)
– A carbon atom may share electrons with another carbon atom
2.4 Organic Molecules
• Many molecules of life are macromolecules.
(macromolecules contain many molecules joined together)
Macro= big Large molecules example: Hemoglobin in RBC carry oxygen.
Hb is huge when compared to water
2.4 Organic Molecules
• Many molecules of life are macromolecules.
(macromolecules contain many molecules joined together)
– Monomers:
Simple organic molecules that exist
individually
– Polymers:
Large organic molecules form by
combining monomers
2.4 Organic Molecules
2.4 Organic Molecules
A meal containing carbohydrates, lipids, and proteins.
2.4 Organic Molecules
• Cells have mechanisms of joining monomers to build
polymers
2.4 Organic Molecules
• Cells have mechanisms of joining monomers to build
polymers
• Dehydration Reaction: an -OH and -H are removed
– Sometimes called dehydration synthesis (joining together by
removing water)
• Hydrolysis Reaction: the components of water are added
– Reversal of dehydration synthesis (split apart – lyse, by adding water
2.4 Organic Molecules
2.5 Carbohydrates
• Some Functions:
– Quick fuel
– Short-term energy storage
– Structure of organisms
– Cell to cell recognition
2.5 Carbohydrates
• Simple Carbohydrates
– Monosaccharides are sugars with 3 - 7 carbon
atoms
2.5 Carbohydrates
• Simple Carbohydrates
– Monosaccharides are sugars with 3 - 7 carbon
atoms
– Pentose refers to a 5-carbon sugar
– Hexose refers to a 6-carbon sugar
2.5 Carbohydrates
Three ways to represent the structure of glucose.
Carbohydrates
• Please note that other monosaccharides may
have the same formula as glucose but have a
different shape and thus are different
altogether
• Glucose, Fructose, Galactose all are Hexoses
with same formula (ratio of C,H,O) but are
different molcules
• Ex: Which is sweeter? Why? (hint;shape)
2.5 Carbohydrates
• Disaccharides contain two monosaccharides.
2.5 Carbohydrates
• Polysaccharides are long polymers that contain many
glucose subunits.
– Starch is the storage form of glucose in plants.
– Glycogen is the storage form of glucose in animals.
– Cellulose can be found in the cell walls of plants.
2.5 Carbohydrates
2.6 Lipids
• This group of macro molecules contains all of
the fats, oils, waxes, sterols
• Some Functions:
– Energy Storage
– Found in the plasma membrane
– Component of steroid hormones
–Lipids do not dissolve in water
2.6 Lipids
• Some Functions:
– Energy Storage
– Found in the plasma membrane
– Component of steroid hormones
Lipids do not dissolve in water
Lipids are electrically neutral
2.6 Lipids
• Fats and Oils
– Fats
• Usually of animal origin
• Solid at room temperature
– Oils
• Usually of plant origin
• Liquid at room temperature
2.6 Lipids
• Functions of Fats
– Long-term energy storage
– Insulation against heat loss
– Protection of major organs
2.6 Lipids
Synthesis and degradation of a fat molecule
2.6 Lipids: don’t dissolve but are
suspended in water by addition of an
emulsifier (soap or detergent)
Emulsification
2.6 Lipids
• Saturated and Unsaturated Fatty Acids
– Fatty acids are hydrocarbon chains that end with COOH. This is a “carboxyl” functional group
2.6 Lipids
• Saturated and Unsaturated Fatty Acids
– Fatty acids are hydrocarbon chains that end
with -COOH.
• Saturated fatty acids: No double covalent
bonds between carbon atoms
• Unsaturated fatty acids: Double bonds
between carbon atoms
2.6 Lipids
Saturated Fatty Acid
Unsaturated Fatty Acid
2.6 Lipids
• Phospholipids
– Comprised of 2 fatty acids + a phosphate group
– Primary components of cellular membranes
2.6 Lipids
2.6 Lipids
• Steroids
– All steroids have four adjacent rings.
– Examples:
 Cholesterol
 Testosterone
 Estrogen
2.6 Lipids
2.7 Proteins – The most “Diverse” of
the Biolmolecules
• Proteins have important functions in cells.
– Proteins such as keratin and collagen have
structural roles.
– Proteins are also enzymes that speed up the
chemical reactions of metabolism.
– Proteins such as hemoglobin are responsible for
the transport of substances within the body.
– Proteins also transport substances across cell
membranes.
2.7 Proteins
• Proteins have important functions in cells.
– Proteins form the antibodies of the immune
system that defend the body from disease.
– Proteins such as insulin are hormones that
regulate cellular function.
– Contractile proteins such as actin and myosin
allow parts of cells to move and muscles to
contract.
2.7 Proteins
• Proteins are comprised of amino acids.
• These amino acids are the “monomer” units
• There are 20 different amino acids in our
protein
• 10 of these 20 are “essential” – must be taken
in preformed in our food
2.7 Proteins
• Amino acids
– Amino group (-NH2)
– Acidic group (-COOH)
– R group (remainder)
2.7 Proteins
2.7 Proteins
• Peptides
– A polypeptide is a single chain of amino acids.
– A peptide bond joins two amino acids.
– So proteins are polymers of amino acids joined by
peptide bonds – polypeptides.
2.7 Proteins – Amino acids joined together
by dehydration synthesis and digested by
hydrolysis
2.7 Proteins
• Levels of Protein Organization
– The structure of a protein has three or four levels of
organization.
– The final shape of a protein is very important
to its function. Beaman “mantra” - shape determines
function
Disrupt or alter shape – loss of function, homeostasis upset
2.7 Proteins
2.7 Proteins
2.7 Proteins
2.8 Nucleic Acids
• DNA (deoxyribonucleic acid)
• RNA (ribonucleic acid)
2.8 Nucleic Acids
• DNA stores genetic information. (one kind)
• DNA codes for the order of amino acids in a
protein.
• RNA is an intermediary in the sequencing of
amino acids into a protein. (3 kinds)
2.8 Nucleic Acids
• Components of a
nucleotide
– Phosphate
– Pentose sugar
– Nitrogen-containing
base
2.8 Nucleic Acids
DNA Structure
2.8 Nucleic Acids
2.8 Nucleic Acids
• ATP (Adenosine Triphosphate)
• The universal “energy” source within cells
– Comparable to Euro in the economy of Europe
2.8 Nucleic Acids
• ATP (Adenosine Triphosphate)
– A high energy molecule
– ATP undergoes hydrolysis and energy is released
2.8 Nucleic Acids