Chapter 2: The
Molecules of Cells
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
2.1
Basic Chemistry
All matter, living or nonliving, is made up of elements.
Elements contain atoms.
An atom is the smallest unit of matter that can enter
chemical reactions
Isotopes
Atoms of the same element that differ in number
of neutrons.
Carbon 14 is unstable and releases energy,
therefore it is a Radioactive isotope. Half life of
carbon is 5,730 years.
Radioactive Isotopes in Science
 Can be used as tracers in the body to detect any abnormal
functions
 Can be used to kill cancer cells .
Cs-131 seeds placed in
prostate gland to kill
cancer cells
Thyroid hormones:
T3 – triiodothyronine
T4 - thyroxin
Radioembolization: beads of Y90 sent to
tumor to block blood flow and kill cancer
cells!
2.2
Molecules and Compounds
Atoms form bonds to fill the outer shell with
electrons.
 two types of bonds (ionic bonds and
covalent bonds) form to create molecules
and compounds
Ionic Bonds
 In ionic bonding, atoms give up or accept
electrons, resulting in ions.
 Metals give up electron and Non-metals accept
electrons
 Ions with opposite charges (- or +) are attracted to
each other and form an ionic bond.
Covalent Bonds
 In covalent reactions, atoms share electrons,
resulting in covalent bonds.
 A non-metal and a non-metal share electrons
 Chlorine gas is a non-polar covalent molecule
Water is a polar
covalent molecule
 Oxygen is more ELECTRONEGATIVE than
hydrogen (it has a stronger attraction to the
electrons)
Hydrogen Bonding
 Hydrogen bonds form when slightly positive
hydrogen is attracted to a slightly negative
oxygen (or nitrogen)
 A weak bond
 Also hold DNA helix together
 Makes water unique
2.3
Chemistry of water
 Water is the most abundant molecule in living
things.
 Water is polar and hydrogen bonded to each other
Important properties of
water
1.
A great solvent (dissociate any ionized or polar
molecules - hydrophilic)
2.
Cohesive and adhesive (hydrogen bonding)

Copy of Properties of Water Lesson - Google Slides
Acids and Bases
 When water dissociates or “ionizes” it releases
hydrogen ions (H+) and hydroxide ions (OH-).
 Acids are molecules that release hydrogen ions in
solution (when mixed with water)
 Bases are molecules that either take up hydrogen
ions or give off hydroxide ions in solution.
2-13
pH Scale
Indicates the concentrations of hydrogen ions or
hydroxide ions
What does pH stand for? (you should know this….)
Potential of Hydrogen
BUFFERS
 Buffers are substances that help to resist change
in pH.
 Carbonic acid and bicarbonate ions are found in
our blood to help maintain our blood pH at 7.4
(HOMEOSTASIS!)
VIDEO
Crash course – Water:
http://www.youtube.com/watch?v=HVT3Y3_gHGg
Properties of water
stations lab
 Use your device and headphones to watch the video
and complete the matching portion of the lab
 Then go into the lab to complete the rest of the
stations
2.4 Organic Molecules
216
 Organic molecules are found in living
things
 Always contains Carbon (C) and
Hydrogen (H)
 The chemical properties of Carbon
allows for the formation of very large
variety of organic molecules found in
living things
 Are Macromolecules
217
A Carbon atom can share
electrons covalently with as
many as 4 other atoms
Carbon atoms are also able to
form long hydrocarbon chains
or even rings
Crash course: Carbon
https://www.youtube.com/watch?v=QnQe0xW_JY4
Hydrocarbon chains can have
functional groups that cause the
macromolecule to behave in a
certain way
218
Macromolecules (polymers) are formed from smaller
2building blocks called monomers.
19
Polymers in our cells are:
Polymer
carbohydrate
Lipids
protein
nucleic acid
Monomer
monosaccharide
glycerol & fatty acids
amino acid
nucleotide
221
2Carbohydrates
22
Functions
 Quick energy and short-term energy storage
 They play a structural role in plants, bacteria
(cell wall), and insects (chitin).
 Act as cell markers for cell-to-cell recognition
Simple carbohydrates / monosaccharides
(monomers of carbohydrates)
• glucose (hexose (6C) sugar)
• fructose
• galactose
• ribose (pentose (5C) sugar)
• deoxyribose
2-A
23
DISACCHARIDE is made from linking two
monosaccharides together.
COMPLEX CARBOHYDRATE
2POLYSACCHARIDE is made from linking many
24
A monosaccharides together
Examples of polysaccharides formed by dehydration
synthesis reaction:
 Starch
 Glycogen
 cellulose
225
Starch
Glycogen
Structure: long chains of glucose with
• few branches
many branches
Function: Storage form of glucose (energy)
• In plant
In animals
Cellulose
Structure: long chains of glucose with
alternating bonds between glucose
molecules
Function: structural component of plant
and bacterial cell walls and
exoskeleton (chitin) of insects / crabs
Is the fiber in our diet as we can not break
the bonds.
(0-7:15) https://www.youtube.com/watch?v=jQi84TnstI4
LIPIDS
fats, oils, phospholipids, waxes & steroids
https://www.youtube.com/watch?v=5
BBYBRWzsLA
Lipids
 Lipids are organic molecules that are nonpolar therefore are insoluble in water
(Hydrophobic)
Making butter:
https://www.youtube.com/watch?v=e
1LYWF8T8g0
Functions of Lipids
229
 Long-term energy storage in cells (Lipids contain
9.1 calories of energy per gram compare to
carbohydrates and proteins with about 4.4
calories per gram)
 Structural component of cell membranes
(Phospholipid bilayer)
 Insulation (blubber)
 Padding (protection for our vital organs i.e
heart)
 Chemical messengers (hormones)
4 main types of lipids
1. Fatty acids
2. Neutral fats or triglycerides
3. Phospholipids
4. steroids
1. Fatty acids
 Long chains of hydrocarbons ending in COOH (Carboxyl group)
 Fatty acids may be saturated fatty acids
or unsaturated fatty acids or trans-fatty
acids
 Saturated fatty acids are SOLID
at room temperature (Lard)
 They do not contain any double
bonds in the hydrocarbon
chain
 Unsaturated fatty acids are
LIQUID at room temperature
(oils)
 They contain 1 or more double
bonds causing the hydrocarbon
chain to bend
Fatty acids
233
Cis and Trans-fatty
acids refers to the
configuration of the
hydrogen atoms
Industrial (artificial) Trans fats are produced by
hydrogenation or chemically adding hydrogen
to convert vegetable fats into solid form in
processed foods (to increase shelf life). These
increase LDL (“bad” cholesterol) in our blood.
2. Neutral fats (Triglycerides)
234
 Storage form of fat (energy) in animals
 Composed of GLYCEROL and 3 FATTY
ACIDS combined together by dehydration
synthesis
The fatty acids may be saturated or unsaturated
235
3. Phospholipids
 Some lipids are phospholipids that form cell
membranes.
 Phospholipids are composed of GLYCEROL, 2
FATTY ACIDS and a PHOSPHATE group
Phospholipids have a POLAR head
and a NON-POLAR tail
236
4. Steroids
 Steroids are lipids derived from cholesterol.
 Steroids are made of carbon rings instead of
chains
 Steroids function as chemical messengers and
important hormones such as estrogen and
testosterone.
Cholesterol
 Cholesterol is also found as part of the
structural component of cell membranes
 Makes vitamin D and bile
https://www.youtube.com/watch?
v=0U7YHRW5dyc&vl=en
Emulsification
 Emulsifiers cause fats to mix with water.
 The molecules of emulsifiers have a polar end
and a non-polar end.
 These molecules position themselves around oils
so that their non-polar end project inwards and
their polar ends project outwards allowing the
oils to become attracted to water
Colours on the move:
https://www.acs.org/content/acs/e
n/education/whatischemistry/adve
ntures-inchemistry/experiments/colorsmove.html
2.7 PROTEINS
Functions of Proteins
VIDEO what are proteins: (:59): https://learn.genetics.utah.edu/content/evolution/proteins/
Structural support (bones, cartilage, tissues)
Movement in muscle cells
Enzymes to speed reactions
Antibodies (immune system proteins)
Transport (hemoglobin, channels in cell
membranes)
Hormones (signals)
Proteins are polymers of amino
acids
An amino acid derives its
name from its amino
group (NH2) and its acid
group (COOH)
There are 20
different amino
acids
241
Examples of amino acids
Structure
Formed from chains of amino acids
connected by peptide bonds (by
dehydration synthesis)
Structure
Proteins have 4 levels of structure /
organization:
primary (1O)
secondary (2O)
tertiary (3O)
quaternary (4O)
Primary Structure (1O)
Refers to the sequence of amino
acids
Note that type, sequence and
length of the amino chain
determines the characteristics of
the protein
Secondary Structure (2O)
Hydrogen bonds between oxygen and
hydrogen atoms cause the protein to assume
either an alpha helix or pleated sheet shape.
Tertiary Structure (3O)
final shape of many proteins
created by the alpha helix folding
on itself.
this shape is held together by
covalent, ionic and hydrogen
(sometime disulfide bridges)
bonding between the “R” groups
of the amino acids
most enzymes have this level of
structure
3O Peptide hormones: ADH,
oxytocin
Quaternary Structure (4O)
proteins that are made up of two or more
different polypeptide chains.
eg hemoglobin, insulin
Denature
When the shape of the protein is changed
due to broken bonds. (hydrogen, ionic,
covalent, di-sulfide linkages)
Caused by: severe changes in
temperature, pH changes or introduction
of heavy metals
2-50
Nucleic Acids
Nucleic acids are polymers of
nucleotides.
2 types of nucleic acids are
Deoxyribonucleic Acid (DNA) and
Ribonucleic Acid (RNA).
DNA: Deoxyribonucleic Acid
 DNA is a double stranded polymer
 Its function is to control the cells activites
 DNA make up chromosomes and genes
RNA: Ribonucleic Acid
 RNA is a single stranded polymer
 Its function is to work with DNA to direct
protein synthesis
Nucleotide
 Composed of a pentose sugar, nitrogenous
base and a phosphate group
 The Carbons in the nucleotide are numbered
1-5.
 The base binds to the Carbon 1 (C1)
 The Phosphate group binds to Carbon 5 (C5)
The polymer forms by
Dehydration synthesis
 Covalent bonds form between
C3 and the phosphate group
2-55
DNA is double-stranded
 The 2 strands of the DNA attach by
forming Hydrogen bonds between its
bases
 This is called
complimentary
pairing
 The strands are
parallel
base
anti-
ϛ+
Bases of DNA
 Consists of 4 bases
Cytosine
Guanine
-
ϛ
-
ϛ+
-
ϛ+
ϛ
ϛ
ϛ+
-
ϛ
-
ϛ
ϛ+
Adenine
Thymine
 Cytosine complimentary base pairs with
Guanine (3 H-bonds form between
them)
 Adenine complimentary base pairs with
Thymine (2 H-bonds form between them)
Bases of RNA
 RNA consists of 4 bases
Cytosine
Guanine
Adenine
Urasil
 Cytosine complimentary base pairs with
Guanine (3 H-bonds form between them)
 Adenine complimentary base pairs with Urasil
(2 H-bonds form between them)
 Complimentary base pairing in RNA only
occurs while RNA is carrying out its function
2-58
Summary of DNA and RNA
2-59
ATP - Adenosine triphosphate
 Some nucleotides also perform functions in
cells.
 ATP is produced by the cell in its mitochondria
 ATP is a “free” nucleotide that functions to carry
and provide energy to the cell
ATP
 The bond between the phosphates are very
high energy, especially between the 2nd and 3rd
 When this bond is broken, energy is released
 About 10 million molecules of ATP are created
and used by each cell every second
Structure of ATP
 Formed of an adenine base, ribose sugar and 3
phosphate groups
 When a phosphate group is lost, the nucleotide
becomes ADP – adenosine diphosphate
 Crash course: DNA (0-8:54) http://www.youtube.com/watch?v=8kK2zwjRV0M