Cells and Cell Chemistry
(rev 9-11)
• All matter consists of elements
– Matter is anything that has mass and
occupies space
– Element is a substance made of one kind of
atom
• Periodic chart contains the 103 known elements,
arranged by similar properties
• Atoms: the smallest functional unit of an
element that still retains the physical and
chemical properties of the element
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– Elements of biological importance:
•
•
•
•
•
•
Carbon-C
Hydrogen-H
Nitrogen-N
Chlorine-Cl
Magnesium- Mg
Sulfur-S
Oxygen-O
Sodium-Na
Calcium-Ca
Potassium-K
Phosphorous-P
Iron-Fe
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Core of the atom is the cell nucleus.
• It consists of:
– Protons: + (positive) charge, have mass (weight-1
AMU)
– Neutrons: have no charge (neutral particle), have
mass (1 AMU)
– Protons and Neutrons are tightly bound together
• Electrons: - (negative) charge, orbit the nucleus, have no
discernable mass (<0.001 AMU)
• Electrons are constantly moving so their actual location
within their specific shell can not be determined
• Atoms and their parts are weighed by AMU-atomic mass
units because they are so small.
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• All atoms are electrically neutral
– Have an equal number of protons and electrons
• Number of protons and electrons determines behavior of
each atom
The Periodic Table of the Elements identifies the
11
composition of each atom.
Na
22.990
– Letters in the middle = the atom’s chemical symbol
– Number on top = the atomic number (# of protons)
(and also the number of electrons—Why?)
– The number on the bottom is the atomic mass;
(use it to figure out the number of neutrons-How?)
• Subtract the atomic number (# of protons) from the atomic mass or
subtract the top number from the bottom number.
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Isotopes
• All atoms of a particular element have the same
number of protons and electrons HOWEVER,
they can have a different number of neutrons,
therefore a different atomic mass (weight)
• These atoms are called isotopes.
• Isotopes tend to be unstable. They are called
RADIOISOTOPES because they give off energy
as radiation until they reach a stable state
– Some of this energy can damage the body
– Some of this can be used in medicine to tag and track
molecules to determine their location in the body
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Electrons have potential energy
– The term “orbital” describes the probable
location of an electron within a “shell”
– The term “shell” refers to the energy level of
electrons
• Each shell further away from the nucleus has a
higher level of energy
-- When an electron moves to a shell closer to
the nucleus it loses energy
--When an electron moves to a shell further
away from the nucleus, it gains energy
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• Atoms are most stable when their outermost occupied
electron shell is completely filled
– An atom with an unfilled outermost electron shell will
try to interact with other atoms in order to fill this
outermost shell
– Atoms try to share electrons with other atoms
• First shell can hold 2 electrons; second can hold 8 electrons; few
atoms have a third shell (can hold a maximum of 18 electrons)
• These interactions will typically cause the atoms to be
bound to each other by a force called a “chemical bond”
• There are 3 principal types of chemical bonds:
– Covalent
– Ionic
– Hydrogen
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• Covalent Bond
– Strong-rarely break apart
– Formed by the sharing of a pair or more of
electrons with another atom (in order to fill the
outermost shell)
– Sharing of 1 pair of electrons is a single bond
– Sharing of 2 pairs of electrons is a double
bond
– Example: Hydrogen gas, oxygen gas, water
molecule
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• Ionic bond- bond between two oppositely
charged atoms or molecules which was formed
by the transfer of one or more electrons
– Atom with nearly full outer shell gains electrons; gives
the atom a net charge due to gain or loss of electrons
• + charge for each electron lost
• - charge for each electron gained
– An electrically charged atom or molecule is called an
ion. Examples: Na+, Cl-, Ca2+
– Bond is of moderate strength
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• Hydrogen Bond
– Weak attraction which occurs between oppositely
charged regions of polar molecules that contain
covalently bonded hydrogen. We see this most often
in a water molecule.
– Water is electrically neutral overall but still has
partially charged ends (called poles). This type
molecule is called a polar molecule.
• Since opposites attract, polar molecules arrange themselves
to that the negative pole of one molecule is facing the
positive pole of another molecule.
– Hydrogen bonds between liquid water molecules are
so weak that they break and reform allowing water to
flow.
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A polar molecule is formed when electrons are
unequally shared between two atoms.
• ThIs occurs because one atom has a stronger
affinity for electrons than the other (yet not
enough to pull the electrons away completely
and form an ion) and the bonding electrons will
spend a greater amount of time around the atom
that has the stronger affinity for electrons.
– An example of this is the hydrogen-oxygen
bond in water.
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Compounds
• Composed of molecules.
– A molecule forms when 2 or more atoms
combine.
• Organic compounds contain the element
carbon
• Inorganic compounds do not contain
carbon
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Life depends on water
• Water is responsible for 60% of our body
weight
• Water molecules are polar
• Water is liquid at body temperature
• Water can absorb and hold heat energy
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Two Biological Functions of Water
1. Water is the biological solvent because it is a
polar liquid at body temperature
– A solvent is a liquid in which other
substances dissolve
– Solute is any dissolved substance.
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2. Water helps regulate body temperature
– Water can absorb and hold heat with only a
small increase in temperature. It prevents
body temperature from rising suddenly.
– Water also holds heat when there is danger
of too much heat loss (on a cold day for
example).
– We can lose heat rapidly by evaporating
water from our body surface.
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So, water is the substance in which many chemical
reactions take place.
– Water is the substance that carries solutes
from one place to another.
– It also fills our intracellular and intercellular
spaces.
• The term hydrophilic refers to polar molecules
attracted to water and interact with it.
• The term hydrophobic refers to nonpolar
molecules that are not attracted to water and
therefore don’t interact with it. (oil and water)
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The Importance of Hydrogen Ions
Despite the covalent bonds between water molecules, the
bonds can be broken into H+ and OH-.
– In pure water, there are only a few dissociated (broken
apart) molecules
• Other sources of hydrogen ions in aqueous solutions:
– Acids are any molecule that can donate a hydrogen
ion (H+ --proton). Produce an acidic solution (which has
a higher concentration of H+ than water)
– Bases are any molecule that can accept hydrogen
ions. Produce a basic or alkaline solution (which has a
lower H+ concentration than water).
• Acids and bases have opposite effects on the H+
concentration of solutions so they “neutralize”
each other
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How to indicate the acidity or alkalinity of a
solution
• pH Scale = measure of hydrogen ion
concentration in a solution
– Scale goes from 0-14; pH of water is 7.0 or
neutral
– Changes in pH of body fluids can affect how
molecules are transported across the cell membrane
and how rapidly certain chemical reactions occur. pH
changes affect the body’s homeostasis.
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Buffers: minimize pH change
• Buffers are essential to maintain homeostasis of
pH in body fluids
– Carbonic acid (H2CO3) and bicarbonate
(HCO3-) act as one of the body’s most
important buffer pairs. They pick up H+ when
fluids are too acidic and release them when
fluids are too basic.
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Organic Molecules of Living Organisms
Organic molecules are molecules that contain
carbon and other elements held together by
covalent bonds.
Carbon is the building block of all organic
molecules.
–
–
–
–
Comprises 18% of body weight
Forms four covalent bonds with other molecules
Can form single or double bonds
Can build micro- or macromolecules
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• Living organisms synthesize 4 classes of organic
molecules:
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
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Living organisms use carbohydrates for energy; plants
also use them for structural support
• Monosaccharides are the simplest carbohydrate
– Glucose, fructose, ribose and deoxyribose are 4 of
the most important monosaccharides in humans
– Oligosaccharides: short chains of monosaccharides
linked together.
• Disaccharides: consist of 2 linked
monosaccharides
examples: sucrose (table sugar), fructose, lactose
• Some oligosaccharides are bonded to cell
membrane proteins; called glycoproteins
– Glycoproteins participate in linking adjacent
cells together and in cell-cell recognition and
communication
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• Polysaccharides: a complex carbohydrate formed when
thousands of monosaccharides are joined together in
long chains and branches
• Extra long chains; energy is stored in the bonds of
the polysaccharide molecule
– Glycogen: most important polysaccharide made in
animals; stores energy
– Starch: most important in plants; stores energy
– Cellulose: Undigestible polysaccharide made in plants
for structural support
• Undigested cellulose in the food we eat is called
“fiber”
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Lipids
• Are relatively insoluble in water
Most Important Subclasses of Lipids:
Triglycerides: energy storage molecules
– Glycerol and 3 fatty acids make up triglyceride;
can be saturated or unsaturated
• Saturated fats are usually solid at room temperature
• Unsaturated fats are usually liquids at room
temperature
– Are stored in adipose tissue
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Phospholipids:
• Are the primary structural component of cell
membranes
• Have a phosphate group (PO4-) at one end; this
negative charge makes the phospholipid a polar
molecule and thus one end of it is soluable in
water. The other end is “neutral” and is not
soluble in water
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Steroids:
• Are classified as lipids because they are
relatively insoluble in water
• Cholesterol is a steroid
• We all need a certain amount of cholesterol
because it:
– is an important part of the cell membrane
– is used in making estrogen and testosterone
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Proteins are macromolecules constructed from
long strings of amino acids
– A string of 3-100 amino acids is called a
polypeptide
– When a polypeptide is longer than 100 amino
acids it is called a protein
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The body has many different proteins; each serves different
functions.
– Structural support
--Muscle contraction
– Part of the cell membrane --Enzymes
• Protein shape can be changed in the presence of polar
molecules.
– The ability to change shape is essential to the
functions of certain proteins.
• Protein structure can be damaged by high temperatures
or changes in pH.
– Denaturation refers to permanent disruption of protein
structure which causes a loss of function i.e. boiling
an egg
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• Enzymes:
– are proteins that function as a biological catalyst (a
substance that speeds up the rate of a chemical
reaction without itself being changed or consumed by
the reaction)
– they speed up a reaction that would have happened
anyway but it would have taken longer
• They serve as catalysts because, as proteins, they can
change shape. This allows them to bind to other
molecules and orient them so they can work with each
other.
• The functional (or changeable) shape of an enzyme is
dependent on:
– temperature of reaction medium
– pH
– ion concentration
– presence of inhibitors
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Other organic molecules:
Nucleic Acids
• DNA: deoxyribonecleic acid
• RNA: ribonucleic acid
Functions:
• DNA directs everything the cell does including the
instructions for producing RNA.
• RNA is a closely related macromolecule and carries out
the instructions of DNA including how to produce
proteins.
• Structure
– Composed of Nucleotides consist of a phosphate
group, a sugar, and a nitrogenous base
– DNA structure is a double helix: two associated
strands of nucleic acids
– RNA is a single-stranded molecule
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Structure of DNA and RNA
• DNA: double-stranded helix
– Sugar: deoxyribose
– Nitrogenous bases: adenine, thymine,
cytosine, guanine (the protein code is actually
contained in the sequencing of nucleotides)
– Pairing: adenine-thymine and cytosine-guanine
• RNA: single-stranded helix
– Sugar: ribose
– Nitrogenous bases: adenine, uracil, cytosine,
guanine
– Pairing: adenine-uracil, cytosine-guanine
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• Adenosine Triphosphate (ATP)
– Nucleotide
– Made up of adenine+ ribose (which is a 5 carbon
sugar). Together these are called adenosine. There
is also a 3 phosphate group called triphosphate.
– Is a universal energy source for cells
• The bonds between the phosphate groups contain
a lot of potential energy
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