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Chapter 2:
The Chemical Level of
Organization
Copyright 2009, John Wiley & Sons, Inc.
Why Chemistry?
Biology based on principles of chemistry and physics
Living organisms are collection of atoms and molecules
Life’s processes dependent on Chemistry
All life composed of Matter (Anything that has mass and
occupies space)
Matter consists of chemical elements in pure
form and in combinations called compounds
•
•
Organisms are composed of matter
Matter is anything that takes up space and has mass
•
Since chemicals compose your body and all body
activities are chemical in nature, it is important to
become familiar with the language and fundamental
concepts of chemistry.
•
We are taking the approach that in order to understand
living systems you have to understand what they are
made of.
How Matter is Organized

Chemical Elements



All forms of matter are composed of chemical
elements which are substances that cannot be
split into simpler substances by ordinary chemical
means.
Elements are given letter abbreviations called
chemical symbols.
Trace elements are present in tiny amounts
Copyright 2009, John Wiley & Sons, Inc.
Periodic Table of the Elements
Structure of Atoms
Units of matter of all chemical elements are
called atoms. An element is a quantity of
matter composed of atoms of the same type.
Atoms contain:
 Nucleus: protons (p+) & neutrons (neutral
charge)
 Electrons (e-) surround the nucleus as a
cloud (electron shells are designated regions
of the cloud)

Copyright 2009, John Wiley & Sons, Inc.
2 Representations of Atomic Structure
Atomic Number and Mass Number


Atomic number is number of protons in the
nucleus.
Mass number is the sum of its protons and
neutrons.
Copyright 2009, John Wiley & Sons, Inc.
Atomic Mass


Mass is measured as a dalton (atomic mass
unit)
Neutron has mass of 1.008 daltons



proton has mass of 1.007 daltons
electron has mass of 0.0005 dalton
Atomic mass (atomic weight) is close to the
mass number of its most abundant isotope.
Copyright 2009, John Wiley & Sons, Inc.
Atomic Number and Mass Number

Atomic Mass


The atomic mass, also called the atomic weight,
of an element is the average mass of all its
naturally occurring isotopes and reflects the
relative abundance of isotopes with different mass
numbers.
The mass of a single atom is slightly less than the
sum of the masses of its neutrons, protons, and
electrons because some mass (less than1%) was
lost when the atom’s components came together
to form an atom.
Copyright 2009, John Wiley & Sons, Inc.
Ions, Molecules, Compounds, Free Radicals
Ions - an atom that gave up or gained an electron
 written with its chemical symbol and (+) or (-)
 Molecule - atoms share electrons (2 or more similar elements)
 written as molecular formula showing the number of atoms of
each element
■ Compound – 2 or more different elements
□ has characteristics different from those of its elements
 Free Radical - an electrically charged atom or group of atoms with
an unpaired electron in its outermost shell
 Unstable and highly reactive; can become stable

by giving up an electron
 taking an electron from another molecule
 Antioxidants are substances that inactivate oxygen-derived free
radicals

Copyright 2009, John Wiley & Sons, Inc.
Chemical Bonds
The atoms of a molecule are held together by forces of
attraction called chemical bonds (union between
electron structures of atoms)
 The likelihood that an atom will form a chemical bond
with another atom depends on the number of electrons
in its outermost shell, also called the valence shell.
 Electrons:
-Carry a negative charge
-Repel one another but attracted to protons in the
nucleus
- It takes energy to hold electrons in place
-Move in orbitals - volumes of space that surround
the nucleus

Copyright 2009, John Wiley & Sons, Inc.
Electrons and Electron Shells

Only outer shell electrons can interact (form
bonds)!





If outermost shell is full, element is stable (He)
If outermost shell is not full, unstable and can
bond
The 1st shell can hold 2 electrons
The 2nd shell can hold 8 electrons
Stability is goal : by gaining, losing or sharing
electrons
Ionic Bonds


When an atom loses or gains a valence electron, ions
are formed
Charge difference attracts the two ions to each other
 Positively and negatively charged ions are attracted to
one another.
 Cations are positively charged ions that have given
up one or more electrons (they are electron donors).
 Anions are negatively charged ions that have picked
up one or more electrons that another atom has lost
(they are electron acceptors).
Copyright 2009, John Wiley & Sons, Inc.
The Ionic Bond
Formation
Covalent Bonds


Covalent bonds are formed by the atoms of molecules sharing
one, two, or three pairs of their valence electrons.
 Covalent bonds are the most common and strongest
chemical bonds in the body.
 Single, double, or triple covalent bonds are formed by
sharing one, two, or three pairs of electrons, respectively.
Covalent bonds may be nonpolar or polar.
 Nonpolar covalent bond -atoms share the electrons equally;
one atom does not attract the shared electrons more
strongly than the other atom
 Polar covalent bond- unequal sharing of electrons between
atoms. In a water molecule, Oxygen has greater
electronegativity & attracts the hydrogen electrons more
strongly;
Copyright 2009, John Wiley & Sons, Inc.
Polar Covalent Bond
Nonpolar Covalent Bond
Copyright 2009, John Wiley & Sons, Inc.
TEST YOURSELF!!
How many covalent bonds can each of these atoms form??
fd
Copyright 2009, John Wiley & Sons, Inc.
Hydrogen Bonds




An attraction between
a slightly positive
hydrogen atom in one
molecule and a slightly
negative atom (usually
oxygen) in another
molecule
weak intermolecular
bonds; serve as links
between molecules.
help determine threedimensional shape
give water
considerable cohesion
which creates a very
high surface tension
Copyright 2009, John Wiley & Sons, Inc.
Chemical Reactions (Metabolism)






When new bonds form or old bonds are broken
Metabolism is all the chemical reactions in the body
Law of conservation of mass = total mass of reactants equals the
total mass of the products
Require a source of energy and a catalyst (enzymes)
Occur in liquid environment – water
Influenced by: Temperature ; Concentration of reactants; Catalysts
Energy and Chemical Reactions




Chemical reactions involve energy changes
Two principal classes of energy:
 potential energy = stored energy
 kinetic energy = energy of motion
Chemical energy is potential energy stored in the bond of
molecules
 digestion of food releases that chemical energy so that it
can be converted to heat or mechanical energy
Law of conservation of energy
 energy can neither be created nor destroyed--just
converted from one form to another
2-25
•
1.
2.
3.
4.
5.
Five Types of Energy
Mechanical - resulting from the position & movement of objects

Ex. Moving a limb
Chemical – energy within chemical bonds

Ex. ATP + H2O  ADP + H2PO4 + E+
Heat - flows between objects that are different temperatures

Ex. Human body’s chemical rxns release heat as a by-product
and this helps to maintain body temperature
Electric - ability of an electric current to produce work, heat, light, or
other forms of energy. It is measured in kilowatthours.
Electromagnetic - reflected or emitted from objects in the form of
electrical and magnetic waves that can travel through space
26
Energy Transfer in Chemical Reactions



Forming new bonds releases energy & breaking old
bonds requires energy
Chemical reactions usually involve both
 exergonic reactions release more energy
 endergonic reactions absorb more energy than they
release
Human metabolism couples exergonic and endergonic
reactions, so that the energy released from one reaction
will drive the other.
 Glucose breakdown releases energy used to build
ATP molecules that store that energy for later use in
other reactions
Activation Energy
Atoms, ions & molecules are continuously moving & colliding
Activation energy is the collision energy needed to break bonds &
begin a reaction
Copyright 2009, John Wiley & Sons, Inc.
Factors that Cause a Collision and
Chemical Reaction




Concentration
Temperature
Catalysts are chemical compounds that speed up chemical reactions
by lowering the activation energy needed for a reaction to occur.
A catalyst does not alter the difference in potential energy between
the reactants and products. It only lowers the amount of energy
needed to get the reaction started.
 A catalyst helps to properly orient the colliding particles of matter
so that a reaction can occur at a lower collision speed.
 The catalyst itself is unchanged at the end of the reaction; it is
often re-used many times.
Copyright 2009, John Wiley & Sons, Inc.
Catalysts and chemical reactions
Copyright 2009, John Wiley & Sons, Inc.
Types of Chemical Reactions
Synthesis Reactions--Anabolism
-Two or more atoms, ions or molecules combine to form new
& larger molecules
-Anabolism - all the synthesis reactions in the body
-Usually endergonic→absorb more energy than they release
-Example combining amino acids → protein molecule
Decomposition Reactions—Catabolism
-Large molecules are split into smaller atoms, ions or molecules
-Catabolism -all decomposition reactions in the body
-Usually are exergonic→release more energy than they absorb
Types of Chemical Reactions
Exchange Reactions


Substances exchange atoms
 consist of both synthesis and decomposition reactions
Example: HCl + NaHCO3 → H2CO3 + NaCl
ions have been exchanged between substances
Reversible Reactions
Reactants can become products or products can revert to the
original reactants
Indicated by the 2 arrows pointing in opposite directions
between the reactants and the products
AB ↔ A + B
Oxidation-Reduction Reactions



Oxidation is the loss of electrons from a molecule (decreases
its potential energy); acceptor of the electron is often oxygen
Reduction is the gain of electrons by a molecule
 increases its potential energy
In the body, oxidation-reduction reactions are coupled & occur
simultaneously
Inorganic Compounds & Solvents


Most of the chemicals in the body are
compounds
Inorganic compounds




usually lack carbon & are structurally simple
Exceptions: CO , CO2 , HCO3
Water, Oxygen, CO2, Salts, Acids & Bases
Organic compounds


contain carbon & usually hydrogen
always have covalent bonds
Water – most abundant & important
inorganic compound in living systems
Characteristics of H2O
Polar molecule:
1.
–
b/c it is polar it forms H+ bonds
with other H2O molecules
forming a lattice structure w/in
the H2O
% of body’s weight
2.
–
–
50% in ♀ (> body fat than ♂)
60% in ♂
% of blood plasma
3.
–
92% H2O
AP1: Ch. 2: Chemical Basis of Life
37
Polar Water Molecules
Copyright 2009, John Wiley & Sons, Inc.
H2O: Functions in living organisms
Stabilizing Body Temp.
1.
–
–
–
H2O has a high specific
heat (meaning it takes a
large amount of e+ to raise
its temperature)
Thus it is resistant to
temperature D’s
H2O also evaporates (thus it
can be sweat used to cool
the body when it evaporates
and takes the “heat” with it)
Protection
2.
–
–
Acts as a lubricant to
prevent damage from
friction
It also forms a “fluid
cushion” around the organs
(ex. CSF)
Chemical Rxns
3.
–
–
–
Reacting molecules must be
dissolved in H2O for many
of the bodies chemical rxns
**Hydrolysis
**Dehydration Synthesis
Mixing Medium
4.
–
Mixture: combination of 2 or
more substances blended
together but not chemically
combined
a.
Solution
b.
Suspension
c.
Colloid
39
3 Common Mixtures
A mixture is a combination of elements or compounds that are
physically blended together but are not bound by chemical bonds.



Solution: a substance called the solvent dissolves
another substance called the solute. Usually there is
more solvent than solute in a solution.
A colloid differs from a solution mainly on the basis of
the size of its particles with the particles in the colloid
being large enough to scatter light.
Suspension: the suspended material may mix with the
liquid or suspending medium for some time, but it will
eventually settle out.
Copyright 2009, John Wiley & Sons, Inc.
Concentration

The concentration of a molecule is a way of stating the
amount of that molecule dissolved in solution.

Percent gives the relative mass of a solute found in a
given volume of solution.

A mole is the name for the number of atoms in an atomic
weight of that element, or the number of molecules in a
molecular weight of that type of molecule, with the
molecular weight being the sum of all the atomic weights
of the atoms that make up the molecule.
Copyright 2009, John Wiley & Sons, Inc.
Acids & Bases
Base
Acid

A proton
(H+)
donor


A proton (H+) acceptor
OH- is what is usually found in
solution that will bind to free H+’s
Strong Acid/Base
• Either will completely
dissociate when put into
H2O, releasing all of the H+
or OH- in their make-up
• The rxn is not freely
reversable
• Ex.
• HCl  H+ + Cl• NaOH  Na+ + OH-
Weak Acid/Base
• A proton (H+) acceptor
• OH- is what is usually
found in solution that will
bind to free H+’s
• Rxn is reversible
• Ex.
•
H3COOH ↔ CH3COO- + H+
42
Dissociation of Acids, Bases, and
Salts
Copyright 2009, John Wiley & Sons, Inc.
pH
pH scale expresses hydrogen ion (H+) concentration in a solution.
scale range = 0-14
neutral = 7
Acids release H+
thus increasing [H+]
pH values < 7
Bases lower [H+]
bond up H+ or
Release OHpH values > 7
Why do we care about pH?
pH can affect:
Shapes and functions of molecules
Rates of many chemical reactions
Ability of two molecules to bind to each other
Ability of ions or molecules to dissolve in water
Organisms usually tolerate only small changes in pH
BLOOD pH MUST BE MAINTAINED AT 7.35-7.45
Buffers help to keep a relatively constant pH
Buffers act as a reservoir for hydrogen ions, donating or removing
them from solution as necessary.
Buffers- convert strong acids or bases→ weak acids or bases
Examples of buffers used by living systems include:

Bicarbonate, Phosphates, Amino Acids, Proteins as Components
↔
H2CO3
Carbonic Acid
H+
+
Proton
Conjugate Acid (H+ donor)
HCO3Bicarbonate Ion
Conjugate Base (H+ acceptor)
b/c the rxn is reversible:




In a  [H+] flow in 
In a  [H+] flow in 
Thus: H2CO3 and HCO3- remain in constant equilibrium
The greater the buffer concentration the more resistant to D, but
pH may still D just not as drastically as seen w/o the buffer
AP1: Ch. 2: Chemical Basis of Life
46
Carbon Dioxide
Oxygen



21% of earth’s
atmosphere is O2
Essential to lives of most
animals
Humans use it in the final
step in a series of rxns in
which e+ is extracted
from food molecules



Byproduct of organic
molecule metabolism
A small % is eliminated
via exhalation
Accumulation of high
amounts is toxic to cells
AP1: Ch. 2: Chemical Basis of Life
47
Carbon is unique in that it can form covalent bonds w/ up
to 4 other atoms allowing the formation of the large,
diverse, complicated molecules required for life.
•
•
These molecules are:
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic Acids
•
Carbon Backbone: series of C atoms bound together
by covalent bonds
•
CB allows for variation in length as well as highly
varied combinations of atoms.
AP1: Ch. 2: Chemical Basis of Life
49
Carbohydrates
Made up of C, H, O in a 1:2:1 ratio
Glucose : C6-H12-O6
•
•
Carbo: Atom
Hydrates: Hydrated
Range from small to large in size
1.
2.
3.
•
Monosaccharide- Mono 1 Simple Sugar
Disaccharide- Di 2
Polysaccharide- Complex Sugar
Functions:
A.
Structural: ribose and deoxyribose (DNA, RNA, ATP)
B.
Energy: simple sugars(monosaccharides) can be used as
an immediate e+ source, complex sugars must be
processed before use
•
Glycogen (polysaccharide) - e+ storage molecule
C.
Bulk: cellulose (polysaccharide) forms the bulk of feces
AP1: Ch. 2: Chemical Basis of Life
50
Monosaccharides = 1 (mono) sugar
Copyright 2009, John Wiley & Sons, Inc.
Disaccharides

Combining 2 monosaccharides by dehydration
synthesis releases a water molecule.



sucrose = glucose & fructose
maltose = glucose & glucose
lactose = glucose & galactose (lactose intolerance)
Copyright 2009, John Wiley & Sons, Inc.
•
•
Polysaccharides (PS) = many (poly) sugars
Many MS’s bound together to form long
chains (can be straight or branched)
3 major types:
–
In animals you find 1 type in plants 2 types
a)
Glycogen: “animal starch”; used as an e+
storage molecule. When quickly
metabolized it results in e+ for cells
b)
Starch: long chains of glucose used for e+
storage in plants
•
Humans can break it down & use it for e+
Cellulose
c)
•
•
Long chains of glucose that fxn as a structural
molecule in plants
Humans can’t break it down & use it for e+,
thus it b/comes bulk of feces
53
Lipids (a.k.a. fats)
•
•
•
•
Major components: C, H, & O
Minor components: P & N
Compared to carb’s, lipids do not have 2:1 ratio of H
to O and have a lower ratio of O to C, this makes
them less polar thus they can be dissolved in nonpolar organic solvents (acetone, alcohol)
4 major groups:
–
–
–
–
Triglycerides
Phospholipids
Steroids
“Other”
AP1: Ch. 2: Chemical Basis of Life
54
•
Fxns of lipids:
Protection: surrounds and protects organs
Insulation: fat under the skin prevents heat loss; myelin
sheaths electrically insulate axons of neurons
Regulation: steroids regulates physiological
processes prostaglandins regulate inflammation
Vitamins: “fat soluble” vitamins do many things
A.
B.
C.
D.
•
•
•
•
E.
Vit A forms retinol req’d for night vision
Vit D Promotes Ca2+ uptake in bone tissue
Vit E Promotes healing
Vit K  necessary to form clotting factors
Energy: can be broken down to yield more e+ than
either carb’s or proteins
AP1: Ch. 2: Chemical Basis of Life
55
Triglycerides
•
•
Make-up 95% of fats in the
human body
1- glycerol + 3 Fatty Acids (FA’s)
FA’s differ from each other by #
of C’s and degree of saturation
–
2 types:
1.
Saturated
•
Fatty Acid
Glycerol
•
Fatty Acid
Only single covalent bond btwn
C’s in the carbon backbone
Unsaturated
2.
•
1 or more double covalent bond
btwn C’s in the carbon backbone
a)
b)
Monounsaturated
Polyunsaturated
AP1: Ch. 2: Chemical Basis of Life
Fatty Acid
56
Triglycerides
Copyright 2009, John Wiley & Sons, Inc.
Phospholipids (PL)

Glycerol + 2 FA’s + phosphate
containing molecule


Polar Molecule:



Notice structurally similar to TG’s
Hydrophilic Head (Polar)
Hydrophobic Tails (Non-polar)
Essential in the cell
membrane’s structure
AP1: Ch. 2: Chemical Basis of Life
58
Chemical Nature of Phospholipids
head
tails
2-59
Steroids
•
•
•
Structurally they are a unique
lipid, but their solubility
characteristics are similar
All composed of C’s bound
together in a 4-ring-like
structure
Important Examples:
–
Cholesterol (building blocks for
other steroids)
Ingest too much  heart disease,
but it is still essential to diet
–
–
–
–
Bile Salts
Estrogen
Progesterone
Testosterone
AP1: Ch. 2: Chemical Basis of Life
60
Other Lipids
•
•
Eicosanoids
–
–
–
–
a)
b)
c)
Group of important
molecules derived from
FA’s
Made in most cells
Important regulatory
molecules
Examples:
Prostaglandins: implicated
in regulation of hormones
for blood clotting, some
reproductive fxns, and
more (*Asprin*
Thromboxanes
Leukotrienes
Fat Soluble Vitamins
–
Structurally not similar to
one another but they are
non-polar molecules
essential to normal body fxn
AP1: Ch. 2: Chemical Basis of Life
61
Proteins



Major components: C, H, O, & N
Minor components: S, P, Fe, and I
Protein’s molecular mass can be huge:



NaCl= 58
Glucose= 108
Proteins  1000 to several million
AP1: Ch. 2: Chemical Basis of Life
62
Fxns of proteins
1.
Regulation
–
Enz’s control chem rxns and hormones regulate many
physiological processes
Transport
2.
–
Can help to transport things in the watery environment of the
blood & can control mvmt in & out of cell
Protection
3.
–
Antibodies and complement system proteins protect against
foreign invaders
Contraction
4.
–
Actin and Myosin and proteins involved in muscle movement
Structure
5.
–
–
Collagen fibers give structural framework
Keratin lends strength to hair, skin, nails
Energy
6.
–
Can be broken down to produce e+ equals the same yield as
carb’s
63
Protein Structure

The building blocks of proteins are
amino acids(AA):



These are made up of a central C with
an Amine group at one end and a
carboxyl group at the other
The R-Group varies from AA to AA
Btwn each AA the Amine and Carboxyl
groups bind to each other and form
Peptide Bonds. Thus the reason
proteins are often referred to as
polypeptides.
64
All 20 Amino Acid Structures
AP1: Ch. 2: Chemical Basis of Life
65
Formation of a Dipeptide Bond


Dipeptides formed from 2 amino acids joined by a
covalent bond called a peptide bond
 dehydration synthesis
Polypeptides chains contain 10 to 2000 amino acids.
Copyright 2009, John Wiley & Sons, Inc.
4 Levels Protein Structure
1.
Primary (1o)
- Sequence of aa bound by peptide bonds
2.
Secondary (2o) a-helix & b-pleated sheet
- Local structure that results from H-bonding
-If these bonds are broken by temperature
or pH D the protein will unfold & become
non-functional
3.
Tertiary (3o)- 3D structure
-Caused by the interactions btwn the
polypeptide and its immediate environment
4.
Quaternary (4o)
-Spatial relationships between individual
subunits
AP1: Ch. 2: Chemical Basis of Life
67
Copyright 2009, John Wiley & Sons, Inc.
Proteins : Enzymes
•
•
•
Protein catalyst that increases the
rate of chemical rxn w/o being Ded
itself
An enz’s 3-d shape is essential for
its fxn
Lock & Key Model (old name)
–
–
•
Induced fit model (new name)
–
–
•
Lock: Active Site
Key: Reactants
more correct term
The enz can D shape significantly to fit
reactants
Enz’s lower activation e+ b/c they
orient the reactant in such a way
that chem rxn is more likely to occur
69





Enzyme binds reactants
Combines reactants
Releases reactant so that it can do it
all over again
It is capable of catalyzing multiple
reactions
Some enz’s require co-factors to fxn
or an organic molecule

Co-factors: ions



Usually finalize the shape of the active
site
Organic Molecule: co-enzymes
-ase …this suffix means enzyme
70
H2O
Substrates
Sucrose and
Water
Enzyme
Sucrase
Active site
of enzyme
1 Enzyme and substrate
come together at active
site of enzyme, forming an
enzyme–substrate complex
3 When reaction is complete,
enzyme is unchanged and
free to catalyze same reaction
again on a new substrate
Products
Glucose
Fructose
2 Enzyme catalyzes
reaction and transforms
substrate into products
Mechanism of enzyme action
Nucleic Acids - Made-up of C,H,O,N & P
•building blocks are called nucleotides
Basic Nucleotide →
Nitrogenous
Base
Phosphate
Group
Pentose Sugar
DNA- genetic code
RNA- mRNA, rRNA, tRNA
Deoxyribonucleic Acid
Double Helix
Ribonucleic Acid
Single stranded
Nitrogenous Organic Bases- 2 types
Pyrimidines




Cytosine
Thymine
Uracil
Purines


DNA bases
• Adenine
• Guanine
• Cytosine
• Thymine
Guanine
Adenine
RNA bases
• Uracil
• Guanine
• Cytosine
• Adenine
AP1

RNA (single stranded)

AP1
DNA (Double Stranded)
DNA
•
•
•
DNA is a double helix
– “twisted ladder”
Vertically nucleotides are held together
via a covalent bond between the
phosphate group of 1 NA and the next
Horizontally, nucleotides are held
together via a H bond between
nitrogenous bases next to each other
*NB’s must have to correct partner to bind to**
→ complementary base pairing
–
DNA :T=A G=C
–
RNA: U=A G=C
DNA
•
•
•
The two opposing strands of DNA
also run antiparallel to each other.
– Meaning the sugar phosphate
backbone of 1 strand runs the
opposite direction of it’s partner
• 5’  3’
• 3’  5’
Within DNA the sequence of bases is
a “code” that stores information used
to determine the structure and fxn of
cells
Gene: sequence of DNA that directs
the synthesis of an RNA molecule
that will become a protein
Adenosine Triphosphate (ATP)
Temporary
molecular storage of
energy as it is being
transferred from
exergonic catabolic
reactions to cellular
activities
Copyright 2009, John Wiley & Sons, Inc.
Formation & Usage of ATP


Hydrolysis of ATP (removal of terminal phosphate group by
enzyme -- ATPase)
 releases energy
 leaves ADP (adenosine diphosphate)
Synthesis of ATP
 enzyme ATP synthase catalyzes the addition of the
terminal phosphate group to ADP
 energy from 1 glucose molecule is used during both
anaerobic and aerobic respiration to create 36 to 38
molecules of ATP
Cyanide Poisoning:
 The way cyanide works is by impeding the production of
ATP within the mitochondria
Copyright 2009, John Wiley & Sons, Inc.