Bio156IN – Human Biology for Allied Health
Chapter 2 – Basic Chemistry
Lab: #2 Atoms, Molecules and Models Part I
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March 1st: Part IV Basic Chemistry
• Lecture Notes: Basic Chemistry
• Atoms Video: (Khan Academy) ?
• Lab 2: Atoms, Molecules, Models Part I
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Learning Objectives:
1.
Define matter, an element, and a trace element.
2.
Define a compound.
3.
Describe the structure of an atom.
4.
Define the atomic number and mass number of an atom.
5.
Define an isotope and explain what makes some isotopes
radioactive.
6.
Explain why radioactive isotopes are important to biologists.
7.
Explain how the electron configuration of an atom influences its
chemical behavior.
8.
Distinguish among nonpolar covalent, polar covalent, and ionic
bonds, noting their relative strengths and functions and the
methods by which they are diagrammed.
9.
Describe the special properties of water that make it vital to
living systems. Explain how these properties are related to
hydrogen bonding.
10. Define a chemical reaction and distinguish between the
reactants and the products.
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The emergence of biological function
starts at the chemical level
• Everything an organism is and does depends
on chemistry
• Chemistry is in turn dependent on the
arrangement of atoms in molecules
• In order to understand the whole, biologists
study the parts (reductionism)
4
• Molecules and ecosystems are at opposite
ends of the biological hierarchy
– Each level of organization in the biological hierarchy
builds on the one below it
– At each level, new properties emerge
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• A biological
hierarchy
starting at
the chemical
level
D. Organ: Flight
muscle of a moth
Rattlebox moth
C. Cell and tissue:
Muscle cell within
muscle tissue
Myofibril
(organelle)
B. Organelle: Myofibril
(found only in muscle
cells)
Actin
Figure 2.1
A. Molecule: Actin
Myosin
Atom
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Life requires about 25 chemical
elements
• 92 naturally occurring elements or atoms
• about 25 different chemical elements are essential
to life
• oxygen, carbon, hydrogen and nitrogen are
particularly abundant making up 96.3% of the
human body
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• Carbon,
hydrogen,
oxygen, and
nitrogen make
up the bulk of
living matter,
but there are
other elements
necessary for
life
Table 2.2
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• Goiters are caused by iodine deficiency
Figure 2.2
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Elements can combine to form
compounds
• Chemical elements combine in fixed ratios to form
compounds
• Example: sodium + chlorine  sodium chloride
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Elements are made up of atoms
• Atoms are the smallest portions of an
element that exhibit the chemical
characteristics of that element
• Atoms cannot be broken down to other
substances by ordinary chemical means
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Atoms consist of:
protons, neutrons, and electrons
• The smallest particle of an element is an atom
• Different elements have different types of atoms
• Atoms are composed of subatomic particles
– Protons
– Electrons
– Neutrons
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• An atom is made up of protons and neutrons
located in a central nucleus
• The nucleus is surrounded by electrons
2
Protons
Nucleus
Figure 2.4A
2
Neutrons
2
Electrons
A. Helium atom
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• Each atom is held together by attractions between
the positively charged protons and negatively
charged electrons
• Neutrons are electrically neutral
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Protons
Nucleus
Figure 2.4B
6
Neutrons
6
Electrons
B. Carbon atom
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• Atoms of each element are distinguished by
a specific number of protons
– The number of neutrons may vary
– Variant forms of an element are called isotopes
– Some isotopes are radioactive
Table 2.4
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16
Electron arrangement determines the
chemical properties of an atom
• Electrons are arranged in shells
–
–
–
–
Each shell or orbital can accommodate a specific # of electrons
The innermost level holds 2 electrons
H has 1 electron in this shell; He has 2
The outermost shell determines the chemical properties of an
atom
– In most atoms, a full outer shell holds eight electrons
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• Atoms whose shells are not full tend to interact
with other atoms and gain, lose, or share electrons
Outermost electron shell (can hold 8 electrons)
Electron
HYDROGEN (H)
Atomic number = 1
First electron shell (can hold 2 electrons)
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8
Figure 2.6
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Atoms react to form molecules
• Reactions involve sharing or transferring
outer electrons
• Atoms with unfilled outer energy levels
become stable by gaining, losing or sharing
electrons with other atoms
• This exchange/sharing of electrons results
in the formation of chemical bonds that hold
molecules together
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Periodic table of elements
• The periodic table shows:
– Symbol and name of element
– Atomic number = # of protons
– Atomic Weight = # protons + # neutrons
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The Periodic Table
Atomic number = # of protons
Atomic weight = # protons + # of neutrons
http://www.webelements.com/
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Compounds
• A compound is a substance consisting of
two of more elements
• Because of their outer electrons some
atoms are very reactive and will readily
combine to form compounds
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Lab 2 Atoms, Molecules, Models
• Define basic chemistry terms
• Calculate the atomic weight and atomic
number of an element
• Be able to identify an element using the
Periodic Table of elements
• Build and identify a model that represents
a water molecule
• Describe the polarity of water using
models
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March 2nd
• Lecture Notes: Water
• Lab 3: Atoms, Molecules, Models Part II
• Video: Properties of Water
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DUE TODAY – March 1st
1.
Hand in completed Lab 1
2.
Read Intro. pp. 1-11; Chemistry pp. 23-39
FOR NEXT CLASS – March 2nd
1.
Read pages 42-47 of text (Organic Compounds to
Proteins
2.
Bring Labs 3, 4 Handouts
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Water
• Like no other common substance, water
exists in nature in all three physical states:
• as a solid
• as a liquid
• as a gas
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• Earth, clouds, and oceans
Figure 2.10x
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Water and hydrogen bonds
• Hydrogen bonds:
– do not create molecules
– can change molecular shapes or pull molecules together
– result in surface tension
• Hydrogen bonds make liquid water cohesive
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Water and hydrogen bonds
• Cohesion is the tendency of water molecules
to stick together
• Surface tension results from the cohesion of
water molecules to each other
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The difference between:
• Cohesion = the attraction between
molecules of the same kind
• Adhesion = the attraction between
different kinds of molecules
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• Trees move water by capillary action
which is the result of both cohesion and
adhesion
Figure 2.11x
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Hydrogen bonds make liquid water cohesive
• Due to hydrogen bonding,
water molecules can move
from a plant’s roots to its
leaves
• Insects can walk on water
due to surface tension
created by cohesive water
molecules
Figure 2.11
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Water in the human body
• Water is the single most important component of
the body
• Accounts for 2/3 of body weight
• Most chemical reactions in the body take place in
water
• Most organic molecules are soluble in water e.g.
sugars and salts
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Water’s hydrogen bonds moderate
temperature
• It takes a lot of energy to disrupt hydrogen
bonds
– Therefore water is able to absorb a great deal of heat
energy without a large increase in temperature
– As water cools, a slight drop in temperature releases a
large amount of heat as hydrogen bonds are formed
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– A water molecule takes a large amount of energy
with it when it evaporates
– This results in evaporative cooling
Figure 2.12
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Ice is less dense than liquid water
• Molecules in ice are farther apart than those in
liquid water
Hydrogen bond
ICE
Hydrogen bonds are stable
Figure 2.13
LIQUID WATER
Hydrogen bonds constantly
break and re-form 38
• Frozen water floats (left)
• Frozen benzene sinks (right)
Figure 2.13x2
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• Ice fishing
Figure 2.13x1
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Water is a versatile solvent
• Solutes whose charges or polarity allow them to
stick to water molecules dissolve in water
– forming aqueous solutions
– e.g. Na+ and Cl- have affinities
for different parts of the water
molecule
Na+
–
Na+
–
+
Cl–
+
–
+
–
+
–
Cl–
Ions in
solution
Figure 2.14
Salt
crystal
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June 3rd Part 3
• Lecture Notes: Chemistry cont.
• Video: Chemical Bonding
• Chapter 2 Study Guide
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Three types of chemical bonds
• There are three types of chemical bonds
involved in the formation of compounds
1. ionic
2. covalent
3. hydrogen
• When chemical bonds are formed – outer
electron orbitals become filled
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1. Ionic Bonds
• Ionic bonds involve the outright transfer of
electrons from one atom to another
• Ionic bonds form ionic compounds = salts
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1. Ionic Bonds
• some atoms have such a strong attraction for
electrons that they will steal them from other
atoms
• the specific structure of an atom determines
whether it will gain or loose electrons to form
an ion
• the number of electrons an atom will lose or
gain depends on the number of electrons in the
outermost shell
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1. Ionic Bonds – cations
• If there are fewer than 4 electrons in the
outer shell the atom will tend to lose them
and form a cation
• A cation is a positively charged ion
• A cation has a positive charge because it
lost an electron
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47
How to remember …
Cations are positively charged
Anions are negatively charged
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1. Ionic Bonds - anions
• if there are more than 4 electrons in the
outer shell the atom will gain electrons and
form an anion
• anions have a negative charge because they
gain electrons
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Ionic bond formation involves 3 steps
1. one atom loses electron to become a cation
2. another atom gains the electron and becomes
an anion
3. the opposite charges draw the 2 ions together
like a magnet
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Ionic bonds are attractions between
ions of opposite charge
• When atoms gain or lose electrons, charged atoms
called ions are created
– An electrical attraction between ions with opposite charges
results in an ionic bond
–
+
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na
Na+
Sodium ion
Cl
Cl–
Chloride ion
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Figure 2.7A
Sodium chloride (NaCl)
• Sodium and chloride ions bond to form
sodium chloride, common table salt
Na+
Cl–
Figure 2.7B
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• Salt (sodium chloride, NaCl) crystals
Figure 2.7Bx
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2. Covalent bonds
• Covalent bonds are formed between pairs of atoms
by the atoms sharing electrons to complete their
outer electron shells
– Atoms joined together by covalent bonds form molecules
– Each pair of shared electrons is the equivalent of 1 covalent
bond
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• Molecules can be
represented in
many ways
• Sharing electrons
creates covalent
bonds. Very
strong bonds that
produce a
molecule
Table 2.8
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• Methane, ball and stick model
Figure 2.8Bx
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Polar Covalent Bonds
• elements differ in how strongly they hold
shared electrons
• oxygen is one of the most electronegative of
all the elements
• it will attract shared electrons more than
other elements
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Polar Covalent Bonds
• When pairs of electrons are shared between
identical atoms they are shared very evenly
– e.g. H2, N2, Cl2
• However, in heteroatomic molecules the electron
pairs are unevenly shared
– e.g. HCl
– the electron pair spends more of its time near the chlorine
atom than near the hydrogen atom
δ+H-Clδ-
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Water is a polar molecule
• In a water molecule, oxygen exerts a stronger pull
on the shared electrons than hydrogen
– This makes the oxygen end
of the molecule slightly
negatively charged
– The hydrogen end of the
molecule is slightly
positively charged
– Water is therefore a polar
molecule
(–)
(–)
O
H
(+)
H
(+)
Figure 2.9
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3. Hydrogen Bonds
• The charged regions on
water molecules are
attracted to the oppositely
charged regions on nearby
molecules
– This attraction forms weak
bonds called hydrogen bonds
Hydrogen bond
Figure 2.10A
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Chemical Reactions
• Processes leading to chemical changes in matter
• Involve the making and/or breaking of chemical
bonds
• Result in the formation of a new substance
• May see bubbles or a change of color or a precipitate
• May feel heat or cold (exothermic or endothermic)
• Chemical reactions do not create or destroy matter,
they only rearrange it
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Chemical Equations
• Are a description of what is happening in
a chemical reaction
• They are a shorthand representation of a
chemical reaction that allow you to
describe complex events in a brief and
precise fashion
• REACTANTS  PRODUCTS
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Chemical Equations
• To write a chemical equation, write an atom
using the chemical symbol for that element
• Use atomic symbols to describe molecules e.g.
– H2O
– CO2
– NaCl
– HCl
– NH3
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Chemical Equations
• Reactants
– Substances participating in a chemical reaction
– Shown on left hand side of equation
• Products
– Substances generated by a reaction
–
Shown on the right hand side of the equation
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Chemical Equations
• Equations must be balanced
• The number and kinds of atoms on each
side of the equation must be the same
• Atoms are neither created or destroyed
during a reaction
• Existing atoms are simply rearranged
into different combinations
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Chemical reactions rearrange matter
• In a chemical reaction:
– reactants interact
– atoms rearrange
– products result
Figure 2.17A
2 H2
+
O2

2 H2O
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Patterns of Chemical Reactions
• Synthesis Reactions
• Decomposition Reactions
• Exchange Reactions
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Synthesis Reactions
• Smaller particles bond together to form
larger, more complex molecules
• Example- Amino acids join together to
form a protein
• A+B
AB
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Decomposition Reactions
• Bonds are broken in larger molecules,
resulting in smaller, less complex
molecules
• Example- Glycogen broken down into
glucose units
• AB
A+B
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Exchange Reactions
• Also called Displacement reactions
• Bonds are both made and broken
• Involves both synthesis and
decomposition
• A+C
AC + B
• AB + CD
AC + BD
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