II. Elements Chemistry Atoms Ch 2: Chemistry Comes … 105 Ch 2 Chemistry.pdfCh 2: Chemistry Comes...
Transcript of II. Elements Chemistry Atoms Ch 2: Chemistry Comes … 105 Ch 2 Chemistry.pdfCh 2: Chemistry Comes...
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Chemistry
Ch 2: Chemistry Comes to Life
Biol 105
Lecture 2
Reading: Chapter 2 (pages 20-29)
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Outline
I. Why study Chemistry
II. Elements
Atoms
Isotopes
Periodic Table
Electrons
Bonding
III. Bonds
Covalent bonds
Polarity
Ionic bonds
Hydrogen bonding
IV. Water
V. Acids and Bases
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Why study Chemistry?
Chemistry is the basis for studying much of biology
The biology of the human body follows the rules of physics and chemistry.
You need to understand enough about chemistry to know what kind of things will cross a membrane, and what biological compounds make up cells, and structures within cells. Eg. What is a protein?
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The Nature of Atoms
Everything that takes up space and has mass is
called matter
All matter is made of atoms, each containing a
nucleus with protons and neutrons surrounded
by a cloud of electrons
Atoms are units of matter that cannot be broken
down into simpler substances by ordinary
chemical means
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TABLE 2.1 Review of Subatomic Particles
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The Atom Cont.
Protons and neutrons are in the center of the
atom (called the nucleus)
Electrons orbit around the outer edge in orbitals
In each uncharged atom the # electrons = #
protons
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Chemistry and Biology
Figure 2.1c
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Shell Model of Electrons
Electrons can be visualized as residing in shells
around the nucleus.
The first shell can have up to two electrons
The second shell can have up to eight electrons
The third, fourth … shells can have up to eight
electrons
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Protons are found in the …
1. Nucleus
2. Orbital shells
Nucleus
Orbita
l shells
50%50%
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How many electrons can be in the 1st shell?
1. One
2. Two
3. Four
4. Eight
One Tw
o
Four
Eight
25% 25%25%25%
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How many electrons can be in the 2nd shell?
1. One
2. Two
3. Four
4. Eight
One Tw
o
Four
Eight
25% 25%25%25%
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The Nature of Atoms
Element
A form of matter that cannot be broken down
into simpler substances
Made of many atoms that are all the same
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Definitions and the Basics
Matter is anything that takes up space and has
mass.
Atoms are units of matter that cannot be broken
down into simpler substances.
An element is a “pure” form of matter containing
only one kind of atom.
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Elements in nature
Text page 22
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Figure 2.2 The Periodic Table (After Dmitri Mendeleev 1869).
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The Nature of Atoms
Each element has an atomic number and atomic
mass
Atomic number
The number of protons in the nucleus
Atomic mass
The number of protons plus the number of neutrons
(note that electrons have an insignificant mass)
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Particle Mass
Proton = 1 amu
Neutron = 1 amu
Electron = negligible
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How many electrons does Be have?
1. 4
2. 5
3. 9
4. 13
4 5 9 13
25% 25%25%25%
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The Nature of Atoms - Isotopes
Elements with the same number of protons but
different numbers of neutrons are called isotopes
Example of Carbon atom
All carbon atoms have six protons in the nucleus
Common isotopes of carbon include 12C (with six
neutrons), 13C (with seven neutrons), and 14C (with
eight neutrons)
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Isotopes of Hydrogen
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Radioactive Isotopes
In 1896, Henri Becquerel placed a rock on unexposed photographic plates inside a drawer. The rock contained uranium.
The isotopes of uranium emit energy.
After a few days the plate had an image of the rock.
A co-worker, Marie Curie, named this radioactivity. This is known as a radioisotope
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Radioactive Isotopes
Radioisotopes are isotopes that are unstable, and become more stable by emitting energy and particles
In contrast, most isotopes are stable
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Radioisotopes in Medicine
PET scans (Positron-Emission Tomography)
Patient is injected with a compound that is labeled
with an unstable isotope
Cancer cells are growing faster and take up more of
the compound than normal cells
Abnormal tissue takes up less of the compounds
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Isotopes in medicine
Figure 2.4
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Isotopes are atoms of the same element that differ in their
number of …
1. Protons
2. Electrons
3. Neutrons
4. None of the above
Proto
ns
Elect
rons
Neutrons
None of t
he above
25% 25%25%25%
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Carbon has 6 protons, 6 electrons and 6 neutrons.
Its atomic number is ___.
1. Six
2. Eight
3. Twelve
4. Twenty-four
Six
Eight
Twelve
Twenty
-four
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Carbon has 6 protons, 6 electrons and 6 neutrons.
Its atomic weight is ___.
1. Six
2. Eight
3. Twelve
4. Twenty-four
Six
Eight
Twelve
Twenty
-four
25% 25%25%25%
The atomic weight = an average of the isotopes
Mass number = round the atomic weight
Mass Number = (Number of Protons) + (Number of
Neutrons)
Number of Neutrons = Mass number - # of Protons
Atomic number
Atomic weight
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How many neutrons does Li have?
1. 3
2. 4
3. 7
4. 10
3 4 7 10
25% 25%25%25%
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Chemical Bonds
Chemical bonds are unions between electron
structure from different atoms
Molecules are when two or more atoms join
together. They can be the same element (H2) or
different elements (H2O)
When different elements join the molecule is
referred to as a compound molecule
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Electrons and Bonding
If the outer shell is full, then it is non-reactive
and stable = does not form chemical bonds.
Incompletely filled outer orbital, then atom
reactive and will form chemical bonds.
How many bonds it can form depends on how
many empty spots in outer shell
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Chemistry and Biology
Figure 2.8
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Chemical Bonds
Covalent bonds
Ionic
Hydrogen
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Covalent bonds
Covalent bonds
The strongest bonds
They form when two or more atoms share the
electrons in their outer shells
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How many bonds can form?
Each atom wants their outer shell filled.
Hydrogen only has one electron in its shell –
wants two, so it can form one bond.
Carbon has four electrons in outer shell,
wants eight, so it can form four bonds.
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Double Bond
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How many bonds can carbon form?
1. One
2. Two
3. Three
4. Four
One Tw
o
Three
Four
25% 25%25%25%
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How many bonds can hydrogen form?
1. One
2. Two
3. Three
4. Four
One Tw
o
Three
Four
25% 25%25%25%
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How many bonds can helium form?
1. None
2. One
3. Two
4. Three
None One
Two
Three
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How many bonds can nitrogen form?
1. One
2. Two
3. Three
4. Four
One Tw
o
Three
Four
25% 25%25%25%
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How many bonds can oxygen form?
1. One
2. Two
3. Three
4. Four
One Tw
o
Three
Four
25% 25%25%25%
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Types of Covalent Bonds
Covalent bonds
• Polar
• Nonpolar
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1. Covalent Bonding
When two atoms with unpaired electrons in the
outer most shell come together and share
electrons
Each atom has an attractive force for the other
atoms unshared electrons, but not enough to
take it completely away
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Covalent Bonding
Covalent bonds can be polar or nonpolar
Nonpolar bonds the atoms have same pull on the
shared electrons (H2)
Polar bonds – the atoms don’t equally share the
electrons (H2O)
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Polar Covalent Bond
Figure 2.11a © 2014 Pearson Education, Inc.
Polarity
Some atoms have a greater pull on shared electron than other atoms
The measure of this pull is electronegativity
When a bond is made between atoms with different electronegativities it is a polar bond
The greater the pull the more electronegative (remember that electrons are negative)
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Polarity Con’t
Polar Covalent Bonding occurs with strong
electrophiles (electronegative): atoms with nuclei
that have a strong pull on electrons. Common
examples in biological molecules include:
Oxygen
Nitrogen
Sulfur (less than oxygen or nitrogen)
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Polarity
The oxygen side of water is slightly negative and
the hydrogen sides are slightly positive
C
H
H H
H
C
H
H O
H
HO
H
H
H3C
H2
C
CH2
C
O
HH3C
H2
C
CH2
C
CH3
O
H3C
H2
C
CH2
H2
C
CH2
H2
C
CH2
CH3
Water Alcohol
Ketone Aldehyde
Hydrocarbons
N
HH
CH3
S
H
CH3
HC
HC
CH
CH
CH
HC
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Biological molecules - functional groups
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Polar Groups
Oxygen containing:
Carboxyl = - COOH
Hydroxyl (alcohol) = - OH
Phosphates = -PO4
Carbonyl
Ketone = - CO
Aldehyde = - CHO
Nitrogen containing: Amino (-NH2)
Sulfur containing: -SH
CH3CH2CH2OH
CH3-O-CH2CH3
CH3CH2CH3
Carboxyl
Alcohol
Ketone
Aldehyde
Ether
Hydrocarbons
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Nonpolar compounds
Hydrocarbons – lots of carbons and
hydrogens bonded together
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Terminology
Hydrophilic (water-loving) – polar molecules that
are attracted to water
Hydrophobic (water-fearing) – nonpolar
molecules that are pushed aside by water
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Chemical formulas
When we write compounds, we often write them
as a formula that tells how atoms many of each
element are present, but not the way the
molecule is put together.
You often can determine the way the molecule is
put together by knowing how many bonds each
element can form.
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Examples
How would you draw this compound?
H2O
O H
H
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Examples
How would you draw this compound?
C4H10
C C C C
H
H
H H H
H
H
H
H
H
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Examples
How would you draw this compound?
C4H8
C C C C
H
H
H H
H
H
H
H
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Examples
How would you draw this compound?
CO2
C OO
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Examples
How would you draw this compound?
C2H4O
C C H
H
H
H O
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2. Hydrogen Bonding
Weak attraction between a hydrogen atom with
a partial positive charge and another atom with a
partial negative charge (electronegative atom
such as oxygen, nitrogen, or sulfur).
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2. Hydrogen Bonding
Individually weak, but many together can be
strong.
Determines shapes of many biological
molecules including proteins and DNA
2. Hydrogen bonds
Figure 2.11b
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3. Ionic Bonds
Ion = atom that has gained or lost electrons, It
no longer has a balance between protons and
electrons, it is positive or negative charge
Ionic bond is an association between ions of
opposite charge
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3. Ionic bond
Figure 2.10
Chemical bonds
Table 2.2
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Water – The Life Giving Molecule
Why are we so interested in finding evidence of water on Mars?
What would it mean if we did not find evidence of water? Or if we find evidence? Does it matter what form the water is?
Life exists here because water is abundant
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Water’s Abundance
71% of Earth’s surface is water
97.5% of the water is salt water
Freshwater only accounts for 2.5% of water
Only 0.53% is available to us to drink (rivers, lakes, ground water)
66% of the human body is water by weight
75-85% of a cell’s weight is water
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The Role of Water in Life
Web Activity: Water and Chemistry © 2014 Pearson Education, Inc.
Water
Water is polar and forms hydrogen bonds
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Hydrogen bonding
Water is a great example of hydrogen bonding,
itis the hydrogen bonds that give water much of
its unique characteristics
O
H
H
OH
H© 2014 Pearson Education, Inc.
Exists in Three Forms
Water exists in three forms
Solid - Ice
Liquid
Vapor
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Properties of Water
1. Water is an excellent polar solvent
2. Water has cohesion
3. Water has high heat capacity
4. Water has high heat of vaporization
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1. Water is an excellent polar solvent
Because water is polar and forms hydrogen
bonds, it acts as a solvent for polar molecules
Like dissolves in like, so polar molecules
dissolve in water
Water is considered the best polar solvent – due
in great part to its ability to form hydrogen bonds
with other molecules
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Why is this property important?
Blood is approx 55% water so the fact that water
is a good solvent makes blood a good way to
transport things around since things stay in
solution.
Cells are made up of mainly water (75-85%), the
water keeps salts in your cells, blood and tissues
in solution (dissolved).
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2. Water has Cohesion
Due to the hydrogen bonding, water has
cohesion (the water molecules cling together)
Cohesion is the capacity to resist breaking under
tension
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2. Water has Cohesion
What allows bugs to walk on water?
Hydrogen-bonds create surface tension
At the surface of water, where water meets air,
the water molecules are being pulled down with
a much greater force than they are being pulled
up towards the air
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Why is this property important?
The cohesion of water allows blood move easier
in the blood vessels.
Also is responsible for moving water in plants
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3. Water has High Heat Capacity
It takes a great deal of energy to raise the
temperature of water as compared to other
compounds.
When you increase the temperature of
something, the molecule in it move faster,
hydrogen bonds keep the water molecules in
place so it takes lots of energy to break the
bonds and heat the water
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Why is this property important?
Water in our bodies keep us at a constant temp.
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4. Water has High Heat of Vaporization
It takes a great deal of energy to make water
evaporate (change water from a liquid to a gas).
Hydrogen bonds must be broken in order to
change water from liquid to vapor
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Why is this property important?
Sweat is mainly water, when we sweat the body
uses its heat to vaporize the water – cooling us
off.
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H2 is a(n):
1. Atom
2. Molecule
3. Compound molecule
Atom
Mole
cule
Compound m
olecu
le
33% 33%33%
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Hydrophobic molecules are __________ by water.
1. Attracted
2. Repelled
Attrac
ted
Repelled
50%50%
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What type of bond between water molecules creates
surface tension that gives water cohesion?
1. Ionic
2. Covalent
3. Hydrogen
Ionic
Covalent
Hydroge
n
33% 33%33%
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Water ….
1. Makes ionic bonds
2. Is nonpolar
3. Is polar
Makes i
onic bonds
Is nonpola
r
Is pola
r
33% 33%33%
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Which property of water provides the cooling effect of
sweating?
1. Cohesiveness
2. High heat capacity
3. High heat of vaporization
4. Excellent solvent
Cohesiveness
High h
eat capac
ity
High h
eat of v
aporizatio
n
Excelle
nt solve
nt
25% 25%25%25%
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Acids and Bases
We are already familiar with acids and bases
Common acids:
Lemon juice
Sodas
Vinegar
Common bases:
Ammonia
Many household cleaners
Bleach© 2014 Pearson Education, Inc.
Acids and Bases
Acids – Substances that donates hydrogen ions
when in solution
Bases – Substances that accept hydrogen ions
when in solution (sometimes we say that bases
release OH- (hydroxyl ions)
In solution:
H+ + Cl- + Na+ + OH- H2O + NaCl
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Ph Scale
The strength of acids and bases is measured using
the pH scale.
pH = -log10[H+]
[H+] = conc in moles per liter
It is inverse relationship:
Higher the pH the lower the concentration of H+
Logarithmic:
Each point increase in pH represents a ten-fold
decrease in H+ concentration. © 2014 Pearson Education, Inc.
Ph Scale
Scale from 0 – 14
0 is the most acidic
14 is the most basic
7 is neutral (pure water)
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Acids and Bases
Table 2.3
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The higher the pH a solution has, the higher the H+
concentration
1. True
2. False
True
False
50%50%
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Is a pH of 8 acidic or basic?
1. Acidic
2. Basic
Acidic
Basic
50%50%
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Biological Fluids
Blood – pH 7.35 Changes in pH of ± 0.1 can damage cells, pH of 7.8 can be lethal
Biological fluids have buffers to keep the pH stable.
Most biological fluids are between 6 – 8
Stomach fluid – pH of under 2
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The Role of Water in Life
Buffers
Prevent dramatic changes in pH
Remove excess H+ from solutions when
concentrations of H+ increase
Add H+ when concentrations of H+ decrease
Many body fluids have the buffering capacity to
maintain a stable internal environment
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Important Concepts
Reading for next lecture: Chapter 2 (pages 29 –
41)
Know what the three particles of an atom are,
where are they located, what is their charge, and
their mass.
Be able to determine how many bonds each
element can form.
Be able to recognize if a molecule is drawn
correctly.
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Important Concepts
Be able to read the periodic table to determine
the number of protons, neutrons and electrons in
the atoms of all the biologically important
elements.
What are the three most common elements in
the human body
Be able to draw the atom of any biologically
important element, with the correct number of
protons, neutrons, and electrons. Be able to
draw the electrons in their correct shell.
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Important Concepts
Be able to identify polar and nonpolar molecules
Be able to describe the types of chemical bonds
What are three electronegative elements found in
biological molecules?
Know the functional groups and if they are polar
Be able to draw a water molecule and hydrogen bonding
between water molecules
Be able to describe the four properties of water and their
importance in living organisms.
Understand the pH scale
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Definitions
Matter, Atom, Element, Isotopes, Radioisotopes,
Chemical bonds, single bond, double bond,
Molecules, Compound Molecules, Ion, Ionic bond,
Covalent bond, Nonpolar bonds, Polar bonds,
electronegativity, Hydrogen bond, Hydrophilic,
Hydrophobic, Cohesion, acid, base, buffers,
logarithmic, inverse, pH, solvent, solute, solution