Study Guide for Anatomy and Physiology - Use With an Open Text !
CHEMISTRY (Chapter 2 of Marieb textbook, see pg. 24, Text)
Atoms - building blocks of matter, smallest units of matter
indivisible
by chemical means.
Elements - composed of like atoms.
Molecules - composed of two or more atoms, H2 is
a diatomic molecule, but also units of the
element Hydrogen (H).
Compounds - composed of like molecules, each of which has two
or more different kinds of
atoms.
Hydrogen - the building block of the universe
The simplest atom is common Hydrogen See below:
Protium,
atomic mass or weight
of 1, has 1 proton and one electron. There are two other, rarer, forms
of Hydrogen:
Deuterium (mass=2) and Tritium (mass=3). They are
called
isotopes
(different forms
according to mass but with the same atomic numbers) of Hydrogen because
they all
have one positive proton and one negative electron. All unreacted
or
uncombined
atoms have # protons = # electrons to create a 0 electrical charge.
How many
neutrons does Protium, Deuterium and Tritium have?
X-rays, gamma rays and ultraviolet rays are mutagenic; that is, they
mutate DNA,
the chemical in our cells that carries the messages of inheritance
that regulate cell growth,
reproduction and metabolic activities. See
http://en.wikipedia.org/wiki/Gamma_ray
Why wear "sun screens?"
See:
http://www.epa.gov/radiation/docs/ionize/ionize2.htm,
http://www.cpc.ncep.noaa.gov/products/stratosphere/uv_index/uv_nature.html
and http://www,epa.gov/radiation/students
. Click on What is Radiation,
Types of Radiation;
Some medical Imaging techniques use forms of radiation produced by
decaying
atomic
nuclei. Some forms are more dangerous than others. In general, short
wavelength forms
have very high energy and can therefore mutate the chemical of
inheritance,
DNA, and
cause cancers or the death of cells.
In radiation therapy, beams of gamma rays are focused
on a tumor to 'burn out'
the cancer cells. One goal of physicians has been to lower the dosage
of medical imaging
x-rays or gamma rays which patients are exposed to during their
lifetime.
Recently,
a breast cancer gene (causative in 10% of all breast cancers) has been
discovered that is
activated by x-rays.
If food is bathed by gamma rays (as in sterilization/preservation),
does that make the food
radioactive?
To study the radiation effects of the atomic bombs dropped on Japan,
see
http://www-sdc.med.nagasaki-u.ac.jp/n50/disaster/medical-E.html
Are there any medical procedures or treatments which do not have
risk?
Is it contradictory that x-rays are used to treat cancer but that
they
can cause cancer?
Einstein discovered that Mass (an amount of matter, on Earth
designated
as weight) can be
converted to energy. Some mass is converted to energy in the Fusion
reaction.
Remember, Einstein said:
Some heavier atoms are cooked up in stars, such as Carbon, Iron,
Silicon,
Nitrogen, Sulfur,
Phosphorus, Aluminum, Copper, et c. Since these atoms are in our
tissues,
Carl Sagan calls us
"Star Stuff." There are several types of energy which are important
for Environmental Sciences.
Atomic energy is stored in atoms, it literally holds the atomic
nucleus together.
When atoms are split (as in an Uranium or Plutonium fission bomb or
nuclear reactor)
or fused (as in the Sun or laser fusion devices)some mass is converted
to energy.
Kinetic energy is the energy that moves atoms or molecules.
Kinetic energy provides the energy to collide reactants A with
B
to react to make C product.
Heat increases molecular motion.
Why is it easier to dissolve corn starch or table salt in warm water rather than cold water?
Chemical energy is stored in chemical bonds. Radiant
energy
(travels in waves, see
above) and electrical energy (carried by moving electrons) will
be considered in this course. .
Periodic Chart: Look up element #19 in the periodic chart in
Appendix D.
Here is #12 as an example. See also
http://www.webelements.com
. Also see p. 26, text.
| 2
8 2 |
12
Mg 24.3 |
(numbers at left represent electron configuration 1st shell = top #)
We will deal with small-medium size atoms. With the Periodic Chart
Handout,
or information
included, you should be able to draw Hydrogen (H), Helium (He); Sodium
(Na); Chlorine (Cl);
Carbon (C) and Oxygen (O). Keep in mind that the first electron shell
(K) contains a maximum
of 2 electrons: the second 8: the third 18 (M) etc. Mendeleev
discovered
that, after Helium that
has 2 electrons, every eighth (increasing atomic mass units) element
were inert or
unreactive, they will not normally combine with other atoms
to make molecules. This is called
"The Rule of Octets or Eights." The modern interpretation is that
after Helium,
nonmetal atoms with eight (8) electrons in their outermost shell
are inert. See
pg. 29.
Draw the following atoms. Include the correct number of protons,
neutrons
and electrons in
their shells.
H
He
Ca
Na
Cl
C
N
O
Ne, for example:
10 + K(1)
L(2) M(3)
10
n
2e-
8e-
0
See: http://rex.nci.nih.gov/
Click
on Radioactive fallout. Then click on press release of I-131 fallout
from nuclear bomb testing. How is I-131 different from I-127? See the
map of I-131 exposure, etc.
Using webelements, identify the Sr 90 as an isotope. What periodic
chart
column is it in? It is a relative
of ___________found in bones.
If one eats plants that have soaked up I-131, Sr-90 and Cs-137, does
one's radioactivity
level increase?
Chemical Bonds
The reason why atoms react or combine to form molecules is that in
reacting,
they reach a more
stable outer shell electron arrangement, 8, the magic number for atoms
stability (and lower
energy level). See p. 33-39.
Ionic bond - If a Na gives away an electron to Cl which keeps
it, notice that both atoms have 8
electrons in their outer shell. Now Na+ has a +1 electrical
charge because it lost one negative
electron and; Cl- has an extra electron and thus has a -1
negative charge. Charged atoms are
called Ions. See page 35//34 of Text. Ionic bonds are
formed when atoms give away or receive
electrons. When atoms lose electrons , an oxidation results,
if atoms gain electrons , they
undergo reduction;
Na0 ---> Na+ (+) 1e- (Oxidation of Na); Cl0 + 1e- ---> Cl- (Reduction of Cl)
Nonmetals generally have 4-8 electrons in the outer shell
hold
on to their electrons and
generally "grab for more". Metals are weak electronegative atoms mean
that the atoms which
give up electrons readily; i.e., Metals generally have 1-3
electrons in their outer shells .
Look at your periodic chart. Are Li, Na, K, Mg, Al and Au (gold)
metals?
_____ How about S, O,
Cl and Ar. What are they, metals or nonmetals? _____
| If you dissolve the ionic compound
NaCl in water,
Na+ and Cl - ions will float free and
be surrounded by spheres of water molecules. See page 42//41. |
| NaCl -----> Na + (+) Cl - |
Solutions of ions are called electrolytes, the presence of
which
we will see is essential for
the operation of muscle and nerve cells.
Covalent bonds share electrons. Two electrons form a pair and
share an orbital path; there
are two shared electrons in one covalent bond represented with
a dash . See page 36//35, Oxygen
and Nitrogen. Notice all carbon atoms share 4 bonds (8e- ).
There are two kinds of covalent bonds:
Nonpolar Covalent, where electrons are shared equally by all atoms, e.g., Methane, CH4
H
|
H -- C -- H; O=C=O is Carbon dioxide
|
H
Both of these heavy gases of our atmosphere, along with SO2
and NO2 , contribute to the
greenhouse effect - abnormal warming of the earth (global
warming) is thought
to occur when these gases,
which concentrate close to the earth's surface, trap heat energy
(infra-red
radiation) . CH4 is
also an ozone layer destroying gas. The ozone (03 ) layer
is thought to protect the earth from
harmful ultraviolet waves which are thought to mutate DNA in skin cell
and cause skin cancer.
Nonpolar bonds cannot normally form ions (electrically charged
atoms)
because they continue
to share electrons. Electrons must be given away and retrieved to form
ions.
Polar Covalent bonds have at least one atom which is an
electron
"bully"; the highly
electronegative atom (usually Oxygen) has a greater share of the
negatively
charged electrons.
.
Because H--O--H is polar as a molecule, meaning that the Oxygen side
of the molecule has a
negative charge and the Hydrogen side has a positive charge. This
characteristic
helps water
dissolve NaCl or table salt. See pg. 36-37.
Water Molecule:
O- Water Molecules
stick
to each other
/
\
with weak hydrogen bonds. The positive
+H
H+ and negative ends of water
molecules
attract each other.
O-
/
\
+H H+
WATER as a Chemical/Molecule/Substance. See page 40.
Characteristics:

Some important facts related to water's cohesion are as follows:

Anecdote
A freshman at Eagle Rock Junior High won first prize at the
Greater
Idaho Falls Science Fair, April 26. He was attempting to show how
conditioned we have become to alarmists practicing junk science
and
spreading fear of everything in our environment. In his project
he
urged people to sign a petition demanding strict control or total
elimination of the chemical "dihydrogen monoxide."
And for plenty of good reasons, since:
1. it can cause excessive sweating and vomiting
2. it is a major component in acid rain
3. it can cause severe burns in its gaseous state
4. accidental inhalation can kill you
5. it contributes to erosion
6. it decreases effectiveness of automobile brakes
7. it has been found in tumors of terminal cancer patients
ACIDS AND BASES - See pg. 41-43.
Acids are substances which produce H+ ions in
solution,
they are proton donors . For example,
HCl is a polar covalently bonded gas molecule but when dissolved in
water makes H + ions and Cl -
ions. Because more molecules of HCl ionize (about 96% generally), HCl
(found in our stomach)
is a strong Acid, However, H 2CO3 , Carbonic
acid, is a weak acid because only about 3% of it's
molecules ionize when in water solution. Carbonic acid is weak; it
is found in carbonated
beverages and your blood! An important point is: the more H+
ions, the more acid is present.
Are H+ ions also protons? ________
100 HCl (in H2O) yields ---> 96 H+ ions
+ 96 Cl - (Chloride) ions: 96 of 100 HCl molecules
break into ions.
| 100 H2 CO3 (in H2O) yields ---> 3H+ ions + 3HCO3- (bicarbonate) ions; | |
| 3 of 100 H2CO3 molecules break up. |
Bases are the opposites of acids, or have OH-
ions,
or will bond to H+ ions/protons. For
example, if a solution had a lot of H+ ions, you could
add OH- ions, react the two and form
HOH or water. NaOH or lye is a common base used for making soap and
cleaning sink drains.
Bases are opposites of acids, they may make OH- ions, all
will bond to H+ ions/protons.
For example, if a solution had a lot of H ions, you could add OH-
ions,
react the two and form
HOH or water. NaOH or lye is a common base used for making soap and
cleaning sink drains,
e.g., NaOH (in H2O) ---> Na + (+) OH -
Any compound which produces OH- is a base.
But is NH3 (Ammonia) a base because NH3 + H +
---> NH4+ (The answer is yes!)
Bases react with acids to produce water or Acid + Base --->
Salt
and H2 O
This is called neutralization.
| e.g., | H+ + OH- ---> H2O; HCl + NaOH ---> NaCl + H2O |
Measure of Acidity
pH is an inverse logarithmic scale of H+ ion
concentration in Moles per liter of solution.
Mathematically, pH=1/log H+ ion concentration in
Moles/liter.
Because the formula is 1 over
the concentration of H+ ion, as H+ ion conc.
increases, pH decreases and vice versa. The pH scale
runs from 0 to 14. A pH of 0 to just below 7, means the solution is
acidic and has more H+ ions
than OH- ions. Above 7.00 means a basic solution where OH
- is more concentrated than H+ .
Note: the scale at first look, appears backwards or if the pH number
is high,
H+ concentration is low; if the pH # is low, H+
concentration
is high! A
simple rule which relates to our study of the metric system in lab
is a pH = 0 means H+
concentration is 100 or 1 mole/liter. A pH of 1 means H+
= 10 -1 mole/l. A pH of 7 means H+ =
10 -7 mole/l. Is 10 -7 a big quantity or a very
small quantity?
Remember: Acid (+) Base yields Salt (+) Water. This is
neutralization.
The pH will be 7 if it
was a complete neutralization with equal amounts of H+ and
OH- resulting.
This buffer pair is found in the blood: H2CO3
(a weak acid) and the basic salt of a weak acid,
NaHCO3 . The weak acid neutralizes bases and the salt
neutralizes
acids. Identify the acid and base
in NaH2P04 /Na2HP04 , NH4+
/NH3 , NH2---/---COOH- .
pH Scale

( H+ ) = hydrogen ion concentration; (OH- ) = hydroxide ion concentration
Hint: since pH numbers are log rhythmic, log of the number 1 = 0,
log
of 0.1 = -1;
log 0.01 = -2, log .001 = -3, etc.
Important Measurements and Figures
Mole = the atomic masses of atoms in a molecule added and converted to grams (above).
1 Mole has Avogadro's Number of Molecules or, to be exact, 6.02
x 1023 molecules-a
huge number!
1 Mole of any compound has Avogadro's Number of Molecules. 2 Moles
have
2 x Avogadro's Number of Molecules.
1 liter of water = 1000 milliliters = 1000 cubic centimeters
(cc) = 1000 grams = 1
kilogram (kg).
1 gram = 1000 milligrams (mg = 1,000,000 micrograms
(ug)
=
1,000,000,000 nanograms (ng).
Exponents and Decimals
100=10+2 10-1 = .1 10-2 = .01 10 3 = .001 10-4 = .0001 10-5 = .00001
10-6 = .000001 10-9 = .000000001 10-10 = .0000000001
Organic Chemistry - the chemistry of the Carbon atom. See p.
43 of text.
The simplest organic molecule is CH4 or methane (above, nonpolar covalent compound).
Major Organic Chemicals -Learn to Recognize!
Carbohydrates - combinations of C and H2O or Cn(H20)x . See page 44 of text.
Sugars - the most basic energy storing food material of cells is glucose, C6H12O6 .

Glucose, fructose and galactose are also C6H12O6
or have the same number of atoms, but
they have different structures. For that reason they are called isomers.
Glucose, fructose and
galactose are also monosaccharides, one sugar 'link.' Fructose is
sweeter
than table sugar
(sucrose), which is sweeter than glucose. Glucose is "blood sugar,"
the basic food material of cells.
Why do cells need glucose and oxygen? To make ATP! See below.

Disaccharides - are composed of two monosaccharide building blocks
or
monomers.
They are
formed by dehydration synthesis - water is removed when the
two monosaccharides are
joined to make a larger molecule. See pg. 45 of text.
sucrose - a disaccharide of glucose and fructose, formed by dehydration
synthesis.
Breaking the glycosidic bond, as occurs in digestion, is the
enzyme assisted,
opposite reaction of hydrolysis.

maltose - disaccharide of glucose formed with alpha glycosidic bonds.

lactose - a disaccharide of glucose and galactose.

Polysaccharides- long chain
of
monosaccharides, or polymer, formed by dehydration
synthesis of monosaccharide monomers
using alpha glycosidic bonds (see disaccharides
above).
Starches - have alpha bonds
between
long chains of glucose molecules twisted into a coil.
Complex carbohydrates are "branched
starches" that have side chains branching off of the 6th
carbon atom. Glycogen (liver or muscle
cell starch) is a branched polysaccharide.
Cellulose or food fiber-
notice
the different bonding pattern (beta glucose bonds). There are
two
types:
soluble (to some degree) and insoluble. They are thought to interfere
with cholesterol absorption.

Lipids - oily compounds that will dissolve in nonpolar solvents. See page 47.
Triglycerides - or neutral
fats
are composed of 3 monomers of fatty acid and one monomer of
glycerol, an organic alcohol. They
are joined by dehydration synthesis making ester bonds.
Unsaturated fats have one or more
double
bonds between C atoms in the chain of fatty acids.


What happens to unsaturated fats
when
they are "hydrogenated" as when vegetable oils are
made in solids for use in "stick"
margarines?
Steroids - large compounds
composed
of 4 rings of carbon atoms. Cholesterol is the building
block of many steroid hormones, like
estrogen and testosterone. See pg. 47, fig. 2.15, c.

Proteins - are formed by dehydration synthesis of amino acid
monomers to form peptide bonds
and long polymers. See page 49-53. There are the
basic structural material of cells. Two
principal types in the body are structural proteins and enzymes (see
below).

Proteins have four levels of Structure
| Primary - | The precise sequence of amino acid
molecules(20
types for cells) is
determined by the "genetic code" in DNA.. |
|---|

This would "read":
methinonine-glycine-alanine-phenylalanine-leucine-
tyrosine-histidine-valine.
| Secondary - | Determined by hydrogen bonding within the polypeptide molecule that forms a helix, a cylindrical, rope-like structure. |
|---|
| Tertiary - | Determined by disulfide bonding and the polarity of amino acids that turns the molecule so that it can become globular. |
|---|

| Quaternary - | A combination of more than two separate polypeptides of protein. Hemoglobin has 4 polypeptides joined by an iron (Fe+2 ) atom. See pg. 50. |
|---|

Enzymes - See pg. 53 of text.
Characteristics:
Enzymes participate in both
constructive
(anabolic, as in making proteins) reactions
and destructive (catabolic, as in
digesting
proteins) reactions.
However, Pepsin, first secreted in
the
stomach glands as the protein pepsinogen,
Must bond with H+ ions in
order to have any activity in digesting protein. In this case
H+ ions are cofactors for
the Pepsin enzyme.
ATP - the source of most chemical
energy stored and used in cells. It is made
in the mitochondria of cells.
ATP stands for adenosine
triphosphate
(see pg. 57 of text). It is composed of
the DNA nucleotide adenosine and three
high energy-bonded phosphate groups.
Chemical energy is stored when
ATP is formed from adenosine diphosphate (ADP),
energy from high energy electrons,
and one phosphate. Energy is released when ATP
is broken down into ADP and a low
energy
phosphate.
Each succeeding
high
energy phosphate bond stores more
energy!

DNA - the chemical of inheritance is significant because it can replicate exactly (with the help of enzymes) and it can direct the synthesis of structural, gene regulatory and enzymatic proteins. See p. 54-56 of textbook.
-

The building blocks (monomers) of DNA
(deoxyribonucleic
acid) are called nucleotides. Each
nucleotide is composed of (1.) a deoxyribose (5C) sugar, (2.)
a phosphate (PO4-3) group, and
(3.) a nitrogenous base of 4 kinds: Cytosine and Guanine
that bind together with 3 hydrogen
bonds, and Thymine and Adenine that bind
together
with 2 hydrogen bonds. Adenine and
Guanine have two rings of mostly carbon atoms and are called purines,
cytosine and thymine
have one ring and are called pyrimidines.
Study Questions
1. What is a radioactive isotope? How is it different from the most
common form of the atom?
2. What forms of electromagnetic radiation are dangerous?
3. What are the building blocks of sucrose, lactose, maltose, starch,
cellulose, glycogen, protein,
neutral fat, DNA, and steroids? Learn to visually recognize each.
4. Compare and contrast the four levels of protein structure.
5. List and explain 4 characteristics of enzymes.
6. Compare hydrolysis and dehydration synthesis (condensation)
reactions.
Where does
each occur for starches and proteins?
7. Explain how ATP stores and releases energy.
8. How is the genetic code derived from the structure of DNA?
Biology Practice Test _______________________________
name
Matching (multiple guess) Hint - use best answer and look at all
answers.
Don't cross answers out.
___1. Tentative and testable explanation. a. Einstein
___2. Building blocks of the universe b. theory
___3. If one neutron was changed to a
proton
c. hydrogen atoms
in an atomic nucleus, you would have....
___4. 2 (Helium) or eight electrons in an
outer
d. hydrogen bonds
atom shell
___5. Discovered Rule of Eights (Octets) e. sunlight
___6. Discovered that mass can be
converted
f. Calorie
to energy
___7. All Carbon atoms have 6.... g. another element
___8. Electrons are given away and
received
h. stable, unreactive atoms
by atoms.
___9. Even sharing of electrons i. hydrogen ions
___10. 1 mole j. electrons
___11. Amount of energy to raise
temperature
k. hypothesis
of 1 g of water 1 degree C.
___12. All acids
make...
l. ions separate when substance dissolved
-
___13. Makes water hard to
boil
m. Avogadro's number of particles
___14. Hydrogen fusion occurs to make... n. Mendeleev
___15. Has substantial evidence, but
still
o. nonpolar covalent bonds
tested
|
X 25.4 |
a. Atoms of element X would tend to give away//share//receive (circle one) electrons
when reacting with another atom with 6 electrons in its outer shell.
b. T or F. X is a metal.______
c. X has _______ (#) electrons?
d. Most X atoms have _______ (#) neutrons?
e. T or F. Some X atoms weigh 26 or more. _______
Fill-in (1 point each)
Pure Aluminum foil would represent a __________ because all it's atoms
are the same.
However, the anti-acid Gaviscon has Al(OH)3 which is
composed
of more than one
species of atom and therefore is a __________. An Aluminum ion, Al+3,
has an electrical
charge because it __________ (gained or lost, choose one) the subatomic
particles called
__________. Any atom called Aluminum must have __________ protons in
it's nucleus.
((Look up Al on your periodic chart or see
http://www.webelements.com )).
True or False (Believe It or Not!)
____ 1. All Scientific Laws remain hypotheses that can be retested.
____ 2. The diatomic molecule of Hydrogen is also a compound
because
it is
composed of more than one atom.
____ 3. All Hydrogen species have one neutron.
____ 4. Ion atoms have their # of protons = # electrons.
____ 5. When the ionic compound NaCl is formed, Na(Sodium)
gives
away an electron to Cl(Chlorine).
____ 6. A pH of 1 is twice as concentrated in H+ ions as a pH of 2.
____ 7. Pure water is a good conductor of electricity.
____ 8. Solid ice is less dense than liquid water.
____ 9. Helium gas is very explosive.
____ 10. Since Chlorine is an element found in the compound table
salt
(NaCl),
as a pure element it is harmless.
Short Discussion
1. Why are covalently bonded compounds generally poor ion formers.
(2 points).
2. In what 2 ways is water considered to be an unusual compound as
compared
to
compounds of similar molecular weight? (2 points)
3. Explain why doesn't Neon Chloride or metalic Sodium exist in
nature.
4. Why is I-129 a radioisotope?
5 . What is radon gas? Describe it as an atom, a radioactive
isotope,
its source and hazards.
List
1. List and define 4 types of mixtures. (4 points)
a.______________________________________________________________
b.______________________________________________________________
c.______________________________________________________________
d.______________________________________________________________