General Biology Notes | Page 1

Chapter 1: Scientific Thinking

I. Introduction What is Science? Science isnt a body of facts or
ideas, but rather an intellectual activity, observation,
description, and experimentation of natural phenomena.
Science helps us understand the world.
Biology (bios = life, ology = study of) the study of living
things. Literacy in science and biology is important in life as
many things in health, society, medicine, politics, economics,
and law rely on analyzing scientific data and theories.
II. Scientific Method The Scientific Method is a process of
examining and discovering natural phenomena with
observations, constructing hypotheses, testing predictions,
experimenting, and drawing conclusions then revising if
needed.
A. Steps of Method
1. Make Observations See phenomena
2. Formulate a hypothesis Prediction of experiment
based on observation.
3. Devise a testable prediction What will happen when
something is done.
4. Conduct an experiment.
5. Draw conclusions and make revisions if needed.
6. Method may not go from Step 1 to Step 5. Some
observations may lead to multiple hypotheses. It
may change from more observations.

B. Make Observations. Scientific studies begin with an

observation, looking for interesting patterns or cause-and-
effect relationships.

C. Formulate a Hypothesis. A hypothesis is a proposed

explanation for observed phenomena. To be useful, a
hypothesis must (1) establish that if the proposed
explanation is not supported by evidence or further
observation, a different hypothesis is a more likely
explanation and (2) it must generate a testable prediction.
Researchers often pose a hypothesis as a negative
statement [this is what isnt going to happen] called a null
hypothesis that proposes a lack of relationship between
two factors.

D. Devise a Testable Prediction. The hypothesis must generate

a prediction that under certain conditions we will be able to
observe a certain outcome.
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E. Conduct a Critical Experiment. A critical experiment is

an experiment that makes it possible to decisively
determine whether a particular hypothesis is correct. [No
room for error, accounting for everything. Only can be one
answer.] If the hypothesis is not true, we will make
observations that compel us to reject that hypothesis.

F. Draw Conclusions and [sometimes] Make Revisions. Once

the results of he experiment are in, researchers analyze
them and look for patterns and relationships in the
evidence they have gathered; they draw conclusions and
see whether their findings and conclusions support their
hypotheses. If an experimental result is not what you
expected, that does not make it a wrong answer. If the
conclusions do not support the hypothesis, then you must
revise your hypothesis, which often spurs you to perform
more experiments. [Do experiment again but change some
conditions.]

G. Hypotheses and Theories. As we have seen, a hypothesis is

a proposed explanation for observed phenomena. A
theory is an explanatory hypothesis for natural
phenomena that is exceptionally well supported by the
empirical data. A theory can be thought of as a hypothesis
that has stood the test of time and is unlikely to be altered
by any new evidence. Theories are viewed by the scientific
community with nearly the same confidence as facts and
tend to be broader in scope than hypothesis. Examples:
Cell Theory and the Theory of Evolution by Natural
Selection. [We are fairly confident in something, but we
dont know exactly so its still a theory.]

H. Controlling Variables in Experiments. (See Handout) It is

important to have a well-planned well-designed experiment
that will allow you to draw correct conclusions. First, lets
consider some elements common to most experiments.
1. Treatment any experimental condition applied to
the research subjects. Example: The Echinacea
[anti-cold medicine] given to an individual. [Conduct
a test to see if the medicine works.]
2. Experimental group a group of subjects who are
exposed to a particular treatment. Example: The
volunteers who were given the Echinacea tablets
(not the ones given the placebo).
3. Control group- a group of subjects who are treated
identically to the experimental group, with one
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exception- they are not exposed to the treatment.

Example: The individuals are given the placebo
tablets.
4. Variables- the characteristics of an experiment that
are subject to change. Example: The dosage of the
Echinacea, the placebo tablet, the severity of the
cold symptoms, and the duration of the symptoms.
5. In our experiment with Echinacea, all volunteers
were given tablets and some people from both
groups probably showed improvements in their
symptoms even though the placebo had no real
medical benefits. This positive response to any
treatment is called the placebo effect. Neither the
volunteers nor the researchers administering the
tablets knew who was receiving the Echinacea or the
placebo. This type of study is called a double-blind
experimental design [neither knows what is
placebo]; had the researchers known which
individuals were receiving the placebo but the
subjects did not know the study would be called a
blind experimental design. These experimental
designs reduce researchers and subjects bias that
could affect the results. The random assignment of
subjects into the groups also further reduces the
influence of the researchers and subjects on the
study. If other groups can repeat the experiment,
showing similar results, then the hypothesis may
gain greater acceptance.

III. Unifying Themes of Biology. Two major themes connect the diverse
topic of biology including the chemistry of life, cell structure and
function, genetics, the diversity of both living and extinct organisms,
and ecology: Hierarchical Organization and Evolution.
A. Hierarchical Organization: Life is organized on many levels
within an individual organism and among groups of
organisms.
1. Atom - the smallest particle of an element that still
retains the properties of the element.
2. Molecule - two or more atoms held together by
chemical bonds.
3. Organelle - [tiny organ] a structure found inside a
cell that performs a specific function.
4. Cell - the smallest unit of life.
5. Tissue - a group of cells that perform a specific
function. [Nervous tissue, muscle tissue]
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6. Organ a structure composed of two or more tissues

that function together.
7. Organism an individual living thing. [Anything from
Cells to Tissues to Organs. Bacteria, fungus, organs.]
8. Population all the members of a species occupying
a given place at a given time.
9. Community all of the populations of all species
occupying a given place at a given time.
10. Ecosystem A community and the nonliving
environmental components with which they interact.
[Many species cannot survive in other ecosystems
easily.]
11. Biosphere the part of Earth inhabited by living
organisms.
B. Evolution. Evolution is the change in genetic characteristics
within populations over time. It accounts for the diversity of
organisms but also explains the unity among them.
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Chapter 2: Chemistry
I. Introduction. Everything, including living organisms, is made
up of atoms. The function of a cell is a collection of chemical
reactions; therefore a better understanding of atoms can help
us to understand how living organisms function. An atom is
the smallest particle of an element that still retains the
properties of the elements.
II. Atoms
A. Structure of Atoms
1. Proton- particles in the nucleus of an atom
that have a positive electrical charge.
2. Neutron- particles in the nucleus of an atom
that have no electrical charge.
3. Electron- negatively charged particles moving
at a distance from the nucleus. The position of
an atoms electrons will determine how it will
react with another atom. Electrons are found in
areas called energy levels (Electron shells). The
higher the energy level of an electron, the
further it is from the nucleus.
B. Elements. An element is a substance that can neither be
broken down nor converted to other substances by
ordinary chemical means. The most common elements in
the living things are Oxygen, Carbon, Hydrogen, and
Nitrogen.
1. Chemical Symbol- a letter or 2 letters [C =
Carbon, H = Hydrogen, He = Helium] that are
used to represent an atom. [First is large,
second/third small.]
2. Atomic number- equal to the number of
protons in an atom of the element. [Carbon =
6]
3. Mass Number- equals the weight of an atoms
protons and neutrons are measured in atomic
mass units (AMU). [Carbon = 12.011]
4. Isotopes 2 atoms with the same number of
protons but a different number of neutrons.
E.g. 12C and 14C
a. Radioactive Isotopes- isotopes that
breakdown (decay) into more stable
atoms (non-radioactive).
III. Chemical Bonds. Chemical bonds are forces that combine
atoms and hold them together. Atoms are bounded together
to form a molecule- a compound of a defined number of
atoms in a defined spatial relationship. Molecular formula
indicates the elements present and the number of each kind
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of atom in a compound. E.g. H2O = 2 Hydrogen atoms + 1

Oxygen atom; CH4 = 1 Carbon + 4 Hydrogen atoms.
A. Covalent Bonds. Covalent bonds are attractive forces
formed between two atoms that share electrons.
Covalent bonds form when atoms get close enough to
other atoms that have unfilled energy levels and share
electrons, thus filling the energy levels of each atom
(e.g. CH4). Certain elements will often form a certain
number of bonds (e.g. Hydrogen = 1, Oxygen = 2,
Nitrogen = 3, Carbon = 4, Phosphorus = 5). Molecules
most often found in living organisms are organic
molecules- molecules having carbon as its main
element. In a double covalent bond, two atoms share
two pairs of electrons (e.g. O2). Sometimes there is an
unequal sharing of the electrons, which causes the
molecule to be polar, have some areas that are
positively and negatively charged.
B. Ionic bonds. Ionic bonds are attractive forces between
ions of opposite charges (e.g. Na+Cl-).
a. Ions- atoms that have either a positive (+) or
negative (-) electrical charge. [Difference in
amount of electrons vs protons I think. 11 protons
10 electrons +1 charge, 17 protons 18 electrons
-1 charge.] This is accomplished by gaining or
losing electrons e.g. F- ([9] 9 protons, 8 electrons.)
and Mg+2 ([12] 12 protons, 10 electrons).
C. Hydrogen Bonds. Hydrogen bonds are weak attractive
forces between atoms already taking part in a polar
covalent bond.
IV. The Importance of Water to Life. Waters covers about 71% of
the Earths surface and humans are 66% water. One of the
characteristics of water that makes it important to life is its
ability to act as a solvent. Water is the best known solvent; it
can dissolve more compounds in greater amounts than any
other liquid.
A. Solutes, Solvents, and Solutions. A solution is a
homogeneous mixture of two or more kinds of
molecules, atoms, or ions. For example, mixture of
sugar dissolved in water is a solution. The substance
being dissolved (the sugar) is called the solute and the
substance in which it is dissolved (the water) is called
the solvent. A solution in which water is the solvent is
referred to as an aqueous solution.
V. pH: Acids, Bases, and Buffers.
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A. Acids. An acid is a substance that releases hydrogen ions

(H+) when dissolved in water (e.g. HCl [hydrochloric acid]
and H2SO4 [sulfuric acid]).
B. Bases. A base is a substance that combines with hydrogen
ions (H+) when dissolved in water (e.g. NaOH [sodium
hydroxide] and NaHCO3 [sodium bicarbonate].
C. pH scale. A pH scale is used to measure the concentration
of free hydrogen ions; pH 0 is the most acidic, 14 is the
most basic, and 7 is perfectly neutral.
D. Buffers. Buffer- a substance that can combine with
hydrogen ions, release them, or both. Buffers help stabilize
the pH of fluids.
CO2 + H2O <===> H2Co3 <===> H+ + HCO3-
VI.
Carbohydrates. Carbohydrate- simple sugars or large
molecules composed of sugar units. Carbohydrates are made
up of C, H, and O, with the number of H atoms being about
twice the number of C and O atoms.
A. Monosaccharide. A monosaccharide is the simplest
carbohydrate, with only one sugar unit e.g. Glucose,
Fructose, Galactose, Ribose, and Deoxyribose.
B. Disaccharides. A disaccharide is a simple sugar made from
2 monosaccharides covalently bonded together. Small
molecules such as monosaccharides are bonded together
by a dehydration reaction in which a hydrogen atom is
removed from one molecule and a hydroxyl is removed
from the other molecule forming water as a byproduct.
Example:
Glucose + Fructose -> Sucrose + Water
C6H12O6 C6H12O6 C12H22O11 H2O
C. Polysaccharides. A polysaccharide is a chain of hundreds
of thousands of covalently linked sugar units, of the same
kind or different kinds e.g. Cellulose, Starch, Glycogen.
VII. Lipids. Lipids- large molecule that are not easily dissolved in
water made up of C, H, and few O. Lipids can be divided into
two groups: lipids with fatty acids and lipids without fatty
acids.
A. Lipids with Fatty Acids.
1. Glycerides (Fats and Oils). Glycerides are made up
of fatty acids attached to a glycerol backbone.
Monoglycerides have one fatty acid, diglycerides
have two fatty acids, and triglycerides have three
fatty acids. Some fats are called saturated fats,
meaning that the fatty acids have the maximum
number of hydrogen atoms attached to them (solid
at room temperature). Others are called
unsaturated fats because the fatty acids do not
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contain the maximum number (have double bonds

between the carbons) of hydrogen atoms (liquid at
room temperatures).
2. Phospholipids. Phospholipids- a lipid made up of
glycerol, 2 fatty acids, and a phosphate group.
B. Lipids without Fatty Acids (Steroids). Steroids- lipid
containing four rings of carbon and no fatty acid tails.
Examples: Some hormones (Testosterone and Estrogen)
and cholesterol.
VIII. Proteins. Protein- large organic molecules composed of one
or more chains of amino acids held together by peptide
bonds.
A. Amino Acids. Amino acid- a small organic molecule having
an amino group, an acid group (carboxyl group), and an R
group covalently bonded to a central carbon atom. There
are only about twenty or so different amino acids.
1. Peptide Bonds. Amino acids are joined together, one
after another, by a covalent bond called a peptide
bond that forms between the amino group of one
amino acid and the carboxyl group of another. This
bond is formed during dehydration synthesis. Three
or more amino acids bonded together form a
polypeptide. Larger chains of amino acids are
called proteins.
B. Protein Structure. The sequence (order) of the amino acids
is called the primary structure of a protein. The primary
structure will determine the shape and function of the
protein. Each protein has its own unique sequence of
amino acids and its own unique shape.
IX. Enzymes. Many chemical reactions are occurring in a cell at
all times. Metabolism is the sum of all chemical reactions
within a cell or within all the cells of a multicellular organism.
Many of these reactions are linked in sequences called
metabolic pathways. Enzymes help regulate the chemical
reactions within a cell. Enzymes are protein that catalyze
(speed up) a chemical reaction (at least a million times
faster). Enzymes work by lowering the activation energy,
the amount of energy required to start a reaction. The
molecule that an enzyme binds to and changes is called a
substrate. The enzyme is not used up (or changed) in the
reaction and can be used many times.
A. Enzyme Structure. Enzymes work on specific substrates
because their three dimensional shapes fit together like
pieces of a puzzle. The active site is the place where the
enzyme bonds to the substrate and causes bonds in the
substrate to break and reform differently.
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B. Enzyme Function. The shape and electrical charge of the

active site force the substrates to enter the enzyme in a
specific orientation. When the substrate enters the active
site, the active site promotes the specific chemical reaction
catalyzed by the particular enzyme. When the chemical
reaction is finished, the enzyme can bond to another
substrate and catalyze another reaction.
C. Regulating enzyme Activity. The metabolic reactions within
a cell must be carefully controlled; they must occur at the
proper rate and with the proper timing. Cells have evolved
several ways of regulating enzyme activity.
D. In some cases, two or more similar molecules can compete
for the active site on an enzyme. When a molecule that is
similar to the substrate binds to the enzyme, it will prevent
the substrate from bonding to the active site and prevent
the chemical reaction from occurring. This is called
competitive inhibition.
E. In some cases called feedback inhibition the activity of
the enzyme is inhibited by its own product, which changes
the shape of the active site.
X. Nucleic Acids. There are 2 types of nucleic acids (1)
Deoxyribonucleic acid, DNA and (2) Ribonucleic acid, RNA.
DAN serves as the genetic material of organisms that is
inherited from each parent and RNA helps DNA during protein
synthesis. Nucleic acids are long chains of subunits called
nucleotides.
A. Nucleotides
1. Sugar. Deoxyribose found in DNA or Ribose
in RNA (monosaccharides).
2. Phosphate group.
3. Nitrogen base. DNA has four kinds of nitrogen
bases: Thymine (T), Adeine (A), Cytosine
(C), and Guanine (G). RNA also has four kinds
of nitrogen bases: Adenine (A), Cytosine (C),
Guanine (G), and Uracil (U).
The nitrogen base and phosphate group are both bonded to
the sugar.
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Chapter 3: Cells
I. Introduction
A. The Cell Theory. The cell theory states that all
organisms are composed of one or more cells and
all cells arise from preexisting cells.
B. Prokaryotic vs. Eukaryotic Cells.
Eukaryotic cells have a true nucleus that
contains the DNA and is enclosed by a membrane.
Prokaryotic cells have no membrane bound
nucleus. Eukaryotic cells are much larger than
prokaryotic cells and have many organelles,
highly organized structures inside a cell that serve
some specialized functions. Prokaryotic cells have
only organelles called ribosomes where proteins
are made. Prokaryotic cells are found only in
bacteria and archeans. Animals, plants, fungi, and
protists have eukaryotic cells.
II. Plasma Membrane. Each cell is surrounded by a thin plasma
membrane that selectively isolates the cells contents from
the external environment, regulates the exchange of
substances between the cell and the environment, and
communicates with other cells. Most cells have internal
membranes as well as a plasma membrane. These
membranes form compartments (organelles) in which
specialized chemical activities occur. All the membranes of a
cell have the same basic structure.
A. Membrane Structure. The most widely accepted
model of cell membrane structure is called the
fluid mosaic model. The term fluid refers to its
components ability to move or flow and mosaic
means the membrane has a patchy appearance.
1. Phospholipids. Phospholipids are the main
component of cell membranes. Phospholipids
consist of hydrophilic (water loving) head and
two hydrophobic (water fearing) tails. The
phospholipid molecules are arranged in two
layers (phospholipid bilayer) with the
hydrophilic heads of each layer pointing in
opposite directions because of the water inside
and outside the cell. The hydrophobic tails of
each layer are in the center, insulated from the
water molecules by the heads. The
phospholipids are not bonded to each other
which allow them to move about within each
layer.
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2. Proteins. Proteins are found embedded in the

phospholipid bilayer and on its surface.
Integral proteins are bound to the
membranes hydrophobic interior some
extending entirely through the membrane,
while others penetrate only part of the way.
Peripheral proteins are found on either sode
of the membrane and are not bound to the
interior but the integral proteins.