Biology Notes

1.01 Exploring Life

 Zoology- study of animals

 Botany- study of plants
 Ecology- study of living things in their environment
 Microbiology- study of microscopic organisms
 Biochemistry- study of the chemical reactions of living things
 Anatomy and Physiology- study of the human body
Science is our knowledge of the natural world and the process
through which that knowledge is built. This knowledge consists of
information gathered over thousands of years and is the result of
observation, inquiry, rational thinking, and questioning. It has developed
from group and individual efforts. It must be able to answer a testable
question using observation and experimentation.
The independent variable is the one factor that a scientist
chooses to change, or alter, in a scientific experiment. 
The dependent variable is the factor that changes in response to
the independent variable, also called the outcome variable.
Controlled variables are the factors that a scientist chooses to keep constant
throughout the experiment.
 1.02 Chemistry of Life
All life on earth is made of carbon-based molecules, sometimes called organic
compounds.
Valence electrons- an electron located in the outermost occupied energy level in an
atom. These are the electrons that participate in chemical bonding between atoms.
The carbon atom has four valence electrons in the outermost
energy level, so it can form up to four covalent bonds with other atoms in
many combinations. The combination of the bond determines the
chemical and physical properties of the created molecule.
The carbon atom can bond with other carbon atoms to form macromolecules. They can
also bond with atoms of different elements, so there is a near-endless variety of carbon-based
molecules that can be formed.
Biological macromolecules- cells make large macromolecules by bonding smaller
molecules into chains called polymers, large molecules composed of many identical or similar
subunits called monomers. There are four categories of biological macromolecules-
carbohydrates, lipids, proteins, and nucleic acids.

 Monosaccharide- the smallest type of carbohydrate molecule. They provide

energy to cells, and they can be used to make other molecules. If they are not
used immediately, they can be stored in larger carb cells for later.
 Disaccharide- carbohydrate molecules made up of two bonded monosaccharide
molecules bonded together. They are usually referred to as “sugars” in biology.
 Polysaccharide- carbohydrate polymers made up of hundreds to thousands of
bonded monosaccharide units.
Four different types of polysaccharide molecules that are produced/consumed by living
organisms are starch, glycogen, cellulose, and chitin. They are all polymers made up of
hundreds to thousands of glucose molecules, but their different structures give them different
properties and functions.
Starch- molecules that are long straight chains of glucose molecules all turned in the
same direction, and some have some branching in their chain.
Starch is largely used by plants to store glucose, in places like
seeds or other specialized organs, some of which humans eat.
When we eat starch, an enzyme found in saliva and the intestines breaks down the starch into
glucose molecules, which are distributed into the bloodstream where energy is needed.
 Glycogen- the polysaccharide molecule that is used to
store glucose in animals. It is a branched chain of glucose
molecules that all face the same direction. Humans and other
animals consume starch for energy, and if there are extra
glucose molecules left over, they are stored in glycogen.
Cellulose- a rigid polysaccharide found in plants. It is made of long chains of glucose
bonded together, alternating where every other molecule is
turned in an opposing direction. This way hydrogen bonds can
form between the cellulose molecules to give strength to plant
cell walls. Cellulose cannot be digested by animals, but it is still
useful because it cleans out our digestive track to keep it clean and healthy.
Chitin- a rigid polysaccharide that also has alternating
arrangements of glucose molecules. It is different than
cellulose because it has amino groups (NH2) bonded to the
glucose. Because it is so strong, it is used to form the
exoskeleton of all arthropods. It cannot be digested by
animals.
The monosaccharides can bond by dehydration synthesis, a process where two
substances bond together by the removal of water. A
hydrogen atom (H) is removed from one monosaccharide,
and oxygen and hydrogen atoms (OH) are removed from
another monosaccharide so that the two molecules can
bond. The hydrogen and oxygen atoms that were removed
can bond to form a water molecule (H2O).
The opposite of dehydration synthesis is hydrolysis.
This is the chemical reaction that breaks down polymers
into smaller monomer units.
Lipids are macromolecules that are not considered polymers because they are not made
up of monomers. They don’t dissolve well in water, which is called being hydrophobic. The
main categories of lipids are fats, phospholipids, and steroids.

 Fats are made of carbon, hydrogen, and oxygen atoms. They are made of smaller
molecules, which is why they are also called triglycerides. Fat serves different
purposes, including storing energy, providing insulation, and cushioning organs.
They are made of one glycerol and three fatty acids.
 Fatty acids can form fat molecules, but they also can control inflammation,
maintain brain health and development, maintain fluidity of cell membranes,
 and prevent blood clots. A fatty acid is a long chain of carbon and hydrogen
atoms with a carboxylic acid group on one
end of the molecule.
 An unsaturated fat is a fat or fatty acid in
which there is one or more double bond in
the fatty acid chain.
 Glycerol has the formula C3H8O3.
Dehydration synthesis occurs to attach fatty acid molecules to glycol. The
process leaves an available location for a covalent bond to form between the
glycerol and fatty acid.
 Phospholipids are like fat, but they have a different composition. They have two
fatty acids and one phosphate group.
 Steroids are mainly hormones that control many of the body’s metabolic
processes. It is structured as four linked rings of carbon atoms.
Proteins are very important to living organisms as they are used for structure,
transporting substances, storage, signaling parts of an organism to another, movement, and
defense against foreign substances. They can only function under
specific conditions, like a small range of temperature and PH.
Proteins are made of smaller molecules called amino acids.
There are 20 different amino acids that all share the same basic
structure, and proteins are made of 50+ amino acids bonded together.
The five parts of the amino acid structure are amino group, carboxylic acid group, side chain,
central carbon atom, and forming a protein.
Proteins and their functions-

 Antibodies- Specialized proteins that help defend organisms

from foreign invaders.
 Contractile Proteins- Proteins responsible for the movement
of muscles. Examples include actin and myosin.
 Hormonal Proteins- Messenger proteins that help coordinate
bodily activities. Examples include insulin and oxytocin.
 Transport Proteins- Carrier proteins that move molecules
from one place to another around the body. Examples include
cytochromes and hemoglobin.
 Structural Proteins- Fibrous and stringy proteins that provide support or protective
coverings like hair, feathers, horns, etc. Examples include collagen and elastin.
 Enzymes- Specialized proteins that speed up reactions by decreasing the energy needed
for the reaction to occur. Examples include lactase and pepsin.
 Receptor Proteins- Sends information from various cells to the brain.
1.03 Earth’s Early Atmosphere
Earth is the ideal home for life because-
  It has liquid water
 An optimal distance from the sun
 An atmosphere that supports life
Any of the other planets have many reasons why humans or any other living forms
could not live there-
Sun Venus Moon Mars Saturn Jupiter
Atmosphere Hydrogen 97% No true Mostly Hydrogen Hydrogen
and carbon atmosphere carbon and and
helium dioxide dioxide helium helium
Temperature About 10k 900 -280 -200 Approx. - Approx. -
degrees degrees degrees to degrees to 285 234
Fahrenheit Fahrenhei 260 80 degrees degrees
t degrees degrees Fahrenheit Fahrenheit
Fahrenheit Fahrenhei
t
Conditions Nuclear Sulfuric Dust storms Frequent 1000 mph High
fission acid rain dust winds winds and
occurs, falls from storms lightning
releasing the clouds are
extreme common,
amounts with a
of energy large
cyclonic
storm.

The Early Earth

Back in the day, earth was likely to be covered with
volcanoes, and with no protective atmosphere, it was
probably steaming hot, like me on a good day, and was
attacked by space rocks. In fact, its atmosphere was so
trashy that it was like volcanic gas (little oxygen, mostly
carbon dioxide, water vapor, and nitrogen). 4.2 billion years
ago, earth finally cooled off enough for the surface to
solidify and for water to form out of vapor.
Organic Molecules- carbon-based molecules that can either be small and simple or long
and branching, consisting of hundreds of atoms. They’re important, thus scientists are very
invested in how they came to existence.
 Two hypotheses were made in the 1920s by A. I. Oparin and J. B. S. Haldane, both
simplifying to the fact that earth favored chemical reactions that made organic molecules from
inorganic molecules from the atmosphere. The low amounts of oxygen, the UV radiation, and
lighting in that level of the atmosphere were all thought to allow the reactions to occur
spontaneously. The scientists said that the reason we don’t see the reactions today is because
the atmosphere has more oxygen gas, which interferes with the creation of carbon-based
molecules.
Some other theories suggested that organic molecules came from meteorites and
comets from space, like organic compounds such as amino acids. When biochemists added the
compounds to water, they formed small groups of vesicles, which could be predecessors to
modern-day cells.
Iron Sulfide Hypothesis- a few years ago, deep sea explorers noticed vents on the ocean
floor where hot water and minerals come through, and where living organisms also stayed.
They hypothesized that the first living cells could have come from these vents. The hot water
from the vents contains iron sulfide, which forms chimneys on the ocean floor when exposed to
cooler water. These chimneys were like honeycomb. Inside of the holes, organic compounds
could react and work together, like a cell membrane. Also, scientists noticed that iron sulfide
contained materials that can speed up reactions such as acetate and pyruvate.
Lipid Membrane Hypothesis- some have proposed that closed membrane vesicles were
a step in the development of early cells. It has been found that lipids can form vesicles, which
are like membranes because they can maintain internal conditions separate from external. Had
lipids been present in early earth, this could have been a predecessor of early cells.
In cells, bonding of macromolecules from smaller organic molecules requires the help of
specialized enzymes, which some scientists have observed could be triggered by hot surfaces.
Using this observation, scientists theorized that organic molecules formed in the ocean,
splashed onto the hot land, and bonded.
Other theories suggest that the first organic molecules were bade of amino acids and
nucleotides, which are a small type of molecule that are used to form RNA and DNA. The
bonding of these two molecules to go from nonorganic to organic cannot happen in today’s
oxygen-rich atmosphere.
DNA- Deoxyribonucleic acid is genetic
material with instructions used in the
development of living things.
RNA- Ribonucleic acid is a
macromolecule made up of nucleotides that is
essential for all known forms of life.
All cells share the same following
things- genetic material, a cell membrane, and an internal metabolism.
 All living organisms use DNA and RNA. The origin of these molecules is important to
know how life began on earth. Using the Miller-Urey experiment, we can hypothesize that the
first large organic molecules to form and replicate were RNA, with DNA following later. This is
called the RNA world hypothesis. This is supported by the replication cycle, which is supported
by polypeptide, a primitive enzyme that aids RNA replication.
It has been observed that RNA is a catalyst in modern cells, meaning it increases the
rate of a chemical reaction without going under any permanent chemical change. This
observation helped scientists realize how all organisms share the same genetic code, because
the RNA self-replicated and made new RNA molecules. While this hypothesis is not widely
accepted, it has substantial evidence. Some other scientists think that simpler self-replicating
molecules formed DNA and RNA.
Some think that groups of molecules called microspheres may
have come before the common cells of today. Microspheres are tiny
bubbles filled with groups of large organic molecules, which form
under very specific conditions. They aren’t cells, but they are a lot like
cells. They can maintain an internal environment separate from the
external surroundings. They also have a simple way of storing and
releasing energy.
They expand by adding more and more molecules until they pop into smaller bubbles.
This isn’t true reproduction or cell division, but it may be a predecessor of it.
This also adds onto the RNA world hypothesis. Every time the bubble popped with the
genetic code inside, it would split into new bubbles, which would explain how all organisms
share a genetic code. This is how evolution really started.
Over time, photosynthetic bacterial cells became more common, using sunlight to
produce food and releasing oxygen. As the oxygen accumulated, the ozone layer formed, and
slowly but surely, the whole atmosphere formed.
Back to around 3.5 billion years ago, prokaryotic, heterotrophic cells lived, and had
internal environment due to the lack of oxygen in the atmosphere. These early cells and some
cells today sometimes need to function with low oxygen. A process called anaerobic respiration
allowed them to get energy when there was no oxygen gas pressent. Scientists believe that old
cells used to get energy in a similar way. Anaerobic respiration produces carbon dioxide gas,
which built up over the atmosphere, letting autotrophic cells make food.
Autotrophic organisms are the top of the food chain, and they take inorganic molecules
and make it into organic nourishment, using light or chemical energy in the process.
 Photoautotrouphs use photosynthesis, which also releases gas into the
atmosphere.
 Chemoautotrophs use light energy and chemosynthesis.
Descendants of Cells- early cells are related to modern-day cells, but they have special
characteristics that let them live under severe conditions. Examples of these include-
  Methanogens- single celled organisms that produce methane in a form of
anaerobic respiration.
 Thermophiles- single celled organisms that live at extremely high temperatures
(113- and 176-degrees Fahrenheit). They are thought to be the first cells on
earth.
 Halophiles- organisms that thrive in environments with high concentrations of
salt.
 Cyanobacteria- photosynthetic prokaryotes that live in the water. They release
oxygen into the atmosphere. Fossils prove that the most abundant autotropic
cells were modern day cyanobacteria. Because of their addition of oxygen, the
atmosphere received more oxygen.
Eventually, the production of oxygen got too high and was probably too toxic for
anaerobic cells, killing them off, while other aerobic cells evolved, carrying out aerobic
respiration rather than anaerobic.

2.01 Properties of Water

Water is everywhere. It is in every cell in existence,
and it can be found in both solid, liquid, and gas form.
 Ionic Bond- A chemical bond in which ions are held together by the attraction between
their opposite charges. During an ionic bond, atoms can gain or lose electrons to become
charged ions.
Covalent Bond- A chemical bond in which atoms are held together by their mutual
attraction for two or more electrons they share. They occur when two atoms overlap their
outer energy levels to share pairs of valence electrons, which are attracted to the nuclei of both
atoms. This forms a covalent compound, otherwise known as a molecule. During the formation
of a chemical bond, the atom may lose, gain, or share electrons.
In water molecules, hydrogen and oxygen atoms form a covalent bond. Hydrogen atoms
get 2 electrons and oxygen gets 8, due to the uneven attraction of the different atoms. This
gives oxygen a slight negative charge and hydrogen positive. Though water has no charge, it has
negative and positive ends. This magnet-like attraction helps water molecules bond, with a
process called hydrogen bonding.
 Cohesion- an attraction of the same particle
 Adhesion- the attraction of water to another substance.
 Surface Tension- the measure of how difficult it is to break the surface of a
liquid. Hydrogen bonds give water a strong tension.
 Capillary Action- the movement of water through a narrow tube. This occurs
when the previous actions work together.
Water expands when it freezes. This is because hydrogen
bonds form rigid structures, which requires more space than
liquid water. This makes ice less dense than water, which makes it
float. If it didn’t float, lakes and ponds would freeze from the
bottom up, killing many ecosystems.
Universal Solvent- Many substances dissolve well in water
because they share the same opposite ended structure as water.
Water also has a neutral PH of 7. Substances with a PH of above 7 are bases, and below
are acids.
High Specific Heat- Specific heat is the amount of energy needed to change the
temperature of 1 gram of a substance by 1 degree Celsius. Water has a high specific heat.
High Heat of Vaporization- Heat of vaporization is the amount of heat energy needed to
convert 1 gram of a liquid into a gas. Water has a high heat of vaporization.
 2.02 Microscopes
A microscope produces an enlarged image of something very small. They usually use
lenses to magnify an image of a small image by focusing light or electrons.
Early microscopes- The first microscope was made by Antonie van Leeuwenhoek which
observed bacteria and blood cells. In
1655, Robert Hooke took Leeuwenhoek’s
ideas and made the first compound light
microscope, which used more than one
lens to magnify on one object. He
discovered how cork, a dead plant material, was made of cells. With each advance in
technology, we learn more about organisms.
Light Microscopes- in a light microscope, light travels through or bounces off the
specimen and into the glass lenses, which magnifies the image through an eyepiece.
 Dissecting Microscope- a type of light microscope that can magnify an image up
to 40x. A beam of light produced above the stage reflects off the specimen’s
surface, passing though the lenses to magnify it. These microscopes are used to
examine organs and tissue during dissections. They are also used to examine
leaves, stems, mold, spores, and other small items.

 Compound Light Microscope- a common light microscope that’s light source is

below the stage, which shines through the specimen and then through the
glasses. Slides are commonly used, and dyes can stain them to view nearly
transparent cells. They can magnify an image from 40x to 1000x. They are used
to examine tissue, blood, pond microorganisms, cells, and details in cells.
 Two important factors in
microscopy are magnification (how
much larger an object appears
compared to its real size) and resolving
power (a measure of the clarity of an
object). Resolving power can be
limited by the properties of light. Increased magnification=decreased clarity, which is why
microscopes don’t usually magnify beyond 1500x. They can’t magnify finer than 0.2
micrometers, which is the size of a small bacterium cell.
Electron Microscope- an electron microscope uses beams of electrons instead of light to
view specimens. The shorter wavelengths of electrons give these a higher resolving power, up
to 0.2 nanometers, 100 times greater than a light microscope. These cannot view living
specimens because the methods preparing them from viewing kill the cells.
These use electromagnets to magnify because electrons can’t pass through glass. The
electromagnets magnify the image by bending electron beams and projecting it onto a screen
for viewing.
 TEM- Transmission electron microscopes pass a beam of electrons through a thin
specimen. Scientists can stain specimens to increase contrast in the image. TEMs
are used to study the internal structures of cells that can’t be viewed in light
microscopes. They are usually in black and white, but scientists use artificial color
to enhance visibility when needed.

 SEM- Scanning electron microscopes are used to study the details of a

specimen’s surface. The electron beam scans the surface, which is coated with a
thin layer of gold. The electrons that scatter off the gold surface are put on a

screen, making a 3D version of the specimen surface.

 2.03 Early Cells
The modern cell theory describes what we currently know about cells. It states-
 All living things are made up of cells
 The cell is the basic unit of structure and function in all living things
 New cells can only be produced from existing cells

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 Prokaryotic and Eukaryotic Cells- These are the two main types of cells. Prokaryotes
don’t have a nucleus, and eukaryotic cells separate their DNA from the rest of the cell by
enclosing it in a true nucleus.
Prokaryotes- prokaryotic cells are small and simple, meaning they don’t contain many
specialized structures within the cell. They are single-celled.
Prokaryotic Cell Structure

 Cell Wall- Semi-rigid structures mostly composed of a sugar. The cell wall function is to
give the cell structure and protection.
 Cell Membrane- Also called a plasma membrane, it is a structure made mostly of fats
and proteins that functions to control what comes in and out of the cell. All cells have a
membrane.
  Cytoplasm- A gel-like substance that functions to
separate the parts inside the cell. It is also a place
where a lot of chemical reactions occur that keep the
organism alive.
 Nucleoid- The area of the prokaryote cell that contains
the DNA.
 Ribosomes- An organelle that is used to make proteins
for the cell.
 Flagella- A long whip like structure used to help the cell
move.
Eukaryotes- Eukaryotic cells are more complex that
prokaryotic cells. Some exist as single-celled cells, and some are multicellular.

Every cell is enclosed in a cell membrane,

which can also be called a plasma membrane. It is
selectively permeable, meaning it lets some
substances pass through, but not others. This is
essential to life. They are made up of carbohydrates,
phospholipids, and proteins.
There are two different ways for cells to
regulate the movement of molecules in and out of the cell, which
are called passive and active transport.
In diffusion, particles move from an area where they are
higher in concentration to where they are lower.
Passive Transport- the movement of materials across a
membrane without the use of energy from a cell. The cell’s
cytoplasm is a solution of many different substances dissolved in
water. In it, particles diffuse.
 Facilitated Diffusion- large hydrophilic molecules are not able to diffuse through the
phospholipid bilayer of the cell membrane because they don’t mix well with the hydrophobic
tails of the phospholipids. Some proteins that make sure only a specific type of molecule in lets
them through the membrane. This process does not require energy from the cell, which means
it’s a form of passive transport. Osmosis is the facilitated diffusion of water, which is difficult in
cells that are protected by a hydrophobic cell membrane. Aquaporins allow water to pass
through the membrane for osmosis.
Active Transport- the movement of materials across the membrane
that requires energy from the cell. It needs energy because it moves energy
against the concentration gradient, which means that it moves from lower
concentration to higher. The transport of ions is carried out by transport, also
called protein pumps, that are found in the membrane. They move ions such as
calcium, potassium, and sodium. Larger materials are transported by
endocytosis (the intake of materials from outside the cell when the membrane
folds around the material and forms a saclike vesicle) or exocytosis (the
discharge of materials to the outside of a cell when a vesicle containing these
materials fuses with the plasma membrane).
Endosymbiosis- when one organism lives inside the other, and they benefit each other
while doing so. This works because years ago, all cells were prokaryotic. Some of these cells
used photosynthesis to make oxygen. According to the endosymbiotic theory, two prokaryotic
cells lived together and performed aerobic respiration and got stronger, later making the
mitochondria in eukaryotic cells. The same is said about chloroplasts and organelles, which are
found in plant cells, which evolved to be inseparable and to work together.
Most of the membrane-bound organelles inside eukaryotic cells seem to have originated
from deep folds in the cell membrane, but the mitochondria and chloroplasts have distinct
properties that make them different. These two organelles have characteristics prokaryotic
cells.
Endosymbiotic Theory- a theory that explains the existence of eukaryotic cells, that did
not have any fossil record until 2 billion years after the first prokaryotic was found. The theory
hypothesizes that modern-day eukaryotic cells were just two prokaryotic cells in an
endosymbiotic relationship.
This theory is supported by scientists that noticed that eukaryotic cells have both a
mitochondria and chloroplasts, similar to prokaryotic cells, they have a similar circular DNA
arrangement, similarly sized ribosomes, and the fact that they are responsible for their own
reproduction.
 2.04 Cell Structure and Function
Eukaryotic cells are more complex than
prokaryotic cells. They contain organelles, which
have specific structures and functions for the
cell. They can be found in animals, plants, fungi,
and protists.
Parts of Cells
Nucleus- controls the activity in the cell.
Most DNA is found here. The nucleus is
protected by a nuclear envelope. The nucleolus is in the center of it and produces ribosomes.
Mitochondria- powerhouse of the cell, provides energy.
Endoplasmic Reticulum- transports materials to and from the nucleus, which has
ribosomes all over it.

 Rough ER- an endoplasmic reticulum covered in small ribosomes. It stores and

makes proteins and makes phospholipids.
 Smooth ER- an endoplasmic reticulum without ribosomes. It participates in
metabolic processes such as the construction of lipids, deconstruction of
carbohydrates, and the detoxification of harmful substances.
Ribosomes- where proteins are made, factory of the cell. They are located both on the
endoplasmic reticulum and throughout the cytoplasm. They are made of RNA and protein.
Golgi Apparatus- packs and distributes proteins, post office of the cell. Works with the
endoplasmic reticulum to transport proteins.
Lysosome- breaks food down in the cell, the digestive system of the cell. It uses
enzymes to break down large molecules.
Vacuole- stores water and food. Plant
cells have a large vacuole to maintain the
shape of the plant, and animal cells have
smaller vacuoles.
Chloroplast- found in plant cells, the
photosynthetic organelle. Makes food during photosynthesis for the plant cell.
Cell Membrane- surrounds the cell as a selective barrier.
Cytoplasm and Cytoskeleton- cytoplasm is the thick fluid that fills up a cell and
surrounds all the organelles. It is made of water, salts, ions, and organic molecules.
Cytoskeletons give the cell shape, anchor many of the organelles in place, and direct organelle
movement.
Cell Wall- surrounds a plant cell for protection. Made of cellulose, polysaccharides, and
imbedded proteins, this can maintain the shape of the cell and prevent excessive loss or gain of
water.
 2.05 Cellular Energy
The human’s “battery” is energized by molecules that we get from eating, such
as carbohydrates and fats. They release energy when digested. They are used to make ATP
molecules from ADP.
ATP- a source of energy for a cell, called
adenosine trisphosphate. It is made up of ribose
and a chain of three phosphate groups.
The bond between the second and third
phosphate groups is broken down easily. When one phosphate is broken off ATP, the remaining
molecule is called adenosine diphosphate, or ADP.
Water molecules and a small amount
of energy are needed to remove a phosphate
from ATP, but the amount of energy released
in the process is more than amount needed to
break the bond. That energy that is released is used by the cell to power processes such as
movement, active transport, or protein synthesis.
The cell can store or release energy by adding or removing the phosphate group. The
ability to form or break this bond makes ATP a renewable resource within the cell.
Our food contains molecules like fats,
carbohydrates, and proteins. They are broken
down during digestion, which releases energy.
That energy can be used to power ATP molecules.
ATP is suited for short term energy storage
because it’s too unstable for long term. Cells use it
to build more stable molecules. Plant cells also use
it to make sugar and starch with their excess energy, which can be stored.
Animals store energy in fat molecules.
 2.06 Cellular Respiration
Cellular Respiration- a process that uses oxygen to harvest the chemical energy stored
in organic molecules. Carbon dioxide is produced as the chemical energy is released from the
organic molecules.
C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy (ATP and heat)
Organic Compounds + Oxygen → Carbon Dioxide + Water + Energy
Adenosine Triphosphate- Food contains energy that is released when their chemical
bonds are broken. During cellular respiration, ATP is used to provide energy needed to harvest
electrons from organic molecules that are used to make ATP.
Reactants- Glucose (found in foods, broken down into carbon-based compounds as
energy is released), Oxygen (makes cellular respiration an aerobic process, needed to perform
respiration)
Electron Carriers- NAD (accepts pairs of high energy electrons to become NADH), NADH
(carries high energy electrons to the electron transport chain where they build ATP), FAD (does
the same as NAD but forms FADH2), FADH2 (carries electrons to the transport chain)
Products- Carbon Dioxide (contains the carbon from glucose, a reactant for
photosynthesis), water (at the end of the electron transport chain, electrons, hydrogen ions,
and oxygen bond together to form water molecules)
Stages
1. Glycolysis- both aerobic and anaerobic, occurs in the cytoplasm. A six-carbon
glucose molecule is broken into two three-carbon molecules called pyruvate, which
go to the mitochondria for the Krebs cycle. This step takes in 2 ATP molecules and
produces 4. This doubling effect is the same with glucose and NAD molecules.
2. Krebs Cycle- aerobic, occurs in the mitochondria. The pyruvate molecules formed
from the glucose molecules convert into two acetyl-CoA molecules. (2 acetyl-CoA + 2
oxaloacetate → 4 CO2 + 2 oxaloacetates + 6 NADH + 2 FADH2 + 2 ATP).
3. Electron Transport Chain- aerobic, occurs in the mitochondria. The chain is made of
three protein pumps embedded in the inner mitochondrion membrane. The NADH
and FADH2 from glycolysis give energy to these pumps. As electrons go through the
pumps, they become energy, which moves positive hydrogen ions from the
mitochondrion’s matric to the intermembrane space. When the amount of hydrogen
ions becomes too large, they diffuse back into the matrix through the ATP synthase,
which produces about 34 ATP molecules. At the end of this chain, hydrogen and
oxygen form water, and the NAD and FAD molecules are sent back to the beginning
of the chain.
 When a cell can’t get oxygen, it can’t perform cellular respiration. There is one way for
glycolysis to occur anaerobically, which is called fermentation. Instead of producing 30 ATP
molecules in exchange for one, fermentation only makes 2. There are two different types of
fermentation- alcoholic and lactic
acid.
Both types regenerate NAD
so it can be used in glycolysis.
Microorganisms like yeast undergo
alcoholic fermentation, which uses
ethyl alcohol and carbon dioxide.
Other organisms like animals
undergo lactic acid fermentation.
This converts pyruvate to lactic acid.
When you work out, you might not have enough oxygen for your torn down muscles to
replenish, and when lactic acid gets to your muscles, it makes you feel the burn.
 2.07 Photosynthesis
Photosynthesis is the process that takes light and converts it into energy. The energy is
stored in glucose and other molecules, which are ingested by animals.
Photosynthesis uses water and carbon dioxide gas and turns it into oxygen and
carbohydrates, using the following reaction.
6CO2 + 6H2O + Energy →C6H12O6 + 6O2
Light-Dependent Reactions- only occur when there is light present. In this form, solar
energy is converted to chemical energy through ATP and NADPH. NADP accepts electrons
released when chlorophyll accepts sunlight and a hydrogen atom to form NADPH, which carries
the electrons and transfers them to other molecules. These light-dependent reactions take
place in thylakoids. When chlorophyll releases electrons after absorbing light, they move
through electron transport chains in thylakoids. These chains use energy from the electrons to
pump hydrogens into the thylakoid from stroma (gel-like substance in the chloroplast), which
fills up the thylakoid. Through diffusion, the hydrogen moves back to the stroma through the
ATP synthase, where, as it moves, it bonds with ADP to make more ATP. At the end of the
electron transport chains, NADP picks up electrons, energy from chlorophyll, and hydrogen to
form NADPH, which carries electrons to the next stage of photosynthesis. To repeat this, a
water-splitting removes electrons from water and gives it to chlorophyll, which splits the water
up into hydrogen and oxygen.
The hydrogen and chlorophyll
can repeat the reaction, and
oxygen is let into the air.
Light-Independent
Reactions- (also known as the
Calvin cycle) occurs without
light. It uses light from light-dependent reactions to power it. They use the chemical energy
(ATP and NADPH) from the previous reaction and carbon dioxide to make glucose and other
molecules. Carbon dioxide enters the Calvin cycle from the atmosphere, which is combined
with other carbon-based molecules by the stroma to make three-carbon compounds which
continue the cycle.
Photosynthesis and cellular respiration work together to harvest the energy from
sunlight, package it into chemical molecules, and break down those molecules to power the
growth, movement, and functions of all organisms and their cells. They also help cycle
important molecules in our atmosphere.
 3.01 Cell Division
Cell Cycle- during the cell cycle, a cell performs
everyday actions, DNA replicates, and the cell divides into
two daughter cells. A cell takes most of the time in
interphase, where it works and grows.
Parts of the Cell Cycle
The cell cycle can be divided into two parts- interphase
and cell division. Interphase has three parts, and most of the
cell’s life take place in it.
G1 Phase- This is the longest stage in interphase.
During it, the cell grows and performs its duties in an organism. They will work and grow until
they get too large to work, so they enter the S phase.
S Phase- The synthesis phase is when the cell makes a copy of chromatin in its nucleus,
which contains the cell’s DNA. After this, the G2 phase starts.
G2 Phase- During the G2 phase, the cell grows and gets further prepared for division. At
the end, its ready to divide.
Cell division is separated into two parts- mitosis and cytokinesis.
Mitosis- In mitosis, the cell distributes genetic material from the S phase into two
separate nuclei. There are four phases- prophase, metaphase, anaphase, and telophase. This
process also exclusively takes place in eukaryotic cells.
 In a prokaryotic cell, mitosis can’t occur, so another process, called binary fission,
occurs.
Binary Fission is when a prokaryotic cell grows too large, replicates
its genetic material, and divides in four steps.
1. The original prokaryotic cell has one single chromosome.
2. The single DNA molecule is replicated or copied.
3. The DNA copies are moved to opposite ends of the cell, where they
are attached to different parts of the cell membrane. Anchoring
the DNA molecules to different parts of the cell membrane helps
ensure that the replicated DNA molecules end up in separate
daughter cells as cytokinesis divides the cell.
4. Cytokinesis divides the cell into two identical daughter cells. Many
prokaryotic cells have a cell wall surrounding the membrane. If a
cell wall is present, a cross-wall forms to divide the cell.
Both in mitosis and binary fission, the cell’s genetic material is copied, separated, and
made into two daughter cells in cytokinesis.
 Cytokinesis- During cytokinesis, the cell divides into two daughter cells, which contain
the same genetic material as the original cell, and they repeat the process over again. In an
animal cell, the cell membrane is pulled inward until the cell is pinched in two, and each new
daughter cell contains its own nucleus and organelles. In a plant cell, a cell plate forms between
the two nuclei, developing into cell membranes. Next, a cell wall forms between the two
membranes to complete the cell division.
Adaptations that increase the ability to survive and reproduce are favored for any
organism. Genetic diversity is important for a species to adopt and evolve. Though prokaryotic
cells reproduce asexually, there are some ways for them to become diverse.
Mutation- a change in the nucleotide sequence of a cell’s DNA, which can result from
insertion, deletion, or substitution of one or a few nucleotides in a gene sequence, or
rearrangements of entire genes within a chromosome. They are often caused by errors in DNA
replications prior to cell division that cause daughter cells that aren’t identical. A mutation can
be harmful, neutral, or beneficial to the organism, and they will be passed down to generations
of cells.
Transduction- when a virus transfers DNA from one
bacterium to another. Bacteriophages are viruses that infect
bacteria. Sometimes when new virus particles are assembled
in a host DNA cell, some of the bacteria’s DNA can get
incorporated in the virus. When the viruses infect new host
cells, the bacterial genes can be inserted into the DNA of the
new host cell.
Conjugation- when genetic material is transferred
between two bacterial cells by a bridge-like connection
between the cells. During this, DNA segments move from one cell to the other through the
bridge. These DNA segments can let bacteria resist antibiotics or survive in a changing
environment. The DNA is passed down to daughter cells during binary fission.
Transformation- Sometimes, DNA fragments are
released into the liquid environment as dead cells break down,
which can be taken into bacteria cells and added to its genes.
Prokaryotic cells multiply quickly. The time taken for a
bacterial cell to divide is called the generation time. They can be
as short as 15 minutes or long as several days. This is how
mutations and diseases spread so quickly in host populations.
 3.02 Meiosis
There are two main types of reproduction- asexual and sexual.
Asexual Reproduction- when a single organism is the sole parent and passes all its
genes into its offspring. Asexual reproduction mostly uses mitosis, so any differences in
offspring are from mutations. Certain organisms benefit from asexual reproduction if they can’t
move and seek a partner, and because it takes less energy and it is faster than sexual
reproduction. A disadvantage of asexual reproduction is a lack of diversity in daughter cells.
There are different types of asexual reproduction, but some examples include-

Binary Fission Used by most bacteria, single-celled organisms can reproduce

asexually through cell division.
Budding A new mass of living cells divides and grows on the side of the
parent, that grows into a mini version of the parent, called a bud,
that detaches and grows on its own.
Gemmules A parent releases a specialized mass of cells into offspring.
Sexual Reproduction- when two parents, usually animals and plants, make a child with a
combination of their genes. Children made with sexual reproduction have different sets of
genes for every trait, called alleles. Each parent gives on allele to the child. This method of
reproduction results in much more variation, which is important for the survival of a species.

Type of Reproduction Asexual Sexual

Number of Parents One Two
Genetic Diversity Identical offspring Diverse offspring
Characteristics Quick, produces large number Usually slower. But genetic
of offspring diversity helps ensure survival of
the species.
Every species has a specific number of chromosomes in its cells. Human cells contain 46
chromosomes, which is a human's diploid (2N) number. Their cells contain two homologous
(chromosomes in which one set came from the male and female parent respectively) sets of
chromosomes, 23 from each parent.
Gametes, which are haploid cells involved in sexual reproduction, carry half the number
of chromosomes as diploid cells. These haploid (N) cells contain a single set of chromosomes to
pass on to their offspring, and they are made in meiosis. When they are made, the diploid
number is cut in half to produce haploid sperm and egg cells. When the sperm and egg cells
fuse, it is called fertilization, which forms a zygote.
Two of the 46 chromosomes are called the sex chromosome, because they determine
the sex of the offspring. Females have XX chromosomes, and males have XY. Sperm cells carry
an equal amount of X and Y chromosomes, which is why there’s a 50:50 chance of heaving each
gender, and an ovum carries only X chromosomes. X chromosomes carry 1,200 genes, and Y
chromosomes carry 140. The rest of the 44 chromosomes are called autosomal chromosomes
or autosomes.
Meiosis Stages
Meiosis I-
1. Interphase I- as the cell prepares for meiosis, the chromosomes replicate. For each
chromosome, a genetically identical sister chromatid is formed.
2. Prophase I- chromosomes condense and become more visible. The sets of sister
chromatids pair up with its homologous pair of chromosomes, which makes four
chromatids. Non-sister chromatids pair up at several places and go through crossing
over, when chromatids of homologous chromosomes cross and hold the four
chromatids together. They then cross over and form new alleles in the cell. As the cells
prepare to divide, spindle fibers form between the centrioles and the nuclear
membrane and nucleolus disappear.
3. Metaphase I- the four chromatids line up along the center of the cell. Spindle fibers
from one pole attach to each set of sister chromatids, while another pole attaches to the
homologous sets.
4. Anaphase I- the spindle fibers pull the chromosomes apart, like mitosis, but the sister
chromatid pairs stay together at their centromeres and move together at the same end
of the cell
5. Telophase I- Each pole now has a haploid set of chromosomes, but each chromosome
still has two chromatids.
6. Cytokinesis I- The cell splits into two daughter cells that have different chromosomes
from each other and from the diploid cell that entered meiosis, thanks to prophase I.
7. Interphase II- In some species, the daughter cells go through this stage, while some do
not, and they go straight to meiosis II.
Meiosis II
1. Prophase II- the chromosomes are still paired as sister chromatids in each of the
daughter cells, and spindle fibers begin to form in them.
2. Metaphase II- the sister chromatid pairs line up across the middle of the cell, and
spindle fibers attach to the centromeres of each chromatid pair.
3. Anaphase II- the centromeres that held the sister chromatids together separates, and
the chromosomes move along the spindle fibers toward opposite ends of the cell.
4. Telophase II- nuclear membranes form around each haploid set of chromosomes.
5. Cytokinesis- The cells divide, forming a total of four haploid daughter cells from the
original diploid cell that entered meiosis I.
In human females, meiosis makes four
haploid nuclei, but the cytoplasm is divided
unequally during cytokinesis is both meiosis I and
II. One egg cell is produces, along with 2 or 3
polar bodies, that break down and never form into gametes. This inequality makes it so that the
ovum is well supplied with cytoplasmic materials that are important for the embryo.
There can be lots of genetic variation in sexual reproduction from the shuffling of
chromosomes during meiosis and fertilization. The main mechanisms that make variation
happen are crossing over, arrangements of chromosomes in metaphase I, and random
fertilization.
During the crossover in prophase I, sister chromatids in each tetrad attach and swap
portions of adjacent DNA molecules. No genes or added or subtracted, but the crossover
increases variation in the sex cells. In metaphase I, the orientation of homologous pairs is
random as they line up, so they can line up in two different ways, which can lead to variation.
Changes in the orientation of tetrads along the center of the cell can vary the combination of
chromosomes in the daughter cells. The fusion of gametes during fertilization adds to variation
because there are eight million possible chromosome combinations in both eggs and sperm
cells respectively, which results in 64 trillion possible combinations.
Mitosis and meiosis both ensure that cells inherit genetic information, but they differ
how that happens.

Event Mitosis Meiosis

DNA replication, Occurs during interphase before Occurs during interphase before
forming sister nuclear division begins. nuclear division begins.
chromatids
Number of One, consisting of prophase, Two, each consisting of prophase,
division cycles metaphase, anaphase, telophase, metaphase, anaphase, telophase,
and cytokinesis. and cytokinesis.
Total number of Two diploid cells, genetically Four haploid cells, containing half
daughter cells identical to the parent cell. as many chromosomes as the
original parent cell.
Importance Production of diploid body cells for Production of haploid gamete
growth and repair. cells for sexual reproduction.

3.03 Mendel
Genetics is the scientific study of genes and heredity. Mendel is a man who changed the
knowledge of genetics forever.
 Mendel’s observations used a pea plant, which reproduces sexually, to observe genetics.
Male flowers make pollen called Stamens, which have sperm, and female produces eggs called
the Carpel. He made them cross-pollenate so that he
could observe how hybrids form, in relation to
genetics. He used flowers that had one difference,
which is called a monohybrid cross. In the experiment,
P was the original flowers, the first generation is F1,
and the second is F2.
After the experiment, seen on the right, was
completed, you can see that the traits in the F1 group
were the dominant (an allele for a trait that is usually is
in the phenotype and masks the recessive trait) traits.
The recessive (an allele for a trait that won’t be shown
in the phenotype unless the organism is homozygous
for the trait) trait was shown in the F2 group.

Mendel concluded that in each monohybrid cross, all the F1 plants were the same as
one parent, but when they self-pollenated, the other trait was in about 25% of the F2 plants.
From this he drew the following conclusions:
1. Different forms of a gene account for variations in the inherited traits- each trait is
controlled by one gene that occurs in two varieties that can result in two different
expressions of it.
2. An organism inherits two genes for each trait, one from each parent.
3. Some alleles dominate over others for a given trait- (this is now called the principle of
dominance.) an organism inherits two of each gene, one from each parent, and the one
with the dominant allele takes over the recessive one. If both are recessive, then it will
be shown.
4. The two genes of a given trait segregate during gamete production- (this is now called
the law of segregation.) each cell made in meiosis is haploid, which means each gamete
will only receive one of the two genes for a given trait that are found in the organism’s
other cells. If it had matching alleles for a trait, then all the gametes will have the same
allele for it, but if differing alleles are present, half will receive the dominant trait and
the other will receive the recessive.

3.04 Heredity Patterns

 Probability- the probability scale ranges from 0% to 100%. For example, a coin has a
50/50 chance of landing on heads or tails. No amount of coin tosses will change this probability.
This is true in genetics as well.
An organism with identical alleles for a trait is homozygous. When organisms sexually
reproduce, they each give a gamete with half of the chromosomes as the organism’s other cells.
Since its homozygous, it will give out gametes that have the same allele for that trait.
An organism with differing alleles for a trait is heterozygous. These organisms are made
from dominant (PP) organisms reproducing with recessive (pp) and making Pp organisms. When
a heterozygous organism makes gametes, the alleles separate. Half of the offspring would get
the dominant, and the other would get the recessive.
There is a difference in the appearance of an
organism and its genetic makeup, so you can’t tell the
genetic makeup of an organism from its appearance. When a
trait is shown in the appearance, it is called a phenotype, but
if it’s in the genetic makeup, it is called a genotype. An
example of this is shown on the right.
Punnett Squares- a way to make predictions about
the outcome of a genetic cross using a diagram.
Test Crosses- a way to determine the genotype of an individual with a dominant trait.
This test crosses an organism with a dominant phenotype and an unknown genotype with an
organism that is homozygous recessive for that trait. You can tell the difference because all
homozygous offspring will have the dominant, and the heterozygous will have half and half.
Dihybrid Cross- a cross used to track two different traits. In Mendel’s studies, he learned
about independent assortment (genes for different traits can segregate independently during
the formation of gametes). It’s basically a bigger Punnett square.
Some of Mendel’s work was flawed. There are a few different ways people have noticed
this:
1. Incomplete Dominance- some traits show incomplete dominance, where the alleles are
neither dominant nor recessive.
2. Multiple Alleles- an individual will only have two copies of each gene, but there are
more alleles of that gene in a population.
3. Codominance- when both alleles are showed in an offspring’s phenotype.
4. Polygenic Traits- traits controlled by two or more genes.
5. Sex-Linked Traits- in humans and other mammals, there are two variations of sex
chromosomes, which are X and Y. Other than determining the sex of the offspring, the
sex chromosomes also contain genes for other traits, which are called sex-linked traits.
Men pass down a Y chromosome to their sons, and females pass down a X chromosome
 to both sexes. Most sex-linked traits are X-linked. If a sex-linked trait is recessive, a
female must be homozygous for the trait to exhibit it.
Pedigree- a diagram that shows relationships in families over multiple generations. They
use squares for males, circles for females, horizontal lines for mating, vertical lines for offspring.
These are used to see things like diseases and how they’re passed down in families by shading
infected individuals’ boxes or circles.

3.05 DNA Replication

Structure of DNA-
  Nucleic Acids- long macromolecules made up of nucleotides covalently bonded
together. They are made of deoxyribose, a phosphate group, and a nitrogenous
base. The nucleotides in a DNA strand are held together by bonds between the
sugar of a nucleotide and the phosphate group of the next, with the nitrogenous
bases sticking out sideways from the chain.
 Nitrogenous Bases- bases that contain nitrogen. The nucleotides that make up
DNA differ by the base they contain, either adenine (A), guanine (G), cytosine (C),
or thymine (T). The different nucleotides can be strung together in many ways.
 Hydrogen Bonding- the nitrogenous bases of each nucleotide stick out from
DNA, and hydrogen bonds from between them. This is weaker than covalent
bonding, which is important because DNA separates a lot.
 Base Pairing- hydrogen bonds only form in two ways; guanine with cytosine, and
adenine with thymine. Cars in the Garage, Apples on the Tree.
DNA can be copied, thanks to base pairing. Each strand of DNA is complementary to the
other because each base can only bond with one other base, so each strand can reconstruct the
other strand through base pairing. Before cell division, it replicates DNA. During this process,
DNA separates into two strands and then, using base pairing, makes new strands. This process
uses enzymes that break hydrogen bonds and join nucleotides. At the end, DNA checks itself to
make sure every base is with its perfect partner.
RNA copies sections of DNA and carries the copies outside the nucleus, which direct the
construction of protein. DNA and RNA differ in the following ways-
1. RNA is single stranded, while DNA is double.
2. The sugar in RNA’s nucleotides is ribose instead of deoxyribose.
3. RNA has uracil instead of DNA’s thymine.
Functions of RNA

 Messenger RNA (mRNA)-RNA that carries genes that contain instructions to

make amino acids into proteins around the cell.
 Ribosomal RNA (rRNA)- RNA that makes up ribosomes, along with up to 80
protein molecules.
 Transfer RNA (tRNA)- transfers amino acids to ribosomes from instructions from
messenger RNA.
The flow of genetic information in a cell goes from DNA to
RNA to protein, through processes called transcription and
translation.
Transcription- when a segment
of DNA is used to produce a mRNA molecule. This process uses
an enzyme called RNA polymerase.
 1. The RNA polymerase binds to a DNA molecule and separates the strands.
2. One strand of DNA is used as a template to assemble complementary nucleotides into a
complementary mRNA strand.
3. Base sequences on DNA called promoters signal where RNA polymerase should
transcribe another section of mRNA. Other base sequences signal that the mRNA
molecule is complete, and the transcription stops.
Translation- when the genetic code
on the mRNA strand is used to direct the
construction of a protein molecule.
1. A ribosome attaches to a mRNA
molecule in the cytoplasm.
2. As each codon passes through the
ribosome, tRNA molecules bring
amino acids in, as well as their three
unpaired nitrogenous bases called anticodon, which is complementary to codon on
mRNA. The other end of tRNA carries only one type of amino acid. In this way, tRNA
translates the code in the mRNA molecule in a pattern of amino acids.
3. The ribosome, and the rRNA molecules it contains, join the amino acids together as
tRNA brings them to them. The protein chain grows until the ribosome reaches a stop
codon from the mRNA molecule, and translation is complete.
Codon- a group of three
nitrogenous bases in mRNA that
codes for a specific amino acid to
be added to the protein molecule.
There are codons that start and
stop the assembly of the protein
molecule, as well. There are 64
possible codons in the genetic
code.

3.06 Mutations
A mutation is a change in a cell’s genetic material. They can be beneficial, bad, or
unnoticeable for an organism.
Chromosomal Mutations- a change in the number of chromosomes.
  Deletion- the loss of all or a part of a chromosome
 Duplication- an extra copy of all or part of a chromosome
 Inversion- reverses the direction of parts of an organism
 Translocation- when a part of a chromosome breaks off and attaches to another
chromosome
Gene Mutations- (also called point mutations) chemical changes in one or more
nucleotides that occur at a single point within a gene. This happens during DNA replication, and
it is passed from the duplicating cell to the new one. This can also happen in sperm or egg cells,
which will pass the mutation onto the offspring, which are called germ line mutations.

 Base-Pair Substitutions- when one base pair is replaced with a different pair of
nucleotides. This sometimes has no effect on the protein if the replaced codon
makes the same amino acid. If it does have an effect, it changes the protein. It
will disrupt the corresponding mRNA, making it signal for synthesis to error. It
can also change the shape and function of a protein.
 Base-Pair Insertions and Deletions- when nucleotides are added or removed
from the DNA sequence. This can affect the protein molecule because the
genetic code will be either under or overloaded with codons, which will signal for
the wrong amino acids.
Without mutations, organisms wouldn’t evolve. Inherited mutations are essential for
variation, but some mutations can’t be inherited if it occurs in a body cell that isn’t used in the
production of gametes. Mutations must be dominant for them to be shown in the phenotype.
Cells can control what genes are expressed (when a gene produces its product and the
product carries out its function) in response to the internal and external conditions. Some
proteins interact with the environment and others determine what genes should be transcribed
and translated. Cells have specified genes for different body actions, and others can turn genes
on and off from internal and external conditions.
Examples of Mutations

 Sickle-Cell- a recessive disease the gives red blood cells a crescent shape rather
than a disk shape, which blocks flow of blood in limbs and organs. It is caused by
a mutation in the gene that makes hemoglobin, which carries oxygen.
 Non-Disjunction- when a gamete has two copies of a chromosome and the other
with no copy, which when used in fertilization, will give a zygote an abnormal
number of chromosomes. This is caused by a homologous pair not separating in
anaphase I of meiosis, or chromatids not separating in anaphase II.
 Cystic Fibrosis- a disease that causes mucus to build up in the lungs and digestive
tract. This is caused by mutations to the gene that codes a protein called CFTR,
that regulates the components of sweat, digestive juices, and mucus.
  Insects- insects benefit from mutations because they help them live in different
environments, but their mutations can be harmful to humans.
 Humans- some humans have mutations that help them resist HIV, and some can
increase bone strength and density.
 Breeding- when people breed animals and fruits, they will breed together two
mutated organisms to pass it down to the offspring.
Mutations that don’t occur naturally come through mutagens, which are physical or
chemical agents that interact with DNA to cause mutations. When mutagens interact with DNA,
they produce mutations at a higher rate. They do this by weakening the DNA strand or through
base pairing.
Cancer- a disorder when body cells can’t control cell growth, so cells divide
uncontrollably. This can form a tumor, that invades and destroys healthy tissue and spreads
across the body, which can stop bodily functions and organs. This can be caused by viruses,
tobacco, radiation, and defective genes, some of which are called p53, which makes cells
unable to respond to the signals that tell them to grow and divide. This can be attempted to
cure by radiation because cancer cells replicate DNA faster than normal cells.

3.07 Biotechnology
A genetic engineer can analyze and change the genetic makeup of cells.
An example of genetic engineering is adding genes from one organism to the DNA of
another organism. This is done by extracting a DNA sequence that has the gene they want to
insert into a cell. When restriction enzymes cut DNA at sequences, they leave sticky ends that
can pair with complementary sequences. This is used to bond sequences together with the help
of DNA ligase, which splices DNA together. At the end, this is called recombinant DNA.
Transgenic Organisms- organisms that have traits produced by recombinant DNA, which
is used to improve plants or animals for agricultural purposes, such as toxins that were bred
into plants to kill of harmful bugs, but not harm humans.
Cloning- when a cell from an adult organism is used to make an identical organism. This
is easy to do on unicellular organisms like bacteria, but harder on multicellular organisms like
animals. Animal cloning uses nuclear transplant, which is when an unfertilized egg is replaced
by the nucleus of a diploid body cell, which makes an embryo that is identical to the original
organism. Cloning allows for passing on of good genetic traits without passing on bad ones.
DNA Fingerprinting- a method to identify individuals based on their genetic makeup.
This is done by breaking down cells from tissue, blood, sperm, or saliva to release DNA, then
separating them by length through gel electrophoresis, when DNA is injected into openings on a
gel tray, where electric currents are applied on the gel, attracting the negatively-charged DNA,
shorter DNA segments first, followed by the longer ones. Finally, a DNA probe is added to the
gel tray, which makes a fluorescent image of the DNA segments. This can be used on crime
scenes to identify people, or to see how people are related to one another. It is also used in
wildlife conservation.

3.08 Health and Genetics

Some diseases are passed down through sexual reproduction, through the combination
of genes and/or alleles passed down by one or both parents.
 Infectious Disease- Infectious diseases are caused by pathogens, which are viruses or
microorganisms that cause disease in a plant or animal host.

Infectious Characteristics Diseases

Agents
Viruses Nonliving pathogens that replicate Common cold, influenza, chicken pox,
by inserting genetic material into a warts
host cell and taking over its
functions. Can spread through
coughing, sneezing, and contact.
Prevented by hand washing,
vaccines, and more.
Bacteria Not all harmful. Breaks down tissue Streptococcus infections, anthrax,
for food or releases toxins that tuberculosis, diphtheria, botulism
stops the host’s functions. Spread
through coughing, sneezing,
contact, and more.
Protists Protists infect organisms through Malaria, African sleeping sickness,
contaminated water or insect bites. intestinal diseases
They take nutrients from the host
and damage cells and tissue.
Fungi Infect surfaces of skin, throat, Ringworm, thrush, athlete’s foot
mouth, fingernails, toenails, and
lungs.
Parasites Small organisms that enter the host Hookworm, trichinosis, elephantiasis
through mouth, nose, skin, or anus.
They stay in the intestinal track and
absorb nutrients.
Preventing Infectious Disease

 Coughing and Sneezing- coughing and sneezing allows for droplets of bacteria
and viruses to go on surfaces and into people’s mouths. This can be avoided by
washing your hands and avoiding infected people.
 Exchange of Body Fluids- STIs can spread through sex, and you usually don’t
know you have it when you do. This can be avoided by using protection.
 Contaminated Water or Food- water can be contaminated by animal feces, and
to avoid getting sick from it you should always have filtered water, and never
wash food in contaminated water.
Not exercising and having a poor diet can lead to sickness as well, such as type 2
diabetes and heart disease. Also staying protected from the sun can reduce the risk of skin
cancer from UV radiation.
 Substance Abuse- drugs can alter normal bodily function, and when you get addicted
and abuse them, they can hurt your body.

Drug Group General Information Effects Drugs in this

Category
Alcohol Not recognized as a Slows down the Beer, wine, liquor
drug but is abused in central nervous
many ways. system, which results
in difficulty walking,
blurred vision,
slurred speech,
slowed reaction
times, and impaired
memory. Also, can
result in alcohol
poisoning, which can
cause extreme
sleepiness, seizures,
difficulty breathing,
unconsciousness, and
even death.
Depressants Drugs that relieve Decreases alertness, Barbiturates, opiates,
anxiety and produce confusion, alcohol, oxycodone,
sleep. drowsiness, lack of Ritalin, Valium,
coordination, Darvon, Xanax,
irritability, poor Rohypnol
coordination, lack of
judgment, loss of
appetite, sleep
disorders, nausea,
addiction, and
possibly can cause
death.
Stimulants Drugs that Speeds up brain Caffeine, cocaine,
temporarily improve activity and spinal crack,
physical or mental cord activity, which methamphetamines
performance. makes the heartbeat
faster, which makes a
person more
talkative, anxious,
and exhilarated.
Excessive amounts of
this can kill you.
Using these drugs
 can cause chronic
nervousness,
excitability, and
paranoia. The effects
may even be
irreversible, and you
cannot live without
the drug.
Hallucinogens Disrupt the nervous Short-term effects LSD, MDMA, PCP
system, which makes include dilated
you see the world pupils, higher body
different. You can’t temperatures,
concentrate, increased heart rate
communicate, or and blood pressure,
sense reality under sweating, loss of
this drug. appetite, dry mouth,
and tremors. Long-
term effects include
flashbacks,
schizophrenia,
depression, and
possible death.
Marijuana Most used illegal Effects include THC, hashish
drug in the US. perception, impaired
coordination,
difficulty with
problem solving and
memory, and
increased rates of
depression, anxiety,
and suicide.
Club Drugs Odorless, colorless, Can cause MDMA, GHB,
and flavorless drugs drowsiness, nausea, Rohypnol, ketamine,
that can be added to vomiting, headache, methamphetamine,
beverages. decreased blood LSD
pressure, visual
disturbances,
confusion, amnesia,
liver and kidney
damage, loss of
consciousness,
impaired breathing,
coma, and possible
death.
Inhalants Substances that Can burn brain cells Common household
produce vapors that faster than any other cleansers, correction
can be inhaled to drug. fluid, glues, gasoline,
alter the mind. Just cooking spray, spray
one use can be paint, hairspray, nail-
deadly. polish remover,
nitrous oxide
Steroids A human made Effects include Testosterone
substance like male increased size and
sex hormones that strength of muscles,
increase hair. hair loss, acne,
aggression, loss of
sex drive, sexual
dysfunction, liver
damage, cancer,
heart disease, and
strokes. They can
stop a women’s
menstrual cycle and
lower their voice, and
it stunts teen’s
growth.
Tobacco A very addictive Causes rapid Cigarettes, cigars,
substance that, heartbeat, increased pipes, snuff,
short-term, causes blood pressure, and smokeless tobacco
blemished skin, bad rapid breathing. Also,
breath, reduced the brain creates
athletic performance, more endorphins,
greater risk of injury resulting in feelings
and slower healing of increased
time, and overall alertness and
increased risk of euphoria.
illness. Long term,
this causes heart
disease, stroke,
emphysema, and
many types of
cancer, including
lung, throat,
stomach, and
bladder.
4.01 Ecology
Biosphere- all living things and the areas where they live
Biome- a large area classified by its climate and the plant and animal life within it.
 Climate- the average temperature, sunlight, wind, and precipitation over an extended
period.
Ecosystem- all living things functioning together with the factors of their environment.
Habitat- a place in an ecosystem where an organism lives.
Community- an area occupied by different groups of interacting organisms.
Population- a unit of species living in the same geographical area.
Species- a group of like organisms that can successfully reproduce with one another.
Abiotic Factors- nonliving things in an environment
Biotic Factors- living things in an environment.
Food Chain- displays the transfer and matter from one species to another in a linear
path.
Producers/
Autotrophs- the first
trophic level, brings energy
into an ecosystem. Photoautotrophs make food from photosynthesis, and chemoautotrophs
make food from chemosynthesis.
Consumers/heterotrophs- use producers and other consumers for food. The types of
consumers are herbivores, omnivores, and carnivores.
Decomposer- consume dead organisms and other organic wastes and break them down
into reusable organic compounds. Detritivores feed on dead plant matter, and saprotrophs
consume the remaining organic material that other scavengers or decomposers cannot.
Energy Pyramid- illustrates the flow of energy passing from one level to the next.

 Producers (100% from the sun)- consists of autotrophs

 Primary Consumers (10% energy)- heterotrophs; herbivores and omnivores
 Secondary Consumers (1% energy)- heterotrophs; omnivores and carnivores
 Tertiary Consumers (0.1% energy)- omnivores and carnivores
 Quaternary Consumers (0.01% energy)- carnivores
Food Web- shows intersecting connections in food chains.
4.02 The Biosphere
Our biosphere overflows with variety, otherwise known as biodiversity, which is all
thanks to earth’s climates. Some things that effect climate are altitude, win, precipitation,
sunlight, and latitude. They are responsible for change in ecosystems and they account for the
range of conditions on earth.
Latitude- a measure north or south on the earth’s surface, measured in degrees from
the equator.
Altitude- distance above sea level
Factors of Climate
Latitude and Sunlight- earth is an oblate
spheroid, meaning it is slightly flattened at its poles
and bulges at the equator (a circle around the earth
that divides it into northern and southern
hemispheres) from the momentum of its rotation.
What this does is it allows the sun to hit the middle of
the earth at almost a 90-degree angle. This area is
called the tropics, are always hot, and are 2.35-
degrees latitude north and south of the equator.
North and south of the tropics are temperature zones, which are between 23.5-degrees
and 60-degrees latitude north and south of the equator. The climate is mild here and can vary
depending on altitude and rainfall. Farther out are the polar circles, which are 60-degrees north
and south latitude. Due to the earth’s axis (a line that runs through the earth that extends
through the north and south poles), which is tilted 23.5-degrees, they receive little sunlight and
are very cold.
Altitude- the height of land above sea level affects the climates of the biosphere. As the
elevation increases, the temperature decreases.
Altitude can also affect humidity.
Wind and Precipitation- warm air rises and cool
air sinks, which is called convection currents. Warm,
moist water rises at the equator and cools, then forms
clouds and precipitates in rain. At 30-degrees latitude,
the dry air sinks. Earth’s rotation also affects this, with
the Coriolis force, where winds in the northern
hemisphere curve left and vise versa.
Biomes are geographical areas that have similar climate and ecosystems. They are
categorized by climate, habitat, and the community of organisms. There are six major biomes in
the world, which are marine, freshwater, desert, grassland, forests, and tundra.
Abiotic factors, such as temperature, precipitation, and topography (the features on the
surface of an area of land) influence the variation and distribution of species within each biome.
Biomes in areas with warmer temperatures and that are moister tend to be more diverse than
the opposite.
Water covers most of the earth, so there are water biomes as well. Three types of water
biomes are lakes, rivers, and oceans. They all depend on temperature, sunlight, and oxygen to
survive. The amount of oxygen in water is influenced by temperature, sunlight, and salinity.
Cool water is perfect for aquatic life because it has the perfect amount of oxygen.
Freshwater Lake- lakes and ponds are lentic ecosystems because they consist of still
water. The elevation of a lake effects the amount of oxygen for aquatic live because higher up
lakes are subject to more atmospheric pressure, which allows for more oxygen. In lakes, since
they’re small, temperatures can change faster. Currents of cold or warm water don’t change
the temperature of lakes unless they’re part of a runoff or tributary system.
The specific heat of water is high. In a lake, both specific heat and water density cause
stratification, which is the layering of water at different densities and temperatures. This
happens in the spring, as ice melts and cold dense water sinks. This mixes more oxygenated
waters with less oxygenated water. In the fall, the opposite happens. Stratification and seasonal
conditions influence the lives of aquatic animals. In the spring, animals lay eggs, and during the
winter, ice insulates water to make it possible for fish to hibernate and survive. Microphytes,
which are microscopic autotrophs, oxygenate water and are a food source for fish. Plants
underwater also can be used as homes for fish.
Coastal Habitats- these are many different habitats that depend on location, water
temperature, salinity, and geography. Coastal ecosystems store and recycle nutrients from the
ocean, filter pollutants from inland freshwater systems, and protect shorelines from erosion.
They are also important to global hydrology, a study of Earth’s waters as a whole and
interconnected body of water. They have lots of phytoplankton, autotrophic organisms that
make food from sunlight, so they provide a lot of oxygen. They are home to many organisms
who are eaten by humans and other animals and provide materials for fertilizer,
pharmaceuticals, cosmetics, household products, and construction materials.
Estuaries- locations where freshwater streams or rivers empty into an ocean.
Freshwater streams carry sediments that can grow vegetation and can form a barrier to protect
from weather and ocean waves. Many organisms live in estuaries. When the tide is high, salinity
is higher, and vice versa.

4.03 Ecosystems
The study of population dynamics is based on population (the amount of like species
that live in the same geographical area) size and makeup. Some things that affect population
size are migration, births, and habitat.
 Migration- the movement of populations from one ecosystem to another. They can be
good or bad, depending if they will harm or help the ecosystem they are entering and leaving.
Leaving an environment is called emigration.
Births- the cycles of birth and death can affect a population. An organism’s natural rate
of reproduction, the ratio of males and females in the population, and the general health of
reproducing species directly impacts the birthrate of a species. 
Habitat- these are where an organism lives, and if there are too many of a species, they
could run out of habitats. Habitats provide food, water, and breeding areas. Not having these
could be bad for a species.
The maximum number of species that can live in an ecosystem
is called the carrying capacity. If the number exceeds the capacity, it
is called a biological surplus, and it can cause animals to migrate to
avoid running out of food. Carrying capacity is determined by tracking
populations over a long period of time and seeing when the
ecosystem stops supporting the population size. Sigmoid and peak
phenomena occur most often in ecosystems.
Sigmoid patterns (k-selection line on the graph) show that population sizes slow as food
becomes less available. The population stabilizes when the
number of births equals the number of deaths and the
population growth gets to zero. Sigmoid patters reveal the
carrying capacity at the stability point. When all
populations stop changing, it is called a climax community.
Peak phenomena patterns (r-selection line on the
graph) show that food guides population growth and that
birth and death don’t stabilize population. It shows that an
abundance of food will boom the population, and a lack will bust it.
Population size is always shifting due to open systems (where matter and energy are
exchanged freely between the ecosystem and the surroundings) for energy and matter.
Sunlight provides energy, and migration can remove energy. Limiting factors, such as seasonal
fluctuations, water levels, and habitat changes, control population growth and decline and the
carrying capacity. If you limit factors, a population can die out.
Abiotic factors can affect animals as well. Events called successions can change
ecosystems in dramatic ways. There are two types of this- primary and secondary.

 Primary Succession- the progression of growth that develops on newly formed

land or surfaces.
  Secondary Succession- the redevelopment of a habitat that has been disturbed
by an event such as a fire or hurricane.
Biotic factors can also affect animals. Factors that help or harm population growth deal
mostly with interactions between species. Animals eating each other is an example of this.
Invasive species can also affect populations. Invasive species are non-native species that
interfere with established niches of an organism. They can disrupt food chains, bring disease, or
alter genetics when they breed with organisms. When these invasive species are away from
their predators, their predators could die out. Invasive species can also dominate and cause
extinction in an organism population.

4.04 Impacts on our Ecosystem

Environmental indicators have shown that
humans have been changing global climates. The
greenhouse effect explains these indicators. These
indicators include land temperatures, precipitation levels, large storm frequency, ocean
temperatures, sea levels, ocean currents, ocean composition, glacier recession, polar ice levels,
animal migration, plant hardiness zones, and flower bloom rates.
Top Five Greenhouse Gases-

 Water Vapor- water is found naturally in the atmosphere, but the burning of
fossil fuels creates steam as its main by-product. This increases water in the
atmosphere, which increases solar radiation, which makes it hotter, which makes
more water vapor, which makes the cycle get worse and worse.
 Carbon Dioxide- another natural part of the atmosphere but burning of fossil
fuels releases carbon dioxide at high amounts.
 Methane- there is less methane in the atmosphere, but it is more dangerous
than both combined. Permafrost releases methane as it melts and mining
releases methane.
 Nitrous Oxide- produced by deforestation and fossil fuel combustion. With less
plants, more nitrous oxide Is less unabsorbed into the atmosphere.
 Ozone- released by vehicle exhaust, and gasoline vapors, and it can be toxic to
animals and plants. It protects earth’s surface from UV radiation. The ozone is
decreasing due to another greenhouse gas, chlorofluorocarbons, which are from
aerosol sprays, refrigerants, and foam production.
Climate change has caused very warm temperatures, that cause higher precipitation.
Sea levels have also risen, which causes higher surface temperatures, raised sea levels, and
changed sea currents, which all harm marine life. Glaciers have also been melting, which raises
sea levels and changes migration patterns.
Catastrophe in Japan- a huge earthquake hit Japan in March of 2011, which destroyed
many buildings. Following the primary quake was a humongous tsunami, that destroyed cars,
boats, and buildings. Many people were injured and killed. After concerns of Japan’s use of
nuclear power for electricity, literally everything exploded, which made everything else fail. The
impact of these disasters are still prevalent, but the crisis itself ended after radioactive water
leaked into the Pacific Ocean. It was just a mess.
Wildfires in California- for weeks in October 2007, fires burned in California, costing
millions in damages. After the fires, citizens wanted more fire protection, like prescribed burns,
fuel breaks, and telling citizens to move to safer areas.
Human Impact on the Ecosystem-

 Human Expansion- the growth of the population means a growth of our habitat,
meaning houses, schools, businesses, parks, and roads, which we clear land used
by other species in order to build. This leads to a loss of rain, habitat for animals,
and a mass extinction of numerous species.
  Our Choices- the small choices we make can harm ecosystems. Things like
pesticides can kill reptiles and amphibians that naturally reduce pets, and
fertilizers can run into water and deplete its oxygen. Wastewater systems
produce pollutants that can kill fish.
 Our Activities- we clear land for things like garbage, chop down trees for paper,
remove land for farms, mine for minerals, and drill for oil. These things are
helpful to us, but are detrimental to the ecosystem.
To sustain the earth from going to absolute trash for future generations, people partake
in substantiable practices, such as avoiding overhunting, helping animals build their habitats,
and farming without harming other animals.

4.05 Recycling
Earth recycles elements such as water, carbon, nitrogen, and oxygen, using
biogeochemical cycles. These are the flow of chemical elements and compounds between
organisms and the environment.
Biogeochemical cycles also move energy through the environment. The energy may
change forms in-between cycles, but it is never lost, due to the law of conservation of energy,
which states that energy cannot be created or destroyed, only changed.
 The Hydrologic Cycle (the water cycle)- the cycle water takes as it moves through the
environment. All organisms take part in it.
Steps of the Water Cycle

Energy Movement in the Water Cycle

The Carbon Cycle- carbon is organic to every living thing on earth. It is the pathway
through which carbon moves between living things and the non-living environment.
Carbon Cycle on Land

Carbon Cycle in Water

 Energy Movement in the Carbon Cycle

Renewable Source- a natural resource that is replaceable through biogeochemical

cycles or sustainable practices. Abiotic factors are renewable, and biotic factors are renewable
if care is taken to protect them from human activities.

Renewable Resources Benefits Costs

Biomass Energy- The burning It is inexpensive, helps with It is not a clean energy
of wood or garbage is used to garbage disposal, and source. It releases
heat homes or power steam reduces the need for landfills, greenhouse gases.
turbines for electrical energy. protecting habitat.
Solar Power- Special panels Clean energy source Expensive setup and
convert energy from the sun maintenance requires lots of
to electrical energy. space for paneling.
Wind Power- Wind turbines Clean energy source Many locations do not have
convert moving wind to the space or available wind
electrical energy. to make turbines cost
effective.
Hydropower- Turbines use It is less expensive than other It needs a dam built across a
flowing water to create renewable energy sources, fast-moving water source.
electrical energy. but it adds water vapor, a Blocking a river causes
greenhouse gas, to the drastic changes to
atmosphere. surrounding ecosystems. It
adds water vapor, a
greenhouse gas, to the
atmosphere.
Geothermal energy- Heat Clean energy source Geothermal power stations
energy from steam surfaces are only built in areas where
from circulating heated groundwater is close
 groundwater, moving to the surface. They are very
turbines and creating expensive to construct and
electrical energy. maintain.

Nonrenewable Source- a natural resource that cannot be readily replaced. Many energy
sources are unsustainable.

Nonrenewable Resources Benefits Costs

Coal- Fossil fuel of solid It is efficient and inexpensive. The burning of fossil fuels
carbon mined from the releases carbon dioxide and
ground. The heat from water vapor, both
burning coal powers steam greenhouse gases. Coal
turbines that produce mining can damage the
electricity. habitat of the surrounding
area.
Petroleum (oil)- Crude oil is It is inexpensive compared to The burning of fossil fuels
refined to produce industrial other fossil fuels. releases carbon dioxide and
oils and oil-based products. It water vapor, greenhouse
is used to power automobiles gases. Oil is a common water
and provide heat for homes. pollutant.
Natural Gas- Gas is often It can be used directly in The burning of fossil fuels
found trapped in the porous homes for heating and releases carbon dioxide and
spaces of sedimentary rock cooking. water vapor, greenhouse
along with petroleum gases.
deposits. It is used for
running steam turbines for
electricity.
Nuclear power- Energy It does not pollute the Nuclear power plants are
source powered by nuclear atmosphere. expensive to build and
fission or fusion. maintain. The process
produces radiation, which is
harmful if leaked into the
environment.

Energy Movement in the Nitrogen Cycle

 5.01 Evolution
Evolution refers to the processes that transform life on earth over time. It is based on
organism interactions and their habitat. Some things that support this are fossils, anatomy,
embryology, biogeography, and molecular biology.

 Botany/Botanist- Botany is a field of science that studies plants. Botanists are

the scientists that work in this field of study.
 Anatomy/Anatomist- The field of anatomy is concerned with the bodily
structures of humans, animals, and other organisms. Anatomists use dissection
as just one of the ways in which they study body structures.
 Biogeography- The field of biogeography studies where on the planet species
live now and where their ancestors lived in the past.
 Astronomy/Astronomer- Astronomy is the field of science that studies outer
space, including the position, distribution, dimensions, motion, composition, and
energy of planets, stars, and other celestial bodies.
  Paleontology/Paleontologist- The field of paleontology is concerned with the
study of fossilized plants and animals. Paleontologists are the scientists who
work in this field.
 Geology/Geologist- Geology is the field of science that investigates the earth's
physical structure, its history, and the processes that act upon it.
 Naturalist- A naturalist is an expert in the study of the natural history of the
Earth.
 Catastrophism- Catastrophism is a theory about the earth's history that says
major changes in the earth's crust result from catastrophes rather than from
slow, gradual processes.
 Gradualism- Gradualism is a theory about the earth's history that says slow but
continual processes can result in large, dramatic changes.
 Uniformitarianism- A theory, built upon gradualism, proposing that the rates of
geological processes that form the Earth are uniform, or constant, throughout
history.
 Punctuated Equilibrium- The theory of punctuated equilibrium proposes that
evolution happens in rare instances of rapid branching evolutionary change in
between long periods of stability. This contrasts with the theory of evolutionary
gradualism.
 Evolution by Natural Selection- Some individuals within a population have traits
that better enable them to survive and reproduce in each environment, while
others may not survive to reproduce. This process is called natural selection, and
it can lead to the evolution of a population over many generations.

Timeline
 Evidence for Evolution

 Fossils- paleontologists have found fossils that prove evolutionary stages. Where
the fossil lies in the earth shows the stage of evolution an animal was in.
 Comparative Anatomy- similar structures that came from a common ancestor
are called homologous structures. These structures have been made through
the years to modify animals to be able to act differently.
 Vestigial Structures- evidence of something that no longer exists.
 Comparative Embryology- closely related organisms go through equivalent
stages of embryonic development.
 Molecular Biology- species with similar DNA sequences share close ancestors.

5.02 Evolutionary Relationships

Charles Darwin traveled on the HMS Beagle for five years to map South America, and so
he could get plants and animals along the route. Through his studies, he noticed three patterns.

 Species Vary Globally.

 Species Vary Locally.
 Species Vary Over Time.
Artificial Selection- breeders can modify species over generations by selecting
individuals with desired traits and breeding
them.
Natural Selection- survival of the fittest
species. Populations evolve, individuals don’t,
and this happens naturally. All species can
overproduce. Adaptations, an inherited trait that
increases an organism’s ability to survive, help an
organism compete for survival. Helpful
adaptations become more common in a
population from breeding. After breeding many times, animals can adapt and evolve into a new
species.
An environment can change while the population is changing. Previously adapted traits
can be unhelpful or detrimental. Species that cannot evolve fast enough may become extinct.
Interbreeding in populations starts gene pools, which is made up of all the alleles
present in a population. Each allele will have a relative frequency in the pool. Small changes in
the allele frequency is a sign of evolution. The introduction of outside alleles is called gene flow
and can increase variation in a gene pool. When this happens in closely related species, it is
called hybridization. Interbreeding and uneven reproduction can lead to genetic drift, which is
when the allele frequency changes in the pool. Organisms with this can lead to overproducing
or underproducing. For gene frequencies to remain unchanged, mating must be random. When
organisms choose who to reproduce with, it is called sexual selection.
A mutation is a change in a cell’s genetic material. These can cause chromosome
malfunctions and can make it harder for an organism to live.
Genetic equilibrium- stability and consistency in the frequency of alleles and genotypes
in a population’s gene pool over generations.
To avoid evolution and maintain genetic equilibrium, populations must randomly mate,
have large populations, not isolate, do not have mutations, and absolutely, God forsakenly, do
not naturally select.
The Hardy-Weinberg principle states that a population's allele frequencies will remain
constant unless one or more factors, such as mutations or natural selection, cause those
frequencies to change.

Gradualism- the pattern of evolution supported by the fossil record that says organisms
have evolved slowly and steadily over time.
The fossil record has also proven the opposite of gradualism. Punctuated equilibrium is
the interruption of equilibrium by periods of rapid change.
 Niche- physical and biological conditions in which an organism lives, and the way in
which the organism uses those conditions to perform a function in the community.
Patterns of Evolution

 Adaptive Radiation- when a single species evolves and diversifies over a short
time into different forms that occupy different niches. This is caused by
migration to an area with new niches and the extinction of another species
leaving new niches.
 Convergent Evolution- when evolution produces similar qualities in different
organisms.
 Co-Evolution- when two species share an environment and depend on each
other for survival. When this happens, they will evolve according to changes in
the opposite party.
Extinction- when a species dies out and there are no longer any living members.

 Background Extinction- ongoing, gradual extinction of individual species due to

environmental or ecological factors such as climate change, loss of habitat,
disease, or competitive disadvantage in relation to other species. 
 Mass Extinction- events where the environment changes so fast that everything
dies. These are things like climate change, ice ages, meteorite crashes, and
volcanic eruptions.
 5.03 Primate Evolution
Primate- a mammal that is characterized by their developed hands and feet, forward-
set eyes and binocular vision, a small nose, and a large brain.

Primates have opposable thumbs, which can be moved opposite of the fingers to grab
things. This is ideal for a tree climber, or arboreal. They have more reliance on sight and less on
smell compared to other animals. Their eyes are
large and face forward, and their nostrils are smaller.
Primates have small litters when they give birth, and
babies take a long time to grow.
The study that studies the human fossil
record is called paleoanthropology, and it is the
combination of anthropology and paleontology. The
evolution from ancient primates is not a direct line, it
is more of a web.
 Radioactive Dating- radioactive elements break down at a predictable rate which makes
it easy for scientists to date fossils and artifacts.
Molecular Clocks- biological molecules change in predictable ways, which means they
can be used to date items. They are based on how DNA sequences or proteins mutate at
constant rates, which is used to date things.
DNA of any species can be mutated, base pairs can be lost, gained, or altered. These
don’t affect the organism, so it doesn’t affect natural selection. Mutations happen at a common
rate, so scientists can look at two organisms and compare who has more mutations, that’d be
the older one.
To be used for a molecular clock, a molecule must be present in all organisms being
studied and it must serve an important function in an organism.
Divergence- the process where organisms evolve into two forms while living under two
conditions. Scientists use other forms of dating to do this than molecular clocks, such as fossil
records and radioactive dating.
Ribosomal RNA Clocks- ribosomal RNA mutates very slowly, which makes it useful to
date old species, and makes it easy to make a phylogenic tree (a diagram that shows the
correlation between different species), the classification of organisms, and the study of forces
that effect evolution.
Mitochondrial DNA Clocks- the mitochondria of DNA have been used recently to study
evolution. The mitochondrial can accumulate neutral mutations, which are studied to use as
clocks.

6.01 Classification of Living Organisms

Aristotle recognized the need for a classification system for living things, so he made a
hierarchy called “The Great Chain of Being”, placing humans on top, and ten less developed
organisms below. A botanist named Linnaeus made the hierarchy of The Seven Major Taxa
1. Kingdom
2. Phylum
3. Class
4. Order
5. Family
6. Genus
7. Species