ICSV
BIOLOGY NOTES
Chapter 1
1.1:
SCIENCE: The study of and the gathering of evidence and
information that explains the natural world around us.
GOALS OF SCIENCE:
1. To investigate and explain the natural world around us.
2. To explain events in the natural world.
3. To use these explanations to make useful predictions.
1.2
SCIENTIFIC PROCESS:
1. Observation: Observe and gather data.
(Quantitative - # - more reliable)
(Qualitative - qualities and non # data - less reliable)
2. Inference: Interpret the situation and the data.
3. Hypothesis: One “if… then” sentence that predicts the
outcome of the experiment. The sentence does not have
to be true, just testable.
4. Controlled experiment: Design an experiment in which
all but one variable is controlled.
Independent variable: The variable that is manipulated
in the experiment.
Dependent variable: The variable that reacts in the
experiment.
5. Collect data: Collect data from the controlled
experiment and insert it into a graph, table, or other
means of displaying the results.
6. Conclusion: Explain what the experiment has shown
and refer back to the hypothesis.
SPONTANEOUS GENERATION: The belief (now disproven)
that bacteria or organisms would generate from non-living
matter, due to the matter becoming aged.
1.3
MAJOR THEORIES IN BIOLOGY:
1. Germ theory
2. Evolutionary their
3. Cell theory
4. Gene theory
THEORY VS. LAW:
Theory: Evolves. A collection of hypotheses from multiple
scientists.
Law: No exceptions. Absolute fact. Has been tested many
times and proven to be true.
LIVING ORGANISMS:
All living organisms have the following characteristics:
1. Are made of cells.
2. Reproduce.
3. Grow and develop.
4. Require energy and matter.
5. Respond to the environment.
6. Change over time. (Evolve)
7. Have a genetic code.
8. Homeostasis
Order of biosphere contents growing from left to right:
Molecules - Cells - Cell Tissues - Organs - Organ systems Organisms - Populations - Communities - Ecosystems Biosphere.
ICSV
BIOLOGY NOTES
Chapter 2
2.1
THE ATOM: Atoms are made of electrons(-), protons(+), and
neutrons(no charge).
The middle of the atom is called the nucleus, which is
composed of protons and neutrons. The nucleus is orbited by
the electrons, with valence electrons on the very edges.
The mass number of the element is the # of protons plus the
# of neutrons.
ELEMENT: A pure substance that consists entirely of one
type of atom.
ISOTOPES: When atoms of the same element differ in the #
of neutrons that they contain. Isotopes still contain the same
amount of protons.
ION: An atom or molecule with a net electric charge due to
the loss or gain of one or more electrons.
CHEMICAL COMPOUNDS: A combination of two or more
elements. (H2O) These compounds are held together by
valence electrons, which are on the outer edge of each atom.
These electrons form the bonds between atoms. A reactive
isotope, unlike an unreactive isotope, wants more electrons.
In other words, it wants to form new bonds.
CHEMICAL BONDS:
Ionic: Stronger than covalent bonds. Instead of sharing
electrons, electrons are taken to form ions.
Covalent: Weaker than ionic bonds. Instead of taking
electrons, these bonds are made by sharing electrons.
Covalent bonds are always formed between nonmetals.
VAN DER WAALS: Van der Waals' forces are the weakest type
of intermolecular force. ... Negatively charged electrons orbit
molecules or ions. The electrons create slightly different
charges from one end of the molecule to the other.
2.2
WATER:
Water has the following properties:
1. Is odorless and tasteless when pure.
2. Has a melting point of 0°C.
3. Has a boiling point of 100°C.
4. Has a very high heat capacity.
5. Has three states: solid, gas, and liquid.
6. Is a universal solvent, which means it dissolves almost
anything. H2O is a polar molecule, while the molecules
in substances like oils are non polar.
7. Is cohesive and adhesive. Cohesive means that due to
hydrogen bonds, the water molecules stick to each
other. A hydrogen bond is when the hydrogen parts of
the water molecule stick to the oxygen parts of the
molecules. Adhesive means that water molecules stick
to other surfaces. An example of this is capillary action.
Capillary action is the force that draws water up
through the roots of plants. Capillary action is caused by
the adhesive properties of water molecules.
8. Is neutral on the Ph scale.
THE PH SCALE: The Ph scale measures the concentration of
H+ ions in a solution (acidity). The scale is numbered from 1
to 14. Each number on the scale increases the concentration
by 10x. The closer you get to 1 on the scale, the more acidic
and more concentrated the solution is. The closer you get to
14, the more basic (alkaline) and less concentrated. The very
middle (7) is neutral.
MIXTURES: A mixture is composed of two or more elements
or compounds. The elements are physically mixed but not
chemically combined. An example of this is a salad or lego
box.
SOLUTION: When all of the components in a mixture are
evenly distributed. An example of this would be salt in water.
SUSPENSION: When materials in the mixture do not fully
dissolve but instead separate into pieces so small that they
do not settle out. An example of this is the pulp in orange
juice.
BASE: A compound that has more Hydroxide ions (OH-) than
Hydrogen ions (H+) in a solution. (OH- is basic)
BUFFER: Weak acids or bases that react with strong acids to
prevent sharp changes in a substance's Ph scale. An example
of this can be found in our digestive system. Without buffers,
when we ate acidic foods, our system would be thrown off
balance.
2.3
CARBON: Carbon atoms always contain exactly four valence
electrons, which allows them to make covalent bonds with
elements like hydrogen or oxygen. Macromolecules make
chains or rings of carbon.
CARBOHYDRATES: Carbohydrates are used for short term
energy in our bodies. They also help create structure. The
elements that carbohydrates consist of are carbon, hydrogen,
and oxygen. The monomers that they are made from are
called monosaccharides (simple sugars). Examples of
carbohydrates would be noodles.
PROTEIN: Proteins are the building blocks of our different
body parts. The elements that make up proteins are carbon,
hydrogen, oxygen, and sometimes nitrogen and sulfur.
Protein’s monomers are called amino acids. There are about
20 kinds of amino acids found in nature, but we only need to
eat nine because our bodies can’t produce them. Amino acids
are chains of the different elements of proteins. These chains
are held together by peptide bonds. A peptide bond is
formed through a process called dehydration. Below is a
diagram of the typical amino acid structure.
Proteins have four levels of structure:
1. Primary structure: amino acid chain.
2. Second structure: Coils of polypeptide chains.
3. Tertiary structure: A 3D polypeptide shape.
4. Fourth quarterly structure: four combined subunits.
An example of protein is meat.
LIPIDS: Lipids are the macromolecule that store up long
term energy for our bodies. They also are a building block for
our cells. The elements that make up lipids are carbon,
hydrogen, and oxygen. The monomers that make them up
are glycerol and fatty acids. There are two kinds of lipid
structures: saturated and unsaturated. Saturated is when all
of the bonds between the carbon atoms are as broken down
as possible (C-C). Unsaturated is when a certain # of the
bonds are not fully broken down (C-C=C-C). It does not
matter if some of the bonds between the carbon and the
hydrogen are not fully broken down (C=H). Below is an
example.
Examples of lipids are fats, oils, and waxes.
NUCLEIC ACIDS: Nucleic acids store genetic information and
genetic code. The elements that make them up are carbon,
hydrogen, oxygen, nitrogen, and phosphorus. Their
monomers are called nucleotides. These nucleotides are
made of three parts: the nitrogenous base, the 5-carbon
sugar, and the phosphate group. Below is a diagram of the
typical nucleotide structure.
Examples of nucleic acids are RNA and DNA.
2.4
REACTANT: The element or compound that enters into a
reaction.
PRODUCT: The element or compound that is produced by a
chemical reaction.
ACTIVATION ENERGY: The energy needed to start a chemical
reaction.
CATALYST: A substance that speeds up the rate of a chemical
reaction.
SUBSTRATE: The reactant in an enzyme-catalyzed-reaction.
ENZYMES: An enzyme is a protein that acts as a biological
catalyst.
The following properties describe enzymes and what they
do:
1. Enzymes are a protein.
2. Our digestive systems are full of them and use them to
break down foods.
3. Enzymes speed up chemical reactions.
4. Enzymes break down chemicals using a lock and key
system. As specific chemicals(lock) enter the active site
of an enzyme(key), the enzyme “unlocks” the chemical
and alters it. This process is displayed below.
5. Enzymes affect how much activation energy is needed
to start a chemical reaction. Below is a graph that
displays two different reactions: One without enzyme
interference, and one with it.
ICSV
BIOLOGY NOTES
Chapter 7
7.1
DISCOVERY OF CELLS:
1. R. Hooke - Discovered the cell.
2. Schwann and Schleiden - Discovered that everything is
made of cells.
3. Virchow - Discovered that cells come from cells.
MICROSCOPES:
Most microscopes use lenses to magnify the image of an
object by focusing light or electrons.
There are two types of microscopes:
1. Compound light microscope: This is the most common
of the two. This microscope is made of two sets of
magnifying lenses. These are called the ocular lenses
and the objective lenses. This kind of microscope works
by a beam of light to magnify the object. Below is a
diagram of this kind of microscope:
2. Electron microscope: This microscope magnifies objects
by focusing beams of electrons and passing them
through the object. There are two types of electron
microscopes:
a. Transmission electron microscope: Runs electrons
through the cells.
b. Scanning electron microscope: Scans the cells using
electron beams.
CELL THEORY:
1. All organisms are composed of one or more cells.
2. The cell is the basic unit of structure and function.
3. All cells come from preexisting cells.
PROKARYOTIC VS. EUKARYOTIC CELLS:
- Eukaryotic: These cells have a membrane-bound
nucleus. They range from 10-100 μm and can be found
in plants, animals, fungi, and protists.
- Prokaryotic: These cells do not have a
membrane-bound nucleus. They range from 0.1-5.0
μm and can be found in algae and bacterias.
7.2 - Our bodies are made of cells, and cells are made of
organelles.
The next page displays names and definitions of a lot of the
key organelles in plant and animal cells. More detailed
descriptions and pictures will follow.
CELL WALL:
The cell wall of a cell, which can only be found in plant cells,
helps to maintain the shape of the cell. It also acts as a layer
of protection for the cell.
CHLOROPLAST:
Chloroplasts only appear in plant cells. They are what
conduct the process of photosynthesis, which captures
energy from the sun and converts it into food for the plant.
This energy is then stored in the chloroplasts.
NUCLEUS:
The nucleus of a cell controls most of the cell processes and
is a protective envelope that contains DNA and nucleolus.
The part of the nucleus called the nuclear envelope has small
pores that allow RNA to enter and exit the nucleus. Below is
a diagram of the nucleus.
NUCLEOLUS:
This part of the cell is located in the middle of the DNA and
nuclear envelope of the nucleus. Like the nucleus, the
nucleolus has small pores which allow the entry and exit of
RNA. The nucleolus’s main job is to create ribosomes, which
are then transported throughout the cell.
RIBOSOMES:
Ribosomes, which can be found floating in the cytoplasm or
attached to the endoplasmic reticulum of a cell are
composed of RNA and proteins. Ribosomes help to decode
peptide bonds and link amino acid chains (protein creation).
MITOCHONDRIA:
The mitochondria is the powerhouse of the cell. It works to
convert chemical energy from food into compounds that the
cell can use. This process is also called cellular respiration.
CELL MEMBRANE:
The cell membrane of a cell is kind of like a protective layer
for the cell. It also provides a fixed environment for the cell
and helps to transport nutrients into the cell and toxins out
of the cell. The cell membrane is flexible and semi-fluid. It is
made out of two layers of phospholipids. Below is a diagram
of the membrane:
As you can see, the cell membrane consists of two layers of
lipids. The lipids themselves consist of two parts: the
hydrophilic head, which loves water, and the hydrophobic
tail, which repels water.
Since the cell membrane is semi permeable (let’s things
through) water is able to be drawn into one side of the
membrane by the head, and then pushed out the other side
by the tail.
CYTOPLASM:
The cytoplasm of a cell is the gel-like substance that fills a
cell. The cytoplasm helps to protect the cell and its different
organelles and also houses many proteins and is involved in
cell reactions.
VACUOLE:
The vacuole is a storage organelle. Although in both plant
and animal cells, a plant cell’s vacuole is much much bigger
than an animal cell’s. In plants, the vacuole actually also
helps to maintain the cell’s rigidity. The vacuole itself is a
sack-like structure that stores any nutrients that a cell might
need to survive, such as water.
VESICLES:
Vesicle is another name for different membrane-bound
organelles in a cell. The vesicles are often part of the process
of transporting proteins within a cell and releasing
substances from the cell.
GOLGI BODY:
The golgi body in a cell is the last stop of any products from
the endoplasmic reticulums. It modifies them, sorts them,
and then transports them to wherever their end destination
is.
LYSOSOMES:
Lysosomes are similar to vacuoles in that they act as storage,
but they also serve as the digestive system of the cell.
Lysosomes take large molecules or cell parts and recycle
them for the cell to use again.
ROUGH ENDOPLASMIC RETICULUM:
The rough reticulum of a cell creates and modifies proteins.
Unlike the smooth reticulum, the rough reticulum has
hundreds of ribosomes on its outer surface. These ribosomes
help to create the proteins, and the rough reticulum helps to
modify and fold them.
SMOOTH ENDOPLASMIC RETICULUM:
The smooth reticulum of a cell serves to produce and export
lipids and proteins, to detox the cell of harmful substances,
and to store certain ions. The smooth endoplasmic reticulum
is also important in creating new cell membranes.
DNA DEOXYRIBONUCLEIC ACID:
Found between the nuclear envelope of the nucleus and the
nucleolus, the DNA of a cell holds all of the genetic
information for the cell. This DNA almost never leaves its
place in the cell and is protected by the nuclear envelope.
CYTOSKELETON:
A network of protein filaments that help the cell maintain its
shape and also helps with movement of the cell. The
cytoskeleton is made of microtubules and microfilaments.
Their traits are listed below.
1. Microtubules
- Are hollow tubes of proteins.
- Help in the process of cell division.
- Help maintain the cell’s shape and serve as “tracks”
on which organelles move.
- Help build cilia and flagella.
a. Cilia: Tiny hairs or “eyelashes” within the
lungs that catch dust. Cilia are found on the
outside surface of the cells.
b. Flagella: A small tail-like appendage of sperm
or certain bacterias. Flagella helps the sperm
or bacteria to move.
- Is about 25 nm.
2. Microfilaments:
- Are long thin hairs.
- Help with the movement and support of the cell.
- Are a tough and flexible framework for the cell.
- Are about 7 nm.
CONTRACTILE VACUOLE:
This is a type of vacuole that absorbs water and then
releases it, which allows the protists (eukaryotic organisms)
to move. If a plant is wilting, then it means that the
contractile vacuoles are not getting enough water. On the
next page is a picture of a contractile vacuole and a diagram
of the water absorption and release process:
PROTEIN BUILDING PROCESS WITHIN CELL:
1. Proteins are assembled in ribosomes.
2. Some proteins complete assembly in rough endoplasmic
reticulum.
3. Proteins are carried to the golgi apparatus in vesicles.
4. The golgi apparatus sorts and packages proteins.
5. Vesicles are shipped to their final destination.
7.3
PASSIVE AND ACTIVE TRANSPORTATION:
1. PASSIVE TRANSPORT: Particles and molecules moving
from high concentration to low concentration without
the use of energy. (Can be related to swimming
downstream.)
a. OSMOSIS: The facilitated diffusion of water through
a selectively permeable membrane.
- Aquaporins: Water channel proteins that allow
water molecules to pass through cell
membranes.
- Osmotic Pressure: The force caused by the net
movement of water by osmosis.
b. OSMOSIS IN CELLS: Diffusion of H2O molecules.
(All to maintain a balanced concentration in the
cell.)
- Hypotonic solution: Cell absorbs too much
liquid and therefore has an unbalanced
concentration. The cell reacts by bursting,
which releases the liquid to balance the
concentration.
- Isotonic solution: H2O flows into and out of
the cell to maintain the cell’s homeostasis and
to keep the concentration balanced.
- Hypertonic solution: Due to a salty substance
surrounding the cell, all of the H2O within the
cell is released, which results in the cell
shriveling. For example, when we eat salty
chips, we end up being thirsty because our
cells have shriveled and are running out of
H2O.
c. DIFFUSION: The process by which particles move
across the cell membrane from an area of high
concentration to an area of low concentration.
d. FACILITATED DIFFUSION: The process by which
molecules that cannot directly diffuse across the
membrane pass through special protein channels.
2. ACTIVE TRANSPORT: Movement of particles and
molecules from low concentration to high concentration
with the use of energy. (Can be related to swimming
upstream.)
a. Protein pumps/carriers: Sodium potassium pumps
that change the concentration of elements in and
around cells. These are mainly used to send signals
in the nerve system and in the brain.
People who are drunk respond to things slower,
because of the fact that alcohol slows down these
pumps which in turn slows down brain signals.
b. Leakage channels: An ion channel in a cell
membrane that is always open, making the
membrane permeable to ions.
3. BULK TRANSPORT: A process in which the entire cell
works to move large molecules and clumps of
materials into or out of the cell.
c. Endocytosis and Exocytosis: Large particles,
molecules, or even liquids are moved into or out of
the cell by endocytosis (in) or exocytosis (out).
When these movements happen, the entire cell is
used to complete the process.
d. Phagocytosis: Type of endocytosis that envelopes
large solids (Ex: White blood cell eating bacteria)
ATP (Adenosine 5'-triphosphate): The principal molecule for
storing and transferring energy in cells. It is often referred to
as the energy currency of the cell and can be compared to
storing money in a bank. ATP supplies transport proteins
with energy, so that they can catch particles on one side of
the membrane and then release them on another.
7.4
HOMEOSTASIS AND CELLS:
1. UNICELLULAR ORGANISMS:
- Also known as a single-celled organism.
- Is an organism that consists of a single cell.
- Every cell has many important functions in their
environments.
- Maintain homeostasis by growing, responding to
the environment, transforming energy, and
reproducing.
- Include prokaryotic and eukaryotic cells.
- Examples include bacteria, protists, and yeast.
2. MULTICELLULAR ORGANISMS:
- We are multicellular organisms
- Are interdependent (depend on each other) and
specialized.
- Each cell has one specific task.
- Maintain homeostasis by communicating with one
another and carrying out their tasks.
- Are organized into groups:
a. Specialized cells: Cells that have one specific
task. (E.g. muscle cells)
b. Tissue: A group of similar cells that perform a
particular function. (E.g. muscle tissue)
c. Organ: A group of tissues working together to
perform a specific function. (E.g. stomach)
d. Organ system: A group of organs that work
together to perform a specific function.
(E.g. digestive system)
- Multicellular organisms communicate with
chemical signals, which are passed from one cell to
another.
a. Certain cells form cellular junctions
(connections) which hold cells firmly together
and allow them to communicate.
b. To receive and respond to a chemical signal, a
cell must have a receptor to which the
signaling molecule can bind.
.
ICSV
BIOLOGY NOTES
Chapter 8
8.1
ENERGY AND LIFE:
Energy: The ability to do work.
Adenosine triphosphate(ATP):
ATP is a chemical compound that cells use to store and
release energy. This energy is used to contract muscles, to
make proteins, and in active transport. The way that ATP
stores and releases energy is through adding and subtracting
phosphate groups from itself. The ATP works somewhat like
a battery. When the molecule has three phosphate groups, it
is fully charged. But when this battery is half used up, it loses
a phosphate group and becomes what is called ADP
(adenosine diphosphate). Below are two diagrams. One of
ATP (fully charged battery), and one of ADP (half charged
battery).
This diagram also shows the process of ADP becoming ATP
through adding a phosphate group.
Below is another diagram, displaying the different parts of
the ADP/ATP molecule:
The energy for the creation of ATP from ADP comes from the
sun, through the process of photosynthesis, which will be
talked about later.
HETEROTROPHS VS. AUTOTROPHS:
Heterotrophs: Organisms that consume other living things to
obtain food. Examples: Humans, cheetahs, and sharks.
Autotrophs: Organisms that make their own food. Our world
depends on autotrophs to get energy through
photosynthesis. Examples: sunflowers and trees.
8.2
PHOTOSYNTHESIS - AND OVERVIEW:
LIGHT:
Photosynthesis depends on the energy from the sun that
arrives in the form of sunlight.
This light can be different colors based on the wavelength of
the light.
PIGMENTS:
The way that plants gather the sun’s energy from this light is
through using light-absorbing molecules called pigments.
Chlorophyll is the principal pigment that is used in the
process of photosynthesis. This pigment is found in the
thylakoids of chloroplasts, which will be talked about later.
This pigment is extremely important for photosynthesis as it
is so good at gathering energy from the sun. This energy is
then directly transferred to electrons in the molecule. This
process raises the energy-level of the electrons, which
produces a steady stream of high-energy electrons to fuel the
process of photosynthesis.
CHLOROPLASTS:
Chloroplasts are the organelles within the cell that conduct
the process of photosynthesis. There are many parts to the
chloroplast, however, that have different roles in
photosynthesis. Below is a diagram of a chloroplast, as well
as several of its different parts:
The three key parts are the stroma, the thylakoids, and the
granum.
Stroma: The stroma is the gel-like substance that fills the
inside of the chloroplast and surrounds the thylakoid stacks.
The stroma is in charge of light-independent reactions in
photosynthesis, which will be talked about later.
Thylakoids: Thylakoids are extremely important in the
process of photosynthesis. Thylakoids are sac-like structures
that hold pigments such as chlorophyll. These are in charge
of the light-dependent reactions in photosynthesis, which
create products to be used in the light-independent reactions
later on. Thylakoids are also where oxygen is created in the
process of photosynthesis.
Granum: Granum are simply stacks of thylakoids within the
chloroplast.
ELECTRON CARRIERS:
As said earlier, when light from the sun is absorbed by the
pigment chlorophyll, the energy from the light excites
electrons in the chlorophyll. When these electrons become
excited (convert to high energy electrons), they require
electron carriers. These carriers, which consist of protein,
carry the high energy electrons from the chlorophyll to other
molecules during the process of photosynthesis. One of these
carriers is called NADP+, which can accept and hold 2 high
energy electrons and one hydrogen ion. Holding these two
things turns the NADP+ into NADPH. (This will be discussed
in detail later)
SIMPLE EXPLANATION OF LIGHT
DEPENDENT/INDEPENDENT REACTIONS:
Photosynthesis involves two sets of reactions:
Light-dependent-reactions: A reaction in which H2O and
light-energy enter the thylakoids, and ATP, O2, and NADPH
are produced. This is a light-dependent reaction because it
requires direct involvement of light.
Light-independent-reactions: In this reaction, which does
not require direct involvement of light, CO2, ATP, and NADPH
are all used to produce high-energy sugars such as glucose.
This reaction takes place in the stroma of the chloroplast.
The connection: Below is a diagram showing the reactants
and products of both reactions, and the connection between
them: (Calvin cycle = light-independent-reactions)
8.3
THE PROCESS OF PHOTOSYNTHESIS:
Summary: Photosynthesis consists of two reactions:
light-dependent reactions and light-independent reactions.
This is the main topic of this section.
LIGHT-DEPENDENT-REACTIONS:
These reactions, which occur in the membrane of Thylakoids,
consist of several steps that each have to do with different
parts of the membrane. Below is a picture of the process to
help you make sense of the steps.
STEP 1: In this step, light and H2O enter photosystem II.
The energy from the light then splits the H2O into two parts:
Oxygen and hydrogen ions. The oxygen immediately leaves
the whole system, but the hydrogen ions remain in the
system to be used later. In this process, electrons in
photosystem II are excited and become highly-energized.
These electrons are the main part of the next step.
STEP 2: The electrons that were charged in photosystem
II are transferred by means of electrons carriers in
electron-transport-chains to photosystem 1. Here they are
recharged and used in a reaction. This reaction produces
NADPH. The reactants are 2 hydrogen ions from
photosystem II, 2 NADP+ molecules, and 4 highly charged
electrons, also from photosystem II. As said before, this
reaction produces NADPH, which is taken to the stroma to be
used in the light-independent reactions.
STEP 3: The hydrogen ions from photosystem II are key
here. These ions are taken to the ATP synthase, where they
travel through the middle of the synthase to the outer
stroma. This movement of hydrogen ions through the ATP
synthase causes the synthase to rotate. This rotation powers
the conversion of ADP to ATP through the process of adding
a phosphate group to the ADP. The ATP is then transferred to
the stroma to be used in the light-independent-reactions.
Photosystem II: Light energy + 2H2O → O2 + 4H+ + 4
charged electrons.
Electron-carrier-chains: Strings of electron carriers that
transfer highly-charged electrons.
Photosystem 1: Electrons are reenergized/4H+ + 2 charged
electrons + 2 NADP+ molecules = NADPH
ATP synthase: ADP + energy + phosphate group = ATP
THE CALVIN CYCLE/LIGHT-INDEPENDENT-REACTIONS:
The calvin cycle uses CO2, ATP, and NADPH to create
high-energy sugars such as glucose. This is called a cycle
because some of its different elements are reused over and
over again. Like the light-dependent-reactions, this cycle has
several steps. Again, below is a picture to help you
understand the steps:
STEP 1 (Carbon Fixation): (Note: the following
numbers of molecules are equal to the amount that would be
used if the cycle ran 6 times. Example: 6 CO2 is really only 1
for one turn of the cycle.) 6 CO2 molecules enter the stroma
and combine with six 5-carbon molecules called Rubisco.
This combination produces twelve 3-carbon compounds.
STEP 2.1 (Reduction Phase): In this step, ATP and
NADPH from the light-dependent reactions are used to
convert the twelve 3-carbon molecules to higher-energy
forms. These forms are called G3P. The ATP and NADPH,
which are now ADP and NADP+ are recycled and returned to
the thylakoids to be used in the light-dependent-reactions.
STEP 2.2: Now G3P, the molecules move on to the next
part of the cycle. Two of the 3-carbon molecules leave the
cycle and form glucose, as well as other compounds and
carbs. (Note: with the numbers being used, the cycle only has
to run once to form the 6 needed carbon molecules for
glucose. In reality, however, quite a few less molecules enter
the system at a time and the cycle has to run six times before
the glucose is completed.)
STEP 3 (Regeneration Phase): The remaining 3-carbon
molecules left over after the reduction phase move on to the
regeneration phase. In this last phase, Rubisco is regenerated
and reformed by ATP and is used to begin the cycle again.
Factors that influence photosynthesis:
- Temperature
- Light intensity
- Availability of water.
C4 and CAM Variations of Photosynthesis:
When the affecting factors of photosynthesis listed above are
too extreme, plants adapt by becoming C4 or CAM plants.
Their qualities are listed below.
C4 plants:
- Mostly appear in tropical areas where there is
high light intensity and high temperatures.
- Have special pathways that allow them to
capture very low levels of carbon for the calvin
cycle.
CAM plants:
- Appear mostly in hot and dry areas like
deserts.
- Only allow air in at night, which helps them
not dry up. This also helps them to be able to
store as much water as possible.
Photolysis: The process of light breaking down the molecules
of water. This process happens in the granum of the
chloroplast.
Chemiosmosis: The osmosis of hydrogen. (Used to make
ATP)
ICSV
BIOLOGY NOTES
Chapter 9
9.1+9.2
CELLULAR RESPIRATION: AN OVERVIEW
DEFINITION: The process of energy conversion that released
energy from food in the presence of oxygen.
EQUATION: C6H12O6 + 6O2 → 6CO2 + 6H2O.
STAGES: Within cellular respiration, there are three stages of
reactions. Below are some pictures to help illustrate these
stages.
STAGE 1: GLYCOLYSIS: This reaction, otherwise known as
“sugar-breaking”, occurs within the cytoplasm of the cell. It is
an anaerobic process, which means that it does not require
oxygen.
Reactants: 2ATP, 2NAD+, 2ADP, Glucose
Products: 2 Pyruvic acid molecules, 4ATP, 2NADH
Net ATP Produced: 2ATP
STAGE 2: KREB’S CYCLE: This reaction occurs in the matrix
of the mitochondria. It is considered an aerobic process,
although oxygen is not directly involved.
Reactants: 2 AcetylCOA enzymes (from Pyruvate),
4 carbon molecules (already in cycle), 2FAD+, 6NAD+,
2ADP
Products: 6NADH, 2ATP, 2FADH2, 4CO2
Net ATP Produced: 2ATP
STAGE 3: ELECTRON TRANSPORT CYCLE AND ATP
SYNTHASE: This reaction occurs in the intermembrane space
of the mitochondria. This stage is an aerobic process.
Reactants: 8NADH, 2FADH2, O2
Products: H2O, ATP
Net ATP Produced: 34ATP
Like some ATP synthase within photosynthesis, in the ETC,
there is also ATP synthase which creates ATP from ADP
through the process of H+ ions flowing through the synthase.
This flow creates rotation which gives the synthase energy to
convert the ADP.
NOTE: The heat in our bodies actually comes from the
energy created when bonds are broken within these
processes.
CALORIE: A unit of energy. The calorie used on food labels is
equal to 1,000 calories. The calorie is also referred to as a
kilocalorie.
9.3
FERMENTATION:
Fermentation releases energy from food molecules by
producing ATP without oxygen. Cells convert NADH to NAD+.
This allows glycolysis to produce a steady stream of ATP.
There are two forms of fermentation. Both start with the
reactants pyruvic acid and NADH. Below is a picture to help
illustrate these two processes.
NOTE: Glycolysis provides the pyruvic acid molecules that
are used in fermentation. Both types of fermentation are
anaerobic processes.
ALCOHOLIC FERMENTATION: Alcoholic fermentation does
not happen in animals, except for rare cases, and starts with
yeast or other microorganisms. Once alcohol is created,
energy is stored in it.
Reactants: Pyruvic acid + NADH
Products: Alcohol + CO2 + NAD+
Examples of use in Industry: Bread products, alcoholic
beverages.
LACTIC ACID FERMENTATION: This type of fermentation
occurs in most organisms, specifically in muscle/animal
cells.
Reactants: Pyruvic acid + NADH
Products: Lactic acid + NAD+
Examples of use in Industry: Buttermilk, cheese, yogurt
IMPORTANT NOTE: For bursts of energy under 90 seconds,
our bodies use ATP already in our muscles, as well as ATP
from lactic acid fermentation. After 90 seconds of using ATP
up, our bodies start burning built up glucose(fat) through
cellular respiration for energy. (Aerobic)
ICSV
BIOLOGY NOTES
Chapter 10
10.1
SEXUAL VS. ASEXUAL REPRODUCTION
Asexual reproduction:
- Single parent produces genetically identical offspring.
- E.g. bacteria or prokaryotes
- Offspring grow very quickly
Sexual reproduction:
- Fusion of two separate parent cells
- E.g. humans, basically all animals
- Offspring are very diverse
- Offspring inherit genetics from both parents
10.2
CHROMOSOMES: In prokaryotic cells, DNA is packaged into a
singular circular chromosome. In eukaryotic cells, DNA is
packaged into multiple chromosomes. Below is a picture of
the makeup of a single chromosome.
THE CELL CYCLE:
CELL CYCLE IN PROKARYOTIC CELLS: The cell cycle in
prokaryotic cells is also referred to as binary fission. It’s
quite a simple process. Below is a picture of it.
CELL CYCLE IN EUKARYOTIC CELLS: The cell cycle in
eukaryotic cells is much more complex than in prokaryotic
cells. It consists of interphase and cell division. Both of these
are separated into several different parts:
INTERPHASE: The longest part of the cell cycle.
G1 Phase: This is the longest phase within the
interphase. In the G1 phase, the cells do most of their
growing and synthesize new proteins and organelles.
S Phase: In this phase, new DNA is synthesized when
chromosomes are replicated. At the end of the S phase,
the cell contains twice as much DNA as it did in the
beginning.
G2 Phase: This is the shortest phase within the
interphase. During G2, organelles and molecules needed
for cell division are created. Basically, G2 is in charge of
preparing the cell for cell division. When G2 is complete
and the cell’s DNA has been checked, the cell can move
on to cell division.
M PHASE: The shortest part of the cell cycle.
Mitosis: Mitosis is the division of the nucleus of the cell,
into two identical nuclei. It is divided into five parts.
Below is a picture of all of them, as well as definitions
further below of each stage. Mitosis is an asexual
process.
Prophase: Chromosomes condense and become
visible, spindles form, and the nuclear envelope
dissolves.
Metaphase: Chromosomes line up at the center of
the cell. The centrioles of the cell are connected to
the centromere of the chromosomes through
spindles.
Anaphase: Chromosomes pulled apart into halves
at the centromere by the centrioles. Then the
halves are pulled towards opposite poles of the cell.
Telophase: The cell begins to divide into daughter
cells, the nuclei are formed, and the nuclear
envelope starts to form.
Cytokinesis: The cell membrane pinches in the
middle to form to separate daughter cells. This is
the end of mitosis.
NOTE: Technically cytokinesis is it’s own part, but it is also
considered part of mitosis.
10.3
REGULATING THE CELL CYCLE AND CELL REPAIR:
Cyclins: Proteins that regulate the cell cycle. Cyclins or some
other type of regulatory protein enter the cell and the cell
starts to divide.
Internal regulators:
- Respond to events inside the cell.
- Let the cell cycle proceed only when certain steps
have already happened.
External regulators:
- Respond to events outside the cell.
- Direct cells to speed up or slow down the cell cycle.
- Affect the growth factor.
Apoptosis:
- A process of programmed cell death.
- Important role in structuring tissues during growth and
development.
- Cell undergoes a series of controlled steps for self
destruction.
- Cell cycle regulators detect problems and start
apoptosis.
Cancer:
- Cancer is uncontrolled cell growth.
- Cancer cells don’t respond to normal regulatory signals
that would normally control cell cycle.
- Cell cycle is disrupted.
- The process of cancer growing and spreading is that
first, cells divide abnormally due to a mutation in their
DNA. Then, the cells produce a tumor due to their
uncontrolled growth. If the tumor is not discovered in
time, the mutation spreads to other parts of the body.
10.5/11.4
CELL DIFFERENTIATION, STEM CELLS, AND MEIOSIS:
During the development of an organism, cells differentiate,
which means that they become specialized. The way they are
able to do this is through what are called stem cells. Stem
cells are basically non-specialized cells that can grow and
undergo differentiation. They are mainly found in embryos,
although a few types are found in adults. Below is a picture
of what they can differentiate into:
There are three main types of stem cells.
Multipotent: These types of stem cells are found in
adults, mainly in bone marrow or hair. They are only
able to differentiate into a couple of other cells. They are
important for cell regeneration in our bodies. When we
get an injury such as breaking a bone, the cells at the
edge of the injury are stimulated to divide rapidly,
therefore making new healthy cells to fix the wound.
Pluripotent: These stem cells are found in embryos.
They are capable of turning into most, but not all types
of cells.
Totipotent: These stem cells can become any kind of
cell. They are adaptive, which means they can be used to
heal any part of the body or to grow new organs.
Totipotent stem cells are found in embryos.
MEIOSIS: Meiosis is a special type of cell division in which
gametes, also known as sex cells, are created. Meiosis only
occurs in the reproductive organs. Part of meiosis is
chromosome crossing over, in which chromosomes trade
DNA, which helps to create genetic variation in the product
of sexual reproduction. Below are some very important
terms for understanding the process of meiosis.
Homologous: Chromosomes with the same genes, one
from each parent.
Diploid: Containing both sets of homologous
chromosomes; 2N. Always an even number.
Haploid: Containing only a single set of chromosomes;
1N.
After the process of meiosis occurs, creating the sperm and
egg cells, both of these cells have only 23 single
chromosomes, aka they are both haploid. Then, when
fertilization occurs and the sperm enters the egg, the
chromosomes combine, creating a zygote. A zygote is the
very first cell of an organism. Due to the combination of the
sperm’s 23 chromosomes and the egg’s 23 chromosomes, the
zygote is diploid and has 23 pairs, or 46 chromosomes in
total. (Egg - 23 chromosomes + sperm - 23 chromosomes =
zygote - 46 chromosomes.) Below is a diagram of the entire
process of meiosis, as well as definitions of each stage:
MEIOSIS l:
Prophase l: Chromosomes condense, nuclear envelope
dissolves, and crossing over of chromosomes occurs.
Metaphase l: Pairs of homologous chromosomes move
to the center of the cell, pulled by the centrioles and
spindles.
Anaphase l: The pairs are pulled apart into singular
chromosomes, and are pulled by the centrioles and
spindles to opposite ends of the cell.
Telophase l/cytokinesis: The cytoplasm divides, the
membrane pinches in the center, the nuclear envelope
reforms, and the dividing parent cell is split into two
daughter cells.
MEIOSIS ll:
Prophase ll: In prophase ll, crossing over does not occur
in the two cells from meiosis l. The only thing that really
happens is that spindles form in both cells.
Metaphase ll: Metaphase ll chromosomes line up in the
centers of the two cells; not in homologous pairs, rather
singular chromosomes.
Anaphase ll: Chromosomes are divided into halves at
the centromeres, and are pulled by the centrioles and
spindles to opposite poles of the cells.
Telophase ll/cytokinesis: Nuclear envelopes reform, the
cells’ cytoplasms divide, and the four new haploid cells
are created.
At the end of meiosis, four genetically unique sex cells, either
sperm or egg cells, have been created, each with only 23
singular chromosomes.
ICSV
BIOLOGY NOTES
Chapter 11
11.1
GENETICS AND THE WORK OF G. MENDEL:
GREGOR MENDEL:
Gregor Mendel, now known as the father of genetics was
born and raised in Austria. Eventually, he ended up in a
monastery, working with pea plants in the monastery’s
garden. Through his experiments with pea plants (using
cross pollination and self pollination to create different
variations and scenarios), we now know a huge amount of
information about how the world of genetics works.
Genetics: The study of genes and heredity.
Cross-pollination: The pollination of a flower or plant with
pollen from another flower or plant.
Self-pollination: The pollination of a flower by pollen from
the same flower or from another flower on the same plant.
True-Breeding: The breeding of organisms with the same
homologous genotype. (Example: TT with TT or tt with tt).
Trait: Specific characteristic (e.g. seed color, plant height) of
an individual.
Hybrid: An organism created from the cross of true-breeding
individuals.
Genes: Genes are passed from one generation to the next and
determine an individual’s characteristics.
Alleles: The different forms of a gene.
Principle of Dominance:
● Some alleles are dominant, some recessive.
● An organism with at least one dominant allele will
exhibit that trait.
● An organism with a recessive allele will exhibit the trait
only in the absence of a dominant allele.
Segregation: The separation of alleles during gamete f
ormation.
11.2
76uAPPLYING MENDEL’S PRINCIPLES:
Probability: The likelihood an event will occur. If you flip a
coin three times, each flip is an individual event. So if you flip
it three times in a row, it has a ⅛ chance of landing on heads
all three times. (½ x ½ x ½ = ⅛)
Genotype: The genetic makeup of an organism.
Phenotype: The physical traits of an organism.
Note: Two organisms can have the same phenotype but have
different genotypes at the same time.
Homozygous: Organism has two identical alleles for a gene.
(Example: TT or tt)
Heterozygous: Organism has two different alleles for a gene.
(Example: Tt)
General info: Inheritance is determined by units called genes,
which are passed from parent to offspring. When more than
one form of gene for a single gene exists, some genes will be
dominant and other recessive. Each offspring has two copies
of each gene—one from each parent. These genes segregate
from each other when gametes are formed. Alleles for
different genes usually segregate independently of each
other.
Punnett Square: Below are pictures that show how to use the
punnett square with monohybrid genotypes such as Bb +
Bb, and dihybrid genotypes such as TtGg + TtGg.
Monohybrid:
Dihybrid:
Independent Assortment: Genes for different traits can
segregate (divide) during gamete formation.
11.3
OTHER PATTERNS OF INHERITANCE:
MODES OF INHERITANCE:
● Complete dominance: In complete dominance, the
dominant allele is completely dominant over the
recessive allele. For example if dimples (capital D) is
dominant over not having dimples (lowercase d), then
any offspring with the genotype DD or Dd will have
dimples. It’s never a mix.
● Incomplete dominance: With incomplete dominance,
neither allele is completely dominant over each other or
recessive. The result is a blend of the parent traits.
Below is an example: (White + red = pink)
● Codominance: In codominance, both alleles are
dominant and the phenotypes for both alleles are
clearly expressed in the offspring. Examples: Feather
color and blood groups (AB). Below is an image of
codominance in chickens.
● Multiple Alleles: Many genes exist in more than two
forms. Example: Blood types (three alleles - A, B, and O),
and fur color in rabbits). In other words, three or more
alleles are needed to express the trait. Below is an image
to display this: (Specifically look at the genotypes such
as Cchd )
● Polygenic Traits: Many traits are produced by the
interaction of several genes (lots of genes working
together). Examples: Eye color in fruit flies, skin color in
humans, or coat color in dogs. Due to the large amount
of genes/alleles, there is a lot of variation. Below is an
example of polygenic traits in human skin tones:
,Genes and the environment:
The phenotype of an organism is only partly affected by the
organism’s genotype. Environmental conditions, such as
temperature, can greatly influence how genes are expressed
and can influence genetically determined traits. Below is a
simple illustration of this: