Biology Notes 2024-2025
Biology Notes 2024-2025
Biology Notes 2024-2025
1. Prokaryotic cells
a. No Nucleus
i. Existed before nucleus
ii. Genetic material has no physical lining and floats free
b. No organelles
c. Cell (Plasma) Membrane
2. Eukaryotic cells
a. True Nucleus
i. Nucleus contains the genetic material
b. Contains Organelles(mini organs)
i. Organelle: specialized membrane-bound structures inside cells
c. Cell (Plasma) membrane
1. Lesson 2 plan
a. Structure of plasma membrane
b. Relate structure to its uses
2. Plasma membrane is a phospholipid bilayer
a. This means it has 2(bi) layers of phospholipids
i. Phospholipids
ii. Phospholipids are made up of two parts
1. Polar(loves water)
a. Phosphate group, glycerol, polar group(at the tip)
2. Nonpolar(hydrophobic)
a. 2 Fatty acid chains
iii. These allow for cell to exist in water while still keeping the water inside
and outside from escaping
3. Plasma membrane also contains
a. Proteins(Most important)
i. Membrane proteins(receptors)
1. They receive signals from the outside of the cell membrane
ii. Transport Protein
1. Act as tunnels to move waste and food from the outside of the
membrane to the inside
iii. Anchors
1. Attach the membrane to the skeleton of the cell inside the
membrane
b. Cholesterol(it's basically lube)
i. Imbedded among the fatty acid tails
ii. It is another lipid(fat)
iii. Nonpolar
iv. Prevents the tails from sticking to one another and keeps it fluid
c. Carbohydrates(bouncers)
i. Found on the outer surface of the membrane attached to the membrane or
the receptors
ii. They act like a bouncer by defining the cells characteristics and
identifying the chemical signals
d. Fluid Mosaic model: Phospholipids in the bilayer as a seas that form
pattern/mosaic on the cell surface
4. Function of plasma membrane
a. Forms a thin, flexible boundary between the cell and the world
b. It has selective permeability(allows only certain things through)
c. Since it can allow how and when certain things enter the substance, it maintains
homeostasis
5. Cellular transport
a. Maintaining homeostasis by removing and accepting substances into the cell
6. Why do particles move
a. Particles are in constant motion due to there thermal energy
7. Because of constant random motion they end up at different quantities at different places
i. Ruins homeostasis by confusing environment
ii. Cellular transport is used to restore homeostasis
8. Diffusion: (Same)substance moving from higher concentrated areas with lower
concentration(it's passive and doesn't require extra energy)
a. Dynamic Equilibrium: Only stops once homeostasis is reached on both
sides(equal on both sides, no need to move anymore)
i. Substance continue to move but they remain equal on both sides
9. Rate of diffusion
a. Concentration
i. More concentration→more collisions→Faster diffusion
b. Temperature/ pressure
i. High T/P→more collisions→Faster diffusion
c. Size/ charge of particles
i. If particles are charged they require extra energy for diffusion(active
diffusion)
ii. Big molecules require a transporter but NOT more energy\
1. When it is big AND charged it does not need a transporter it
simply needs the extra energy
10. Protein Transporters
a. Channel protein: the proteins are filled with water and they open and close to
allow specific substances to diffuse through the membrane
b. Carrier protein: proteins that attach to the substances so that they can cross and
they change shapes as they diffuse
c. Water SOMETIMES does emulsion. Water seeps through the nonpolar fatty acids
and goes into or escapes the cell.
11. This is called Osmosis!!!!
12. Osmosis: The diffusion of water across the semipermeable membrane to restore
homeostasis
a. When water leaves the cell the cell becomes more concentrated and the outside
becomes more dilute.
i. Cholesterol levels and space in between the fatty acid effect how osmosis
occurs
ii. Changes depending on membrane
b. Osmosis fixes the ratio of substances to water/concentration which makes it even
concentration. Which means osmosis goes from the highest concentration of
water to the lowest concentration to make both concentrations equal.
13. Isotonic Solution: Same concentration of solute inside and outside the cell
a. Water is entering and leaving the cell at the same rate(concentration)
b. Same shape
14. Hypertonic solution: More concentration of solute outside of the cell
a. Water leaves the cell to go outside and balance the concentration
b. Causes wilting in plants
c. Cell loses water
15. Hypotonic solution more concentrated solute inside the cell
a. The cell gains water to balance the solute inside it
b. Cell gains size and pressure because it's so full(osmotic pressure)
16. Active transportation helps with homeostasis but uses energy.
a. It moves a substance from a lower concentration to a higher concentration
b. Many times it uses carrier proteins(pumps) to do so
17. This is active transport because it requires energy^^^^^^*(
18. Once the Na+ is outside the cell it renders by coupling with the sugar and enters through
a coupled channel.
19. Endocytosis: Substances are encircled by the plasma membrane and then chopped off
encased in membrane into the cell
20. Exocytosis: Is when the opposite happens and substances are absorbed into the membrane
and then let out
a. Exocytosis is mainly use on waste and hormones
b. They both require energy
c. Both substances are very large for this to happen.
21.
Organelles
1. Organelle: A structure that is membrane bound and only found in eukaryotic
cells.(except ribosomes who are not membrane bound)
2. Cytoplasm: the semifluid material that makes up the inside environment of the
cell(made of cytosol, organelles, and soluble substances)
a. Prokaryotes chemical processes take place inside the cytoplasm
b. Eukaryotic have organelles that do the chemical processes but the
organelles are in the cytoplasm
3. Cytoskeleton: it is the skeleton of the cell, it is made up of long, thin protein fibers
that make a frame for the cell, it also anchors the organisms, it is also involved in
movement and division of the cell.
a. Microtubules: hollow protein cylinders that form a skeleton for the cell
and moves things around the cell
b. Microfilaments: Shapes the cell and helps it to move
c. Actin Filaments:
d. Centrioles: Groups of microtubules that are used for cell division
4. Cilia & Flagella are made out of a 9+2 configurations
a. Extensions of the cell membrane
b. Cilia: Many short microtubules that look like hair and move together like
oars on a rowboat.
i. Always in groups
ii. Used more for sweeping substances
c. Flagella: Longer cilia but there are les per cell. They move like a whip.
i. Used for transportation
5. Cell wall: Rigid mesh fibers that surround the outside of the plasma membrane
a. Protects to cell
b. Gives structure
c. Made from carbohydrates called cellulose
d. Prokaryotic cells also have a cell wall
i. It protects the cell
ii. Gives it structure
iii. It is mae from peptidoglycan
6. Nucleus: contains most of the cell's DNA, which determines the cell's growth,
development, and function. Surrounded by a double membrane called a nuclear
envelope
a. Nuclear pores: large sized substances can move in and out
b. Nucleolus; Makes ribosomes and contains most of the cell’s genetic
material
7. Endoplasmic reticulum: membrane systems that are interconnected and make the
proteins and lipids.
a. rough Endoplasmic Reticulum(rER)
i. Ribosomes(the little dots) are attached to these which makes it
rough and makes protein
b. smooth Endoplasmic Reticulum(sER)
i. Ribosomes are not connected which makes it smooth, makes
carbohydrates and lipids
8. Ribosomes: Organelles that make proteins, are not membrane bound and are made
of proteins and RNA. Some roam free and so are attached to the rER.
9. Mitochondria: powerhouse of the cell. Convert fuel(sugar) into ATP. They have
an outer membrane for protection and a larger more folded membrane which
allows for lots of surface area so that it can break the bonds that hold the sugar
together.
10. Golgi apparatus: A group of stacked membranes that sorts and packages proteins.
Packaged proteins are called vesicles which can then fuse into the plasma
membrane which will release the proteins into the environment.
11. Chloroplasts: Use photosynthesis to create sugar and oxygen. Small discs inside
are called thylakoids which contain the color green(chlorophyll) which captures
the light.
12. Vacuole: Plants cant do photosynthesis during night so they store excess sugar in
the vacuole for times of need. They also store enzymes and waste.
13. Lysosomes: Vesicles that eat the old organelles or food particles. They are the
cleaners. They break down bacteria or viruses that invade the cell.
14. Difference between animal cells and plant cells?
a. Plants have chloroplasts, cell walls, and they do not have cilia or flagella.
Both have vacuoles but a cell’s vacuole is much larger and an animal cell’s
vacuoles are much smaller.
3.
a. Energy Change in Chemical Reactions
4.
i. The graphs both show chemical reactions and they both need a certain
activation energy
1. The graph on the left shows an exothermic reaction, which is a
reaction that has less energy in the products then in the reactants
since it releases energy
2. The graph on the right shows an endothermic reaction. An
endothermic reaction occurs when the products have more energy
than the reactants, or absorption of energy.
3. Every chemical reaction has a change of energy due to the
breaking of bonds whether it be exothermic or endothermic.
5. Enzymes
i. All living things are driven by chemical reactions.
ii. Chemical reactions take energy which can take some time to acquire
iii. Certain substances are utilized in living organisms to speed up chemical
reactions.
1. These are called catalysts
a. Catalysts do not increase the products and it is not used up
in the chemical reaction
2. Enzymes are living organisms' own catalyst proteins .
a. Enzymes are extremely needed for any living organism
6.
a. Enzymes are not used up and can be utilized over and over
again in multiple reactions
i. Ex. Amylase is an enzyme that is found in saliva. It
speeds up the chemical reaction with amylose
which is part of starch.
ii. Just like amylase, enzymes are usually only utilized
for one type of reaction. (Lipase breaking down
lipids, Proteas breaking down proteins, etc.)
iii. Substrates: Reactant that bind to enzymes
iv. Active cite: The specific place where the reactant
binds to the enzyme
v. The active site and substrate have specific
configurations which only allows for the same type
of molecules to bind to them.
b. Enzyme substrate complex: the shape the active site
morphs into once the substrate has binded. The enzyme
catalyzes the reaction and then releases the products and
waits for new reactants to bind.
b. Factors that affect Enzyme Activity
i. Temperature. Ex: Humans’ enzymes are most active at about 37oC
ii. pH levels/ levels of acidity
1. As pH or temperature moves away from an enzyme’s optimal
levels, enzymes become less active.
iii. Inhibitors: Reduce or block enzyme activity by blocking or morphing the
active site
Water and its Solutions
1. Atoms have the property of electronegativity
a. Electronegativity: attraction of the electrons to the atoms nuclei
i. Stronger electronegativity means more electrons which means δ-
ii. Weaker electronegativity means less electron which means δ+
iii. In covalent bonds if atoms have different electronegativity, then the
compound becomes polar.
b. Polar molecules: they have two ends that have unequal sharing of electrons
making them oppositely polar
i. When polar compounds become close they act like magnets.
ii. Van Der Waals forces: slight electrostatic forces between polar compounds
1. The attractions influence physical characteristics through
molecular attraction
Module 8
Lesson 1 (How cells get energy)
1. Energy: Ability to do work
2. Thermodynamics: How the energy flows and transforms in the universe
a. Laws of thermodynamics
i. 1st Law is the Law of conservation of energy: energy cannot be created or
destroyed only transferred from one thing to another
ii. 2nd Law: Energy cannot be converted without loss of some usable energy,
the lost energy is usually converted to thermal energy
b. All organisms need energy, whether indirectly or directly they get it from the sun
i. Autotrophs: Make their own food, either from the sun or from inorganic
substances (Ex. plants)
1. Photoautotrophs: Make their own food using energy from the sun
2. Chemoautotrophs: Make their own food using inorganic things like
salts or minerals
ii. Heterotrophs: eat food to obtain energy (Ex. humans)
c. Metabolism: Chemical reactions that happen in a cell
d. Metabolic pathway: a series of chemical reactions in which the product of one is
the reactant for the next.
e. Two types of metabolic pathways
i. Catabolic pathways: release energy by breaking down larger molecules
into smaller ones
ii. Anabolic pathways: use energy (from catabolic pathway) to build larger
molecules
1. Anabolic pathways get their energy from catabolic pathways to
store it in bonds that make larger molecules
f. Photosynthesis: an anabolic pathway in which light energy from the sun is
converted to stored chemical energy for use by the cell by converting
g. Cellular respiration: catabolic pathway in which organic molecules are broken
down to release energy for use by the cell.
h. Adenosine triphosphate (ATP): the most important and most abundant biological
molecule that provides chemical energy, aka energy carrier, and is found in all
types of organisms
i. ATP is a nucleotide
ii. Structure: Made of adenine base, ribose sugar, and three phosphate groups
iii.
d.
7. Phase One: Light Reactions
a. Light-dependent phase: light energy is captured and converted into molecules of
ATP and NADPH that will be used in the 2nd phase.
b. It takes place in the Thylakoids membrane as they contain the pigments that
capture light energy
c. The structure of the thylakoid membrane is the key to an efficient energy transfer
d. H2O light→ H+ + e- + O2
e. ADP + P → ATP
f. NADP+ + H+ → NADPH
8. Thylakoid membrane
a. Large surface area:
i. Providing the space needed to hold a large number of electron-transporting
molecules
b. Photosystem I and Photosystem II
i. These are protein complexes containing light-absorbing pigments and
proteins essential for the reaction.
9. Chemiosmosis
a. Chemiosmosis: the mechanism by which ATP is produced as a result of the flow
of electrons down a concentration gradient.
10. Phase Two: The Calvin Cycle
a. The second phase of photosynthesis aka the Calvin Cycle takes place in the
stroma
b. ATP and NADPH provide cells with large amounts of energy but they are not
“stable” enough to store the energy for long periods of time hence the need for a
2nd phase where this energy carried by ATP and NADPH would be stored in
organic molecules like glucose.
c.
d. The first step of the Calvin cycle is carbon fixation
i. CO2 molecules combine w/ 5-carbon molecules (ribulose 1,5 biphosphate)
to form 3- 3-phosphoglycerate (3-PGA)
e. In the second step, the chemical energy stored in ATP and NADPH is transferred
to the 3-PGA to form glyceraldehyde 3-phosphate (G3P)
f. In the third step, some G3P molecules leave the cycle to be used for the
production of glucose and other organic compounds
g. In the fourth step, an enzyme called ruBisCo converts the G3P molecules into
5-carbon molecules called ribulose 1,5-biphosphates (RuBP). These molecules
combine with new CO2 and continue the cycle
h. Note: Rubisco is one of the most important bio enzymes because it turns
inorganic CO2 into organic molecules used by the cell
i. Note: The sugars formed during the Calvin cycle are used by plants both as a
source of energy and as building blocks for more complex carbs.
11. Alternative Pathways other than photosynthesis
a. C4 Plants
i. This pathway allows plants to maintain photosynthesis while reducing
water loss
ii. C4 plants have significant structural modification in the arrangement of
cells within the leaves
iii. They store the light energy in the photosystem during the daytime, and the
main process is done at night.
iv. They restructure the leaves so that the top layers of the leaves will be very
thin so that light will go through very quickly without having to go to
many layers to get to the stomata to avoid losing water
b. CAM Plants
i. Crassulacean acid metabolism (CAM) is found in desert plants ex. Cacti,
orchids
ii. These plants collect CO2 at night and store it in organic compounds
iii. During the day, the plants release CO2 from organic compounds for the
light-dependent cycle of photosynthesis.
iv. Light-dependent phase happens during the day, and the Calvin cycle
happens during the night
Lesson 3: Cellular Respiration
1. Cellular respiration: the process by which organisms obtain energy by breaking bonds of
food using O2
2. Cellular respiration transfers energy from good molecules to usable energy (ATP)
3. The equation for cellular respiration is the opposite of photosynthesis
a. C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy
4. Cellular respiration has two main parts
a. Glycolysis: an anaerobic process in which it doesn’t require oxygen in the
cytoplasm
b. Aerobic respiration involving the Krebs cycle and electron transport chain, is an
aerobic process, which means it requires oxygen in the mitochondria
c.
5. Glycolysis
a. Is the process of breaking down glucose in the cytoplasm, releasing energy as
ATP and NADH
b.
c. Glycolysis produces 2 ATP, 2 NADH, and 2 pyruvate molecules for each glucose
molecule that is broken down.
i. Note: Pyruvate still contains 90% of the energy stored in glucose
ii. This 90% of energy still in pyruvate will go to aerobic respiration in
mitochondria.
1. Krebs cycle
2. ETC
d. The preparatory reaction takes place after glycolysis
i. Pyruvate + CoA(Co-enzyme A) → Acetyl CoA
ii. Carbon dioxide is given off by the cell.
6. Krebs cycle
a. In the presence of O2, Pyruvate is transported into the mitochondrial matrix
where it’s broken down through a series of reactions called the Krebs cycle,
which is aka the tricarboxylic acid (TCA) cycle and the citric acid cycle.
b. If the O2 is not available or is low, glycolysis is followed by an anaerobic
pathway called anaerobic respiration which is aka Fermentation
c.
d.
e. Steps
i. Acetyl CoA combines with a 4-carbon compound to form citric acid
ii. Citric acid is broken down, releasing CO2 and generating 1 ATP, 3 NADH,
and 1 FADH2
iii. Finally, acetyl CoA and citric acid are generated and the cycle continues
f. Note: Since 2 pyruvate molecules were formed through glycolysis, there will be 2
turns of the Krebs cycle for each glucose molecule
g. The net yield from the Krebs cycle is:
i. 6 CO2 = 2x 3CO2 → to the atmosphere
ii. 2 ATP = 2x 1 ATP → staying in the cell
iii. 8 NADH and 2 FADH2 = 2x 4 NADH + 1 FADH2 → electron carriers
7. Electron Transport
a. The electron transport takes place in the crests of the mitochondrial inner
membrane
b. It starts with the e- carriers releasing their e- that move along ETC
c.
d. Note: in the mitochondria, O2 is the final e- acceptor in the ETC, H+ and e- are
transferred to O2 to form H2O
e. The overall ATP production by Cellular Respiration in eukaryotes is
i. 32 ATP from the ETC
ii. 2 ATP from the Krebs Cycle
iii. 2 ATP from glycolysis (4-2=2)
iv. Total=36
8. Prokaryotic Cellular Respiration
a. Some prokaryotes also undergo aerobic respiration
b. Since they don’t have organelles, the whole process takes place in the cellular
membrane saving the cell 2 ATP consumed in the beginning of glycolysis and
yielding 38 ATP at the end of the process.
9. Anaerobic Respiration
a. When O2 is unavailable or low, cells can’t follow glycolysis with aerobic
respiration which causes a few problems
i. Glycolysis only provides 2 ATP per broken-down glucose
ii. The cell has a limited amount of NAD+ so glycolysis will stop when it’s
used up
b. So, some cells function for a short time by following glycolysis with an
anaerobic process called anaerobic respiration or fermentation
c. Fermentation occurs in the cytoplasm of the cell and produces NAD+ and ATP
d. Two types of fermentation
i. Lactic Acid Fermentation → animals
1. Enzymes change the pyruvate made during glycolysis into lactic
acid
2. Skeletal muscles produce lactic acid when the body cannot supply
enough O2, such as during periods of strenuous exercise, making
muscles fatigued and sore
ii. Alcohol Fermentation → Prokaryotes, “non-animal” eukaryotes
1. This process occurs in yeast and some bacteria
2. It changes pyruvate into ethyl alcohol and carbon dioxide
iii. When oxygen is not enough, fermentation can occur
iv.