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The Cell and Organelles

Methods & tools for studying cells

Understand the differences between the following types of microscopes:

  • Light microscope 

  • Electron microscope (EM), including scanning electron microscope (SEM) and transmission electron microscope (TEM) 


Know the theory of endosymbiosis

Eukaryotic vs. Prokaryotic cells: 

This concise article explains this perfectly and has a great diagram, too

  • Eukaryotes = more complex cell structure; have an endomembrane system with different organelles; has a membrane-bound nucleus

  • Prokaryotes = has no nucleus; has a nucleoid instead, which contains circular DNA.  Has no membrane-bound organelles

Surface area to volume ratio = important to understand, as this is a recurring theme in biology.  Cells need to maintain a relatively high surface area to volume ratio so that materials can easily be transported in and out.  This is why cells are so small

Cell Organelles has a great overview of each of the organelles, with several labeled diagrams


  • Know the differences in organelles and overall cell structure for animal versus plant versus bacteria cells

  • Know the structure and function of all the organelles below.  It is super helpful to draw out a diagram of the cell on your own and label the name and function of each organelle:

  • Cell membrane -- in all types of cells

  • Cell wall

  • Nucleus (and don’t forget the nucleolus)

  • Endoplasmic reticulum -- understand the differences between the smooth and rough ER

  • Golgi apparatus

  • Mitochondria -- in both plant and animal cells; not in prokaryotes

  • Chloroplast -- generally in plants only

  • Vacuole

  • Ribosomes -- in all types of cells

  • Lysosomes

  • Peroxisomes
    *Tip: know the difference between lysosomes and peroxisomes

  • Central vacuole -- in plants only

  • Cell walls -- in prokaryotes, plants, and fungi; not in animal cells

Know the components of the extracellular matrix (ECM):

  • Collagen -- fibrous, stretchy protein strands

  • Proteoglycan

The ECM is different from the cytoskeleton!  Typically, only animal cells have ECM, which is like a substitute for the cell wall.  It provides structure and protection

Know the components and structure of the cytoskeleton:

  • In contrast to the ECM, the cytoskeleton is located within the cell, close to the cell membrane

  • It has several functions: maintains cell shape, anchors organelles in the cell, helps with cytoplasmic streaming (to help the cell move), and anchors the cell itself in place

  • It is made of microtubules, intermediate filaments, and microfilaments (know the general structure and relative thickness of these structures)

Animal cell organelles

This is a diagram of an animal cell.  Notice that it does not have a cell wall, and it does have a a nucleus, which is surrounded by the nuclear envelope (membrane).  Courtesy of Vecteezy

The Cell Membrane

Overview of the cell membrane structure:

  • Fluid mosaic model, made of a phospholipid bilayer with cholesterol molecules embedded, selectively permeable

  • Cholesterol helps maintain and adjust membrane fluidity

  • The cell membrane also contains integral proteins, peripheral proteins, and protein channels (for transport)


Functions of membrane proteins:

  • Transport (EX: sodium-potassium pump, aquaporins)

  • Enzyme activity 

  • Signal transduction.  EX: GCPR (G protein-coupled receptor)

  • Cell to cell recognition.  EX: Glycoproteins

  • Cell to cell attachments.  EX: Desmosomes

  • Help attach cytoskeleton and extracellular matrix to the cell membrane


Types of transport in/out of the cell:

  • Passive = simple and facilitated diffusion, osmosis.  Requires no energy

  • Active = requires energy in the form of ATP, electrons, or other source.  Examples: ion pumps, cotransport, endocytosis/exocytosis, pinocytosis.  In general, movements involving bulk transport or going against a concentration gradient requires energy


Cell junctions allow communication between adjacent cells.  Know the structure and function of the following types of junctions:

  • Tight junctions

  • Desmosomes

  • Gap junctions

  • Plasmodesmata (in plants only)

*Use the link above to view diagrams of each junction


Osmosis can cause the following to happen with cells:

  • Plasmolysis -- in plant cells only; occurs when the cell shrinks away from the cell wall

  • Lysis -- occurs in animal cells when too much water enters the cell

Three scenarios with osmosis in cells:

  • Hypertonic cell = cell has higher concentration of solutes compared to surroundings

  • Isotonic cell = same concentration of solutes

  • Hypotonic cell = lower concentration of solutes

*Think about how the water will always try to move toward the area with higher solute concentration.  Then as a result of the water movement, will the cell shrink, expand, or stay the same?


Relative to the upcoming chapters, this one does not have many processes or new terms to remember.  Here’s what you should know:

  • Metabolism: what it is, and why it is important.  Also know some examples of biological metabolic pathways

  • ATP = the source of energy that our cells use for everyday processes.  Understand how ATP gets used (hint: a phosphate group is removed).  Also know the structure of ATP well

  • Know the difference between anabolic vs. catabolic pathways, and specific biological examples of each

  • The First and Second Laws of Thermodynamics.  Also know what a spontaneous process is, which relates to the second law

  • Enzymes: they are extremely important throughout biology, so it’s important to understand the following:

    • They are proteins that act as biological catalysts and follow an induced-fit model of binding their substrates

    • They lower activation energy of a reaction, therefore speeding up the reaction

    • They are very sensitive to pH and temperature

    • They can be regulated through allosteric or competitive inhibition, as well as cooperativity.  It’s important to understand each one of these regulation methods

Image by National Cancer Institute

Fluorescently labeled cells.  Can you spot several that are undergoing cell division?

The Cell Cycle

Mitosis (part of the M phase in the cell cycle)

  • The process starts with a diploid somatic (body) cell and ends with two genetically identical daughter cells 

  • Know what happens in each stage of mitosis: prophase, metaphase, anaphase, and telophase (PMAT).  There is a lot of vocabulary in this section.  Know all the bolded terms in the AP Biology textbook
    *Tip: draw out the different mitosis stages, explain what’s happening in each stage, and label all the different structures involved (e.g., centromere, kinetochore, mitotic spindles, cleavage furrow, etc.)

  • Know what cytokinesis is, and how it differs slightly in plant vs. animal cells


Other phases of the cell cycle to know:

  • G0 = cell is dormant, not growing or dividing

  • G1, G2 = cell is growing.  In G2, it is getting ready for mitosis 

  • S = DNA synthesis occurs to produce another copy of the DNA, in preparation for cell division


Regulation of the cell cycle:

  • Checkpoints at the end of almost every phase in the cell cycle.  Without checkpoints, the cell could continue dividing and/or growing uncontrollably.  In fact, mutations in cell cycle checkpoints is what often leads to cancer

  • Cyclin and CDK.  Cyclin levels spike right before mitosis begins and then it quickly degrades in each cycle.  CDK (cyclin-dependent kinase) is always present, but is only activated when bound to cyclin

Cell Respiration

  • Know the overall equation for cell respiration and the goal of the process.  Know that the process in eukaryotes depends on mitochondria

  • Understand the differences in the process for prokaryotes vs. eukaryotes.  Remember that prokaryotes do not have mitochondria

  • Know exactly where and when each of the 4 key steps happens, as well as the specific inputs and outputs of each step (how much NADH/FADH and ATP produced):

  1. Glycolysis

  2. Pyruvate oxidation

  3. Krebs cycle (also known as Citric Acid cycle, both terms are used often)

  4. Electron transport chainChemiosmosis occurs here.  This is the most complex step and should be studied carefully.  What is the final electron acceptor?  What is the purpose of the electrons flowing through there, and where did they come from?  What powers the hydrogen pumps?  What powers the ATP synthase?

  • Understand the process of fermentation, where it occurs, how it differs in bacteria vs. humans, and why it is much less efficient than aerobic cell respiration.  Understand how the byproducts (either lactic acid or ethanol) are produced in fermentation


  • Know the overall equation for photosynthesis and the goal of the process.  This process occurs in the chloroplast, which typically only present in plants and algae

  • Know exactly where and when each of the 2 key steps happens, as well as the specific inputs and outputs of each step (how much NADPH and ATP produced):

    • Light reactions = occurs in the thylakoid membranes and involves two photosystems.  You should know exactly what goes on in the light reactions, and understand the similarities and differences compared to the cellular respiration’s electron transport chain

    • Calvin cycle = occurs in the stroma.  Know the enzyme rubisco’s role in the Calvin cycle

    • Understand the differences between cyclic and linear electron flow in photosynthesis, and the advantages of each.  When would a plant want to switch to cyclic flow?

  • Understand the causes and drawbacks of photorespiration

  • There are C4 and CAM plants, which have developed special adaptations that allow for more productive photosynthesis.  Understand why they developed these adaptations, and what these special features are.  For instance, C4 plants have bundle-sheath cells and CAM plants only open their stomata during the night

cell comm.PNG

This diagram shows how neurotransmitters act as a type of cell signaling molecule, allowing communication between neurons (brain cells).  Image courtesy of Openstax Biology

Cell Communication

Understand the different types of cell signaling.  There are 4 main types (autocrine, paracrine, endocrine, and direct contact signaling), which are described here with helpful diagrams


Overview of the signal transduction pathway

*Tip: studying the diagrams of the process in the article linked above will really help.  Try drawing out the processes yourself too


Signal Transduction Pathway Steps:

  1. Signal.  The ligand binds to the receptor.  The ligand can be a hormone, neurotransmitter, or another signaling molecule

  2. Transduction.  There are several important vocabulary terms here to know here.

    • Types of receptors: GPCRs (G protein-coupled receptors), receptor tyrosine kinases, and intracellular receptors.  Know the transduction mechanism for each 

    • Second messengers.  The most common examples to know are cAMP and Ca2+ (calcium ions).  Know how the DAG pathway with Ca2+ and IP3 works

    • Phosphorylation cascade = a chain of phosphorylation (adding a phosphate group to a molecule, a protein in this case), which often occurs as part of transduction.  The purpose of the phosphorylation cascade is to amplify the original signal

  3. Response.  This can be turning off expression of a particular gene, increased uptake of an ion, increasing production of a specific enzyme, or many other changes 


Kinase = enzyme that adds a phosphate group to another molecule, usually to activate it

Phosphatase = enzyme that removes a phosphate group from another molecule

Kinases and phosphatases work together to activate and deactivate molecules in the signal transduction pathway

signal pathways.PNG

The signal transduction pathway using cAMP versus Ca++.  Both molecules are common second messengers.  It is important to know both of these pathways well.  Image courtesy of Libretext Biology

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