Module 3: The Cell Notes

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• Module 3 heading: THE CELL.
• Introduction cues: check current text chapter, upcoming quiz, and EXAM 1 updates.
• Exam logistics: eCampus review posted after everyone completes the exam; option to review during office hours.
• Topic focus: MODULE 3 — THE CELL.

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• The cell is an integrated system of working parts called organelles.
• Organelles are specialized structures that perform distinct jobs inside cells.
• Each organelle has a unique function, which gives each cell a unique job and leads to different cell types with different functions.

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• Three domains of life:
  • Bacteria and Archaea: domains containing single-celled prokaryotes.
  • Eucarya (Eukarya): domain containing multicellular eukaryotes.
• Simple schematic: Single-celled prokaryotes vs multicellular eukaryotes (Us!).

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• Prokaryotes vs. Eukaryotes:
  • Prokaryotes (bacteria and archaea) are the earliest form of life.
  • Eukaryotes came later and include fungi, plants, and animals.

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• Primary distinctions:
  • Eukaryotes have a membrane-bound nucleus; prokaryotes have a free nucleoid.
  • Prokaryotes lack most of the organelles that eukaryotes possess.

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• Eukaryotic cells (plants and animals):
  • Animal cells tend to be larger and more rounded.
  • Plant cells tend to be smaller and more rectangular (square-like).
  • Plant cells have two major components not typically found in animal cells: cell walls and chloroplasts.

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• Typical cell sizes:
  • Most plant and animal cells: between $10\text{-}100\ \mu\text{m}$.
  • Bacteria are smaller.
• How many cells in the body? Approximately $3.72\times 10^{13}$ cells (often quoted as 37.2 trillion).
• Why so many, and why small? Small cell size helps conserve cell metabolism because a higher surface area-to-volume ratio facilitates exchange of nutrients and wastes; metabolism is the process by which food sources are converted to energy.

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• Organelle cards:
  • Located in this module on eCampus under outcomes/activities and end-of-module checklist.
  • Not all organelles will be discussed in depth in lecture; emphasis is on how organelles work together.
  • Students are responsible for studying the cards and knowing the structure and function of the listed organelles and the cell types they’re found in.
  • You’ll be tested on this information in the future.

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• Quick check: Unknown cell type contains a membrane-bound nucleus, ribosomes, and mitochondria.
  • A: prokaryote
  • B: eukaryote
  • C: could be either
• Conclusion: Presence of a membrane-bound nucleus indicates a eukaryote (answer: B).

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• Quick check: If a cell has a cell wall, what can you conclude?
  • A: Plant cell
  • B: Animal cell
  • C: Could be either plant or animal cell
• Conclusion: A cell wall strongly suggests a plant cell (answer: A).

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• How do organelles work together? The endomembrane system (endo = within) is a coordinated system of organelles in eukaryotes.
• Role: Modify, package, and transport proteins.

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• Endomembrane components – Endoplasmic Reticulum (ER):
  • DNA in the nucleus is transcribed to RNA.
  • RNA is sent to the ER and used to make proteins.
  • Two kinds of ER:
  • Rough ER: studded with ribosomes (hence the name).
  • Smooth ER: lacks ribosomes.
• Ribosomes are enzymes that are part protein, part RNA.
• Summary: ER is a primary site of protein synthesis and processing in cooperation with ribosomes.

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• Main endomembrane components:
  • Vesicles: small membrane-bound bubbles that carry proteins.
  • Some proteins are packaged into vesicles for specialized functions.
  • Lysosomes: digest materials.
  • Peroxisomes (not shown): detoxify hazardous contents.

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• Golgi apparatus:
  • Receives packaged proteins from the ER.
  • Performs quality control to check for errors.
  • Re-packages proteins and prepares them for final destinations.

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• ER signal sequence map (conceptual):
  • Presence of a transmembrane signal sequence acts as a “zip code.”
  • If a signal sequence is present, ribosome docking at the rough ER occurs, leading to protein deposition into the rough ER via the ribosome.
  • Proteins are transported to the Golgi via vesicles.
  • If no signal sequence is present, the protein is synthesized in the cytoplasm.
  • The diagram contrasts the options for a protein as it travels through the endomembrane system.
• Note: This page emphasizes how the presence or absence of signal sequences guides the trafficking path of newly synthesized proteins.

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• Endomembrane system at work (stepwise):
  • Proteins begin their journey at the rough ER.
  • Ribosomes deposit proteins inside the rough ER.
  • A signal sequence guides targeting; the Signal Recognition Particle (SRP) binds this sequence.
  • SRP then binds its receptor on the rough ER membrane.
  • If there is no signal sequence, the ribosome remains in the cytoplasm and the protein is not targeted to the ER.

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• If there is a mutation in the signal sequence or in SRP or the SRP receptor: the protein would remain in the cytoplasm (i.e., would not be directed to the ER).
• Question exercise: A mutation in any of these components would prevent proper docking and translocation.

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• Golgi apparatus structure within endomembrane system:
  • cis-face: the receiving side of the Golgi (cis = same).
  • trans-face: the shipping side of the Golgi (trans = opposite).
• Golgi role: final modifications of proteins.
• Exit from Golgi occurs at the trans-face.

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• Vesicle movement within the cell:
  • Vesicles travel through the endomembrane system with help from motor proteins like kinesin.
  • Kinesin carries vesicles along microtubule tracks; kinesins are motor proteins composed of a head, stalk, and tail.
  • ATP is used by kinesin to function; chemical basis: \mathrm{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi} + \Delta G_{hyd}}.
  • Microtubules form long tracks that provide structural support and rigidity for transport.

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• Vesicle trafficking from Golgi to lysosome or other destinations:
  • If proteins exit the Golgi in a lysosome, they are used for digestion.
  • Lysosomes have a very low (acidic) pH that enables digestion of materials.
  • Autophagy: internal digestion of cellular components for reuse.
  • Phagocytosis: uptake of external cellular material (external food) by the cell.

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• Not all proteins go to lysosomes; some are destined for other organelles provided they contain a special “zip code” sequence.
• Three alternate jobs for proteins with targeting signals:
  1) Transfer to other organelles.
  2) Become transmembrane proteins embedded in the phospholipid bilayer; their polar/non-polar properties determine how they sit in the bilayer.
  3) Secretion/export out of the cell.
• Targeting signals allow recognition between proteins and organelles.

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• If a protein is not a transmembrane protein, it can be secreted outside the cell.
• Secreted proteins can interact with other cells and participate in cell-cell communication.
• Endomembrane system at work: further trafficking can lead to secretion.

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• Recap of not-all proteins remaining in lysosomes: some are exported out of the cell for intercellular communication.
• Emphasis on the breadth of protein destinations within the cell and beyond.

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• Why should you care?
• Proteins are the functional entities within cells.
• Without the endomembrane system, the fate and proper localization of proteins would be compromised.

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• ER signal sequence map (revisited):
  • Present? Ribosome docking at rough ER occurs when a signal sequence is present.
  • Trans-membrane protein? Signal sequence presence influences integration into membranes.
  • Zip code signal sequence present? YES/NO determines routing.
  • Protein deposited into rough ER by ribosome; transported to Golgi via vesicles; final destinations determined by sorting signals.
• This page is a prompt to fill in a chart (blue boxes) detailing choices proteins make as they travel through the endomembrane system.

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• To-do list for Module 3:
  • Complete 2 module quizzes: Cells & organelles quiz; Cell membranes quiz.
  • Review the organelle cards (linked in Module 3 outcomes/objectives tab); essential study resource.
  • Read selected sections of Chapters 7 and 6B in Mastering Biology; readings supplement course material and chapter questions.
  • Complete relevant Chapter questions in Mastering Biology; questions are numbered the same as the readings.
  • Optional practice materials: Practice questions 4 (Cells & organelles), Practice questions 5 (Membranes), Practice worksheet 3 (Cells & organelles), Practice worksheet 4 (Transport & osmosis).
  • Reminder: Course schedule provides structure for quizzes and readings; assignments are due the night before the exam for that unit, though completing tasks per the schedule helps manage workload.