Unit 3: Cell transport/early life/organelles

What is organelles and its properties?

Organelles are specialized structures within a cell that perform distinct functions, such as energy production, protein synthesis, and waste processing. They help maintain cellular organization and efficiency. Organelles are surrounded by membrane similar to strucuture as the plasm membrane, exception ribosome.

What is the Cell membrane?

Surrounds the cell and remains homeostasis

Nuceleus

The house for genetic material.

Nucleolus

Site of ribosome production

Centrioles

Found in thee centrosome and is used to help move chromosomes during cell division.

Vesicles

moves molecules inside and out the cell

Smooth Endoplasmic Reticulum

• Produces phospholipids, cholesterol, steroids, and some CBHs

• Stores calcium in skeletal muscle cells for contraction of the muscle

• metabolizes(breaks down) some drugs and toxins (alcohol)

Rough Endoplasmic Reticulum

• Synthesizes proteins for secretion from the cell or for the cell membrane(ribosomes)

• Helps to correctly fold proteins

• Chemically modifies proteins 

• Helps to make sure the proteins get to the right place (part of the endomembrane system)

Ribosome

Reads mRNA and produces polypeptide chains

Golgi apparatus

• Many different compartments (cisternae) each with different job-all contain enzymes

• Receives proteins & lipids from ER-Chemically modifies them(cleave polypeptides, add CBHs/monosaccharides)to make glycoproteins & glycolipids, adds sulfate groups and phosphate groups, continues the folding process

• Chemical tags for destination in or out of the cell

• Manufactures polysaccharides & lysosomes

• part of the endomembrane system

What is the endomembrane system?

• The smooth and rough endoplasmic reticulum(ER), the golgi, and vesicles are all part of the endomembrane system

• This system works together when products need to be secreted from the cell, for example insulin. All cells need insulin, which is produced by cells in the pancreas. 

• Animation

• Animation

• For example: DNA’s instructions coded into RNA in the nucleus. mRNA goes leaves nucleus, goes to RER where ribosomes read and make protein. Protein secreted in a vesicle, goes to Golgi. Golgi chemically alters protein, puts it in a vesicle, secretes it out the cell

Mitochondria

the site of cellular respiration-breaks down organic molecules to produce ATP in animals AND PLANTS

Mitochondria cristae

inner membrane

Chloroplast

SITE of photosynthesis-uses sunlight to produce sugars-PLANTS ONLY

Lysosome

• Membrane filled with various digestive enzymes

• primary responsibility is catabolic degradation of proteins, polysaccharides and lipids into their respective building-block molecules: amino acids, monosaccharides, and free fatty acids

Peroixomes

• Enzymes to breakdown uric acid, amino acids, fatty acids into H2O2, then catalase breaks down H2O2

• Because they breakdown fatty acids,, they help produce energy for the cell(NOT ATP, but FAs can be used to produce ATP)

• They also synthesize lipids, bile & cholesterol

• Provide energy during germination

• have same GENERAL function as lysosomes, however, they break down different things and are NOT part of the endomembrane system

Cell Wall

• provides the cell with structural support, shape, protection, and functions as a selective barrier

•  help the cell withstand osmotic pressure and mechanical stress

Cytoskeleton

• Microtubules, intermediate filaments actin

• Muscle contraction, mitosis(spindle & cleavage furrow), organelle movement, support(gives the cell shape so it’s not a blob), amoeboid movement, cilia/flagella, etc

BASAL BODY

• anchors cilia/flagella, embedded in cell membrane

cytosol-liquid, cytoplasm liquid plus organelles-

• cytosol and cytoplasm are NOT organelles

Centrosome

• general area outside the nucleus where centrioles are found-also not considered an organelle 

Describe conditions on early Earth before and during the evolution of the first cell. Why were these conditions important to the development of life?

The conditions on early earth had a lot of energy (UV, heat, electrical, radioactive elements) , had a large presence of HONC, Volcanic Ash. These conditions made is important to due development of life due to formation of organic compounds from inorganic compounds

1. Describe the series of events leading to the formation of the first cell (Oparin & Haldane’s chemical evolution theory).

Repetitive reproduction was the series of events leading to the formation of the cell. Because of all these weather events it is creating new molecules. For example in water there were formations of Carbon and Hydrogen, which in a warmed pit by the crust starting forming fatty acids. Later after fatty acids started forming then it created micelles/ protocells. Over time they started creating RNA then eventually a prokaryotic cell. 

Describe the experiments of Miller & Urey, and their significance. 

• Goal: Simulate early Earth’s atmosphere and test if organic molecules (like amino acids) could form spontaneously.

• Atmosphere simulated: A mix of methane (CH₄), ammonia (NH₃), hydrogen (H₂), and water vapor (H₂O) — believed to reflect Earth’s primitive conditions.

• Energy source: Electric sparks mimicked lightning, providing energy to drive chemical reactions.

• Closed system: Gases circulated through a loop containing a boiling flask (water) and a spark chamber. 

• It support the chemical evolution theory and that earth’s early environment was very chemically active

1. Relate the significance of phospholipids structure and behavior in water to the development of the first cell.

Phospholipids structure and behavior in water led to the development of the first cell because phospholipids have hydrophilic heads and hydrophobic tails, forming micelles.

1. Describe protobionts(now called protocells). 

Protocells are membrane-bound structures that form spontaneously from organic molecules under the right conditions. They resemble simple cells in that they can:

• Maintain an internal environment distinct from their surroundings

• Absorb and concentrate molecules

• Undergo simple growth and division

• In some models, even carry out rudimentary metabolic reactions

1. Differentiate between autotrophs (chemotrophs, phototrophs) and heterotrophs.

1. Phototrophs

• Use light energy to convert CO₂ and water into glucose via photosynthesis.

• Found in: plants, algae, cyanobacteria

• Equation:

6CO2+6H2O+light→C6H12O6+6O26CO_2 + 6H_2O + \text{light} \rightarrow C_6H_{12}O_6 + 6O_2

2. Chemotrophs

1. Use chemical energy from inorganic compounds (like hydrogen sulfide or ammonia) to make food via chemosynthesis.

2. Found in: deep-sea bacteria, archaea in extreme environments

3. Example: Bacteria near hydrothermal vents using H₂S to produce glucose.

Heterotrophs: consuming must eat other organisms for energy

Describe the first cells on Earth., the common ancestor to all current cells. What structures and processes would they have had? What structures and processes would they not have had?

The first cells on Earth — often referred to as LUCA (Last Universal Common Ancestor) — were simple, microscopic life forms that emerged over 3.5 billion years ago. They represent the shared ancestor of all modern cells, from bacteria to human neurons. Here's a detailed look at what they likely had and did not have, based on evolutionary biology and molecular evidence:

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🧬 Likely Structures and Processes LUCA Had

Feature	Description
Cell membrane	Made of a lipid bilayer, allowing compartmentalization and selective transport.
Cytoplasm	A gel-like interior where chemical reactions occurred.
Ribosomes	Essential for protein synthesis — translating RNA into proteins.
RNA and DNA	Likely used RNA for early genetic coding and catalysis; eventually evolved DNA for stable inheritance.
Basic metabolism	Could extract energy from simple chemical reactions (e.g., fermentation or redox reactions).
Enzymes	Protein catalysts that sped up metabolic reactions.
Genetic code	Used a universal code to translate nucleotides into amino acids — still used by all life today.
Binary fission	Reproduced by simple cell division, copying genetic material and splitting.

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🚫 Structures and Processes LUCA Did Not Have

Feature	Why It Was Absent
Nucleus	LUCA was prokaryotic, so DNA floated freely in the cytoplasm.
Membrane-bound organelles	No mitochondria, chloroplasts, ER, or Golgi — these evolved later in eukaryotes.
Complex multicellularity	LUCA was a single-celled organism.
Photosynthesis	Likely absent or primitive — early cells relied on chemical energy, not sunlight.
Oxygen-based respiration	Earth’s atmosphere lacked oxygen; LUCA used anaerobic metabolism.

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🌍 Why LUCA Matters

• LUCA is the starting point for all cellular life — its core features are preserved in every living organism today.

• Studying LUCA helps scientists understand how life evolved from chemistry to biology, and how complex cells (eukaryotes) later emerged through processes like endosymbiosis.

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Would you like to explore how LUCA connects to archaea, bacteria, and the rise of eukaryotes? Or how scientists reconstruct LUCA’s genome using modern bioinformatics? I’d love to dive deeper!

Explain how cyanobacteria changed Earth’s atmosphere. 

IT changed the earth’s atmosphere because of the addition of oxygen. It used sunlight, water, carbon dioxide to produce oxygen and glucose through photosynthesis. This was toxic to most organisms because they were anaerobic organisms. 

1. Compare and contrast prokaryotes and eukaryotes. 

1. Explain the endosymbiont theory, including 2 pieces of evidence to support it.

The endosymbiont theory is that the eukaryotes exist due to them consuming prokaryotes because of the similar properties within each type of cell. Mitochondria and Chloroplasts are two pieces of evidence because they have the same properties, being able to produce glucose, produce energy, have their own cell division, a membrane as a bacterium cell would have, own DNA, two cell membrane.. 

Why are cells usually microscopic? Explain in terms of surface area and volume.

Cells are usually microscopic because cells are required to be small to be able to fulfill the nutrients needed to keep the cell alive or they will die. In addition, the surface area and volume of a cell needs to have a large ratio but cannot be too large.

Describe the function of the cell membrane. What does selectively permeable mean

The function of the cell membrane is to regulate what molecules are coming inside and outside of the cell. Selectively permeable means that the cell membrane( the phospholipid bi layer) ONLY can intake small, no polar molecules. If not then they cannot pass through the cell membrane and need to go to a membrane protein. 

1. Describe the function and structure, including chemical constituents, of the following cell membrane parts; phospholipids,

Phospholipids: Made out of glycerol backbone, two fatty acids tails and a phosphate group, Chemical constituents: Carbon, hydrogen, oxygen, phosphorus, Function: to form the phospholipid bilayer and create a semi permeable barrier allowing selective movement of substances

Describe the function and structure, including chemical constituents, of the following cell membrane parts; glycolipid,

Strutucutre: A phospholipid with a carbohydrate chain attached to its hydrophilic head. Chemical constituents:Lipids+ carbohydrates (sugar like glucose or galactose) Function: Involved in cell regition, communication and stabilizing the membrane, often as cell markers.

Describe the function and structure, including chemical constituents, of the following cell membrane parts; cholestrol

Strucutre: A rigid ring shaped lipid embedded between phospholipids. Chemical constituents: Carbon, hydrogen, oxygen( a type of steroid). Function: regulates membrane fluidity: it prevents it from becoming too rigid in cold or too fluid in heat. Adds stability without making the membranee brittle.

Describe the function and structure, including chemical constituents, of the following cell membrane parts; hydrophilic and hydrophobic portions

Hydrophilic: The phosphate heads of phospholipids face outward toward water. Hydrophobic: the fatty acid tails face inward, away from water. Function: This dual nature creates the bilayer sand drives selective permeability, only certain molecules can pass through without help.

Describe the function and structure, including chemical constituents, of the following cell membrane parts;integral proteins

• Structure: Span the entire membrane (transmembrane) or are deeply embedded.

• Chemical constituents: Chains of amino acids with hydrophobic R groups in the membrane-spanning region and hydrophilic R groups on the ends.

• Function: Act as channels, carriers, or receptors. Crucial for transport, signal transduction, and cell communication.

Describe the function and structure, including chemical constituents, of the following cell membrane parts; peripheral proteins

• Structure: Loosely attached to the surface of the membrane (either side).

• Chemical constituents: Amino acids, often with polar side chains.

Function: Provide structural support, anchor the cytoskeleton, or assist in cell signaling. They don’t span the membrane

Describe the function and structure, including chemical constituents, of the following cell membrane parts; gylcoproteins

• Structure: Proteins with carbohydrate chains attached.

• Chemical constituents: Amino acids + sugars (oligosaccharides).

• Function: Involved in cell-cell recognition, immune response, and receptor activity. Like glycolipids, they act as ID tags for the cell.

Describe the function and structure, including chemical constituents, of the following cell membrane parts; carbohydrates 

• Structure: Short branched chains of sugars attached to lipids (glycolipids) or proteins (glycoproteins).

• Chemical constituents: Monosaccharides like glucose, galactose, mannose.

Function: Form the glycocalyx — a sugary coating that helps with protection, lubrication, and cell recognition

1. How is the membrane fluid & mosaic?

• The phospholipid bilayer is made of molecules that are not rigidly fixed — they can move laterally within the layer.

• This movement gives the membrane a fluid, flexible nature, like a thin oil film.

• Cholesterol molecules are embedded between phospholipids to help regulate fluidity — keeping it from becoming too stiff or too loose depending on temperature.

• The membrane isn’t just phospholipids — it’s a patchwork of proteins, carbohydrates, and cholesterol.

Be able to explain in detail the structure and function of all plant and animal cell organelles.

1. Shared organelles handle core functions like energy production, protein synthesis, and transport. Plant cells specialize in photosynthesis and structural rigidity. Animal cells focus on mobility, digestion, and rapid response. Plant cells have chloroplasts, cell walls, central vacuole, plasmodesmata.Animal cell have lysosomes and centroles. 

Compare and contrast mitochondria & chloroplast with respect to structure & function.

1. Mitochondria are like the cell’s power plants, burning fuel to make usable energy (ATP).

2. Chloroplasts are like solar panels, capturing sunlight to make fuel (glucose).

3. Both have double membranes, own DNA, and ribosomes, hinting at their evolutionary origin from ancient prokaryotes (endosymbiotic theory).

1. What is meant by the endomembrane system? Explain how it regulates protein traffic and performs metabolic functions within the cell.

he endomembrane system is a system of creating needed molecules inside the cell. It inclusdes the Rough ER< smoothER, the golgi apparatus and the vestivles. The rough ER creates proteins due to ribosomes and the smooth ER creates lipids. They both send it to the golgi apparatus by a vesticle (a membrane sack)  to refold/rearrange any of the foldings or to add auditions to it like glucose to make it a glycoprotein. Then it tags it and sends it by a vesicle wherever its destined to go.  

1. Explain in detail how a pancreas cell secretes insulin into the bloodstream. Include a description of all organelles, membranes, and processes involved.

the endoplasmic reticulum, Golgi apparatus, and secretory vesicles to package the hormone, and the plasma membrane, mitochondria, and ion channels to trigger its release via exocytosis

1. Compare and contrast tight junctions, gap junctions, plasmodesmata & desmosomes with respect to structure & function.

Tight junctions, desmosomes, gap junctions, and plasmodesmata are cell junctions with different structures and functions. Tight junctions create watertight seals to prevent leakage. Desmosomes act as spot welds, providing mechanical strength to hold cells together. Gap junctions and plasmodesmata (in plants) form channels that allow communication and transport of small molecules between cells. 

1. Describe what is happening chemically during diffusion.  Include concentration gradients in your explanation.

Diffusion is the passive movement of molecules from an area of high concentration to an area of low concentration, driven by the molecules' kinetic energy. No energy input (like ATP) is required — it's a spontaneous process.

Relate the structure of the cell membrane to its selectivity in terms of what can and cannot pass through. Why are proteins necessary?

1. Phospholipids have hydrophilic (water-loving) heads and hydrophobic (water-fearing) tails, forming a bilayer that acts as a semi-permeable barrier.

Membrane proteins are essential because they:

Facilitate transport of molecules that can’t cross the lipid bilayer (e.g., channel proteins for ions, carrier proteins for glucose).

Act as receptors for signaling molecules (like hormones).

Help with cell recognition and immune responses.

Maintain homeostasis by regulating what enters and exits the cell.

1. Compare and contrast the movement of hydrophilic molecules and hydrophobic molecules across the membrane.

Hydrophilic molecules are essential but need transport proteins to cross safely.

Hydrophobic molecules slip through easily, which is why gases like O₂ and CO₂ diffuse quickly.

1. Compare the arrangement of hydrophobic and hydrophilic R groups of integral proteins in relationship to the phospholipid bilayer.

Integral proteins have hydrophobic proteins inside of the cell membrane, the phospholipid bilayer so it can be attached to it. The hydrophilic R groups of integral proteins are on the outside of the cell membrane and it can interact with the water like environment and allows them to communicate and interact with ions. 

1. compare and contrast the following: simple diffusion, facilitated diffusion, osmosis, active transport. 

Simple diffusion	A simple diffusion requires no proteins, no energy and High to low concentration. It just occurs through the phospholipid bilayer
Facilitated diffusion	Facilitated diffusion requires proteins, no energy, H to L concentration. This occurs because it is ions/ larger molecules.
Osmosis	Osmosis is the diffusion of water from a H to L in a cell membrane.
Active transport	Active transport requires energy to diffuse molecules through the cell membrane, it has to be with the protein. It goes from a L to H concentration.

1. Why is osmosis a form of diffusion?

Passive process: Both osmosis and diffusion do not require energy (ATP).

Driven by concentration gradients: Molecules move to equalize concentrations on both sides of a membrane.

Goal is equilibrium: Both processes continue until the concentrations are balanced.

1. Give 2 specific examples of substances which would be transported into/out of a cell using each of the above methods. Explain why the substance would need to be transported in that way. 

Water can be transported through osmosis through aquaphorins.  

The bacteria/ waste entering the white blood cells after being digested, exists the cell.

1. The inside of a red blood cell has a solute concentration of .9%. What would happen if the RBC was placed in the following solutions; .2%, .12%, .9%? Use diagrams and the terms hypertonic, hypotonic, and isotonic to explain your answer.

.2% and .12% are both hypotonic so this would cause  water to diffuse into the red blood cell. The .9% is isotonic meaning there wil be no change. 

1. Why does an animal cell need to be in an isotonic solution, while a plant cell needs to be in a hypotonic solution? Explain in terms of turgor pressure.

Animal cells need to be in an isotonic solution to prevent cyclosis and bursting. While plant cells because of their cell wall it creates turgid pressure on the cell which is a good thing because it keeps the cell upright, firm and happy. 

1. In general terms, what is vesicle-mediated transport? How is it different from the other types of transport in question 5?

Vesicle mediated transport are transports like endocytosis, exocytosis which requires vesicles to move large molecules in or out the cell. They don’t rely on concentrations nor active and its not moving substances through a pump

Compare and contrast the following, endocytosis/exocytosis, phagocytosis/pinocytosis, receptor-mediated endocytosis. E

1.  Endocytosis is a process of moving large molecules inside the cell. Exocytosis is a process of moving large molecules outside the cell. Phagocytosis is the movement of solids inside the cell while pinocytosis is the movement of liquids inside the cell. Receptor - mediated endocytosis is a process where receptors on the outside of the cell attach to large molecule and create clathrin pit, forming a vesticle with receptors and ligands inside and chalrid outside. The chalrids deattach and the vescticle attachs to a endosome which separates the receptors and the ligands. Later putting the receptors in a transport vesicles back to the cell membrane and the ligands to the lysosome to be digested. 

1. How does a coated vesicle form?

1. Cargo Selection

• Specific molecules (like proteins or lipids) are selected to be transported.

• These cargo molecules bind to receptor proteins on the inner surface of the membrane.

2. Coat Protein Recruitment

• Proteins like clathrin, COPI, or COPII assemble on the cytoplasmic side of the membrane.

• These coat proteins form a scaffold that helps shape the membrane into a bud.

3. Membrane Budding

• The coated area begins to curve outward, forming a bulge.

• The coat proteins stabilize this curvature and help concentrate cargo.

4. Vesicle Pinching Off

• A protein called dynamin (in clathrin-coated vesicles) helps pinch the vesicle off from the membrane.

• The vesicle is now free-floating in the cytoplasm, surrounded by its protein coat.

5. Uncoating

• Once the vesicle is formed, the coat proteins disassemble.

• This exposes the vesicle’s surface so it can fuse with its target membrane (like the Golgi or plasma membrane).

1. Give 2 specific examples of substances which would be transported into/out of a cell using each of the above methods. Explain why the substance would need to be transported in that way. 

Bacteria or debris( in immune cells) need to be transported inside the cell because they need to be digested by the white blood cells lysosomes. Neurons Transmitters like dopamine, too large to pass through membrane channels (requiring a vesicle) 

1. Explain how the breakdown and elimination of a bacterial cell by a macrophage involves both endocytosis and exocytosis.

he macrophage detects the bacterial cell with its receptors. Then it engulfs it inside and creates a vesicle, hagoosis. Then after entering the lysosomes it breaks down the bacterium then releases them into vesicles outside of the cell.