Unit 2: Textbook/slide definitons

Cell theory

(what are the three parts?)

1. All living things are made of cells.

2. The cell is the fundamental unit of life

3. All cells come from pre-existing cells

Basic unit of life

Cells

Prokaryotic cells

Cells that lack a nucleus

EX: Bacteria, Archaea

Eukaryote cells

Cells that have a nucleus

EX: Plants, Animals, Fungi & Protists

Nucleoid

Found in prokaryotic cells (where DNA is found)

Flagella

Structures that extend that allow them to move

Organelles

Small structures inside a cell that perform specific functions to keep the cell alive

Transcription

Making mRNA from a DNA template

✅ Happens in the nucleus
✅ DNA → mRNA (message to build a protein)

Translation

Where ribosomes read mRNA to build a protein using amino

Happens in the cytoplasm
✅ Uses mRNA, tRNA, and ribosomes
✅ Each 3-letter mRNA code = 1 amino acid

Process of transcription/translation in Eukaryote cells

Transcription in nucleus > translation later in cytoplasm

Process of transcription/translation in Prokaryote cells

Translation occurs as soon as mRNA is transcribed from the DNA template

The main component of cell membranes

Lipids

Their properties form a barrier in an aqueous (watery) environment

(creating the cell membrane)

Major types of lipids found in cell membranes

Phosolipids

Amphipathic

Hydrophilic and Hydrophobic groups being in the same molecule

Cell membrane (aka plasma membrane)

Thin, flexible outer layer that surrounds the cell

• It controls what goes in and out of the cell

• Made mostly of phospholipids (a type of lipid)

• Found in ALL cells

Phosolipid

Type of lipid with a hydrophilic head and two hydrophobic tails

Shapes of structures phospholipids can form

1. Micelles

2. Bilayer

3. Liposomes

These are the shapes a cell membrane can form into

Micelles

Wedge-shaped and packed into spherical structures

(Bulky heads and a single hydrophobic tail are packed)

Bilayer

Structure of two layers where the phospholipid heads are on the outside and the tails are in the inside

Liposome

A cell like structure sphere made up of phospholipid bilayers

Two features that affect the membranes fluidity

1. Length/number of carbon-carbon double bonds in fatty acid tails

2. The longer the fatty acid tails

Explanation:

The longer the fatty acid tails, the less fluid in the membrane

The shorter the fatty acid tails, the more fluid in the membrane

Longer fatty acid tails have more surface area, so they stick together more through Van der Waals forces, making the membrane less fluid

also: the less carbon-carbon double bonds, the less fluid in the membrane

How do saturated and unsaturated fatty acids affect membrane fluidity?

• Saturated fats → less fluid (tails pack tightly)

• Unsaturated fats → more fluid (tails prevent tight packing)

Major component of animal cell membranes

Cholestreol

(also amphipathic)

What chemical group is cholesterol in?

Hydroxyl group (-OH)

How does temperature affect cholesterol’s membrane fluidity?

• Reduces fluidity at moderate temperatures.

• Prevents solidification at low temperatures.

💡 Think of cholesterol as a buffer:

It helps the membrane stay just right — not too fluid, not too rigid — across temperature changes.

Lipid rafts

Small, organized patches in the cell membrane made of tightly packed lipids and proteins.

They gather special lipids that help stabilize and organize parts of the membrane
They help with cell signaling and membrane organization.

FACT: Most membranes contain proteins as well as lipids`

Membrane proteins serve different functions

main functions of membrane proteins are?

1. Transport

2. Enzymatic activity

3. Signal transduction

4. Cell-cell recognition

5. Intercellular joining

6. Attachment to the cytoskeleton and extracellular matrix (ECM)

Transporter proteins

Moves Ions or molecules across the membrane

• Channel proteins- Hydrophilic tunnel

• Aquaporins- Transport water

• Carrier proteins- Shape changers and shuttles

(May be passive or active)

Receptors

Allows the cells to recieve signals form the environment

Enzymes

Catalyze (speed up) chemical reactions

Anchors

Attaches to other protiens and help maintain cell structure + shape

Intergral membrane proteins

Proteins that are permanently embedded in the membrane and can’t be removed without damaging it

Partially or fully inside membrane

Peripheral membrane proteins

Proteins temporarily attached to the membrane, easily removed, and involved in signaling or support

Transmembrane protein

A TYPE of integral protein that spans the entire lipid bilayer with both hydrophilic and hydrophobic regions (Fully crosses from one side to the other)

Key Function:

• Transfers signals or materials from one side of the membrane to the other

What does FRAP show about membrane proteins?

That they are mobil and can move within the membrane

FRAP: is a technique use to test whether proteins moved around in the cell membrane

How it works:

• Proteins in the membrane are tagged with fluorescent dye.

• A laser bleaches one section so it loses its glow.

• Over time, if unbleached (glowing) proteins move into the bleached spot, it proves proteins are mobile.

Main takeaway:
FRAP shows that membrane proteins are not locked in place — they can move within the membrane.

KEY POINT: Endomembrane system

• A specific group of membrane-bound organelles in eukaryotic cells that:

  • Make, modify, and move proteins and lipids

  • Use vesicles to transport materials

  • Work together as a connected team through membranes

  (Found in eukaryotes (not common in prokaryotes)

Examples: Rough/Smooth ER, Golgi apparatus, Lysosomes, plasma membrane, etc.

(Inside/functions within cells)

Nuclear envelope (double membrane)

Double membrane surrounding the nucleus

• The nuclear envelope has two phospholipid bilayers
  (inner membrane + outer membrane)

• It’s like the nucleus is wearing two jackets, not just one

Thats why we say double membrane

Nucleus function

Stores DNA and controls gene expression

Nuclear pores

Controls what leaves/enters the nucleus

mRNA leaves through pores to go to ribosomes for protein synthesis

Endoplasmic Recticulum (ER)

It makes proteins (rough ER) and lipids (smooth ER), and helps with detox and calcium storage

Connected to the nuclear envelope

Rough ER

Makes proteins, helps fold and modify them, send them to Golgi in vesicles

Has ribosomes attached (that’s why it looks “rough”)

Smooth ER

Makes lipids, Detoxifies harmful substances, Stores calcium

Has no ribosomes

Golgi apparatus

Modifies and ships proteins to the cell membrane

Functions:

1⃣ Modifies proteins and lipids received from ER.
2⃣ Sorts and packages them into vesicles for delivery.
3⃣ Adds carbohydrates to proteins/lipids (glycosylation) to form glycoproteins & glycolipids.

4⃣ Directs proteins to:

• Cell membrane

• Lysosomes

• Other organelles

• Secretion outside the cell

Lysosomes

Break down waste, damaged cell parts, and other materials using digestive enzymes

Vesicles

Transport materials between organelles or to/from ER > Golgi > its other destinations

Vesicle Transport = Tiny workers carrying boxes inside the store (cell)

• Vesicles are like delivery trucks or employees

• They move materials between departments (organelles)

• Or carry stuff to/from the "storefront" (cell membrane)

---

🔁 What vesicles do:

• Pick up stuff from the ER

• Drop it off at the Golgi

• Then deliver it to the membrane, lysosomes, or storage areas

They never float randomly — they move on tracks (cytoskeleton) or fuse with membranes on purpose.

What is the role of the cell membrane in the endomembrane system?

It’s the outer boundary that helps regulate what enters and exits the cell; part of the system's transport and signaling

Cell wall

Provides structure and support to the plant cell and protects against damage

(found in plants)

Large vacuole (stores water)

Stores water, nutrients and wast; helps maintain turgor pressure

Turgor pressure is the pressure of the water pushing against the inside of a plant cell’s cell wall.

It happens when the large central vacuole fills with water, causing the cell to swell slightly and stay firm.

Why it matters:

• Turgor pressure helps keep plants upright

• Without it (like in drought), plants get wilted and floppy

(found in plants)

Chloroplasts (photosynthesis)

Chloroplasts convert sunlight into chemical energy through photosynthesis

By chemical energy take away:

• They take light energy from the sun

• And turn it into energy stored in molecules (aka chemical energy)

Specifically:
They make glucose (sugar), which is a chemical energy source the plant can later use to make ATP through cellular respiration.

Plasmodesmata

Channels that connect plant cells and allow molecules like proteins and mRNA to pass between them

Exocytosis

vesicle fuses with the membrane to release contents outside the cell

Endocytosis

vesicle buds inward from the membrane to bring things inside

the membrane itself folds inward to create the vesicle.

Physical separation in cells

• Inside organelles

• Cytosol (fluid outside organelles but inside the cell)

Molecules are restricted to specific areas unless moved by vesicles

Cytosol

Fluid outside organelles but inside the cell

(In both Prokaryote and Eukaryote cells)

What is the cytosol vs cytoplasm?

Cytosol = fluid portion; Cytoplasm = cytosol + all organelles except the nucleus

Glycosylation

• As proteins and lipids pass through the Golgi → enzymes attach sugars to them.

• This creates:

  • Glycoproteins (protein + sugar)

  • Glycolipids (lipid + sugar)

Apoptoisis

Programmed cell death where the cell safely destroys itself to protect the organism

Chromosomes

carry genetic info

Cytoskeleton

Network of fibers inside cystoplasm

• Organizes the cell’s structures and activities, anchoring many organelles

plays a role in:

1. shape

2. cell motility

3. regulation of biochemical activities

Cystoskeleton components

1. Microfilament

• double helix of acting monomers

• Shape, movement, muscle contraction

2. Intermediate filament

• A strong fiber composed of intermediate filament protein subunits

• Strength, anchor nucleus

3. Microtubule

• A hallow tube formed from tubulin dimers

• Movement, shape, chromosome separation

Cristae

Inner membrane folds inside mitochondria

Matrix

Fluid-filled space inside mitochondria

Stroma

Fluid-filled space inside chloroplast

Thylakoid

Disc-like sacs inside chloroplast where light reactions happen

Granum

Stack of thylakoids (Disc-like sacs inside chloroplast where light reactions happen)

Autophagy

Process where lysosomes break down damaged organelles

Phagocytosis

Phagocytosis = “cell eating.”
It’s a type of endocytosis where the cell engulfs large particles (like bacteria, dead cells, or food).

A type of endocytosis where the cell engulfs large particles by surrounding them and bringing them into the cell.

Step-by-step:

1⃣ Cell extends its membrane outward → forms pseudopodia ("arms").
2⃣ Surrounds the particle.
3⃣ Membranes fuse and form a vesicle (phagosome) inside the cell.
4⃣ The vesicle often fuses with a lysosome to break down whatever was eaten.

Peroxisomes

Organelles that detox & break down fatty acids

Hydrolytic enzymes

Enzymes that break down molecules using water

• Found in lysososmes

Motor Proteins

Proteins that move things along cytoskeleton tracks

3 Types of cell junctions

• Desmosomes

• Tight junctions

• Gap junction

Desmosomes

Anchor cells together using strong proteins > gives tissues strength & flexibility

Example:
Skin, heart muscle → tissues that stretch or handle mechanical stress.

Tight junctions

Structures that connect cells together or allow communication

Example:
Intestines → keeps food/waste in gut from leaking into body.

Gap junctions

Form channels (pores) between cells → allows small molecules, ions, and signals to pass directly from one cell to another.

Example:
Heart muscle → allows electrical signals to pass quickly for synchronized beats.

Chart of permeability

Channel proteins (type of transport protein)

• Act like a tunnel/pore for molecules to pass through.

• Usually for small ions or molecules.

• Hydrophilic tunnel → allows polar/charged molecules to move through membrane.

Aquaporins (a type of transport protein)

• Special type of channel protein.

• Specifically for water transport.

• Allow rapid movement of water across membrane.

Carrier proteins (a type of transport protein)

• Bind to molecules.

• Change shape to shuttle molecules across the membrane (conformational change).

• Work for slightly larger or specific molecules.

Types of transport

• Passive transport (req no energy)

• Simple diffusion (small, hydrophobic molecules)

• Facilitated diffusion (Large, polar, or charged molecules) (They use transport proteins for this)

• Osmosis (Facilitated diffusion of water across selectively permeable membrane)

Simple diffusion

Small, hydrophobic molecules

Molecules move down their concentration gradient to establish equilibrium

Facilitated diffusion = PASSIVE transport aided by proteins

• Channel prteins

• Carrier proteins

Tonicity

The ability of a surrounding solution to cause a cell to gain or lose water

membrane potential

Established by having different concentrations of ions on each side of the membrane

(create potential energy for active transport)

Electrochemical gradient

Drives the diffusion of ions across a membrane

• 2 forces:

  1. Concentration gradient

  2. Membrane potential

Electrogenic pump (this establishes membrane potential)

Transport protein that generates voltage across a membrane; help store energy that can be used for cellular work

• Major electrogenic pump in animal cells = sodium-potassium pump

• Major electrogenic pump in plants, bacteria and fungi = proton pump

Sodium potassium pump (Primary active transport)

Establishes membrane potential in resting cells

Secondary Active Transport (Cotransport)

Uses energy from one molecule’s gradient to move another molecule.

Ex: H⁺ gradient helps move other substances.

Bulk transport

For moving large molecules (proteins, polysaccharides)

• Requires energy.

1⃣ Exocytosis:

• Vesicle fuses with membrane → releases contents outside.

2⃣ Endocytosis:

• Membrane folds inward to bring material in:

  • Phagocytosis ("cell eating"): engulfs large particles.

  • Pinocytosis ("cell drinking"): engulfs fluids.

  • Receptor-mediated endocytosis: highly specific intake using receptors.

Cell Junctions

allows
passage of signaling
molecules w/out crossing
plasma membrane

Cell-Cell Recognition

Direct contact between membrane-bound molecules.

Paracrine Signaling

Local regulators affect nearby cells (ex: growth factors).

Synaptic Signaling

Nerve cells release neurotransmitters to target nearby cells.

Autocrine Signaling

Cell signals to itself.

Endocrine signaling (Long-distance signaling)

Hormones travel via bloodstream to distant cells

3 stages of signal transduction

1⃣ Reception:

• Signal (ligand) binds to receptor protein.

• Binding is highly specific.

• Receptor shape changes (conformational change).

2⃣ Transduction:

• Signal relayed through proteins (relay molecules).

• Signal amplified like falling dominoes.

3⃣ Response:

• Cellular activity changes (e.g. movement, gene expression, division, death).

Stages of cell signal image

Receptors

• Receptors are proteins in or on the cell membrane (or sometimes inside the cell).

• They receive signals from outside the cell — these signals are called ligands (like hormones, neurotransmitters, etc).

Types of receptors

Receptor Type	Function
G Protein-Coupled Receptors (GPCRs)	Most common; 7-pass membrane proteins that activate G proteins.
Ion Channel Receptors	Act as gates for ions.
Intracellular Receptors	Inside cell; activated by small/hydrophobic ligands (ex: hormones).

G Protein-Coupled Receptors (GPCRs)

What it is:

• The most common type of receptor in your body.

• Found in the cell membrane.

What does "7-pass transmembrane protein" mean?

• The protein crosses (passes through) the membrane 7 times like a snake weaving back and forth.

• Basically, parts of the protein stick out both inside & outside the cell.

How it works:

1. A ligand (signal molecule) binds to the outside part of the receptor.

2. The receptor changes shape.

3. This activates a G protein inside the cell.

4. The G protein triggers other molecules inside to create a bigger response (like enzymes, second messengers, etc).

Purpose:

• Start many important processes: smell, taste, adrenaline response, etc.