Korean, Edit

Chapter 2. Cell Theory

Higher category : 【Biology】 Table of Contents

1. Overview

2. Structure 1: Endomembrane

3. Structure 2: Organelles of Cellular Metabolism

4. Structure 3: Broad meaning of cytoskeleton

5. Structure 4: Cytoplasm

1. Overview

⑴ Cell : Functional and structural unit of all living organisms.

⑵ Cell theory:

① George Palade: Father of cell biology. Personally developed the electron microscope.

② Content 1: All living organisms are composed of cells.

○ Cell: A compartment where life processes occur, surrounded by a cell membrane.

○ Cells are composed of organelles.

○ Organelles are composed of common biomolecules.

③ Content 2: All cells come from pre-existing cells.

○ Exception: Theory of chemical evolution.

⑶ Number of cells:

① The human body is composed of approximately 260 types of cells.

② The adult body is composed of approximately 100 trillion cells.

⑷ Cell size:

① Increasing factor: Cell size must be large enough to accommodate DNA, proteins, and other components necessary for cell activity.

② Decreasing factor (Surface-to-volume ratio hypothesis): Cell size must be small enough to increase the efficiency of cellular activities (∝ surface area ÷ volume).

③ The actual size of a cell is determined by the balance (trade-off) between the increasing and decreasing factors.

⑸ Types of cells: Prokaryotic cells and eukaryotic cells.

① Prokaryotic cells: Bacteria, cyanobacteria, etc.

○ The earliest type of cell on Earth.

○ Diameter: Approximately 1 μm to 10 μm.

○ Common features: Cell membrane, genome, ribosomes.

○ Unique features: Flagella, pili, cell wall, capsule surrounding the cell wall.

○ Difference 1: Lack of membrane-bound organelles.

○ Difference 2: Absence of a true nucleus. Instead, they have a nucleoid.

○ Difference 3: Most prokaryotic cells, such as E. coli, have one circular DNA molecule, while some have multiple circular DNA molecules.

② Eukaryotic cells: Animal cells, plant cells, fungi, most protists, etc.

○ Diameter: Approximately 10 μm to 100 μm.

○ Animal cells are round, while plant cells are rectangular.

○ Common features: Cell membrane, genome, ribosomes.

○ Some have flagella, pili, cell wall, and capsule surrounding the cell wall.

○ Difference 1: Presence of membrane-bound organelles.

○ Difference 2: Presence of a nuclear membrane.

○ Difference 3: Composed of multiple linear DNA molecules.

⑹ Types of cells: Animal cells and plant cells.

⑺ Cell structure:

① Endomembrane

② Organelles of cellular metabolism

③ Broad sense of cytoskeleton

④ Cytoplasm

2. Structure 1: Endomembrane

⑴ Nuclear envelope (plasma membrane or cell membrane)

① Composition: Lipids, proteins

② Functions: Material transport, shape maintenance, signal transduction, muscle contraction, nerve stimulation

○ Membrane structure: [Phospholipid head - Hydrophobic tail] + [Hydrophobic tail - Phospholipid head]

○ Spontaneous membrane formation by phospholipid bilayer: Phosphate heads face the aqueous surface, and hydrophobic tails point toward the interior of the membrane.

○ Fluid mosaic model

○ Membrane proteins move within the fluid phospholipid bilayer like a mosaic.

○ Revealed by FRAP (Fluorescence Recovery After Photobleaching) and FLIP (Fluorescence Loss In Photobleaching) experiments.

○ Lateral movement of the membrane: 10^5 to 10^7 times per second.

③ Membrane permeability:

○ Hydrophilic and hydrophobic substances diffuse through the membrane.

○ Selective permeability: Allows the passage of soluble molecules.

○ Reason: Hydrophobic molecules can pass through the cell membrane via simple diffusion, as the hydrophobic tails are longer than the hydrophilic heads.

④ Fluidity factor 1: Melting temperature (Tm)

○ Sudden temperature change that converts the rigid state of the cell membrane into a fluid state.

○ Related to gel-sol transition.

⑤ Fluidity factor 2: Restricted movement of membrane proteins attached to the cytoskeleton (e.g., caveolin).

⑥ Fluidity factor 3: Restricted movement of membrane proteins due to tight junctions.

⑦ Fluidity factor 4: Cholesterol

○ Cholesterol: Limits the movement of phospholipids, preventing excessive fluidity at high temperatures and preventing solidification at low temperatures, thereby maintaining membrane fluidity. Not permeable to hydrophilic substances.

○ Regulates fluidity by changing the content and length of unsaturated fatty acids (increases fluidity) in phospholipids according to temperature.

⑧ Asymmetry of phospholipids: Phospholipid vesicles produced in the endoplasmic reticulum (ER) are initially symmetrical. Asymmetry is created after vesicles fuse with the plasma membrane through the action of flippases and floppases.

○ Flippase: Enzyme that facilitates the movement of phospholipids from the outer layer to the inner layer.

○ Floppase: Enzyme that facilitates the movement of phosph

○ Examples of phospholipid asymmetry.

○ Disruption of asymmetry leads to cell death signaling. The flip-flop process is involved.

○ Flippase is also involved in membrane elongation in the process of vesicle formation.

⑨ Patch clamp method: Experimental technique used to study electrophysiology by attaching a patch to the cell membrane of living cells.

⑵ Nucleus

① Component 1: Nuclear envelope (double membrane). Numerous nuclear pores with selective permeability.

○ Outer membrane of the nuclear envelope is connected to the endoplasmic reticulum, and the inner membrane is supported by intermediate filaments.

○ Nuclear pores: Channels for nucleotides, amino acids, glucose, and other monomers.

② Composition 2. Nucleoplasm

③ Composition 3. Nucleolus: The part where chromatin is gathered

○ rRNA synthesis, telomerase synthesis, and assembly site of ribosomal subunits

○ No curtain. a strong look

○ the most easily observed structure inside a nucleus

⑶ ribosome

① Found in every cell

② a workstation for protein synthesis

③ Classified into free ribosomes and bound ribosomes

⑷ Endoplasmic reticulum (ER): A large network of membranes that extends into the cytoplasm while connected to the nuclear membrane

① Rough ER (RER): A vesicle embedded with ribosomes. Protein secretion

○ The part where the bending occurs in the vesicle is smooth without ribosomes

○ Function 1. Formation of vesicles and cell membranes

○ Function 2. Primary glycosylation: N-linked protein glycosylation. Asparagine, etc. are involved

○ Example: Mannose, blood type

○ Function 3. Removal of the vesicle signal sequence: It takes place before protein is delivered to the vesicle, but it is generally considered to be the role of a rough vesicle

○ Function 4. Disulfide Combination

② Smooth ER (SER): Ribosomal-free vesicle

○ Function 1. Lipid and phospholipid synthesis, extension of fatty acid length, and unsaturated fatty acid

○ Usually synthesized from saturated fat to unsaturated fat

○ Late stage live vesicles synthesize sterols

○ Function 2. Calcium storage (Ca2+ pump) and release (IP3 dependent Ca2+ channel)

○ Example: Sarcoplasmic reticulum (SR)

○ Function 3. Cytochrom p450: Toxic removal. Extracellular release by attaching -OH group to fat-soluble material. OH group increases reactivity

○ Function 4. Control of blood sugar level: glycogen phosphate

○ Function 5. Glucose New Synthesis: glucose-6-phosphatase (only in the liver)

③ alcohol breakdown and hangover

⑸ Golgi apparatus: Absent in red blood cells

① Structure

○ Cisternae structure: CGN (cis-Golgi network) + medial + TGN (trans-Golgi network)

○ One side continuously receives (cis) while the other side continuously sends vesicles (trans)

② Formation

○ Cisternal maturation model: The trans portion of the Golgi apparatus disappears, and cis becomes trans. Vesicles from the endoplasmic reticulum become cis.

○ Vesicular transport model: Small molecules are transported directly through vesicles without undergoing Golgi maturation, resulting in faster transport.

③ Secretion pathways

○ Constitutive secretory pathway: Continuous secretion of membrane proteins and extracellular matrix (e.g., collagen, proteoglycans)

○ Signal-mediated secretory pathway: Secretion of proteins mediated by hormones

○ Lysosome pathway

④ Function 1: Protein sorting - Lysosomes

⑤ Function 2: Secretion to intracellular destinations

⑥ Function 3: Protein cleavage → Activation of proteins - Insulin cleavage, digestive enzyme cleavage

⑦ Function 4: Secondary glycosylation - O-glycosylation (O-linked protein glycosylation). Involves serine and threonine.

○ Example of O-glycosylation: O-GlcNAcylation

○ Examples of products: Core proteins and chondroitin sulfate, keratin sulfate

⑧ Function 5: Synthesis of pectin and hemi-cellulose in plant cells

○ Cellulose is produced by cellulose synthase in plant cell walls.

⑨ Function 6: Generation of exosomes

⑩ Function 7: Other post-translational modifications after translation

○ O-sulfation

○ Phosphorylation

⑹ Lysosome

① Single-membrane vesicles containing over 50 types of acid hydrolases

○ Lipofuscin, etc.

○ Plant cells do not have lysosomes; vacuoles serve as substitutes.

② Function

○ Digestion of target molecules, damaged receptors, and damaged organelles

○ Referred to as a “suicide capsule”

③ 1st step: Immature lysosomes acquire a 5-carbon sugar called mannose (glycosylation) on the surface of immature lysosomal hydrolases in the trans-Golgi network. Involves flippase.

④ 2nd step: Immature lysosomal hydrolases move from the trans-Golgi network to the Golgi cis-Golgi network.

⑤ 3rd step: Mannose in the Golgi apparatus is phosphorylated by UTP, resulting in M-6-P (mannose-6-phosphate).

⑥ 4th step: When M-6-P reaches the Golgi trans, it binds to M-6-P receptors on the membrane surface.

○ Binding of M-6-P to receptors leads to the delivery of hydrolases into the lysosome.

⑦ 5th step: Proteins tagged with mannose are enclosed in vesicles and bind with mature endosomes that have budded off from the cell membrane.

○ Endosomes: Vesicles where endocytosis occurs. They have H+ pumps.

○ If there is a problem with the enzyme that tags proteins with M-6-P, acidic hydrolases cannot be sent to the lysosome.

⑧ 6th step: Lysosome maturation: When the internal pH reaches 5 due to the functioning of H+ pumps, M-6-P is released from the receptor.

⑨ 7th step: Bacteria or other substances enter the cell through phagocytosis, forming a phagosome.

⑩ 8th step: When the phagosome containing organic material encounters the lysosome, it becomes a phagolysosome.

○ Lysosomal hydrolases inside the lysosome degrade all organic material.

○ The low pH inside the lysosome aids in hydrolysis.

⑪ 9th step: The remaining debris is expelled from the cell through exocytosis.

⑫ Inhibitors

○ Mannan: Inhibitor of mannose receptor-mediated endocytosis.

○ Bafilomycin: Lysosomal inhibitor.

⑬ Lysosomal diseases

○ Mechanism: Decreased lysosomal hydrolases → Accumulation of degradation products → Increased lysosome concentration → Influx of water → Lysis → Damage to surrounding cells

○ Example 1: Tay-Sachs disease: Newborns experience blindness or hearing loss.

○ Example 2: Pompe’s disease: Occurs in muscles.

○ Example 3: gouty: Related to acidity

⑺ Vacuole

① Characteristics

○ Generated from the golgi apparatus with similar functions/origins as lysosomes

○ Found only in plant cells

○ Focuses on recycling rather than digestion

○ Plant cells lack lysosomes and vacuoles take their place

② Type 1: Storage vacuole

③ Type 2: Contractile vacuole: Protozoa have contractile vacuoles to expel internal water

④ Type 3: Central vacuole: Stores various molecules including water, pigments, digestive enzymes, toxins, and waste. Helps maintain internal pressure and supports plant structure

⑻ Peroxisome: Prevents the formation of oxygen radicals by breaking down hydrogen peroxide

① Single-membrane vesicles that contain about 50 different enzymes, including enzymes involved in the glyoxylate pathway

② Generation: Generated from vesicles. Golgi apparatus does not generate peroxisomes.

③ Enzymes

○ Superoxide dismutase (SOD): 2O₂^- + 2H⁺ → O₂ + H₂O₂

○ Catalase: 2H₂O₂ → 2H₂O + O₂. Not found in other cell organelles.

④ Reaction

○ Reactive oxygen species (ROS): Highly reactive chemical species generated from oxygen

○ Radical: Superoxide (O₂^·-), hydroxyl radical (^·OH)

○ Nonradical: Singlet oxygen (1O2), hydrogen peroxide (H2O2)

○ ROS cascade reaction

○ O₂ + e^- → O₂^·-

○ 2H⁺ + 2O₂^·- → H₂O₂ + O₂

○ H₂O₂ + e^- → HO^- + ^·OH

○ 2H⁺ + 2e^- + H₂O₂ → 2H₂O

○ Fenton reaction: Iron ions can generate ROS

○ Fe²⁺ + H₂O₂ → Fe³⁺ + HO● + OH^-

○ Fe³⁺ + H₂O₂ → Fe²⁺ + HOO● + H⁺

○ HO● + HOO● + H₂O → 2H₂O₂

○ Haber Weiss reaction : If there is a free ion in the amount of catalyst, the next reaction will occur

⑤ Functions

○ Oxidation of fatty acids

○ Removal of H₂O₂

⑥ Animal cells: 25-50% of beta oxidation occurs in peroxisomes, the rest occurs in the intermembrane space of mitochondria

○ Liver cells have more peroxisomes compared to other cells

⑦ Plant cells: 100% of beta oxidation occurs in peroxisomes

⑧ Zellweger syndrome: Multiple empty peroxisomes are found

⑼ Glyoxysome

① Peroxisomes found only in germinating or germinated seeds, with different enzymes

② Peroxisomes and glyoxysomes

○ Exist as peroxisomes in light conditions suitable for photosynthesis

○ Exist as glyoxysomes in conditions where photosynthesis is not possible

③ Glyoxylate cycle: A metabolic pathway that converts fat to sugar in seed endosperm

⑽ Mesosome

① Organelle found only in bacteria

② Part of the cell membrane that forms a folded structure or a stalk-like membrane organization

⑾ Lipid droplet (LD)

① Surrounded by a phospholipid monolayer

② Generally 0.1-5 μm in size, 100 μm in fat cells

③ Formation

○ Formation of triglycerides inside LD: Involves DGAT (diacylglycerol acyltransferase) in the endoplasmic reticulum (ER)

○ Formation of cholesterol esters inside LD: Involves ACAT (acyl-CoA:cholesterol acyltransferase) in the ER

④ Functions

○ Storage of lipid esters

○ Defense against lipotoxicity

○ Lipolytic activity: Involves ATGL (adipose triglyceride lipase), HSL (hormone-sensitive lipase), MAGL (monoacylglycerol lipase)

○ Storage site for preventing protein degradation

○ Stores toxic saturated fatty acids under hypoxic conditions: These acids are reduced in the absence of oxygen, gaining hydrogen and losing oxygen

⑤ Disposal

○ Lysosomal acid lipase (LAL)

○ Chaperone-mediated autophagy (CMA)

○ Heat shock protein 70 (HSP70): Lysosomal proteolysis mediated by HSP70

○ LAMP-2A (lysosome-associated membrane protein 2A)

3. Structure 2: Metabolic cell organelles

⑴ Mitochondria: Energy-generating cell organelles in eukaryotic cells

① Double-membrane structure: Outer membrane, inner membrane, and intermembrane space

② Outer membrane

○ Pores (open channels) exist: Substances smaller than 5,000 Da (e.g., ions) freely diffuse

○ TOM, SAM (sorting and assembly machinery) are present

○ TSPO (translocator protein)

○ Transport of cholesterol into the mitochondria

○ Utilized in porphyrin movement, heme synthesis, steroid synthesis, etc.

○ Involved in apoptosis, proliferation, etc.

○ Outer membrane proteins used as biomarkers for neuroinflammation, tumors, etc.

○ High concentration of H+ in the intermembrane space cannot exit through the pores

③ Inner membrane

○ Resembles the primitive plasma membrane of prokaryotes

○ Limited substance transport with cardiolipin. Decreases membrane permeability. Mainly exists where the electron transport chain is present.

○ Types of transport proteins: H+-pyruvate symport (active transport), H+-Pi symport, succinate transporter, ADP-ATP antiport, shuttle, ATPase, citrulline and ornithine (freely diffuse)

○ TIM, OXA (oxidase assembly) are present

④ Matrix

○ Mitochondrial DNA (circular), RNA, ribosomes (70S)

○ Mitochondrial Genetics

○ 50-75% of β oxidation occurs in animal cells

⑤ Cristae: Folded structures inside the mitochondria

⑥ Intermembrane space

○ Mia40, etc., are present

⑦ Characteristics

○ Mitochondria can replicate themselves

○ Carbon diffusing into the mitochondria through simple diffusion can be up to 12-C

⑧ Functions

○ ATP production

○ Fatty acid oxidation

○ Acetyl-CoA synthesis

○ Ketone synthesis

⑵ Chloroplast: Not present in animal cells

① Double membrane (outer membrane, inner membrane), intermembrane space

② Stroma

○ Chloroplast DNA (circular), RNA, ribosomes (70S)

○ Cytosolic proteins have primary signal sequences that target them to the stroma and remove signal proteins.

③ Granum: Stacked (lamellar structure) portion where thylakoids are present

○ Stroma lamellae: Region in contact with the stroma on the thylakoid

○ Granum lamellae: Region in contact with the granum on the thylakoid

④ Thylakoid: Unit where photosynthesis occurs. Contains cardiolipin in the membrane.

○ Cytosolic proteins have secondary signal sequences that target them to the thylakoid membrane and remove signal proteins.

○ ATP synthase is located in the inner mitochondrial membrane and thylakoid membrane.

○ Mitochondria: Acidic environment → Placed in an alkaline environment initiates ATP synthesis.

○ Chloroplasts: Alkaline environment → Placed in an acidic environment initiates ATP synthesis.

⑤ Functions

○ NADPH, ATP production

○ Glucose synthesis

○ Fatty acid synthesis

⑥ (Note) Chloroplast genomics

⑦ (Note) Leucoplast: No chlorophyll, converts glucose into starch. Present in plant cells. The white portion of fruits and tubers.

⑧ (Note) Plastids (colored plastids)

○ Contains carotenoids (orange) and xanthophylls (yellow)

○ Found only in plants; abundant in carrots, peppers, tomatoes, etc.

○ Involved in fatty acid synthesis, pentose phosphate pathway

⑶ Cell Fractionation

① Cell homogenate → Nuclei + Supernatant: 1000 g, 10 minutes

② Supernatant without nuclei → Chloroplasts + Supernatant: 3000 g, 10 minutes

③ Supernatant without chloroplasts → Mitochondria + Supernatant: 20000 g, 10 minutes

4. Structure 3. Broad meaning of cytoskeleton

⑴ Cytoskeleton: Present only in eukaryotes, divided into microtubules, intermediate filaments, microfilaments

⑵ Microtubules: Diameter of 25 nm. Present in animal and plant cells.

① Function: Maintains cell shape, intracellular transport, formation of cell structures

○ Centrioles, flagella, cilia

② Composition 1: Tubulin heterodimers comprising α-tubulin and β-tubulin

○ (-) End (negative end): End where α-tubulin terminates

○ Faster depolymerization rate

○ (+) End (positive end): End where β-tubulin terminates

○ Faster polymerization rate

○ Both assembly and disassembly rates are faster at the (+) end

○ Neurons have (-) end at the cell body and (+) end at the axon

○ Structure: Protofilaments composed of tubulin polymers form a cylindrical structure

③ Composition 2: Motor proteins capable of moving along microtubules

○ Dynein: Moves from a distant point to a nearby point from the centrosome, involved in protein transport in the nucleus

○ Kinesin: Moves from a nearby point to a distant point from the centrosome, involved in exocytosis protein transport

○ Myosin

④ Polymerization experiment: Nucleation - Elongation - Steady state

○ α-tubulin: GTPase activity

○ β-tubulin: Can bind to GTP or GDP

○ When the GTP bound to the β-tubulin at the (+) end is hydrolyzed to GDP, a new β-tubulin (GTP) binds to α-tubulin

○ GTP cap: β-tubulin at the (+) end is in the GTP state, while the remaining β-tubulins are in the GDP state

○ Microtubule formation over time: Tubulin heterodimers, GTP, Mg2+ as materials. Can grow up to 25,000 nm

○ Treadmilling: (-) end shortens while (+) end elongates

○ Catastrophe

○ Rescue

⑤ Tension-compression length experiment

○ Catastrophe

○ Rescue

⑥ Type 1: Centriole

○ Not present in prokaryotes, fungi, or plant cells. The exact necessity has not been determined

○ Structure: 9 microtubule triplets, ring-shaped structure with a funnel shape

○ Centrosome: 2 centrioles in the S phase become perpendicular and attach to each other, causing microtubules to elongate and form the spindle apparatus

○ Basal body: Modified form of the centriole. Consists of 9 microtubule triplets. Through elongation, forms flagella and cilia

○ Flagella, cilia: 9 + 2 doublets

○ Function: Cell motility, movement of fluids

○ Principle: When a dynein attached to one doublet walks on an adjacent doublet, the two doublets bend

○ Primary Ciliary Dyskinesia:

○ Genetic condition where cilia are absent resulting in impaired ciliary movement in the respiratory tract

○ Impairs respiratory function

○ (Reference) Flagella of prokaryotes: Move by rotational force due to a hydrogen ion gradient

○ Similar mechanism to ATPase

○ Wider than flagella of eukaryotes

○ Unlike eukaryotes, not covered by a primitive plasma membrane

○ Composed of flagellin, not tubulin

⑦ Microtubule destabilizing agent: Destabilizes microtubules during their synthesis, hindering their function

○ vinca alkaloid: vinblastine, vincristine, vinorelbine, vindesine, vinflunine

○ colchicine: Used for polyploidization in plant breeding. Cannot be used as an anticancer agent because it inhibits leukocytes.

⑧ microtubule stabilizing agent: Stabilizes microtubules when they are disassembled, impeding microtubule function.

○ taxol: Extracted from the Pacific yew tree. Used as an anticancer agent.

○ paclitaxel, docetaxel, eleutherobins, epothilones, laulimalide, sarcodictyins

⑨ microtubule breaking agent

○ nocodazole: Destroys microtubules.

⑶ intermediate filament: Diameter of 8 to 12 nm.

① Functions

○ Maintains cell shape and positions organelles: Nuclear lamins, etc.

○ Desmosome: Supports cell-cell adhesion.

○ Hemidesmosome: Supports cell-ECM adhesion.

○ Present only in animal cells.

② Subunits

○ Structure: N-terminus + α-helix + C-terminus, 32 subunits form one filament.

○ Intermediate filaments contain specific proteins depending on the cell type.

○ Type 1: Nuclear lamins - Maintain nuclear envelope structure.

○ In animal cells, the nuclear lamina consists of lamin proteins.

○ In many protists, fungi, and plant cells, the inner surface of the nuclear envelope is unrelated to lamins.

○ Lamin proteins anchor the nucleus in place.

○ Type 2: Keratin - Observed in the cytoplasm, abundant in epithelial cells.

○ Keratin intermediate filaments connect the basal layer of the epidermis to the epidermis, protecting the dermis.

○ Skin, hair, nails, etc., are mostly composed of dead cells filled with keratin.

○ Type 3: Vimentin - Abundant in mesenchymal cells, used as a marker.

○ Type 4: Desmin - Abundant in muscle cells.

○ Type 5: Neurofilaments - Observed in axons of neurons.

○ Type 6: GFAP (glial fibrillary acidic protein) - Abundant in glial cells.

③ Characteristics 1: Resistant to destruction, except during cell division and blistering disorders.

④ Characteristics 2: Calcium is involved in stabilizing intermediate filaments.

⑤ Tension-extension experiments

○ Catastrophe

○ Rescue

⑷ microfilament: Diameter of 7 nm.

① Composed of actin filaments and myosin filaments.

○ Actin filaments: Account for 10-15% of cellular proteins.

○ Myosin filaments: Much less abundant.

② Functions: Perform functions not only in muscle cells but also in non-muscle cells.

○ Maintains cell shape: Concentrated below the plasma membrane. Mainly associated with cadherins and actin filaments’ attachment.

○ Signaling between the cell surface and the nucleus: Mainly associated with integrins and actin filaments’ attachment.

○ Adherens junctions, adhesion belts, focal contacts, etc.

○ Fixes the centrosome during cell division.

○ Actin filaments in muscle: ATP-dependent. Myosin, a motor protein, interacts with actin.

○ Non-muscle cell movements: Amoeboid locomotion, etc.

○ 1^st. Inside the amoeba, the cytoplasm is in the sol state, and the outside is in the gel state.

○ 2^nd. The amoeba flows the internal fluid in the direction of pseudopod formation, followed by gelation.

○ 3^rd. In the opposite direction of pseudopod formation, actin contracts and detaches from the substrate.

○ Cytoplasmic streaming in plant cells.

○ Contraction ring in animal cell division.

③ Structure 1: Monomer - Actin monomer.

○ (-) end (minus end): Higher polymerization rate.

○ (+) end (plus end): Higher polymerization and depolymerization rates than the minus end.

○ Microfilaments form a double helix with a repeating period of 37 nm, consisting of two actin monomers twisted together.

④ Structure 2: Fimbrin - Connects actin filaments to each other, making them more resistant to tension and less elastic.

○ Example: Microvilli are formed by actin.

⑤ Polymerization experiment: Nucleation - Elongation - Steady state.

○ 1^st. ATP-bound G-actin attaches to the plus end of F-actin, forming actin filaments.

○ 2^nd. ADP-bound G-actin has weak interactions between monomers and easily dissociates from the polymer.

○ 3^rd. Dissociated ADP-bound G-actin binds to ATP, replacing ADP, and attaches to the growing end of actin filaments.

○ Polymerization experiment: Faster initial polymerization rate in the presence of nuclei.

○ Critical concentration: Concentration of G-actin at equilibrium with actin filaments.

○ Actin filaments can form above the critical concentration.

○ The critical concentration at the plus end, i.e., the concentration of G-actin that polymerizes or depolymerizes (Cc+), is low (strong attachment).

○ The critical concentration at the minus end, i.e., the concentration of G-actin that polymerizes or depolymerizes (Cc-), is high (weak attachment).

○ If the concentration of G-actin is higher than Cc+ and lower than Cc-, the plus end undergoes polymerization and the minus end undergoes depolymerization.

○ Treadmilling phenomenon: The appearance of microfilaments moving due to polymerization and depolymerization at the mentioned concentrations.

⑥ Tension-extension experiments

○ Catastrophe

○ Rescue

⑦ Polymerization promoters and inhibitors

○ Polymerization promoter: Profilin

○ Polymerization inhibitor: Thymosin, cytochalasin

○ Depolymerization inhibitor: Jasplakinolide

⑸ Cell wall

① Found outside the plasma membrane in plant and bacterial cells.

② Abundant in cellulose.

③ Functions to support the plant body, which stands upright against gravity.

④ Plasmodesmata: Cell junctions that allow signaling and material exchange between plant cells.

○ Cell junctions between plant cells that can send and receive signals and substances

○ The protoplasmic reticulum is connected

○ Plant virus moves to adjacent cells via protoplasmic contact

⑤ Primary cell wall: Cellulose + pectin + hemicellulose.

⑥ Secondary cell wall: Primary cell wall + lignin. Thicker.

⑹ Extracellular matrix (ECM): Only present in animal cells. Functions in support, adhesion, movement, and regulation.

① Basal lamina: Sheet-like structure surrounding epithelial cells.

○ Mainly composed of the multi-adhesive protein laminin.

② Collagen: Strong fibers that connect cells.

○ Present in all animals except sponges. Collagen accounts for one-third of the proteins in vertebrates.

○ Formation:

○ 1^st. Released in the form of procollagen.

○ 2^nd. Some amino acids at the N- and C-termini of procollagen are cleaved by procollagen peptidases.

○ 3^rd. Crosslinking occurs, forming insoluble complexes (collagen).

○ Structure:

○ Each α chain, consisting of 100 amino acids, is in a left-handed helix.

○ Three α chains mix to form a triple helix with a plateau structure: Length of 280 nm, diameter of 1.5 nm.

○ The third amino acid of each α chain is glycine, which is essential for the triple helix formation.

○ Bundles of three α chains form collagen fibers: Diameter of 1-20 μm.

○ Each α chain is originally right-handed but hindered by unique amino acid composition, resulting in a left-handed helix.

○ Collagen fibers are made up of multiple collagen fibrils.

○ Type

○ Type I: Secreted by osteocytes and others. Found in bones and ligaments.

○ Type II: Secreted by chondrocytes.

○ Collagen in cancer cells

○ Normal fibroblasts express both COL1A1 and COL1A2.

○ Therefore, the collagen produced by normal fibroblasts consists of two α1 chains and one α2 chain.

○ In cancer fibroblasts, COL1A1 is expressed while COL1A2 is suppressed by DNA methylation.

○ Therefore, the collagen produced by cancer fibroblasts is composed of three α1 chains.

③ Elastin

○ Engaged in elasticity, bending, etc

○ Observation on ligaments, vascular walls, lung tissue, epidermis, and force load

○ Rarely present in tendon and limb ligaments

○ Proportion significant in elastic ligaments such as ligamentum flavum

④ Integrin: Transmembrane proteins

○ Induces cell-matrix adhesion through the integrin motif containing the RGD sequence.

○ RGD: Arginine - Glycine - Aspartic Acid

○ Consists of 18 α subunits and 8 β subunits, both having various forms.

Table. 3. Subunits of integrin</center> > ○ **Function 1:** Anchors cells by binding fibronectin outside the cell and actin microfilaments inside the cell. > ○ **Function 1-1:** Connectivity with fibronectin >> ○ Fibronectin and integrin are connected by non-covalent binding. >> ○ Since it is reversible binding, it is involved in attaching cells to the basement membrane or moving them to other locations. >> ○ Involved in plantar movement. > ○ **Function 1-2:** Connectivity with actin: Connected to multiple actin filaments, providing cushioning against impact. > ○ **Function 2:** Transmits intracellular changes to the outside of the cell. > ○ Signal transduction by integrin.

Figure. 12. Signal transduction by integrin > ⑤ Fibronectin: Binds with integrin. Involved in signal transduction. > ⑥ Vitronectin: Performs functions similar to collagen and elastin. > ⑦ Transmembrane proteoglycan: Involved in cell-matrix adhesion. >> ○ Connected to transmembrane receptors without RGD sequence and low affinity transmembrane proteoglycan. >> ○ Transmembrane proteoglycan binds to matrix proteoglycan, collagen, growth factors, etc. > ⑧ CAM (cell-cell adhesion molecule): Involved in cell-cell adhesion. >> ○ Ca²⁺ independent >> ○ Example: N-CAM acts on nerve cells as an Ig-superfamily CAM. > ⑨ Cadherin: Involved in cell-cell adhesion. >> ○ Ca²⁺ dependent >> ○ Acts as a homodimer. >> ○ Example: E-cadherin (epithelial cadherin)

Figure. 13. Comparison of CAM and cadherin > ⑩ Glycoprotein >> ○ Important for cell-cell recognition. >> ○ Exposed on the outer side of the cell membrane. >> ○ Example 1: Lectin >> ○ Example 2: Selectin >> ○ Example 3: Galectin >> ○ Example 4: Hemagglutinin >> ○ Example 5: Neuraminidase > ⑪ Laminin >> ○ Protein present in the basal lamina of the basement membrane. >> ○ Forms a network of three short arms consisting of α chain, β chain, and γ chain, enabling binding between ECM and cells. > ⑫ Dystrophin >> ○ A connecting protein between the muscle cell membrane and the cytoskeleton that regulates calcium ion channels. >> ○ Connects actin filaments and membrane glycoproteins, stabilizing the structure of muscle cells. > ⑬ Fibrillin > ⑭ Tenascin > ⑮ Matrigel >> ○ Commercialized ECM that induces cell differentiation and morphological changes. >> ○ Forms a grid-like network in epithelial cells and endothelial cells. ⑺ Junctions

Figure. 14. Types of junctions
> ① Type 1: Tight junction >> ○ **Function 1:** Seals the space between cells, preventing the passage of substances. >> ○ **Function 2:** Involved in the polarization of membrane proteins (e.g., in the digestive tract). >> ○ Transmembrane tight junctional proteins present in the cell membranes of adjacent cells form continuous bands, leading to **membrane fusion**. > ② Type 2: Anchoring junction: Forms cell-cell and cell-matrix connections through the cytoskeleton. >> ○ Composed of intracellular attachment proteins and transmembrane linker glycoproteins. >> ○ Type 2-1: Anchoring junction using intermediate filaments. >> ○ Type 2-1-1: Desmosome: Connects cells to each other. >>> ○ Prevents tearing even under strong shear stress (e.g., in the skin, muscles). >>> ○ Involves plaque and cadherin. >>> ○ Cadherin: Stabilized by calcium ions. N-cadherin (neural), P-cadherin (platelet), E-cadherin (skin). >>> ○ Keratin: Intermediate filament. Holds plaques together. >>> ○ Desmosomes also increase during epithelial cell differentiation. >>> ○ Characteristic: Unlike tight junctions, **membrane fusion** does not occur. >> ○ Type 2-1-2: Hemidesmosome: Connects cells to the matrix. >> ○ Type 2-2: Anchoring junction using actin filaments. >>> ○ Cell-cell junction: Adhesion belt, etc. >>> ○ Cell-matrix junction: Focal contact, etc. > ③ Type 3: Communicating junction >> ○ Type 3-1: Gap junction >>> ○ Forms cylindrical structures where adjacent cell membranes meet, creating channels between cells through which small molecules can pass. >>>> ○ Cell membranes are not connected. >>> ○ Function: Exchange of substances between cells. Only allows small molecules to pass. >>> ○ Connexon: Each channel is composed of connexins. >>>> ○ Connexin: Molecular weight ranges from 24,000 to 46,000. >>>> ○ Gap junctions open and close depending on the structural changes of connexin proteins. >>> ○ Gap junctions can also be found in electrical synapses. >>> ○ Type 3-2: Chemical synapse >>> ○ Type 3-3: Plasmodesmata: Exists only in plant cells.

## **5. Structure 4.** Cytosol ⑴ Function 1: NADPH production: Pathway where malate becomes NADPH in the oxidative pentose phosphate pathway, C4 plants, etc. ⑵ Function 2: Synthesis of fatty acids ⑶ Function 3: Synthesis of isoprenoids and steroids
--- *Input: January 15, 2019, 14:53* *Modified: May 2, 2020, 21:23*