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cellular organization

Cell Structure and Basic Components

  • A cell is the smallest, basic unit of life. It has three main parts:

    • Cell membrane – controls movement of substances in and out of the cell.

    • Cytoplasm – the fluid portion of the cell containing organelles like the mitochondria, Golgi complex, endoplasmic reticulum

    • Nucleus – contains the cell’s genetic material.

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  • Overall concept: the cellular level of organization includes the plasma membrane, cytoplasm with organelles, and nucleus, which together enable metabolism, growth, and reproduction.

  • Rough ER- has ribosomes

  • Smooth ER- no ribosomes

  • Lysosome- degrade anything thats not needed for the cell.

  • Centrosome- pulls the chromosomes apart during cell division.

Plasma Membrane and Phospholipid Bilayer

  • The cell membrane is a phospholipid bilayer with many molecular components, including proteins and cholesterol, some with carbohydrate groups attached.

  • Phospholipid structure:

    • Polar phosphate head: hydrophilic.

    • Non-polar lipid tail: hydrophobic.

  • The bilayer consists of two adjacent sheets of phospholipids arranged tail-to-tail. The hydrophobic tails form the interior; polar heads contact the intracellular and extracellular fluids.

  • Additional components include: proteins, cholesterol, and carbohydrate groups (glycoproteins/glycolipids) attached to the membrane.

  • Functions include forming a barrier and facilitating selective transport and communication.

  • selectively permeable

  • Regulates what’s allowed into the cell, keep unwanted substances out.

  • The head of the phospholipid is hydrophilic, while the non-polar lipid tail with fatty acids is hydrophobic.

  • Channel proteins and integral membrane proteins are what allow substances in & out the cell.

Transport Across the Membrane: Why It Matters

  • The transport of solutes across the cell membrane is essential for metabolic processes, such as:

    • Maintaining cell size and volume.

    • Exchange of gases (e.g., oxygen) and removal of wastes (e.g., carbon dioxide).

    • Movements are always down a concentration gradiant

  • Two main transport types:

    • Passive transport: movement without cellular energy (ATP). Based on concentration gradient. Includes Simple Diffusion and Facilitated Diffusion.

    • Active transport: movement using energy from ATP like for Sodium-potassium pumps.

Simple Diffusion and Facilitated Diffusion

  • Simple diffusion:

    • The cell membrane is semi-permeable; only some ions pass down a concentration gradient (from high to low concentration).

  • Facilitated diffusion:

    • For substances that cannot pass by simple diffusion due to size, charge, or polarity.

    • Requires proteins and does not use ATP.

    • Two protein types:

    • Channel proteins: less selective than carrier proteins, usually takes based on size & charge

    • Aquaporins (allow water only).

    • Carrier proteins: bind specific molecules via binding sites and shuttle them across the membrane; more selective.

    • Example: Movement of glucose into the cell for ATP production.

  • Glucose uses facilitated diffusion to enter cells

  • Pneumonia would increase the thickness of the respiratory membrane, which would decrease the rate of diffusion of oxygen and carbon dioxide.

Real-Life Channel Proteins: CFTR and Salt Balance

  • When you eat salty foods, blood salt concentration rises.

  • Water balance is restored by water movement through Aquaporins to balance osmolarity and maintain blood pressure.

  • Channel: CFTR (Cystic Fibrosis Transmembrane Conductance Regulator): a chloride channel.

    • Mutations block chloride and water transport across epithelial cells.

    • Result: Thick, sticky mucus builds up in lungs and digestive tract → breathing problems, chronic infections, poor nutrient absorption.

Osmosis Concepts and Tonicity

  • Concentration of Solutions (effects on cells):

    • Hypertonic: solute concentration inside the cell is higher than outside; water moves out; cells shrink.

    • Isotonic: solute concentration inside equals outside; cells are happy.

    • Hypotonic: solute concentration is lower inside; water moves in; cells may swell or burst.

Endocytosis and Exocytosis

  • Endocytosis (active transport): taking into the cell then destroying it.

    • Three forms:

    • Phagocytosis: nonselective uptake of large particles into the vacuole.

    • Pinocytosis: uptake of small particles in fluid into the vesicle.

    • Receptor-mediated endocytosis: highly selective uptake triggered by ligand binding to receptors. When external receptors bind a specific ligand, the cell responds by endocytosing the ligand.

  • Exocytosis: reverse of endocytosis. Vesicles fuse with the cell membrane to release contents into the extracellular space.

    • Enzymes are enclosed in vesicles is to keep them protected from things that want to destroy them.

      • Example: Digestive enzymes from pancreatic and stomach cells are released via exocytosis.

  • Pancreatic acinar cells produce and secrete digestive enzymes; secretory vesicles contain enzymes that are exported by exocytosis.

The Eukaryotic Cell and the Endomembrane System

  • Eukaryotic cells have an endomembrane system: a group of membranous organelles that regulate protein trafficking and metabolism.

    • Key components include:

    • Nucleus

    • Endoplasmic reticulum (ER)

    • Golgi apparatus

    • lysosomes (derived from Golgi)

    • Also includes the plasma membrane and vesicles that shuttle between organelles.

  • Cytosol: An aqueous, water-based solution that bathes organelles.

  • Extracellular fluid: outside the cell.

  • Intracellular fluid (cytosol) vs extracellular fluid distinction.

  • Nucleus: stores genetic material (DNA); site of DNA replication and RNA synthesis (transcription).

  • Nuclear envelope, chromatin, nuclear pores, nucleolus (rRNA synthesis).

Endoplasmic Reticulum (ER) and Its Roles

  • ER is a winding network of thin membranous sacs near the nucleus.

  • Rough ER: studded with ribosomes; sites of protein synthesis (translation). receive info from nucleus.

  • Smooth ER: synthesizes phospholipids and steroid hormones; regulates intracellular Ca++; metabolizes some carbohydrates; breaks down certain toxins.

  • ER lumen: internal space of the ER.

Golgi Apparatus and Lysosomes

  • Golgi apparatus processes products from the rough ER; also produces new organelles called lysosomes. From Rough ER through transport vesicles to golgi Apparatus.

    • Transport vesicle: carries products from rough ER to golgi

    • Secretory vesicle: carries finished golgi products outside the plasma membrane.

      • Two faces of Golgi:

      • Cis face: Receives newly made proteins and lipids from the ER

      • Trans face: Sorts, modifies, and packages proteins and lipids into vesicles for transport to their final destinations.

  • Functions:

    • Modifies, packages, and tags proteins and lipids for delivery to their destinations.

    • Some products are exported from the cell via exocytosis.

  • Lysosomes: enzymatic compartments produced by the Golgi; involved in intracellular digestion. produce the enzyme lysozyme that degrade bacteria

Mitochondria: Energy Production

  • Mitochondria are the energy-conversion factories of the cell.

  • Mitochondria has its own DNA.

  • The heart, brain, and skeletal muscles require the most energy, therefore are the first organ systems to go down when mitochondrial diseases occur.

  • Structure: two lipid bilayer membranes.

  • Cristae: the folds in the inner-membrane of the mitochondria, where ATP molecules are produced.

  • Inner membrane contains molecules that drive ATP production, the cell’s major energy currency.

The Nucleus and Genetic Material

  • The nucleus is the control center of the cell; contains the genetic material that encodes the cell’s structure and function.

  • DNA is organized with histones into chromatin, which condenses into chromosomes during cell division.

  • Skeletal muscles are multi-nucleated.

DNA Organization and Chromatin

  • DNA macrostructure: strands wrapped around histones to form chromatin.

  • Chromatin condenses into chromosomes when the cell is ready to divide.

  • DNA double helix consists of two complementary strands bonded by hydrogen bonds between nitrogenous bases.

  • DNA is made up of Nitrogenous base, a sugar, and a phosphate group. gives the double helix structure.

  • Nucleotide = base + sugar

  • One strand runs from 5’ to 3’, the other strand from 3’ to 5’

  • the numbers is given based on the positioning of the carbon atoms in the sugar molecule.

  • Complimentary strands are opposite of each other

  • A & G = purines

  • G & T = pyrimidines

  • central Dogma- sequential events that have to happen in that order for your cells to survive and replicate

    • DNA to RNA = transcription

    • RNA to Protein = translation

    • every 3 bases in your DNA, theres 1 protein.

From DNA to Protein: Transcription and Translation

  • DNA holds genetic information to build proteins.

  • The nucleotide sequence of a gene is translated into an amino acid sequence of the corresponding protein.

  • Transcription (in the nucleus): DNA is transcribed into mRNA.

  • RNA processing/modification occurs, then mRNA is transported to the cytoplasm.

  • Translation (in the cytoplasm): Ribosome reads mRNA; tRNA brings amino acids; amino acids are linked to form a polypeptide (protein).

  • DNA replication duplicates the entire genome of the cell.

  • Enzymes separate the two strands, each serving as a template for a new complementary strand. Each daughter DNA has one old strand and one new strand → replication is semiconservative

  • Unzipping of the DNA is done by the enzyme Helicase.

  • The enzyme Primase adds new bases to the strand that is being produced

  • DNA polymerase guides the Primase into the correct spot

  • Ligase cuts and seals whatever gaps there are in the new DNA strand.

  • When the original is strand is unzipped, the top strand has the leading strand and the parent strand.

  • The bottom strand has the parent strand and the lagging strand

  • gene = 3 base pairs

The Genetic Code and Protein Synthesis

  • The genetic code maps nucleotide triplets (codons) in mRNA to amino acids in proteins.

  • DNA holds all the genetic info to build a cell’s protein

  • Translation requires:

    • mRNA template

    • Ribosome (protein synthesis machinery)

    • tRNA molecules delivering specific amino acids

  • Post-translational processing may modify proteins before they become functional.

  • DNA transcription to mRNA, then mRNA to ribosome is translation.

  • Transcription is in the nucleus

  • translation happens in cytoplasm, outside the nucleus

The Cell Cycle and Cell Division

  • The cell cycle is the sequence of events from cell creation to division into two new cells.

  • Phases:

    • Interphase: G1, S, G2

    • Mitosis: Nucleus divides

    • Cytokinesis: Cytoplasm divides into two distinct cells

  • Interphase subphases:

    • G0 (resting phase): cells may exit the cycle and not divide for a period (hours to days depending on cell type). no active cell division, start preparing, may consume more energy to prepare.

    • G1 (First gap): cells grow and perform normal functions; may not divide during this phase. (2 hours to days)

    • S (Synthesis): DNA replication; duration about 8-10 hours.

    • G2 (Second gap): cell prepares for division; duration about 5\ \mathrm{hrs}.

  • M phase includes mitosis and cytokinesis.

Mitosis: Stages and Chromosome Dynamics (General Overview)

  • Mitosis is followed by cytokinesis, ensuring equal distribution of genetic material.

  • A homologous pair of chromosomes consists of two homologous chromosomes, each with its sister chromatid (produced by DNA replication) forming the familiar X-shaped structure.

  • Sister chromatids are identical copies held together at the centromere until separation.

  • Prophase: Chromosomes condense, spindle fibers begin forming, and the nuclear envelope starts breaking down.

  • Prometaphase: Nuclear envelope fully breaks down; spindle fibers attach to chromosomes at the kinetochores.

  • Metaphase: Chromosomes line up along the equator (metaphase plate) of the cell.

  • Anaphase: Sister chromatids separate and are pulled to opposite poles.

  • Telophase: Nuclear envelopes reform, chromosomes de-condense, and spindle fibers disassemble.

  • Cytokinesis: Cytoplasm divides, creating two identical daughter cells.

  • Centromeres: hold chromatids together.

Regulation of the Cell Cycle

  • The cell cycle is controlled by molecules such as cyclins and cyclin-dependent kinases (CDKs).

  • Cyclins: Proteins that control cell cycle timing by activating CDKs, which drive progression through different phases. Checkpoints.

    • Cancer patients have hijacked cyclins, causing cells to divide uncontrollably.

  • These regulators determine whether the cell is ready to move to the next stage of the cycle.

  • Cyclin A CDK2 Inhibits S phase

Stem Cells and Therapeutic Potential

  • Stem cells have the capacity to differentiate into specialized cells.

  • They hold potential for therapeutic applications aiming to replace damaged cells in various tissues.

  • Embryonic stem cells can be found in bone marrow and fetal/placental blood. Can add a growth factor, grow these cells to match an organ system. (Magical cell).

Quick Reference: Key Definitions and Concepts

  • Cell membrane: phospholipid bilayer with embedded proteins and cholesterol; semi-permeable barrier.

  • Phospholipid: polar head (hydrophilic) and non-polar tail (hydrophobic).

  • Passive transport: diffusion without energy; includes simple and facilitated diffusion.

  • Active transport: energy-dependent transport (ATP usage).

  • Aquaporins: channel proteins that facilitate water movement.

  • CFTR: chloride channel; mutation leads to cystic fibrosis.

  • Hypertonic/Isotonic/Hypotonic: describe solute concentrations relative to cell interior and effects on cell volume.

  • Endocytosis: uptake of material via vesicle formation; phagocytosis, pinocytosis, receptor-mediated endocytosis.

  • Exocytosis: export of materials via vesicle fusion with plasma membrane.

  • Endomembrane system: network of membranes coordinating protein trafficking and metabolism (nucleus, ER, Golgi, lysosomes, vesicles).

  • ER: Rough (ribosomes, protein synthesis) and Smooth (lipid synthesis, Ca++ regulation, detoxification).

  • Golgi: modifying, sorting, and shipping proteins; lysosome production.

  • Mitochondria: ATP production via inner membrane processes; two membranes.

  • Nucleus: stores DNA; site of replication and transcription.

  • DNA: double helix; packaged with histones into chromatin; condensed into chromosomes during division.

  • DNA replication: semiconservative; each daughter genome contains one existing strand and one newly synthesized strand.

  • Central dogma: DNA -> RNA (transcription) -> Protein (translation).

  • Cyclins & CDKs: key regulators of cell cycle progression.

  • Stem cells: undifferentiated cells with potential to differentiate into multiple cell types.