Lesson 1: Life is Compartmentalized

Eukaryotic Cell Parts and Their Functions Flashcards

  1. Nucleus

    • Function: Contains genetic material (DNA) and controls cell activities.

  2. Mitochondria

    • Function: Produces energy (ATP) through cellular respiration.

  3. Ribosomes

    • Function: Synthesizes proteins from amino acids.

  4. Endoplasmic Reticulum (ER)

    • Function: Synthesizes proteins (rough ER) and lipids (smooth ER).

  5. Golgi Apparatus

    • Function: Modifies, sorts, and packages proteins and lipids for secretion.

  6. Lysosomes

    • Function: Digests waste materials and cellular debris.

  7. Plasma Membrane

    • Function: Regulates the movement of substances in and out of the cell.

  8. Cytoplasm

    • Function: Jelly-like substance where cell components are suspended.

  9. Cytoskeleton

    • Function: Provides structural support and aids in cell movement.

  10. Chloroplasts (in plant cells)

    • Function: Conducts photosynthesis to convert solar energy into chemical energy.


Plant cells have several unique structures, including:

  • Cell Wall: A rigid outer layer made of cellulose that provides support and protection.

  • Chloroplasts: Organelles that contain chlorophyll for photosynthesis.

  • Central Vacuole: A large vacuole that stores nutrients and waste products, and helps maintain turgor pressure.

  • Plasmodesmata: Channels that allow communication and transport between adjacent plant cells.

These structures differentiate plant cells from animal cells.

Lesson 1: Life is Compartmentalization



Five Fundamental Characteristics

  1. Cellularity

  2. Information Processing

  3. Energy Utilization

  4. Replication

  5. Evolution



4.3: Overview of Cell Structure and Function



Introduction

  • Structure and Function Determined by:

    • Matter

      • Composed of atoms, molecules, and macromolecules

    • Energy

    • Organization

      • Protein-protein Interactions: Specific interactions between proteins that occur during many critical cellular processes

    • Information

      • DNA

        • Genome: The complete genetic material of an organism or species (each living cell has a copy of the genome)

        • Genes: A unit of heredity. At the molecular level, a gene is an organized unit of base sequences in a DNA strand that can be transcribed into RNA and ultimately results in the formation of a functional product.



Prokaryotic Cells Have a Simple Structure

  • Prokaryotic Cells: A cell lacking a membrane-enclosed nucleus and cell compartmentalization; the cells of all members of the domains Bacteria and Archaea are prokaryotic cells. 


Bacteria/Archaea are very small, between 1-10 micrometers in diameter. 

Inside a Prokaryotic Cell: 




  • Plasma Membrane: double layer of phospholipids and embedded proteins that separates the internal part of the cells from the external environment

  • Cytoplasm: The region of the cell that is contained within the plasma membrane, site of metabolism 

  • Nucleoid: Site in a bacterial cell where the DNA is; not a membrane-bound compartment

  • Ribosomes: A structure composed of proteins and rRNA that is the site where translation of mRNAs and synthesis of polypeptides occur. 

  • Cell wall: Relatively rigid, porous structure located outside the plasma membrane of prokaryotic cells and cells in plants, fungi, and certain protists; provides support and protection. 

    • Commonly contains peptides and carbs

    • Relatively porous

  • Glycocalyx: An outer viscous covering surrounding bacterium that traps water and helps protect the bacterium from drying out/A carb-rich zone on the surface of animal cells (cell coat)

    • Capsule: A very thick, gelatinous glycocalyx produced by certain strains of bacteria that may help them avoid being destroyed by an animal's immune system. 

  • Pili: Threadlike surface appendages that allow bacteria to attach to each other during conjugation or to move across surfaces

  • Flagella: Relatively long cell appendages that facilitate cellular movement or the movement of extracellular fluids



Eukaryotic Cells are Compartmentalized by Internal Membranes to Create Organelles 

  • Eukaryotes: The distinguishing feature is the cell compartmentalization; include a cell nucleus; protists (algae), fungi, plants, and animals

    • 10-100 micrometers in diameter

  • Possess a true nucleus

    • Type of Organelle: membrane-bound compartment with its own unique structure and function

  • These cells have extensive compartmentalization, so they have many membrane-bound organelles that separate the cell into different regions 

  • Plant Cells

    • Similar to animals cells, but have chloroplasts, central vacuole, and a cell wall

    • Lack lysosomes and centrioles 

Animal Cell


Plant Cell

Droplet Organelles Are a Category of Organelles Whose Boundary is Due to Phase Separation



  • Liquid-liquid phase separation: Aggregated solutes, like proteins and RNA molecules, separate from the bulk solvent, and form a droplet 

    • Droplet Organelle Potential Purpose

      • Molecules brought close together to assemble into complexes

      • The environment in the droplet is chemically different from the surrounding medium, affecting RNA folding



Cell Characteristics Determined by the Proteins it Makes

  • Genome vs Proteome

    • Proteome: the complete set of proteins that a cell is currently making or an organism can make

      • Largely responsible for determining the structure and function of that cell

      • Largely responsible for determining the trains of organisms

  • Why the cells’ protein compositions are different (Skin cells and neurons, but applies to all)

    • Certain proteins found in skin cells may not be produced in neurons, and vice versa

    • Skin cells and neurons may produce the same proteins but in different amounts

    • The amino acid sequences of particular proteins can vary in skin cells and neurons

    • Skin cells and neurons may alter their proteins in different ways. 



Surface Area and Volume are Critical Parameters that Affect Cell Sizes and Shapes

  • Why are cells so small?

    • To survive, cells have to import substances across their plasma membrane and export waste. A very large cell would require more nutrient uptake and waste export. 

    • As cells get larger, their plasma membrane surface area increases, along with the volume, so the surface area:volume ratio gets smaller. 

      • A high surface area/volume ratio is required for cells to have adequate nutrient uptake/waste support. 



4.4 The Cytosol



Synthesis and Breakdown of Molecules Occur in the Cytosol

  • Metabolism: the sun of the chemical reactions by which cells produce materials and utilize the energy necessary to sustain life. 

    • Metabolic pathway

      • Catalyzed by a specific enzyme: protein that accelerates the rate of a chemical reaction

      • Some pathways involve breakdown into smaller components (catabolism) in order to utilize energy and generate molecules that provide building blocks to construct macromolecules. 

      • Other pathways involve the synthesis (building), of molecules and macromolecules (anabolism)

        • Exa: to make proteins, amino acids are covalently connected to form a polypeptide, using the information within an mRNA. 

  • Cytosol - central coordinating region for many metabolic activities



Cytoskeleton Provide Cell Shape, Organization, and Movement

  • Cytoskeleton: a network within the cytosol consisting of three protein filaments called microtubules, intermediate filaments, and actin filaments.

    • Microtubules: hollow protein filament with tubulin proteins; part of the cytoskeleton

      • 25 nm

      • Functions: cell shape, cell organelle organization, chromosome sorting during cell division, intracellular movement of cargo, cell motility ( cilia and flagella)

      • Assembly of tubulin to form microtubules results in a structure with a plus and minus end.

        • Only grow at plus end, can shorten at either end

          • Dynamic Instability: the oscillation of a single microtubule between growing and shortening phases; important during chromosome sorting at cell division

        • Where these form varies among types of organisms. 

          • Microtubule-organizing center (MTOC): site in eukaryotic cells where microtubules grow

            • Non-dividing animal cells contain a single MTOC near the nucleus called centrosome: A single structure often near the nucleus of a eukaryotic cell that forms a nucleating site for the growth of microtubules; also called a microtubule-organizing center.

            • In the centrosome are centrioles: In animal cells, microtubule growth starts at the centrosome and anchors the minus end there. But most plants/protists lack centrosomes and centrioles, so they are created at sites throughout the plant cell. 




  • Intermediate Filaments: twisted filament in the cytoskeleton of animals cells; helps maintain cell shape and rigidity

    • 10 nm

    • Composed of keratin, lamin, and others

      • Keratins form filaments in skin, intestinal, and kidney cells; important for cell shape and mechanical strength

      • Keratinocytes: cells that synthesize large amounts of keratin

        • Dead ones make up hair, nails, and skin surface

    • Functions: cell shape, cell mechanical strength, anchorage of cell and nuclear membranes

    • Found in cell nucleus

      • Nuclear lamins form a network of these filaments that line the inner nuclear membrane and provide anchor points for nuclear pores. 

      • Not found in all animal species

    • Tension -bearing fibers to maintain cell shape/rigidity

    • Lengths are relatively permanent

  • Actin Filaments: Spiral structured thin protein filament composed of actin proteins; supports plasma membrane; key role in cell strength, shape, and movement

    • Also known as microfilaments as they are the thinnest cytoskeletal filaments

    • 7nm

    • Like microtubules, they have a plus and minus end

      • Grow at the plus end by addition of actin monomers

      • Plus end grows towards plasma membrane; play key role in cell shape and movement 

    • Composed of actin proteins

    • Function: cell strength, muscle contraction, intracellular movement of cargo, cell movement (amoeboid movement), cytokinesis in animal cells 

    • Tend to be concentrated near the plasma membrane

    • Sides of these are often anchored to other proteins near the plasma membrane




Motor Proteins + Cytoskeletal Filaments Promote Movement 

  • Use ATP as a source of energy 

  • Three domains to a motor protein, form a “lever arm”

    • Head- Site where ATP binds and is hydrolyzed to ADP and organic phosphate

    • Hinge - Bends due to ATP binding and hydrolysis

    • Tail - Attached to other proteins/cellular molecules

      • How they cause movement (like walking)

        • Head released from filament

        • Head cocks forward and binds to farther up part of filament

        • Head cocks backward, moving tail from left to right


  • Cause three kinds of movement

    • Movement of Cargo

      • Motor protein kinesin (exa is microtubule)

    • Movement of Filament

      • Motor protein myosin (exa is on actin filament)

      • Occurs during muscle contraction

    • Bending of Filament

      • Motor protein dynein

      • If motor protein and filament are restricted in movement due to linking proteins, when motor proteins attempt to walk toward minus end they exert a force that causes the microtubules to bend





Cilia and Flagella Allow Cells to Move


  • Flagella (flagellum, single):  cell appendages that cause cellular movement, or moving of surrounding fluids

  • Cilia (Cilium, single): Appendages that have the same internal structure as flagella but are shorter and more numerous 

  • Both have the internal structure axoneme: structure of eukaryotic flagella and cilia that contains microtubules, the motor protein dynein, and linking proteins)

    • In most organisms, the microtubules form a 9+2 arrangement array

      • Outer nine are doublet microtubules (partial microtubule attached to a complete one)

      • 2 central microtubules are single ones

      • Radial spokes project from the outer ones towards the central ones

        • Key protein is called SAS-6


    • Microtubules emanate from basal bodies: at the base of flagella/cilia where the microtubules grow; are anchored on the cytosolic side of the plasma membrane

      • Microtubules form a striplet structure

        • Like in the centrosome of animals cells, basal bodies provide site for microtubules to grow


  • Movement involves a bend that begins at the base of the structure and proceeds towards tip

    • Occurs because dynein walks toward the minus end of microtubules, exerting force that causes a bend. The dyneins at the base of the flagellum or cilium are activated first, then progressively closer to the tip



4.5 The Nucleus and Endomembrane System

Introduction 

  • Nucleus: (biology) An organelle in eukaryotic cells that contains most of the cell’s genetic material

  • The membranes enclosing the nucleus are part of a larger network of membranes called the endomembrane system: a network of membranes that includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, peroxisomes, and plasma membrane


The Eukaryotic Nucleus  Contains Chromosomes 

  • Nuclear Envelope: a double membrane structure that encloses the cell’s nucleus 

  • Nuclear Pores: passageway for movement of molecules and macromolecules in and out of the nucleus; formed where the inner + outer membranes make contact




  • In the nucleus are chromosomes and a filamentous network of proteins called the nuclear matrix 

    • Chromosome: a discrete unit of genetic material composed of DNA and associated proteins. Eukaryotes have chromosomes in their cell nuclei and in plastids and mitochondria 

      • Composed of genetic material and proteins to compact the chromosome to fit in the nucleus. This complex is called chromatin: the complex of DNA and proteins that makes up eukaryotic chromosomes. 

    • Nuclear Matrix: filamentous network of proteins found inside the nucleus and lines the inner nuclear membrane. It organizes the chromosomes.

      • Two parts

        • Nuclear Lamina: collection of protein fibers that line the inner nuclear membrane

        • Internal nuclear matrix: connected to the lamina and fills the interior of the nucleus 

    • Primary functions of the nucleus: 

      • Protection

      • Organization

      • Replication

      • Expression 

        • … of genetic material 

      • Also…

        • Assembly of ribosomal subunits, which are cellular structures that produce polypeptides during translation.

          • The assembly of these units occurs in the nucleolus, a droplet organelle in the nucleus of non-dividing cells 

          • Ribosomes are composed of two subunits, one small and one large. Each contains 1+ RNA molecules and different types of proteins. 

            • Most RNA molecules are made in the vicinity of the nucleolus. 

            • Ribosomal proteins are produced in the cytosol and imported into the nucleus through the pores.

            • The proteins and molecules enter the nucleolus and move through pores into the cytosol, where they carry out polypeptide synthesis 



Endoplasmic Reticulum Initiates Protein Sorting and Carries out Metabolic Functions 

  • Endoplasmic Reticulum (ER):  a network of membranes in a cell’s cytoplasm that form flattened, fluid-filled tubules/cisternae 

  • Lumen: the internal space of an organelle/organ

    • Single compartment of ER membrane called the ER lumen

  • Two types of ER 

    • Rough ER: The part of the ER whose outer surface is studded with ribosomes; this region plays a key role in the initial synthesis and sorting of proteins that are destined for the ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane, or extracellular environment.

      • Sorts proteins destined for ER, golgi, lysosomes, vacuoles, plasma membrane, or extracellular environment

        • Proteins packed into membrane vesicles, and moved from one endomembrane system to another 

      • Also inserts new proteins into the ER membrane 

      • Also attaches carbs to proteins and lipids, process called glycosylation

    • Smooth ER: The part of the ER whose outer surface is not studded with ribosomes. This region is continuous with the rough ER and functions in diverse metabolic processes such as detoxification, carbohydrate metabolism, accumulation of calcium ions (Ca2+), and synthesis and modification of lipids.

      • Lacks ribosomes

      • Metabolism

        • Detoxifies harmful organic molecules

        • Carbohydrate metabolism

          • Liver cells in animals store energy as glycogen, which sit close to the smooth ER membrane. When chemical energy is needed, enzymes are activated that break down the glycogen into glucose-6-phosphate. An enzyme removes the phosphate group and is exported from the cell into the bloodstream. 

      • Storage of Ca^2+ oons

        • In all eukaryotes, the smooth ER accumulates calcium, and through calcium pumps transports it into the ER lumen. The regulated release of calcium into cytosol is important for many vital cellular processes like muscle contraction

      • Lipid synthesis and modification 

        • Enzymes in the smooth ER modify lipid cholesterol to produce steroid hormones 



Golgi Apparatus 

  • Golgi Apparatus: stack of flattened, membrane bound compartments perform secretion, processing, and protein sorting 

    • Cis golgi: near ER membrane

    • Trans golgi: closest to plasma membrane

    • Medial golgi: found in the middle 

  • Processing Events

    • Carbs can attach to  proteins and lipids in the ER

    • Glycosylation

      • A protein or lipid is transported from via vesicles from the ER to the cis golgi

      • Most glycosylation occurs in the medial Golgi 

    • Proteolysis: A processing event within a cell in which enzymes called proteases cut proteins into smaller polypeptides.

  • Golgi packages materials into secretory vesicles that fuse with the plasma membrane, releasing contents outside the cell. 




Lysosomes Involved in Intracellular Digestion of Macromolecules 

  • Lysosomes: Small organelles found in animal cells that contains acid hydrolases (hydrolytic enzymes that use a molecule of water to break a covalent bond) that degrade molecules and macromolecules 

    • Acid hydrolases function best at an acidic pH

      • In a lysosome it is 4.8, but the cytosolic PH is neutral so if the lysosome brakes, the enzymes are not active because the neutral pH buffers them

    • Digests substances taken up from outside the cell via endocytosis 

    • Breaks down intracellular molecules and macromolecules to recycle building blocks to make new ones (process called autophagy)



Vacuoles: Storage, Regulation of Cell Volume, Degradation

  • Vacuoles: Special organelles in eukaryotic cells functioning in storage, regulation of cell volume, and degradation

    • Tend to be smaller in animal cells vs plant cells

    • Commonly used to temporarily store/transport

    • Space Filling helps to maintain structure due to turgor pressure, align with drives the expansion of the cell wall

    • Helps maintain cell volume by expelling excess

    • Helps to break down food

Peroxisomes Catalyze Detoxifying Reactions

  • Peroxisomes: relatively small organelle found in all eukaryotic cells that catalyzes detoxifying reactions 

    • Single membrane encloses a fluid-filled lumen

    • Metabolize fats and amino acids

      • Plant seeds have glyoxysomes: a specialized organelle that contains enzymes to convert fats to sugars

    • Peroxisome Formation


Plasma Membrane 


  • Selectively permeable 



Lesson 1 Textbook Video: Cell Structure



All cells have:

  • Cell membrane

  • Cytoplasm

  • DNA (genetic material)



Two Types of Cells

  • Eukaryotic Cells

    • More complex

  • Prokaryotic Cells

    • Don’t have nucleus/membrane bound organelles

    • Unicellular



Organelles:

  • Little organ

  • Nucleus:

    • DNA

    • Chromatin: spread out form of DNA in nuclear membrane

    • When the cell is about to divide, DNA condenses into chromosomes

    • Nucleolus (where ribosomes are made)

      • Ribosomes make proteins

        • Outside they float  around in cytoplasm, or on the ER

  • ER

    • Rough ER: has ribosomes

    • Smooth ER: no ribosomes

    • Pathways for transporting materials through vesicles, to the golgi where it receives them. Here the proteins are customized into forms the cell can use. 

      • Golgi folds the protein into shapes, or adds other materials (carbs, lipids, etc.)

  • Vacuoles

    • Stores stuff

  • Lysosome

    • Animal cell

    • “Garbage collector” damaged or worn out cells

    • Filled with enzymes to break down debris

  • Mitochondria: powerhouse of the cell

    • Cellular respiration: makes ATP

    • More energy = more mitochondria

  • Cytoskeleton

  • Chloroplasts 

    • Plants

    • Where photosynthesis happens

  • Cell wall (plant cells)

  • CIlia

    • Move cells, helps to catch particles

  • Flagella

    • Moves cells



Lesson Lecture 1:



Learning Goals

  1. Differences between prokaryotic and eukaryotic cells. Why do they exist?

  2. Function of the organelles and consequences of them not functioning properly

  3. Differences between plant and animal cells and how the differences affect their functions



Cell Theory: 

  1. All living organisms have 1+ cells

  2. Cells are smallest units of life

  3. New cells only come from pre-existing cells by cell division



Rural City: Prokaryotic Cells

Urban Cities: Eukaryotic Cells (plant and animal cells)

Viruses:

  • Protein encapsulated genetic material

  • Not a cell - not living

    • No organelles/membrane

    • Classified as obligate parasites - they require a host for replication of their genome

  • Inject genetic material into host cell, which provides all replication machinery for the virus

  • Can infect both prokaryotes or eukaryotes