Prokaryotic and Eukaryotic Cells

• Chapter 3 focuses on cells and the methods used to observe them.
• The chapter includes the study of prokaryotic and eukaryotic cell structures
• It covers similarities and differences between these cell types, microscopy principles, specimen preparation, and common staining methods.

Prokaryotic and Eukaryotic Cell Similarities

• Both cell types are made up of cells, containing a cell membrane, cytoplasm, DNA, and RNA.
• They share organizational levels such as population, community, ecosystem, and biosphere.
• Both participate in life processes like reproduction, growth & development, metabolism, communication, response to stimuli, and adaptation.
• Both cell types can include some pathogens.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic cells belong to the Kingdoms Bacteria and Archaea.
• Eukaryotic cells belong to the Kingdoms Protista, Fungi, Plantae, and Animalia.
• Prokaryotic cells are generally smaller than eukaryotic cells.
• Prokaryotic cells do not have a nucleus or membrane-bound organelles.
• Eukaryotic cells have a nucleus and membrane-bound organelles.
• Prokaryotic cells are unicellular.
• Eukaryotic cells can be unicellular or multicellular.
• Prokaryotic cells have a single circular chromosome.
• Eukaryotic cells have multiple linear chromosomes.
• Prokaryotic cells have 70S ribosomes; eukaryotic cells have 80S ribosomes.

Outer components of bacterial cells

• All bacterial cells have a cell membrane.
• Outside the cell membrane are the cell wall and glycocalyx.
• Some bacterial cells have pili or fimbriae for adhesion.
• Some bacterial cells have flagella for movement.
• Archaea have cannulae and hami, which are singular-hamus

Cytoplasmic Membrane of Prokaryotes

• The cytoplasmic membrane structure and chemistry in prokaryotic cells relates to membrane permeability.
• The cytoplasmic membrane is involved with proton motive force.
• Prokaryotic cells use specific systems to move small molecules across the cytoplasmic membrane.
• Prokaryotic cells secrete certain proteins.

Cytoplasmic Membrane Composition

• Cytoplasmic membrane defines boundary of cell
• The cytoplasmic membrane is a phospholipid bilayer embedded with proteins.
• Hydrophobic tails face inward, and hydrophilic tails face outward.
• Proteins in the membrane have various functions, including selective gates, sensors, and enzymes.
• The "fluid mosaic model" describes proteins drifting within the lipid bilayer.

Membrane of Bacteria and Archaea

• Bacteria and archaea have the same general structure
• The phospholipid composition is different in bacteria and archaea
• Lipid tails of Archaea are not fatty acids but are isoprenoids.
• They are connected differently to glycerol: Bacteria has an ester linkage, Archaea has an either linkage
• Extreme environmental stability ensured via diversity of structure and composition

Permeability of Cytoplasmic Membrane

• It is selectively permeable.
• Gases, small hydrophobic molecules, and water pass freely.
• Water passage facilitated by aquaporins in some cells.
• Transport systems necessary for other molecules to move across membrane.

Transport Across The Membrane

• Passive transport goes down the concentration gradient, and requires no ATP
• Active transport goes against the concentration gradient, and needs ATP.

Permeability of Cytoplasmic Membrane - Diffusion

• Simple diffusion involves the movement of molecules from a high concentration to a low concentration until equilibrium is reached.
• The rate of diffusion is affected by the concentration gradient.
• The rate of diffusion is affected by temperature and mass.
• Lower temperatures and heavier molecules result in slower diffusion.

Permeability of Cytoplasmic Membrane - Osmosis

• Osmosis involves the diffusion of water across a selectively permeable membrane due to unequal solute concentrations.
• Water diffuses from high water concentration (low solute concentration) to low water concentration (high solute concentration).
• Water flows water from hypotonic to hypertonic solution.
• There is no net water flow occurring between isotonic solutions.
• Environment of prokaryotes are typically dilute (Hypotonic) related to cytoplasm
• Water flows into the cell where cytoplasm is a concentrated solution (hypertonic)
• Cell wall prevents cell from bursting
• High salt/sugar used in food to prevent bacterial growth

Small Molecule Transport

• Cells use transport systems - transporters, permeases, or carriers - to move nutrients and other small molecules across membranes.
• Highly specific, generally moves one molecule type

Facilitated Diffusion

• Facilitated diffusion is a form of passive transport.
• Molecules move down the concentration gradient, and no energy in the process is required.
• It is not typically useful in low-nutrient environments.
• Channel proteins are involved.

Active Transport

• Requires energy to move material against concentration gradient
• The energy is sometimes driven by proton motive force, with an example of efflux pump.
• Sometimes driven by ATP (ABC transporter)

Protein Secretion

• It involves the active movement of proteins out of the cell for exoenzymes and external structures.
• It involves polypeptides tagged for secretion via signal sequence of amino acids.

The Cell Wall of Prokaryotic Cells

• The chemistry and structure of peptidoglycan differ between Gram-positive and Gram-negative cell walls.
• The cell wall of archaea is different than that of bacteria.
• The cell wall affects susceptibility to particular substances such as penicillin and lysozyme
• The cell wall affects Gram Staining characteristics.
• Lipid A and the O antigen of LPS are significant regarding cell wall

Cell Wall Functions

• Cell walls are a strong, rigid structure preventing bursting.
• They distinguishes two main types of bacteria: Gram-positive and Gram-negative.
• Some bacteria also have no cell wall- Mycoplasma.

Peptidoglycan Composition

• A peptidoglycan layer is in the cell walls for both of gram-negative and gram-positive bacteria.
• The Gram-Positive Cell Wall is relatively thick
• Teichoic acids extend above the layer.
• Teichoic acids are important for cell wall integrity, pathogenesis, sensitivity of temperature and salt concentration
• Gel-like material called periplasm lies below peptidoglycan layer.
• Alternating series of subunits form glycan chains- N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG).
• Tetrapeptide chains attach to NAM and link glycan chains together via direct link or peptide inter-bridge.

The Gram-Negative Cell Wall

• The peptidoglycan layer is thin.
• There is a unique outer membrane beyond the peptidoglycan layer in gram negative cells.
• Lipopolysaccharide (LPS) is in the outside layer, signaling immune invasion
• Even a small amount eliciting can initiate an immune response to eliminate an invader.
• It is called endotoxin, playing a role in infection and survival in the host.
• Lipid A in LPS is hydrophobic, anchors the LPS to membrane, is conserved and is recognized by the immune system among gram negative bacteria
• O antigen is used to identify bacterial species or strains.
• The outer membrane blocks passage, including certain antimicrobial medications, but small molecules and ions cross via porins
• Periplasm lies specifically between cytoplasmic and outer membrane and has binding proteins of transport

Antibacterial Substances and Peptidoglycan

• Interference with peptidoglycan can weaken the cell wall and allow cell to burst.
• Antibiotics can inhibit different steps in peptidoglycan synthesis
• Penicillin interferes with peptidoglycan prevents cross-linking of adjacent Chains; more effective against Gram-positive bacteria but can be modified to cross
• Lysozyme breaks bonds linking glycan chains, which leads to damage of integrity, is more effective against gram-postive bacteria

Bacteria Lacking Cell Walls

• Mycoplasma species lack a cell wall, with one species causing a mild form of pneumonia
• They are flexible because of not having rigid wall.
• Penicillin nor lysozyme does not affect these organisms.

Non-Typical Cell Walls

• Some bacterial groups lack wall- i.e Mycobacterium and Nocario
• Atypical Gram-positive cell wall structure includes lipid mycolic acid (cord factor)
• Pathogenicity and high degree of resistance to certain chemicals and dyes result.
• A basis exists for acid-fast stains to be used for diagnosis of infections caused by these microorganisms

Cell Walls of Archaea

• Archaea have variety of cell walls, ranging of environments
• The variety is due to the extreme environments they are often in
• Generally, Archaea is less well studied relating to bacteria, compared
• There is no peptidoglycan
• Some archaeal cell walls have similar molecule pseudopeptidoglycan (or pseudomerin).
• S-layers on the cell walls self-assemble.

Structures Outside Cell Wall

• Compare and contrast of the capsules and slime layers in Bacteria
• Different structures like the flagella are involved in chemotaxis
• Fimbriae and sex pili help in mobility, chemotaxis

Capsules And Slime Layers

• Located outside cell wall and protects or allows attachment
• A capsule is distinct and gelatinous.
• A slime layer is diffuse and irregular in shape
• Capsules and slime layers are mostly composed of glycocalyx (sugar shell)
• Some capsules allow bacteria to evade host immune system.
• Biofilms are cells once attached to Surface

Flagella

• It is involved in motility, moving cells with spin
• Important in disease Helicobacter pylori
• Numbers/Arrangements help with characterization of bacteria
• Peritrichous - flagella covers surface
• Polar (monotrichous) - a single flagellum at one end

Flagella Parts

• Part of bacteria only
• Basal body: anchors to cell wall and cytoplasmic membrane.
• Hook is also present.
• Filament: made up of subunits (flagellin) use energy from motive force instead of ATP
• Archaella: are unique and differ chemically
• Archaella uses energy from ATP instead of proton motive force"

Chemotaxis

• Chemotaxis enable bacteria to sense a chemical and move toward it (nutrient) or away from it (toxin).
• Movement series of runs and tumbles due to flagella arrangement
• Aerotaxis: response to O2 —Magnetotaxis: earth’s magnetic field response
• Thermotaxis: responses to temperature
• Phototaxis: responses to light

Pili

• Pili (pl. pilus) compared to flagella are a more thinner, smaller entity.
• Fimbriae attaches to bacterial cells.
• Cell motility also depends on them; cell motility with twitch
• Some cells transfer DNA via bacterial conjunction (sex pili)

Cannulae and Hami

• These are unique outer structures of archaea
• Cannulae can aid connection cells to surface.
• Hami can help form a community of cells.

Internal Components of Prokaryotic Cells

– DNA – Plasmids – Cytoskeleton – Ribosomes – Storage granules, inclusion bodies, protein compartments – Endospores in some

DNA, Chromosomes, Plasmids

• Chromosomes are double-stranded, circular and single for DNA molecules and also supercoil. No histones like eukaryotes for chromosome/plasmid structure
• In plasmids however, they might be transferred between. Bacterial con. Also they not for encode genetics but add “advantages, with genetic engineering, are easy for genetic

Ribosomes

• 30s/50s = 70s subunits
• Eukaryotic ribosome = 80s.
• Antibiotics are easy to control to affect 70s ribosomes, can do antibiotics, but hard to affect 80s, but still try to modify them

Cytoskeleton

• Interior protein framework and proteins similar to eukaryotic proteins and cytoskeleton
• Help cell divide/maintain shape

Energy Synthesis

• Nutrients from cell excess
• glycogen, B-hydroxybutyrate for metabolism (red stain w/ blue methyl for cytoplasm
• Protein-bases/separations of functions
• Protein is subunited and semi-permeable and less recognition

Protein based Compartments

• gas vessels - provides with an aquatic buoyancy for prokaryotes and to get close to the the column
• Bacterial micro-compartments provide enzymes to contain enzymes required for some metabolism and also help against harm
• Encapsulin nanostructure is used to contain iron binding protein

Endospores

– Can form resistance and dormant structures when cell/env. Is not ready – Bacteria and bacillus is resistant to heat and chemicals etc because of layer

• Can not eliminate using pasteurization and can germinate vegetative cells from multi
• Can be found literally anywhere
• Sporulation triggered by limited carbon/nitrogen
• Endospores: 8 process to protect itself/DNA from core state
• dipicolates form and prevent replication (not a means of repro.)
• Genetic info
• Septum form The cell compartments are the source for the next endospore

Eukaryotic cell structures

• The eukaryotic cell structure and their functions includes self-contained protozoa but not animal cell walls
• They are vary in fungi with Chitin

Eukaryotic cells

• larger and more complex than Prokaryotic cells
• Has membrane-enclosed compartments called organelles
• Organelles- cell's DNA is stored in the structure of DNA

commonalities

• cell to organism will still vary and cells will tissue to the organ

Eukaryotic cell commonalities

• All "cells" from chromosomes, ribosomes etc
• The DNA in eukaryotes goes through cell walls, peroxisomes, plasmodesmata
• Uniqueness is defined through animal vs plants The cell walls of plants cell walls can be changed using the endoplasmic and Golgi-system

Eukaryotic Cytoplasmic membrane

• Compare/contrast to pro counterpart