Biol 3400Tortora et al – Chap 4
Functional Anatomy of Prokaryotic and Eukaryotic Cells
I. Introduction
Prokaryotic and eukaryotic cells are similar in a number of ways including Chemically similar – contain macromolecules: Nucleic acids, proteins, lipids and polysaccharides’ Similar metabolic reactions to metabolize food, synthesis proteins and nucleic acids and store energy Contain a membrane, cytoplasm, DNA and ribosomes
Prokaryotic and eukaryotic cells differ in a number of ways (Table 4.2) including
Prokaryotic cells DNA is usually in the form of a single circular dsDNA chromosome and not enclosed in a
membrane DNA is not associated with histones; other proteins are associated with DNA They lack membrane bound organelles Usually divide by binary fission
Eukaryotic cells DNA is usually in the form of multiple linear dsDNA chromosomes found in a membrane
bound nucleus The DNA is consistently associated with chromosomal proteins called histones and with
nonhistone proteins They may have a number of membrane bound organelles, including endoplasmic reticulum,
Golgi complex, lysosomes, vacuoles, mitochondria and chloroplasts Cell division usually involves mitosis
Prokaryotic cells: Archaea (member of Archaeal domain = archaeon) and Bacteria (member of Bacterial domain = bacterium)
Prokaryotic cell structures include the following (Fig. 4.6; Note: Underlined structures are found in all prokaryotic cells): Plasma membrane Cytoplasm Nucleoid region Ribosomes Cell wall (and periplasmic space) Flagellum Pili and Fimbriae Inclusions Gas vacuole Capsule and slime layers Endospores
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Eukaryotic cells: Protozoa, Fungi and Algae
Eukaryotic cell structures include the following (Fig. 4.22; Note: not all cells possess all of these structures at all times): Plasma membrane Cell wall True nucleus - membrane bound nucleus Ribosomes Membrane bound organelles
chloroplast mitochondrion endoplasmic reticulum vacuoles golgi apparatus lysosomes peroxisomes
Cytoskeleton Flagellum/Cilium
II. Cell Morphology
A. Prokaryotic CellsTwo most common cell shapes coccus (pl. cocci) e.g., bacillus (pl. bacilli) e.g.,
Other shapes include: spirillum (pl. spirilli) e.g., Mycelial – e.g., Actinomycetes Stalked – e.g., Caulobacter, Hypomicrobium Plates Star shape
Some prokaryotes are variable in shape and lack a single characteristic form = pleomorphice.g.,
B. Eukaryotic Cells Highly variable: cell shapes vary in shape from sphere and cylinders to very irregular nerve cells.
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C. Cell Size Cells come in a variety of sizes & shapes Size limit is set by the logistics required to carry out metabolism
The smallest cells are nanobacteria (diameter of 0.05 to 0.2 µm). Mycoplasmas = 0.2 µm in diameter
What factors constrain the lower size limit of cells? Most bacterial cells are 10 times larger than mycoplasmas (1 to 10 µm in diameter) Eukaryotic cells are typically 10 times larger than bacteria (10 - 100 µm in diameter).
What factors constrain the upper size limit of cells?
Generally prokaryotic cells are smaller than eukaryotic cells. But there are exceptions.
e.g., Epulopiscium fishelsoni size up to 80 x 600 µmThiomargarita namibiensis size up to 750 µm in diameter
Nanochlorum eukaryotum 1 to 2 µm in diameter
Generally cells are microscopic. But there are exceptionsLoligo - Atlantic squid has neurons with axon diameters as large as 1.0 mm. Ostrich egg
III Cell Components
A. Plasma membrane Every cell is surrounded by a plasma membrane (also known as a cytoplasmic or cell membrane) Encloses the cytoplasm This is an important feature distinguishing archaea from bacteria and eukaryotes Membranes are selectively permeable barriers - Why?
What is the function of the plasma membrane?
Fluid mosaic model (Fig 4.14) S.J. Singer and G. Nicolson (1972) Dynamic structure bifacial quality – sidedness 5 – 10 nm thick
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1. Membrane components
i. Lipids backbone or basic fabric often as a lipid bilayer (amphipathic)
hydrophobic corehydrophilic exterior surfaces
ii. Proteins integral (70 to 80 % of the membrane proteins) peripheral (20 to 30% of the membrane proteins)
Functionso Transport – import and exporto Enzymeso Receptorso Intracellular junctionso Cell to cell recognitiono Metabolic processes
iii. Carbohydrates Usually associated with the outer surface of the membrane
2. Differences between bacterial, eukaryotic and archaeal membranes
i. Bacterial membranes Like eukaryotes, most of the membrane lipids are phospholipids unlike eukaryotes bacteria lack sterols such cholesterol but contain sterol like compounds called
hopanoids. The role of hopanoids is likely similar to steroids – stabilized membranes. Some bacteria may have extensive in folding of the plasma membrane to increase membrane surface
area for the purpose of greater metabolic activity
Glycerol diesters (phospholipids)
o Glycerol bonded to phosphate (negatively charged) and two fatty acids o Linkage between fatty acids and glycerol is an ester linkage
O ||
Ester linkage R-O-C-(CH2)n CH3
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Environmental conditions affect fatty acid composition of membranes
o Fatty acids are generally unbranched and 16 to 18 carbons longe.g., palmitic acid CH3(CH2)14 COOH
stearic acid - 18 carbons
o Fatty acids may be saturated or unsaturated
Membrane composition also varies with species and these differences can be used to identify bacteria (Fatty acid methyl ester analysis - FAME).
ii. Eukaryotic membraneso generally the same structure as bacterial membranes including phospholipids but differs in the
major lipids: phospholipids, sphingolipids and cholesterol. o Microdomains that differ in protein and lipid composition may be found – lipid rafts – span
membrane and appear to be involved in a variety of cellular processes (e.g., signal transduction and cell movement)
Sterols o compounds consisting of carbon skeleton of 4 interconnected rings o targets for polyene antibiotics - damage cell membraneso Mycoplasmas acquire sterols from eukaryotic cells
iii. Archaeal membranes Many are thought to be “Extremophiles” Membranes are distinctive Phospholipids are not the main structural components Have branched chain hydrocarbons attached to glycerol by ether linkages
Glycerol diethers
Ether linkage R-C-O-C-R
Bilayers o glycerol bound to branched hydrocarbons (e.g., phytanyl) by ether linkageo glycerol diethers
Monolayers o diglycerol tetraether o often found in extreme thermophiles
Phosphate, sulfur and sugar containing groups are attached to the third carbon of glycerol resulting in a polar lipids that are the predominant lipids (70 – 93%) in the membrane
Nonpolar lipids (squalene derivatives) make up the rest of the membranes
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3. The movement of materials across membranes
Review this material on your own – it is largely review from Biol 1010. You should be familiar with the following
Passive Transport Simple diffusion Facilitated diffusion
o Transporter proteins Osmosis
o Aquaporino Osmotic pressure
Active Transporto Group translocation
B. Cell walls
1. Bacterial cell walls
Functions Define cell shape Protection from osmotic shock (turgor pressure) and toxic substances Point of anchorage for flagella May contribute to pathogenicity Most bacteria have cell walls but there are exceptions – e.g., mycoplasmas Forms a strong, protective layer that is relatively porous, elastic and somewhat stretchable
Gram positive and Gram negative (Fig. 4.13)
Can be differentiated through the Gram stain - an important diagnostic tool. Gram negative Gram positive Gram variable
i. Peptidoglycan (murein) Components a. Polysaccharide 1,4 linkages between N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) monomers
(Fig 4.12). Note : N-acetylmuramic acid is found only in Bacteria Polymers 10 to 65 monomers long
...NAM – NAG - NAM - NAG - NAM - NAG...
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b. Peptide chains
Tetrapeptide chains linked to M residues - composed of unusual amino acids (D- amino acids) – Why? L-alanine D-glutamic acid L-lysine (Gram positive) or diaminopimelic acid (DAP; Gram negative) D-alanine
There are either peptide interbridges (G-G-G-G-G: Gram positive) or direct peptide linkages (Gram negative) between tetrapeptides Results in a strong multilayer sheet or sacculus
Autolysins - enzymes used by the bacteria to recycle, reshape or restructure cell wall
Lysozyme Hydrolyes the 1,4 linkages between M and G monomers
Sources of lysozyme predators tears saliva chicken egg white
spheroplast - partial removal of cell wall
protoplast - complete removal of cell wall
Penicillin Prevents formation of peptides cross linkages between tetrapeptides Penicillin binds to transpeptidase Not effective against bacteria lacking cell walls such as mycoplasmas
ii. Gram positive cell wall Up to 20% of the organism peptidoglycan represents 50-90% of this structure relatively thick (ca. 40 nm – ranges from 20 to 80 nm) a thick peptidoglycan layer is more resistant to desiccation Polysaccharides such as teichoic acids (e.g., glycerophosphate or ribitol phosphate residues –
negatively charged) or teichuronic acids are bonded to the peptidoglycan or plasma membrane lipids
Putative function - bind to cations and regulate movement into and out of the cell- Prevent extensive cell wall lysis
Responsible for cell wall’s antigenicity
e.g., Bacilli, Staphylococci, Streptococci
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iii. Gram negative cell envelope more complex than Gram positive cell wall
Cell wall thin layer of peptidoglycan (ca. 2 to 7 nm) 1 - 10 % of the cell wall lipoproteins instead of teichoic acids
Outer membrane - lipid bilayer phospholipids proteins - e.g., porins lipoproteins – anchored to peptidoglycan The outer membrane may be linked to the plasma membrane in a number of places lipopolysaccharides (LPS)
composed of i) lipid A, ii) the core polysaccharide and iii) the O polysaccharide side chain. main structural component of outer half of outer membrane believed to aid in creating a
permeability barrier as well as contributes to negative charge of the cell surface. Protects pathogenic bacteria from host defenses The LPS (Lipid A componenet in particular) is frequently toxic to animals and known as
endotoxin (i.e., because it is still attached to cell). O polysaccharide is an antigen that is used to distinguish species of bacteria
The outer membrane is more permeable than the plasma membrane to most small molecules due to the presence of porin proteins
Less permeable than the plasma membrane to hydrophobic and amphipathic molecules - makes cells less susceptible to certain antibiotics.
Keeps periplasmic enzymes from diffusing away.
Periplasmic space (30 - 70 nm wide) Gel-like in consistency due to abundance of proteins
Import region where number of chemical reactions occur: oxidation-reduction reactions osmotic regulation solute transport hydrolysis protein secretion
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2. Archaeal cell wall No peptidoglycan, in particular lacking in N-acetylmuramic acid May be composed of
Pseudopeptidoglycan – N-acetylglucosamine and N-acetyltalosaminuronic acid linked by 1,3 linkages
Protein or glycoproteins - most common form of cell wall Polysaccharide
NOTE: Some Bacteria and Archaea do not have cell wallse.g., mycoplasma
Thermoplasma
3. Eukaryotic cell wall Like Bacteria and Archaea, not all eukaryotes have cell walls
Algal cell wall Polysaccharides are the major components
e.g., cellulose May contain high concentrations of calcium or silicon - diatoms
Fungi Many contain chitin - polysaccharide consisting of N-acetylglucosamine monomers. Composition is used in classification schemes
e.g., primitive Chytridiomycetes fungal cell walls lack chitin but contain cellulose
Protists Many protists have a pellicle for support – rigid layer of components beneath the plasma membrane. Pellicle is composed of protein
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C. Layers External to the Cell Wall
Prokaryotes Prokaryotes have a variety of layers outside the cell wall
Functions protection
ingestion dehydration loss of nutrients
attachment pathogenicity
Form thick or thin, rigid or flexible layers depending upon composition Variable composition – glycoproteins and polysaccharides
1. Capsule Rigid – tight matrix that excludes particles protein or polysaccharide
2. Slime layer loosely bound layer – easily deformed
3. Extracellular Polymeric Substance (EPS) glycocalyx that helps cells bind to surfaces and other cells – formation of biofilm
Glycocalyx – term that collectively refers to both capsule and slime layer
3. Surface layer (S-layer) nearly all bacteria and Archaea crystalline protein layer unknown function – may function as permeability or protective barrier
D. Genetic InformationDeoxyribonucleic acid (DNA) - macromolecule consisting of nucleotide monomers Backbone = 5'...-Phosphate-Sugar-Phosphate-Sugar -Phosphate-Sugar-…3'
Nucleotide = nucleoside plus phosphate
Nucleoside = deoxyribose + nitogenous base
Purines – adenine & guanine
Pyrimidines - cytosine & thymine
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Review structure of DNA – Chapter 2
1. Bacterial and Archaeal DNA These organisms do not have a nucleus – the bulk of the genetic material is found in the nucleoid
region
Chromosome single double stranded DNA molecule in the form of a covalently closed circular chromosome –
also known at the genophore Exceptions : Borrelia burgdorferi and some Streptomyces spp. have a linear chromosome;
Rhodobacter sphaeroides has two circular chromosomes
usually only one chromosome and it may be present as multiple copies in rapidly growing cells
DNA arranged into supercoiled domains that are stabilized with structural proteins
In some Archaea – DNA is extensively complexed with proteins that closely resemble histone proteins of eukaryotic organisms
Plasmids autonomously replicating units that usually contain only a few genes (< 30; 1 – 5% of the size of the
chromosome). Most the bacterial and archaeal genomes sequenced contain plasmids Usually covalently closed circles (CCC) but may be linear May contain one to many plasmids Range in size from several kbp to Mbp
Examples of plasmid coded factors (Table 3.3)1. R-plasmids - antibiotic resistance genes2. Bacteriocins3. Conjugal factors 4. Metabolic factors - substrate utilization or fixation5. Virulence factors - toxin production
2. Eukaryotic DNA Most possess a nucleus that contains the bulk of the genetic material Nucleus contains a number of linear chromosomes Chromosomes composed of DNA complexed with protein chromatin DNA associated with Histones in structural subunits called nucleosomes
Chloroplasts and mitochondria also contain small circular genomes
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E. Ribosomes Sites of protein synthesis Approximately 20 - 25 nm in diameter Large numbers may be present in cells (>10,000 in bacterial cells and more in eukaryotic cells) Number varies depending on the level of protein synthesis going on in the cell.
Bacteria and EukaryaArchaea
Ribosome 70 S* 80S
Large subunit 50 S 60S23S rRNA and 5S rRNA 25 - 28S rRNA and 5.8S rRNA Large number of proteins Large number of proteins
e.g., 34 proteins in E. coli
Small subunit 30S 40S16S rRNA 18S rRNALarge number of proteins Large number of proteins
e.g., 21 proteins in E. coli* Svedberg units (S)
Eukaryotic organisms have 70S ribosomes in their mitochondria and chloroplasts Implications in the endosymbiotic theory
Practical implications of ribosome structural differences
Antibiotic treatment
chloramphenicol all bind 70S bacterial tetracycline ribosomes and disrupt protein kanamycin synthesiserythromycinstreptomycin
diptheria toxin bind 70S archaeal and 80S eukaryotic ribosomes and anisomycin disrupts protein synthesis
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F. Cytoskeleton
Prokaryotic Cells For many years it was thought that prokaryotic cells lacked cytoskeletal elements. Recently homologues
have been discovered for all three elements of the eukaryotic cytoskeletone.g., FtsZ – tubulin homologue; widely observed in Bacteria and Archaea
MreB – actin homologue; Many rod shaped cellsCrescentin – intermediate filament proteins; Caulobacter
Eukaryotic Cells Have a well developed three dimensional network of fibrous proteins (microtubules, microfilaments and
intermediate filaments Microtubules and microfilaments are very dynamic structures – can be quickly disassembled and
assembled elsewhere
Functions Support Maintenance of cell shape Cell movement - e.g., muscle cell contraction, amoeboid movement, cilia Cell division (mitosis, cytokinesis and meiosis) Cell wall deposition Provides spatial organization and movement of organelles and cytosolic enzymes Regulation of biochemical activities in the cell – mechanical signaling
Cytoskeleton components
a) Microtubules thickest cytoskeletal elements - hollow rods - 25 nm found in the cytoplasm of all eukaryotes composed to and tubulin dimers readily assembled and disassembled grow by addition of subunits to ends centrosome - microtubule organizing centre (MOC) important in cell division a pair of centioles (9 sets of microtubule triplets) often found in the centrosome region of animal
cells. Replicate during cell division. May function in cell division but not necessary as they are generally not found in plant cells.
Functions compression resisting function cell motility (flagella and cilia) chromosome movement organelles movement cell shape
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b) Microfilaments thinnest cytoskeletal element - 7 nm in diameter composed of protein called actin readily assembled and disassembled
Functions tension bearing function muscle contraction (myosin motors molecules-burn ATP) cytoplasmic streaming (myosin motors molecules-burn ATP) cell motility (pseudopodia) cell division cell shape – three dimensional network just inside the plasma membrane
c) Intermediate filaments 8 to 12 nm in diameter diverse class composed of different protein subunits including keratins more permanent structures not readily assembled and disassembled like microtubules and
microfilaments
Functions tension bearing function maintenance of cell and organelle shape e.g. nuclear lamina fixing positions of certain organelles
G. Motility
Bacterial and Archaeal Movement
1. Flagellum (pl. flagella) one to many flagella up to 60 cell lengths/s
Atrichous – no flagellaMonotrichous - single polar flagellumAmphitrichous - single flagellum at each poleLophotrichous - polar tuft of flagellaPeritrichous - multiple flagella disgributed over the entire cell
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Parts of a prokaryotic flagellum (Fig 4.8)i. filament - whiplike extension that rotates - helical in shape – 15 to 20 µm long
composed of flagellin – highly conserved in bacteria
ii. curved hook - single protein - connects filament to motor
iii. Basal apparatus or motor composed of many proteins (~30) central rod a series of rings embedded in the cell wall, plasma membrane and outer membrane (Gram negative cells). This structure is around 20 nm in diameter
Mot proteins drive the flagellar motor - energy comes from proton motive force (about 1000 H+/rotation)
Fli proteins act as a switch
> 40 genes (fla, fli, flg) required for synthesis and motility (structural, export of components and timing of synthesis)
2. Gliding cells glide along a surface. Mechanism is unknown but there are several models
a) excreted slime adheres to surface pulls cells along - cyanobacteriab) movement of surface proteins - Flavobacterium
3. Gas Vesicles confer buoyancy on cells and allow to move up and down in a water column composed of two types of protein (97% of the gas vacuole is composed of GvpA (-sheets). The
remainder is made of GvpC (-helix) that acts like a cross linker between the GvpA molecules
4. Behavioural Responses to Stimuli In a heterogenous environment prokaryotes are capable of movement (taxis; pl. taxes) towards or
away from stimuli (light, heat, chemicals and electricity)
Chemotaxis movement towards or away from a chemical stimulus (chemoattractant or chemorepellent). Respond to temporal gradient Respond to very low levels of some materials – 10-8 M for some sugars
Types of Taxesphototaxis - light stimulus
scotophobotaxis - entering darkness has a negative effect on a cell
geotaxis - gravitational stimulimagnetotaxis - magnetic stimuliaerotaxis – oxygen stimulus
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osmotaxis – high osmotic strength stimulus
Bacteria lack spatial sensing capabilities- they are too small to sense a gradient along the cell length. Consequently they respond in a temporal fashion.1. Periodically sample environment e.g., chemoreceptors – sensory proteins2. Process information through a signal transduction pathway3. Control of direction of flagella rotation
Movement is through a series of a) alternating runs (straight line movement- counterclockwise rotation of flagella) and tumbles (reversal of
direction of flagella rotation) b) The direction of the next run is random; however, if there is a gradient of a chemical attractant or
repellent present, the random movements become biased If the organisms sense an increase in attractant concentration then this results in longer runs and
tumbles are less frequent. This is also the case if the cell senses a decrease in repellant concentration
Eukaryote Movement Cilia and flagella are the most prominent structures for movement
Cilia (sing. - cilium) and Flagella (singl. - flagellum) are composed of microtubules
Cilia and flagella are 0.25 µm in diameter A plasma membrane encases a core of microtubules arranged in the 9 + 2 pattern (Fig 4.23): and
outer ring of 9 evenly spaced doublets around 2 two single microtubules radial spokes and cross-linking proteins connect the microtubules; dynein arms (named after the protein composing these structures) connect microtubules anchored to cell by a basal body - identical in structure to centrioles chemical energy required for movement
Comparison of Flagella and CiliaLength Number Movement
Cilia 2 - 20 µm large number back and forth - rowing(100-1000’s)
Flagella 10 - 200 µm 1 to several undulating or snakelike(sperm cell)
The eukaryotic flagellum is much different in structure than prokaryotic flagella (Another difference between Prokaryotes and Eukaryotes!)
H. Attachment Structures of Prokaryotes
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Glycocalyx – discussed already
Pili and/or Fimbriae hair like proteinaceous projections used as attachment structures
fimbriae Slender tubes (3 – 10 nm in diameter) composed of helically arranged protein subunits function in attachment and twitching movement more numerous than pili
pili generally longer and thicker than fimbriae but fewer in number attachment between mating bacterial cells consist of phosphate-carbohydrate-protein (single type of pilin) F pilus - important structure involved in bacterial mating (conjugation) which is carried exclusively
by the donor cell
I. Inclusion bodies of Prokaryotes
Storage of energy or structural compounds Often form in response to excess or imbalance in nutrients that are available Usually bounded by a thin non-unit membrane
examples phosphate – polyphosphate – metachromacit granules sulfur glycogen or starch poly--hydroxyalkanoates (e.g., poly--hydroxybutyric acid - PHB) are common carbon reserves
produced by Bacteria and Archaeae.g., B. thuringienisis
YPD mediium – very rich medium – PHBNA medium – spore formation
J. Spores
Functions• reproduction• dispersal - fungi and some actinomycetes produces spores that are readily dispersed• survival under adverse conditions
1. Bacterial endospore
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Differentiated cells Formed within the cell – refractile body Dormant structures that are highly resistant to heat, desiccation, UV irradiation, chemical
disinfectant – Not a reproductive structure Found commonly in soil Contains little water Complex multilayer spore coat contains peptidoglycan and calcium dipicolinate (required for heat
reistance) in its core
Endospore producing bacteria - at least 16 genera, including Bacillus Clostridium Sporosarcina Oscillospira Desulfotomaculum
i) Endospore Structure
Exosporium thin delicate proteinaceous covering
Spore coat several protein layers Impermeable and responsible for spores resistance to chemicals
Cortex up to half the spore volume peptidoglycan (less cross linked than vegetative cell)
Core or spore wall c) usual cell wall
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Spore core plasma membrane, cytoplasm, nucleoid energy supply phosphoglycerate contains Ca2+ complexed with dipicolinic acid 10 – 30 % water content of vegetative cells – water moves freely in and out of endospores heat resistance of endospore is determined by state and amount of water in core pH is one unit lower than vegetative cells contains small acid-soluble spore proteins (SASP) which bind DNA and protect it from damage due
to UV, heat and desiccation. May also serve as a carbon and energy source during germination Ca2+ dipicolinic acid complexes and SASP form a gel in cytoplasm – gel like material excludes water
from the endospore protoplasm Low metabolic activity, no macromolecule synthesis and few or no mRNA molecules The core also contains DNA repair enzymes that repair the the DNA once the spore germinates
ii Sporulation (sporogenesis) a very complex inducible process and is controlled by > 200 sporulation specific genes. triggered by environmental conditions which are unfavourable for vegetative growth. In Bacillus
species C, N or P limitation. a multistage process (seven stages have been described for Bacilli) that can last up to 8 hours or
more. Vegetative cell or mother cell becomes compartmentalized forming a spore compartment through invagination of the plasma membrane (sporangium).
Endospores dormant for many years
If conditions become favourable for vegetative growth then the endospore can rapidly convert back to a vegetative cell.
Three stagesi) Activation prepares endospore for germination reversible process treatments like heating conditions endospore to germinate when placed in a nutrient solution
ii) Germination breaking of an endospore’s dormant state, germinants - such as glucose and certain amino acids may
induce gemination characterized by
loss of refractility loss of resistance to heat and chemicals loss of Ca dipicolinate and cortex components, and degradation of SASPs and increased ability to be stained by dyes
iii) Outgrowth develops into a vegetative cell uptake of water swelling macromolecule synthesis vegetative growth until encounters environmental triggers again
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K. Additional Features of Eukaryotic Cells
Review cell structures and concepts including Endomembrane system and all of its components Mitochondria Chloroplast Endosymbiotic theory – eukaryotic cells arose from larger cells engulfing smaller cells
Mitochondria and chloroplasts contain DNA – closed covalently circular form contain their own ribosomes – 70 S protein synthesis in these organelles is affected by antibiotics such as streptomycin that also kill
or inhibit bacteria rRNA sequences of mtDNA and cpDNA are more closely related to bacteria rRNA
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