MICR2208 Lecture 3: Prokaryotic Structure and Function 1

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1 MICR2208 Lecture 3: Prokaryotic Structure and Function 1 Diversity of Prokaryotes Size Not all prokaryotes are similar in size as they all differ, however, most of the prokaryotes cannot be seen from the naked eye (except the adult roundworm) Most of the prokaryotic cells, such as bacillus megaterium, Escherichia coli and mycoplasma are smaller than the eukaryotic cells (yeast) and can be viewed under a light microscope Shape There are 5 basic shapes for prokaryotic cells. They can be: - Spherical Coccoid look like a coccus,.e.g. staphylococcus spherical in shape - Cylindrical Rod/Bacillus only see a side/top view when viewed under a microscope seen as a rectangle, e.g. Ecoli - Spiral Spirillium looks like a snake - Helical Spirochete looks like bends in between - Square only one square in shape haloquadratum an archaea seen in aquatic environments

2 Some prokaryotic cells are Pleomorphic they do not have a definite shape as they have changes in their morphological structure depending on their environment, e.g. actinomyces israeli: Arrangement e.g. Coccoidal (spherical) shaped cells may be categorized in one group because of their shape, however, there are different subgroups classified according to their arrangement of subunits. (a) Chains - A coccus can divide in one plane as when it divides it may remain as a chain of coccus (cocci) if the replication is really fast or a coccus does not detach to itself (streptococci) or it may form a diplococcus (Neisseria species Neisseria gonorrhea and Neisseria meningitis) (b) Packets a coccus that may divide in 2 or more planes perpendicular to one another forming a packet of cocci e.g. sarcina (c) Clusters a coccus divides in several random planes forming a cluster of cocci but in unusual irregular shapes e.g. staphylococci Binary Fission Bacteria

3 When one bacterial cell undergoes repeated rounds of division on a solid surface, it results in a single colony composed of identical cells. This repeated dividing mechanism is a very fast process (e.g. Escherichia coli undergoes one round of cell division in 20 min). Process: 1) DNA duplication of the prokaryotic chromosome in the bacterial cell 2) After DNA duplication is over, there is cell elongation process by which signals are sent to elongate the cell (widen) at which proteins attach to the cell wall and start manufacturing peptidoglycans and elongate/spread out the cell wall. 3) Once the cell has been elongated to a particular length required for cell division, the cell will signal a particular protein to form a ring at the middle of the cell as this protein is known as FDZ protein 4) As the ring is formed by the protein, the protein will pinch the 2 cells in between, separating the single cell to form 2 identical replicas and gradually the new cell walls forms and 2 new cells are formed with identical DNA. Composition The bacterial cell is composed of water (70%) and dry weight (30%): Dry weight is composed of: (a) DNA 3% (b)rna 12% - more abundant (c) Protein (70% of the dry weight in 30%) - Found in ribosomes (10 4 RNA protein particles involved in protein synthesis, MW = 3 x 10 6 ) while other proteins are in the form of enzymes (catalyse biochemical reactions within the cell). Some are also in the form of porins. (d)cell Wall and cell membranes (15% of the dry weight in 30%) - Polysaccharides (5%) - Lipid (6%) - Phospholipid (4%) Structure 1) Nucleoid - The space where genetic information is stored, in the form of DNA

4 - The nucleoid consists of doublestranded DNA in a chromosome. The DNA is deoxyribonucleic acid (dsdna) as it can be circular, linear, depending on the situation used such as the relaxed or may have nature. multiple such as in supercoiled - Complexed to basic proteins that enable supercoiling size <0.2 um in diameter - Different lengths (measured in 1000 base pair units = kilobase) - Encodes genes which are essential for life important for survival of bacterium There is a second type of double-stranded DNA that is seen in a bacterial cell as this is the Plasmid: - Circular (single or multiple copies of DNA within a plasmid of the bacterial cell) - Supercoiled dsdna (2-200kb) - Replicate independently of the host chromosome (host chromosome replicates only when the cell undergoes division - however plasmids are able to replicate independent to the signals sent for cell division) - Carries genes which are not essential to the host but may be useful in certain environments sexual reproduction (e.g. F plasmid fertility plasmid bacterial can undergo sexual reproduction sharing of plasmids) resistances, e.g. antibiotics, pesticides Virulence genes enhance the metabolism allows the bacteria to live in variety of environments 2) Cytoplasm - The site where all the metabolic reactions take place

5 Composition: - 70% water - contains ribosomes: composed of proteins/ribonucleic acid (RNA) 2 protein subunits: 30S and 50S (total = 80S) essential for protein synthesis - Highly organized cytoskeletonlike system within the matrix full of proteins for cell division allows the cell structure to remain in shape while moving and also makes use of the proteins for the cell division Optional: the cytoplasmic matrix has a variety of inclusion bodies specific to different bacteria. These can be organic (contain carbon) or inorganic inclusion bodies: (a) Organic Inclusion bodies - Glycogen a(1-4) glucose polymers with branching side chains function: energy reserve example: clostridium pasteurianum - Poly-beta-hydroxybutyrate (PHB)- ester linked beta-hydroxybutyrate polymers function: energy reserve example: ferrobacillus ferrooxidans - Cyanophycin polypeptides of arginine and aspartic acid function: nitrogen reserve example: cyanobacteria - Carboxysomes polyhedral paracrystalline arrangement of ribulose-1,5-biphosphate carboxylase function: carbon dioxide fixation - Gas vacuole containing lots of gases such as CO 2 function: flotation creates buoyancy - allows the cells to move up and down (b) Inorganic Inclusion bodies - Polyphosphate granules (volutin) e.g. corynebacterium diphtheriae - Sulfur granules e.g. purple photosynthetic bacteria, such as Thiomargarita - Magnetosome found in magnetic based bacteria intracellular chains of magnetite (Fe 3 or Fe 4 )

6 Fe 3 - bounded by a membrane e.g. aquaspirillium magnetotacticum Some bacterial cells have internal membranes as most common cells are photoautotrophs which have: Thylakoid membranes: - Important in Photosynthesis - Lined with phycobilisomes containing pigments required for photosynthesis (chlorophyll AMC) - E.g. synechocystis sp. 3) Plasma membrane Composition: - Amphipathic phospholipids (head hydrophilic (polar) and tail hydrophobic (non-polar)) organized as a bilayer - Proteins variety of proteins differing in shape and function Function: - Selectively permeable allows certain molecules in and out of the cell (having proteins that act as porins that guard the entry and exit of the cell). Controls the exchange of gases, nutrients etc. Hence, nutrient transport and energy metabolism - Involved in first step in transport of proteins out of the cell - Invaginations, termed mesosomes, are used for DNA replication during cell division 4) Cell wall (Envelope) - All bacterial cells have a cell wall except mycoplasma - Made of peptidoglycan but this can be used to differentiate between a bacterium as gram positive or gram negative - It is rigid as it maintains the shape of the bacterium - Prevents the cell from lysing (swelling up with too much water intake) - It provides protection from: osmotic shocks action of anti-bacterial agents (e.g. antibiotics, antiseptics etc.) - Contains components contributing to pathogenicity, in particular, inflammation endotoxin (lipopolysaccharide - LPS) 5) Optional

7 - Vacuoles, capsules, slime layers, pili, flagella and endospores Gram Staining Gram staining is a technique used to differentiate a bacterium from gram negative or gram positive cells: 1) A cell is fixed onto a slide (with a layer of bacteria) and fix the slide by pulsing the slide through fire 2) And then we add crystal violet to the slide crystal violet binds to the peptidoglycan layer 3) Then we treat the slide with iodine this chemical causes crystal violet to remain stuck to the peptidoglycan layer 4) We then decolorize the cell by adding 100% alcohol as the alcohol takes away crystal violet with the iodine also. HOWEVER: - In gram positive because there is a lot more peptidoglycan density (layer) as compared to gram negative, the gram positive bacterial cell is not decolorized completely, leaving purple in color. - In gram negative because there is very thin peptidoglycan density (layer) as compared to gram positive, the gram negative bacterial cell decolorizes completely. Therefore, we then use a counter stain (such as carbol fuchsin) to stain the cells that are not purple, to pink. Therefore, in the slide, some cells will appear purple, some as pink. As we know, purple cells are gram positive and so pink cells are gram negative. Gram Positive cell wall: - Cytoplasmic membrane with the transport proteins embedded within - Peptidoglycan (cell wall) with teichoic acid the cell wall is thick (30-60nm) with layers of N-acetylglucosamine acids N-acetylmuramic acid e.g. bacillus, staphylococcus, streptococcus

8 Gram negative cell wall: - Inner cytoplasmic membrane with the transport protein embedded within - Very thin peptidoglycan (cell wall) 2-3nm. This peptidoglycan layer lies in a space called the periplasm as this space is between the inner membrane of the cytoplasmic membrane and the outer membrane of the cytoplasmic membrane - Outer cytoplasmic membrane with porin proteins and lipoproteins embedded within and lipopolysaccharide (LPS) system extending outwards responsible for causing inflammation (endotoxin) - e.g. escherichia, Neisseria, pseudomonas

9 Detailed Comparison table End of Lecture 3: Prokaryotic Structure and Function 1

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