Bacterial Cell Structure, Metabolism, and Nutrition

Posted on Dec 8, 2024 in Biology

Peptidoglycan: Chemical Composition

The repeating unit is:

  • N-acetylglucosamine (NAG)
  • N-acetylmuramic (NAM)

These are joined together by β (1→4) bonds. The various disaccharide units are joined together by β (1→4) bonds. This link may be broken by lysozyme. The tetrapeptide chain running from the -COOH group of each NAM lactyl often contains:

  • L-alanine
  • D-glutamic acid
  • m-DAP
  • D-alanine

The Peptidoglycan of Gram-Negative Bacteria

  • Usually, peptidoglycan (PG) has one layer.
  • The chains are joined by peptide bonds directly between the α-NH2 of m-DAP in one string with the -COOH of D-alanine of another string.
  • It forms a loose mesh with large pores: 50% of NAM lacks tetrapeptides.
  • In spirochetes, the diamino acid in position number 3 is L-ornithine (instead of m-DAP).

Global Peptidoglycan Structure in Gram-Positive Bacteria

  • Multiple layers of PG (different levels, up to 50 in some Bacillus species).
  • Crossovers between chains of the same level and from one level to the next higher or lower.
  • Most have tetrapeptides in NAM.
  • Most links are involved in tetrapeptides.
  • The result is a thick three-dimensional network, with smaller pores, more compact than in Gram-negative bacteria.

Structure-Function Relationships in Peptidoglycan

  • High stiffness to endure protoplast osmotic forces (5-15 atm). Stiffness comes from:
    • The degree of crosslinking.
    • The β (1→4) link is very compact.
  • The alternating NAM and NAG give more stability than alternating L- and D-amino acids (side chains on the same side, forming hydrogen bridges).
  • At the same time, greater flexibility to support changes in protoplast osmotic pressure and cell shape.
  • It is very permeable.
  • It can act as an endotoxin (somatic antigen O).

Walls of Acid-Fast Bacteria (AFB)

Special walls in certain Gram-positive bacteria like Nocardia and Mycobacterium resist decolorization with hydrochloric ethanol (acid-fast). This property is derived from mycolic acids (waxes).

Mycolic Acids

β-hydroxy fatty acids are branched, very long-chain glycolipids. They form part of a very peculiar skeleton of the cell wall:

PG → arabinogalactan → mycolic acids

Role Conferred by the AFB Wall

  • Elements and waxy consistency of colonies in Petri dishes.
  • In liquid form, they grow in clumps.
  • Great impermeability and resistance to desiccation.
  • Resistance to antibacterial agents, detergents, oxidizers, and bases.

Bacterial Nutrition

Autotrophy and heterotrophy. Macronutrients and micronutrients. Universal and particular nutrients. N2 fixation. Growth factors.

Concepts

  • Phototrophy: Capturing light energy.
    • Photolithotrophy: Capturing light energy exclusively for nutrition from inorganic substances.
    • Photoorganotrophy: Capturing light energy with the requirement for organic substances.
  • Chemotrophy: Obtaining energy from chemicals.
    • Chemolithotrophy: Obtaining chemical energy from inorganic substances.
    • Chemoorganotrophy: Obtaining chemical energy from organic substances.
  • Fermentations: The regeneration of NAD+ and fermentation products.
  • Some types of fermentation: lactic, alcoholic, mixed acid, butylene glycol, acetone-butyric.

Oxygen Needs

  • Aerobic bacteria: Those that require O2 for metabolism. They perform the oxidation of organic matter in the presence of molecular O2, i.e., they perform cellular respiration.
  • Anaerobic bacteria: Those that do not use molecular O2 in their biological activity. Energy production is carried out by fermentative catabolism. We can distinguish two groups within them:
    • Facultative anaerobic bacteria: They can live in environments with or without oxygen.
    • Strictly anaerobic bacteria: They can only survive in environments lacking oxygen. As an example, Clostridium.

Temperature Needs

  • Psychrophiles (0º – 20ºC)
  • Mesophiles (20º – 40ºC)
  • Thermophiles (40º – 90ºC)

Most bacteria are mesophilic, especially human pathogens that require 37°C.

Basic Concepts

  • Nutrition: Capturing substances from the environment to grow (= nutrient).
  • Nutrients are needed for:
    • Energy (in chemotrophs) → maintenance.
    • Biosynthetic purposes (anabolic, plastic reactions).
  • Catabolism and anabolism: The role of energy production in linking these processes.
  • Macronutrients: C, H, O, N, P, S, K, Mg.
  • Micronutrients (trace elements): Co, Cu, Zn, Mo, etc.

The microbial world has a surprising metabolic diversity. Some metabolisms have evolved only in prokaryotes. Examples:

  • In heterotrophs: From methylotrophic (using C1 compounds) to the versatile Pseudomonas, using more than 100 types of organic C, including aliphatic and cyclic hydrocarbons.
  • Chemolithoautotrophs grow in darkness on media based solely on mineral salts.
  • N2 fixation has only evolved in prokaryotes.

Specific Classes of Nutrients

  • Universal, required in this form for all prokaryotes: H2O, CO2, PO43-, and minerals.
  • Specific elements that can be captured in different ways, depending on the species:
    • N: As inorganic N (oxidized or reduced), organic N, or N2 fixation (in the absence of combined N).
    • S: As inorganic or organic S.

Growth Factors

  • They are specific organic molecules that bacteria cannot produce for themselves and must be taken from the environment.
  • They are required in very small quantities.
  • They do not have a plastic function, nor do they act as a source of energy.
  • They are usually coenzymes or their precursors, such as vitamins.
  • Examples:
    • Brucella requires biotin, niacin, thiamin, and pantothenic acid.
    • Haemophilus needs heme and pyridine nucleotides.

Antibiotics and the Rise of General Microbiology

Antibiotics

  • Domagk (1935): Red Prontosil against pneumococci.
  • The era of sulfonamides.
  • Development of asepsis.
  • Fleming (1929): Crude extract of penicillin (from the fungus Penicillium notatum).
  • Chain and Florey (1940-4): Purified penicillin. Use in World War 2.
  • Waksman (1944): Discovery of streptomycin from Streptomyces griseus.
  • After the war, many antibiotics were found, produced mainly by actinomycetes.

Development of Antibiotics

The rise of general microbiology: lithotrophy and autotrophy.

Sergei Winogradsky

  • 1888: Bacteria thrive on iron ore.
  • 1889: Sulfur bacteria oxidize sulfide or S and get energy from it (lithotrophy).
  • 1890: Nitrifying bacteria fix CO2 with the energy of the oxidation of ammonium or nitrate (chemolithoautotrophy).
  • First isolation of nitrogen-fixing bacteria (Clostridium pasteurianum).
  • Explained N cycling in the biosphere.

The Rise of General Microbiology: Nitrogen-Fixing Bacteria

  • Beijerinck:
    • Discovery of Azotobacter (1901).
    • Shows that it incorporates atmospheric N (1909).
  • Beijerinck (1888) and Hellriegel & Willfahrt (1888):
    • Role of Rhizobium in legume-fixing symbiosis.
  • Incorporation of microbiology into agricultural colleges and experimental stations.

Differences Between Prokaryotes and Eukaryotes

Prokaryotes

  • Chromosome:
    • A single circular DNA chromosome.
    • No nuclear membrane (no authentic nucleus).
    • No histones.
    • Replication: No mitosis.
  • Cytoplasmic Organelles:
    • No eukaryotic-type organelles.
    • No cytoskeleton.
    • 70S ribosomes.

Bacterial Size, Shape, and Groups

Size of Prokaryotes

  • Usually smaller than eukaryotic cells.
  • But there are bacteria:
    • Giants (≥ 0.5 mm).
    • Dwarfs (< 0.1 micron).
  • A typical size: 0.5 x 3 microns.

Small size has methodological implications:

  • Microscopes and stains are usually used.
  • The vast majority of studies are performed with vast populations, from which averages are taken.
  • It is very rare to study an individual bacterium.

Typical Shapes

  • Cocci
  • Bacilli
  • Spirilla
  • Vibrios
  • Rings
  • Other shapes: Filaments, almost closed with extensions (prosthecae).

Bacterial Capsule: Chemical Composition and Structure

Chemical Composition

  • Hetero-anionic polysaccharide capsules.
  • Neutral hetero-polysaccharide capsules (levan, dextran, pentanes, cellulose).
  • Alginate capsules.
  • Polypeptide capsules (in Bacillus).
  • Capsular K antigens.

Role and General Properties Conferred by the Capsule

  • Improves diffusion of nutrients.
  • Protection against desiccation.
  • Prevents phagocytosis.
  • Protection against antibacterial agents.
  • Adhesion to substrates.

Role of the Capsule in Adhesion to Substrates

  • To substrates, forming microcolonies of the same species and consortia of different species, with metabolic benefits. This has economic consequences: corrosion of pipes, the formation of dental plaque and caries, and the formation of biofilms on catheters and prostheses.
  • To living substrates: They act as adhesins, with beneficial effects such as colonization of native flora in the intestine of mammals. In pathological systems, they act as virulence factors, sometimes used to escape the immune system.

Bacterial Groups

  • A single plane of division:
    • In two cells: Diplococci, diplobacilli.
    • Chains of various cells: Streptococci, streptobacilli.
  • Two or more planes of division (in cocci):
    • Two perpendicular planes: Tetrads.
    • Three orthogonal planes: Sarcinae (cubic packages).
    • Many random planes: Staphylococci.

Structure of the Prokaryotic Cell

  • Capsule.
  • Cell wall.
  • Cytoplasmic membrane.
  • Cytoplasm includes:
    • Genome (nucleoid), consisting of a chromosome.
    • Ribosomes.
  • May also exist: Plasmids, flagella, fimbriae (= pili), spores.

Capsules and Mucilaginous Layers: General Concepts

  • Capsules are strictly rigid and comprehensive.
  • Mucilaginous layers are flexible and peripheral.
  • Glycocalyx: Surface layers composed of polysaccharides.
  • Important for adhesion between cells and colonization of niches. Many pathogens also use them to protect themselves from antibacterial agents.