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Introduction
1. Anatomy
2. Microbiology
2.1 General bacteriology
2.1.1 Structure of bacteria and appendages
2.1.2 Virulence factors, extracellular products, and toxins
2.1.3 Bacterial growth and metabolism
2.1.4 Bacterial genetics
2.1.5 Bacterial replication
2.1.6 Mechanism of action of antibiotics
2.1.7 Antibiotics inhibiting bacterial protein synthesis
2.1.8 Mechanism of antibacterial resistance in bacteria
2.1.9 Additional information
2.2 Introduction to systemic bacteriology
2.3 Gram positive cocci
2.4 Gram negative cocci
2.5 Gram positive bacilli
2.6 Gram negative bacilli
2.7 Other important bacteria
2.8 Virology
2.9 Parasitology
2.10 Mycology
3. Physiology
4. Pathology
5. Pharmacology
6. Immunology
7. Biochemistry
8. Cell and molecular biology
9. Biostatistics and epidemiology
10. Genetics
11. Behavioral science
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2.1.1 Structure of bacteria and appendages
Achievable USMLE/1
2. Microbiology
2.1. General bacteriology

Structure of bacteria and appendages

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Bacteria can be classified by shape as follows:

  1. Cocci (spherical)
  2. Bacilli (rod shaped)
  3. Spirochetes (coiled)
  4. Pleomorphic (variable shapes)

Depending on their arrangement, bacteria can be:

  1. Diplococci (pairs of bacilli)
  2. Streptococci (chains of bacilli)
  3. Staphylococci (grape like clusters)

Bacterial cell wall

  1. All bacteria are bounded by a cell wall except Mycoplasma (they have only a cell membrane and no cell wall).
  2. The cell wall is made of an inner peptidoglycan layer, and outside that is the outer membrane.
  3. The peptidoglycan layer is much thicker in Gram positive compared to Gram negative bacteria. It has a carbohydrate backbone composed of alternating units of N Acetyl Muramic Acid and N Acetyl Glucosamine. Attached to the Muramic Acid molecules is a tetrapeptide made of both D and L amino acids. D Alanine is responsible for cross links between tetrapeptides.
  4. The outer membrane consists of Lipopolysaccharide (LPS), Lipoprotein, and Phospholipids. It contains Porin proteins, which act as channels for the transport of sugars, amino acids, antimicrobials, etc.
  5. LPS has three components - Phospholipid A (endotoxin action), core polysaccharide, and outer polysaccharide (somatic or O Antigen).
  6. Between the outer membrane and cytoplasmic membrane is the periplasmic space, which contains enzymes such as beta lactamase.
  7. The outer membrane and periplasmic space are absent in Gram Positive bacteria.
  8. Acid Fast Bacilli cannot be stained by the Gram stain, but they appear pinkish when counter stained with carbol fuchsin (a red-pink stain), and they resist decolorization with acid alcohol. This is due to their cell wall being rich in special lipids called Mycolic Acids.
Gram positive versus Gram negative cell wall
Gram positive versus Gram negative cell wall

Bacterial ribosomes

  1. Bacterial ribosomes are 70S in size, with 50S (large) and 30S (small) subunits.
  2. 50S unit components: 23S rRNA (has peptidyl transferase activity) and 5S rRNA (confers stability to the 3D structure of ribosomes) and involved in signal transmission during translation).
  3. 30S unit has 16S rRNA, which has the substrate binding A, P and E sites.

Bacterial DNA

It is a single, circular DNA molecule with about 2000 genes. No histones or nucleoli are present.

Plasmids

  1. Extrachromosomal, circular, double stranded DNA that is capable of replicating independently of the bacterial chromosome.

  2. They may exist independently of nuclear DNA, or sometimes they may be integrated into nuclear DNA.

  3. Types

    1. Transmissible Plasmids: Can be transferred between cells by conjugation, large, present in 1-3 copies per cell, carry genes for sex pilus and transfer enzymes.
    2. Non Transmissible Plasmids: Cannot be transferred between cells, small, exist in 10-60 copies per cell.

  4. Plasmids carry genes for antibiotic resistance, resistance to heavy metals, genes for Pili (bacterial adherence) and Exotoxins among others.

Transposons

  1. “Jumping Genes” that can move between nucleus to plasmid and vice versa both within and between cells.
  2. Have short DNA sequences called Inverted Repeats at each end.
  3. Replicative Transposition is when transposons move by replicating their DNA.
  4. Direct Transposition is when they are excised from their original site to attach to a new site without being replicated.
  5. Transposons code for antibiotic resistance enzymes, toxins etc.
  6. They cannot replicate independently.
  7. Insertion Sequences are smaller transposons with fewer bases (about 1000 base pairs).

Capsule

  1. Polysaccharide covering present outside the cell wall of some bacteria.
  2. In Bacillus anthracis the capsule is made of D Glutamic Acid.
  3. Capsule is a virulence factor for bacteria as it protects from phagocytosis.

Flagella

  1. Flagella are whiplike appendages made up of protein flagellin. They use ATP for energy needed for movement. They are composed of a Filament, Hook and Basal Body.
  2. Axial Filaments are internal flagella seen in Spirochetes.
  3. Because they help bacteria move, they are important in the pathogenesis of diseases like UTI, Typhoid etc.
  4. The protein flagellin is a PAMP (Pathogen Associated Molecular Pattern), and it induces innate immunity.

Pili

  1. Hair like structure present on bacterial cell wall made of protein Pilin.
  2. Involved with bacterial adhesion and colonization.
  3. Pili are antigenic.
  4. Not involved with motility.
  5. Sex Pilus is involved in conjugation.

Spores

  1. Dormant, highly resistant structures formed by bacteria in response to lack of nutrients or adverse environmental conditions.
  2. Composed of a thick keratin coat and dipicolinic acid (calcium ion chelator), which makes it resistant to heat, radiation, chemicals, dehydration and antibiotics.
  3. Spores can be killed by steam sterilization for 20-30 mins under pressure (autoclave) at 121 degree celsius.
  4. Depending on location and shape spores can be classified as follows:
Central/Equatorial Clostridium bifermentans (spindle shaped)
Sub Terminal Clostridium perfringens (club shaped)
Terminal and oval Clostridium tertium (tennis racket)
Terminal and spherical Clostridium tetani (drumstick)

Bacterial classification by shape and arrangement

  • Shapes: Cocci (spherical), Bacilli (rod), Spirochetes (coiled), Pleomorphic (variable)
  • Arrangements: Diplococci (pairs), Streptococci (chains), Staphylococci (clusters)

Bacterial cell wall

  • Absent in Mycoplasma; all others have peptidoglycan layer
  • Gram positive: thick peptidoglycan, no outer membrane/periplasmic space
  • Gram negative: thin peptidoglycan, outer membrane with LPS (Phospholipid A = endotoxin), porins, periplasmic space (beta lactamase)
  • Acid Fast Bacilli: mycolic acid-rich wall, resist Gram stain, stain with carbol fuchsin

Bacterial ribosomes

  • 70S ribosome: 50S (23S rRNA—peptidyl transferase, 5S rRNA—stability/signal) + 30S (16S rRNA—A, P, E sites)

Bacterial DNA

  • Single, circular chromosome (~2000 genes)
  • No histones or nucleoli

Plasmids

  • Extrachromosomal, circular, double-stranded DNA
  • Types:
    • Transmissible: conjugation, large, 1-3 copies, sex pilus/transfer genes
    • Non-transmissible: not transferred, small, 10-60 copies
  • Carry genes for antibiotic resistance, heavy metal resistance, pili, exotoxins

Transposons

  • “Jumping genes”—move between chromosome and plasmid
  • Inverted repeats at ends
  • Replicative (copy) or direct (cut-paste) transposition
  • Code for resistance enzymes, toxins; cannot replicate independently
  • Insertion sequences: small transposons (~1000 bp)

Capsule

  • Polysaccharide layer outside cell wall (D-glutamic acid in Bacillus anthracis)
  • Virulence factor—protects from phagocytosis

Flagella

  • Whiplike, made of flagellin (PAMP), ATP-driven movement
  • Structure: filament, hook, basal body
  • Axial filaments (internal) in spirochetes
  • Motility aids pathogenesis (e.g., UTI, typhoid)

Pili

  • Hairlike, made of pilin
  • Function: adhesion, colonization, antigenic
  • Not for motility
  • Sex pilus: conjugation

Spores

  • Dormant, highly resistant (keratin coat, dipicolinic acid)
  • Survive heat, chemicals, dehydration, antibiotics
  • Killed by autoclave (121°C, 20-30 min)
  • Classified by location/shape (e.g., central—spindle, subterminal—club, terminal—tennis racket/drumstick)

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Structure of bacteria and appendages

Bacteria can be classified by shape as follows:

  1. Cocci (spherical)
  2. Bacilli (rod shaped)
  3. Spirochetes (coiled)
  4. Pleomorphic (variable shapes)

Depending on their arrangement, bacteria can be:

  1. Diplococci (pairs of bacilli)
  2. Streptococci (chains of bacilli)
  3. Staphylococci (grape like clusters)

Bacterial cell wall

  1. All bacteria are bounded by a cell wall except Mycoplasma (they have only a cell membrane and no cell wall).
  2. The cell wall is made of an inner peptidoglycan layer, and outside that is the outer membrane.
  3. The peptidoglycan layer is much thicker in Gram positive compared to Gram negative bacteria. It has a carbohydrate backbone composed of alternating units of N Acetyl Muramic Acid and N Acetyl Glucosamine. Attached to the Muramic Acid molecules is a tetrapeptide made of both D and L amino acids. D Alanine is responsible for cross links between tetrapeptides.
  4. The outer membrane consists of Lipopolysaccharide (LPS), Lipoprotein, and Phospholipids. It contains Porin proteins, which act as channels for the transport of sugars, amino acids, antimicrobials, etc.
  5. LPS has three components - Phospholipid A (endotoxin action), core polysaccharide, and outer polysaccharide (somatic or O Antigen).
  6. Between the outer membrane and cytoplasmic membrane is the periplasmic space, which contains enzymes such as beta lactamase.
  7. The outer membrane and periplasmic space are absent in Gram Positive bacteria.
  8. Acid Fast Bacilli cannot be stained by the Gram stain, but they appear pinkish when counter stained with carbol fuchsin (a red-pink stain), and they resist decolorization with acid alcohol. This is due to their cell wall being rich in special lipids called Mycolic Acids.

Bacterial ribosomes

  1. Bacterial ribosomes are 70S in size, with 50S (large) and 30S (small) subunits.
  2. 50S unit components: 23S rRNA (has peptidyl transferase activity) and 5S rRNA (confers stability to the 3D structure of ribosomes) and involved in signal transmission during translation).
  3. 30S unit has 16S rRNA, which has the substrate binding A, P and E sites.

Bacterial DNA

It is a single, circular DNA molecule with about 2000 genes. No histones or nucleoli are present.

Plasmids

  1. Extrachromosomal, circular, double stranded DNA that is capable of replicating independently of the bacterial chromosome.

  2. They may exist independently of nuclear DNA, or sometimes they may be integrated into nuclear DNA.

  3. Types

    1. Transmissible Plasmids: Can be transferred between cells by conjugation, large, present in 1-3 copies per cell, carry genes for sex pilus and transfer enzymes.
    2. Non Transmissible Plasmids: Cannot be transferred between cells, small, exist in 10-60 copies per cell.

  4. Plasmids carry genes for antibiotic resistance, resistance to heavy metals, genes for Pili (bacterial adherence) and Exotoxins among others.

Transposons

  1. “Jumping Genes” that can move between nucleus to plasmid and vice versa both within and between cells.
  2. Have short DNA sequences called Inverted Repeats at each end.
  3. Replicative Transposition is when transposons move by replicating their DNA.
  4. Direct Transposition is when they are excised from their original site to attach to a new site without being replicated.
  5. Transposons code for antibiotic resistance enzymes, toxins etc.
  6. They cannot replicate independently.
  7. Insertion Sequences are smaller transposons with fewer bases (about 1000 base pairs).

Capsule

  1. Polysaccharide covering present outside the cell wall of some bacteria.
  2. In Bacillus anthracis the capsule is made of D Glutamic Acid.
  3. Capsule is a virulence factor for bacteria as it protects from phagocytosis.

Flagella

  1. Flagella are whiplike appendages made up of protein flagellin. They use ATP for energy needed for movement. They are composed of a Filament, Hook and Basal Body.
  2. Axial Filaments are internal flagella seen in Spirochetes.
  3. Because they help bacteria move, they are important in the pathogenesis of diseases like UTI, Typhoid etc.
  4. The protein flagellin is a PAMP (Pathogen Associated Molecular Pattern), and it induces innate immunity.

Pili

  1. Hair like structure present on bacterial cell wall made of protein Pilin.
  2. Involved with bacterial adhesion and colonization.
  3. Pili are antigenic.
  4. Not involved with motility.
  5. Sex Pilus is involved in conjugation.

Spores

  1. Dormant, highly resistant structures formed by bacteria in response to lack of nutrients or adverse environmental conditions.
  2. Composed of a thick keratin coat and dipicolinic acid (calcium ion chelator), which makes it resistant to heat, radiation, chemicals, dehydration and antibiotics.
  3. Spores can be killed by steam sterilization for 20-30 mins under pressure (autoclave) at 121 degree celsius.
  4. Depending on location and shape spores can be classified as follows:
Central/Equatorial Clostridium bifermentans (spindle shaped)
Sub Terminal Clostridium perfringens (club shaped)
Terminal and oval Clostridium tertium (tennis racket)
Terminal and spherical Clostridium tetani (drumstick)
Key points

Bacterial classification by shape and arrangement

  • Shapes: Cocci (spherical), Bacilli (rod), Spirochetes (coiled), Pleomorphic (variable)
  • Arrangements: Diplococci (pairs), Streptococci (chains), Staphylococci (clusters)

Bacterial cell wall

  • Absent in Mycoplasma; all others have peptidoglycan layer
  • Gram positive: thick peptidoglycan, no outer membrane/periplasmic space
  • Gram negative: thin peptidoglycan, outer membrane with LPS (Phospholipid A = endotoxin), porins, periplasmic space (beta lactamase)
  • Acid Fast Bacilli: mycolic acid-rich wall, resist Gram stain, stain with carbol fuchsin

Bacterial ribosomes

  • 70S ribosome: 50S (23S rRNA—peptidyl transferase, 5S rRNA—stability/signal) + 30S (16S rRNA—A, P, E sites)

Bacterial DNA

  • Single, circular chromosome (~2000 genes)
  • No histones or nucleoli

Plasmids

  • Extrachromosomal, circular, double-stranded DNA
  • Types:
    • Transmissible: conjugation, large, 1-3 copies, sex pilus/transfer genes
    • Non-transmissible: not transferred, small, 10-60 copies
  • Carry genes for antibiotic resistance, heavy metal resistance, pili, exotoxins

Transposons

  • “Jumping genes”—move between chromosome and plasmid
  • Inverted repeats at ends
  • Replicative (copy) or direct (cut-paste) transposition
  • Code for resistance enzymes, toxins; cannot replicate independently
  • Insertion sequences: small transposons (~1000 bp)

Capsule

  • Polysaccharide layer outside cell wall (D-glutamic acid in Bacillus anthracis)
  • Virulence factor—protects from phagocytosis

Flagella

  • Whiplike, made of flagellin (PAMP), ATP-driven movement
  • Structure: filament, hook, basal body
  • Axial filaments (internal) in spirochetes
  • Motility aids pathogenesis (e.g., UTI, typhoid)

Pili

  • Hairlike, made of pilin
  • Function: adhesion, colonization, antigenic
  • Not for motility
  • Sex pilus: conjugation

Spores

  • Dormant, highly resistant (keratin coat, dipicolinic acid)
  • Survive heat, chemicals, dehydration, antibiotics
  • Killed by autoclave (121°C, 20-30 min)
  • Classified by location/shape (e.g., central—spindle, subterminal—club, terminal—tennis racket/drumstick)