WEEK 2: INTRODUCTION TO BACTERIAL STRUCTURE AND CLASSIFICATION

Question 1

What is microbiology?

Answer 1

‘The study of living organisms which are too small to be viewed by the ‘unaided eye’ but visible with a microscope ‘

Question 2

Outline organisms which can be studied in micro-biology.

Answer 2

Range from tiny viruses to larger bacteria, protozoa, algae, fungi & some parasites.

Question 3

Microorganisms: WHY STUDY THEM?

Answer 3

Their pathogenicity, transmissibility & provocation of the immune system make them significant in medicine.

Question 4

Give 5 characteristics of Pro-karyotes.

Answer 4

Prokaryotes:

Cell Structure: Prokaryotic cells are typically smaller and simpler in structure than eukaryotic cells. They lack a true nucleus and membrane-bound organelles.

1. Nucleus: Prokaryotic cells do not have a well-defined nucleus.

Instead, their genetic material is typically a single, circular DNA molecule located in the nucleoid region of the cell.

-Double-stranded
–Single chromosome aggregated in cytoplasm
Haploid – single copy of each gene
-Most bacteria have autonomous smaller circles of DNA ‘plasmids.

Carry genes which confer special properties i.e., antibiotic resistance.

*Transcription coupled to translation in cytoplasm

Membrane-bound Organelles: Prokaryotes lack membrane-bound organelles such as mitochondria, endoplasmic reticulum, and the Golgi apparatus.

Ribosomes: They have smaller ribosomes (70S) compared to eukaryotic cells (80S).
Cell Wall: Many prokaryotes have a cell wall, which can be composed of different materials, including peptidoglycan in bacteria and pseudomurein in archaea.

Reproduction: Prokaryotes reproduce through binary fission, a process in which one cell divides into two genetically identical daughter cells.

Prokaryotes are represented by two major domains: Bacteria and Archaea. They are abundant and diverse and can be found in various environments, including soil, water, and the human body.

Many prokaryotes are unicellular, although some can form multicellular structures.

Question 5

Prokaryotes are represented by two major domains.

Name them.

Where are they abundant?

Answer 5

Prokaryotes are represented by two major domains: Bacteria and Archaea.

They are abundant and diverse and can be found in various environments, including soil, water, and the human body.

Question 6

Give 5 characteristics of eukaryotes.

Answer 6

Cell Structure: Eukaryotic cells are typically larger and more complex. They have a well-defined nucleus that contains the genetic material (DNA).

Nucleus: Eukaryotic cells have a true nucleus enclosed by a nuclear membrane, which separates the genetic material from the rest of the cell.

-Double stranded with associated proteins
-Packaged into linear chromosomes
-Diploid – 2 copies of each gene
-Several chromosome pairs e.g., baker’s yeast-16 pairs; human cells- 23 pairs

Key processes in distinct areas:
DNA replication; transcription-nucleus
Protein synthesis/translation-cytoplasm

Membrane-bound Organelles: Eukaryotes have various membrane-bound organelles, including the endoplasmic reticulum, Golgi apparatus, mitochondria, chloroplasts (in plants), and lysosomes, among others.

Ribosomes: They have larger ribosomes (80S) compared to prokaryotic cells (70S).

Cell Wall: While some eukaryotes have cell walls (e.g., plants and fungi), many do not, and the composition of their cell walls varies.

Reproduction: Eukaryotes can reproduce asexually and sexually. Asexual reproduction may involve processes like mitosis, while sexual reproduction involves the fusion of gametes.

Eukaryotes are a diverse group of organisms that include plants, animals, fungi, and various protists. They can be unicellular (e.g., yeast and some protists) or multicellular (e.g., humans, trees, and animals).

The distinction between prokaryotes and eukaryotes is a fundamental concept in biology and reflects the two primary cellular architectures found in the natural world.

Question 7

Eukaryotes are a diverse group of organisms.

Give the 4 main kingdoms under eukaryotes.

Answer 7

Eukaryotes are a diverse group of organisms that include plants, animals, fungi, and various protists.

They can be unicellular (e.g., yeast and some protists) or multicellular (e.g., humans, trees, and animals).

Question 8

The pro-karyotes has 3 main groups. Achaea and Bacteria.

What is the similarity between the 2 groups?

Answer 8

Single-celled
No nucleus membrane
No organelles (except ribosomes)

Question 9

State the 4 characteristics of Archaea.

Answer 9

Archaea
1. Extremophiles
(Extreme: temperatures, pH, salinity, high hydrostatic & osmotic pressures)

2. Lipids, cell walls & flagella different to Eubacteria
3. Not associated with human disease
4. Some have significant role in gastrointestinal tract of ruminant animals.

Question 10

Describe Eubacteria under the following subtopics.
1. DNA
2. Cytoplasm
3. Ribosomes
4. Cell wall

Answer 10

1. DNA:
   -Double-stranded
   -Tightly coiled into a region termed ‘nucleoid’ - no nuclear membrane
   -Extrachromosomal DNA present as small circular DNA –’plasmids
2. Cytoplasm
   Generally, no organelles except ribosomes (protein synthesis)
3. Ribosomes
   Different structure in pro & eukaryotic cells i.e., 70S vs. 80S
   (50S & 30S) in prokaryotes (60S & 40S) in eukaryotes
4. Cell wall
   Comprises ‘peptidoglycan’ which surrounds the cytoplasmic membrane.

(Capsules, flagella & pili variable-important role in diagnosis & pathogenicity

Question 11

In eukaryotes essential cellular processes occur in organelles e.g., mitochondria, endoplasmic reticulum But
Bacteria lack most organelles.

Where do most cellular functions occur?

Answer 11

In eukaryotes essential cellular processes occur in organelles e.g. mitochondria, endoplasmic reticulum

But
Bacteria lack most organelles, most cellular functions occur in the cytoplasmic membrane

Cytoplasmic membrane: a phospholipid bilayer (common to all living organisms)

Question 12

Unlike eukaryotes, bacteria don’t have mitochondria. CM= site for energy production i.e., electron transport system (ETS) & ATP synthetase.

What powers these single-celled living organisms?

Answer 12

The ETS pumps protons across the CM creating a ‘proton gradient’ & ‘pH gradient’. Accumulation of protons (H+) externally vs. hydroxyl ions (OH-) internally causes a charge across the CM i.e. proton motive force-PMF.

External surface of CM ‘charged positive’ vs. inner surface is ‘charged negative’, like a battery (also outside of the CM is acidic vs. inside which is alkaline).

The PMF used in bacteria provides energy for various activities incl. rotation of the flagellum, active transport of certain solutes

PMF also used in making ATP by the ATPase which uses the protons when synthesizing ATP from ADP & phosphate

PMF is an area of research as a possible a “antimicrobial target.”

Question 13

What is a cytoplasmic membrane?

CM phospholipids vary across bacteria
e.g., phosphatidylethanolamine, phosphatidyl glycerol, cardiolipin

Other macromolecules within the CM include:

Less common lipids e.g.

-Hopanoids (polycyclic lipids)

-Poly isoprenoid carriers

-Proteins

What are their functions?

Answer 13

It is a lipid bilayer.

CM phospholipids vary across bacteria.
e.g., phosphatidylethanolamine, phosphatidyl glycerol, cardiolipin

Other macromolecules within the CM include:
Less common lipids e.g.

-Hopanoids (polycyclic lipids): confer strength.
-Poly isoprenoid carriers involved in carriage of sugars for cell wall biogenesis
-Proteins i.e. involved in energy production; lipid biosynthesis; secretion & transport

Question 14

State the functions of the cytoplasmic membrane.

Answer 14

1. Permeability barrier: hydrophobic portion is a tight barrier to counteract diffusion of these substances (except H2O).
2. Anchor for transmembrane proteins (e.g., transport proteins for solutes; nutrients; hydrophobic molecules).
3. Site of generation energy for the cell.

Question 15

State the 3 types of transport proteins found on the cytoplasmic membrane.

Answer 15

Types of transport proteins:
Uniporteri.e. unidirectional transport of across the CM e.g. K+ uniporter

Symporter/ or co-transporter i.e. two solutes transported in the same direction e.g. lactose permease, phosphate symporter

Antiporter/exchange diffusion i.e. one solute transported in direction & simultaneously 2nd solute is transported in opposite direction e.g. Na+-H+ antiporter

Question 16

What does high concentration of solutes within cytoplasm causes?

Answer 16

High concentration of solutes within cytoplasm, causes high osmotic pressure.

Question 17

What are the functions of a cell wall.

What is the cell wall of the eubacteria composed of?

Answer 17

In addition to the CM there is a rigid layer i.e., the cell wall (CW) which also deters possible bursting of the cell.

CW composed of peptidoglycan.

Question 18

What the 4 functions of the cell wall peptidoglycan.

Answer 18

*Semi-permeable

*Anchors macromolecules e.g. teichoic acids, proteins & polysaccharides

*Cell growth, division & diffusion of molecules

*Cell-to-cell signaling.

Question 19

State 2 components that make up linear glycan strands of peptidoglycan.

What kind of bond connects the NAM-NAG?

Answer 19

Linear glycan strands composed of

-N-acetylglucosamine (NAG)

-N-acetylmuramic acid (NAM)

Rigidity of peptidoglycan conferred by cross linking in X & Y directions:

NAM-NAG connected by glycosidic covalent bonds

NAM-NAG chains cross-linked by amino acids i.e. L-alanine; D-glutamic acid; L-lysine; D-alanine (vary by no. & type across diff. bacterial species)
Further cross-linked by ‘glycine interbridges’

Question 20

Structure & configuration of bacterial cell wall is vital for bacterial survival.

Breakdown in cell wall integrity is bactericidal.

Name a group of antibodies that target the bacterial cell wall.

Answer 20

Target for beta-lactam antibiotics

Question 21

During bacteria cell wall synthesis, what is the function of:

*Transpeptidases-TP (Penicillin Binding Proteins-PBPs)

*Glycosyltransferases (GT)

Answer 21

During bacteria cell wall synthesis:

Transpeptidases-TP (Penicillin Binding Proteins-PBPs) catalyse cross-linking of glycan chains by removal of terminal D-alanine in the peptide chain

Glycosyltransferases (GT) exist as separate subunits or tightly associated with transpeptidases (e.g., PBP-2) catalyze formation of covalent bonds between NAM & NAG

Question 22

Describe the MOA of Beta lactam antibiotics in the cell wall synthesis.

Answer 22

Note: D-Ala-D-Ala in the CW peptide structure is the substrate for transpeptidase/PBP

The core structure of beta-lactam antibiotics is the ‘-lactam ring’ an analogue of terminal D-Ala-D-Ala in peptidoglycan

-lactam antibiotics bind to active site of transpeptidase/PBP & inhibit cross linking of peptide chains in peptidoglycan.

Question 23

Describe mechanism of antibody resistance in beta lactam antibodies.

Answer 23

Beta lactamases
Most common mechanism for drug resistance to β-lactam antibiotics
Break the -lactam ring by hydrolysis.

Porins
Gram -ve bacteria have porin channels within outer cell membrane. These inhibit passage of beta-lactams into periplasmic space where the cell wall is located.

Pumps
Gram -ve bacteria can express ABC transporters in the outer membrane that function as ‘efflux pumps.
Transport -lactam antibiotics out of the periplasmic space to the outer environment

Mutated PBPs e.g. PBP2a in MRSA
Mutation in binding site leads to lower affinity to β-lactam antibiotics.

Absence of a peptidoglycan e.g., mycobacteria

Question 24

What are lipoteichoic acid (LTA)?

Answer 24

Lipoteichoic acid (LTA): a Gram +ve cell wall component that is anchored in the cytoplasmic membrane & extends through the CW. Teichoic acids covalently bound to CW.

Question 25

State the functions of the LTAs.

Answer 25

LTAs recognized as antigens by immune cells: bind to Toll-like-receptor-2 (TLR-2) & trigger increased inflammation e.g., release of TNF-α, IL-1, IL-6

Aid in binding Ca2+ & Mg2+ for transport into cell

Question 26

Cachectic (tumor necrosis factor-alpha/TNF-α):

Answer 26

a cytokine predominantly produced by macrophages. Upregulates the immune response: induces fever & facilitates increased production of other pro-inflammatory cytokines

Question 27

IL-1

Answer 27

release triggered by immune system detection of LTAs & LPS (in CW of Gram-ve). Induces fever & acute inflammation i.e recruitment of WBCs by inducing vasodilation & diapedesis of WBCs, immune cells by activating endothelium of blood vessels.

Question 28

IL-6

Answer 28

a cytokine produced by macrophages & monocytes, causes fever & facilitates in the production of several acute phase reactants.

Question 29

State the 2 main components of the gram +ve cell wall.

Answer 29

Gram positive cell wall comprises:

Peptidoglycan: THICK/several sheets of peptidoglycan

Teichoic & lipoteichoic acids – virulence factors unique to Gram+ve bacteria cell wall

Question 30

How is the cell wall of a gram -ve different from that of a gram +ve?

Answer 30

In contrast to Gram+ve bacteria, Gram-ve bacteria have an additional membrane as part of the CW: “outer membrane.”

Question 31

In contrast to Gram+ve bacteria, Gram-ve bacteria have an additional membrane as part of the CW: “outer membrane.”

Describe the components of the outer membrane.

Answer 31

Asymmetric bilayer structure:

Inner leaflet – phospholipids

Outer leaflet: primarily LIPOPOLYSACCHARIDES with hydrophobic & hydrophilic properties

Proteins:
Transmembrane proteins e.g., ‘porins’ for diffusion of hydrophilic molecules

Structural proteins, receptor molecules for bacteriophages & other ligands

Question 32

Outer leaflet of LPS consists of three parts.

Describe them.

Answer 32

Outer leaflet of LPS consists of three parts:

*Lipid A, hydrophobic membrane forming the outer leaflet of the OM.

*Phosphorylated, non-repetitive core oligosaccharide (core-OS) connects lipid A & O-antigen.

*O-antigen (O polysaccharide) chain of several types of repeating sugar units.

Lipid A & core-OS are conserved among Gram-ve species, in contrast to the O-antigen, which is highly variable across Gram-ve species.

Question 33

LPS is an endotoxin- causes fever & shock.

How does that come about?

Answer 33

O-antigen consists of several repeats (variable) of oligosaccharide units & recognized by antibodies.

Variability of O-antigen provides basis for serotyping assays for Gram-ve bacteria.
Also associated with the morphology of bacterial colonies i.e., ‘smoothness’ or roughness on colonies on culture media

Lipid A: powerful immune response stimulator
Induces macrophages to release IL-I, IL-6, TNF & other factors. Activates B cells.

Question 34

What is sepsis?

Describe mechanisms of action of LPS in causing sepsis.

Answer 34

Sepsis is your body’s extreme reaction to an infection.

1. Immune cells such as macrophages, bind to LPS via Toll-like receptor 4 (TLR- 4) together with accessory proteins: CD14 & MD-2.
2. Triggering microbiocidal activities within macrophages & the release of pro-inflammatory cytokines, to destroy the pathogen.
3. LPS can directly activate the ‘complement system’ resulting in the formation of “membrane attack complex” (MAC). MAC integrates into the outer membrane & forms pores leading to bacterial lysis. The complement system also facilitates phagocytosis of the pathogen through its effect as an opsonin by binding to the pathogen.
4. Activated complement component C5a induces recruitment of host defense cells i.e., neutrophils which are stimulated to secrete granular contents & produce reactive oxidative intermediates that lead to lysis of the bacteria.

5.BUT during severe infections by Gram-ve bacteria, macrophages & endothelial cells are greatly stimulated by released LPS. This inflammatory response can produce localized tissue damage as well as vasodilatation.

6. Abundant secretion of several cytokines by macrophages i.e., IL-1, IL-6 & TNF-α. This can contribute to the pathophysiology of septic shock.

Question 35

Outer membrane is as an anchor for other macromolecules e.g. proteins, almost exclusively β-barrel proteins – Outer membrane proteins (OMPs) & some lipoproteins

Whereas the cytoplasmic membrane exclusivelycontains transmembrane α-helical proteins.

Describe the B-barrel proteins.

What is their function?

Answer 35

β-barrel proteins form ‘cylinders’ & generally referred to as outer membrane proteins (OMPs) many are ‘porins’

Selectively regulate exchange of anions, cations & other solutes across the bacterial OM

Question 36

State the functions of the following B-barrel proteins (OMP)

1. OmpA
2. OMPLA
   3.FepA

Answer 36

Examples of ‘porins’ in E. coli:

1.OmpAprotein in E. coli serves as a receptorfor a bacteriophage, others include OmpF, OmpC allow diffusion of amino acids & mono or disaccharides.

2. OMPLA protein in E. coli is a lipase.
3. A porin inRhodobacter capsulatus forms water-filled pores in outer membrane, allowing certain hydrophilicsolutes to cross
4. FepA transport protein inE. coli transports iron ions

Other OMPs in E. coli include: LamB & PhoE allow diffusion of maltose, maltodextrins & phosphate respectively.

Question 37

Cell wall proteins crosslinks confer stability to the cell wall.

Describe how that is achieved.

Answer 37

Cell wall proteins crosslinks confer stability to the cell wall e.g.:

‘Braun’s lipoprotein’ (Lpp)/ murein lipoprotein– crosslinks outer membrane (OM) & underlying peptidoglycan

Most abundant protein in E. coli cell wall, forms covalent links with peptidoglycan – vital to structural integrity of OM

Amino terminus attached to lipids in OM & carboxy terminus covalently attached to peptidoglycan peptide cross bridge.

Question 38

Other proteins form non-covalent links with peptidoglycan e.g.:

Give examples.

Answer 38

Other proteins form non-covalent links with peptidoglycan e.g.:

OmpA (Outer-membrane protein A) – a porin

Tol-Pal lipoprotein complex:
TolA, TolB, TolQ, TolR & Pal span from PG across the periplasm to the cytoplasmic membrane & also to inner leaflet of the outer membrane (structure & synthesis of OM)

Question 39

Describe the periplasm.

What is its function?

Answer 39

Periplasm: densely packed with proteins & more viscous than the cytoplasm.

Cellular degradative enzymes e.g., RNAse; alkaline phosphatase

Periplasmic binding proteins: function in sugar & amino acid transport

Chemotaxis & chaperone-like molecules: function in cell wall biogenesis

Question 40

Differentiate between gram negative and positive bacteria.

Answer 40

Gram positive
1. Peptidoglycan: THICK/several sheets of peptidoglycan.
2. No outer membrane
3. Teichoic & lipoteichoic acids
Important virulence factors & aid in binding Ca+ & Mg2+ for transport into cell
4. No Periplasmic space

Gram negative
1. Peptidoglycan - THINNER
2. Outer membrane external to peptidoglycan made of Lipopolysaccharide.
3. No teichoic or lipoteichoic acids
4. Periplasmic space

Question 41

There are atypical bacteria that have unique cell walls OR don’t have a cell wall at all, so they do not stain well with the Gram’s stain & need alternative staining techniques for viewing.

Give examples of those.

Answer 41

Mycobacterium species

Mycoplasma spp.

Ureaplasma spp.

Treponema spp

Chlamydia spp.
Borrelia spp.

Anaplasma spp.

Leptospira spp.

Bartonella spp.

Ehrlichia spp.

Rickettsia spp.

Question 42

Outline the 3 essential macromolecules of mycobacteria cell wall.

Answer 42

Peptidoglycan
Arabinogalactan (D-arabinose & D-galactose)
Mycolic acids (long chain fatty acids)

Contribute to pathogenicity & persistence during infection.

Mycolic acids form inner leaflet of pseudo ‘myco-membrane’. Outer leaflet comprises lipids & glycolipids.

Question 43

Name 2 species which are included under spirochetes.

What diseases do they cause?

Answer 43

Spirochetes include the species: Treponema pallidum & Borrelia burgdorferi the pathogens causing Syphilis & Lyme disease

Question 44

Describe the Structure of spirochetal membrane & cell wall.

Answer 44

Similar to Gram-ve bacteria, as have an outer membrane but don’t Gram stain well due to thin CW) but it consists of some LPS & other different macromolecules e.g. glycolipids, lipoproteins.

Periplasmic space contains ‘endo-flagellum’, allowing corkscrew movement.

Distribution of lipoproteins varies among spirochetes & may be present in different cellular compartments i.e., extracellularly in the outer membrane, or intracellularly in the periplasmic space.

Question 45

Some bacteria able to exist without cell wall. How do they achieve rigidity and strength?

Answer 45

Able to exist without cell walls as contain sterols in their cytoplasmic membranes which confer strength & rigidity.

Question 46

Name the main classes of bacteria without a cell wall.

Answer 46

Mycoplasma & Ureaplasma species – are commensals of the urogential tract but also can be pathogenic.

Mycoplasma pneumoniae – cause respiratory infections.

Mycoplasma hominis - genitourinary tractinfections.

Mycoplasma genitalium – associated with cervicitis, endometritis.

Ureaplasma urealyticum - genitourinary tractinfections

M. hominis can grow on standard culture media but commonly Eaton agar, SP4 glucose agar used. Depicts ‘small, fried egg colony morphology’. Takes ~2-4 days; aerobically/37°C.

Ureaplasma species don’t grow on standard media. A8 agar recommended culture media. Depicts small, punctate colonies on A8 agar. Takes ~2-5 days; aerobically/37°C.

Question 47

What is a capsule?

Answer 47

Secreted polysaccharide structure located outside the cell wall of certain bacteria.

Question 48

State 5 uses of a capsule.

Answer 48

Virulence factor

Hinders phagocytosis by impeding opsonization (coating of microbes with ‘opsonin’s/ serum molecules’ to render them more recognizable to phagocytes)

Facilitates adherence to surfaces.

Resistance to desiccation of cell: Removal of moisture from the cell.
Provides protection from free radicals & heavy metal irons.

Question 49

State examples of clinically relevant encapsulated bacteria.

Answer 49

Group B streptococcus
Streptococcus pneumoniae
Haemophilus influenzae type b
Neisseria meningitidis
Salmonella spp.
Klebsiella pneumoniae
Pseudomonas aeruginosa

Question 50

What are biofilms?

Answer 50

Secreted polysaccharide materials on cell surface. Not considered part of cell envelope as do not confer ‘structural strength’. Slimy or sticky, loosely attached & can be lost from cell surface.

Question 51

State the 2 functions of biofilms.

Answer 51

*Attachment to hospital equipment e.g., ventilators, tubing’s, catheters. Biofilms on implanted prosthetic devices, results in infections, which are very difficult to treat.

*Difficult for antibiotics to penetrate through.

Question 52

What is a flagellum?

Answer 52

Flagella (singular,flagellum) long, thin filamentous appendage for locomotion towards or away from stimuli (some bacteria)

Question 53

Where does a flagellum originate?

Answer 53

Originates in bacterial cytoplasm, anchored
in cell membrane & extends through cell wall

Question 54

May be 1- 20 flagella/cell.

Arrangement may be:
Polar:
Liphotrichous:
Amphitrichous:
Peritrichous:

Answer 54

May be 1- 20 flagella/cell.

Polar Flagellation: In polar flagellation, one or more flagella are located at one or both ends (poles) of the bacterial cell. This arrangement allows the bacterium to move in a specific direction, usually by rotating the flagella at the poles.

Lophotrichous Flagellation: In lophotrichous flagellation, a tuft of flagella is located at one or both ends of the bacterium. This arrangement is similar to polar flagellation but involves multiple flagella concentrated at the same pole, providing enhanced motility.

Amphitrichous Flagellation: Amphitrichous bacteria have a single flagellum at each end of the cell. These flagella can rotate to move the bacterium in opposite directions. Amphitrichous flagellation is less common than polar or peritrichous flagellation.

Peritrichous Flagellation: Peritrichous flagellation is when numerous flagella are distributed all over the surface of the bacterial cell. This arrangement allows the bacterium to move in multiple directions and is characteristic of many motile bacteria.

Flagella are essential for bacterial motility, enabling them to move towards or away from various stimuli such as nutrients or harmful substances. The arrangement of flagella can vary between bacterial species and can be a useful characteristic for classification and identification.

Question 55

What are fimbriae and Pilli?

State the 2 basic types of pilli.

Answer 55

Fimbriae & pili: thin, protein tubes originating from the cytoplasmic membrane of many bacteria (shorther than flagella).

Facilitate adherence of bacteria to surfaces but Fimbriae: more numerous (e.g. 100-500).

Present in many Gram-ve bacteria, less so in Gram+ve

Pili are typically longer & fewer than fimbriae.

Two basic types of pili: short attachment pili & long conjugation pili.

Have a shaft comprising ‘pilin’(a protein). End of shaft acts as an adhesive that binds to specific glycoprotein or glycolipid receptors on host cells.

Mediate adhesion between bacteria & facilitate genetic exchange between bacterial cells. Thus, conferring pathogenicity e.g., Salmonella species & Neisseria gonorrhoeae

Question 56

In adverse conditions some bacteria stop actively growing & enter a dormant phase/ sporulation
NB. a single vegetative cell forms a single spore.

What triggers spore formation?

What does a spore gives rise to?

Answer 56

Triggered by lack of nutrients in the environment. Highly resistant to harsh conditions.

Produced by a few generations of certain Gram-+ve bacteria e.g., Bacillus & Clostridium species.

In more optimal conditions, subsequent germination each spore gives rise to a single vegetative cell, which can then replicate.

Question 57

Bacteria cell shapes are extensively conferred by cell wall/ peptidoglycan configuration.

State the 2 basic shapes.

What are other variants shapes?

Answer 57

Two basic shapes:
Spherical- Coccus
Rod shaped- Bacillus.

Variants:
Comma shaped- Vibrio.
Spiral- Spirillum & Spirochaete
Filamentous

Question 58

During cell division, 1 cell becomes 2 (’generation time’)

What does generation time dependent on?

Under optimal conditions, Escherichia coli have a generation time of ____________ vs. Mycobacterium tuberculosis ______________.

In a new environment bacterial growth has a characteristic pattern:

State the 4 phases.

Answer 58

During cell division, 1 cell becomes 2 (’generation time’)

Generation time dependent on growth medium & incubation conditions.
Under optimal conditions, Escherichia coli have a generation time of ~20-30 min vs. Mycobacterium tuberculosis ~12-15 hours

In a new environment bacterial growth has a characteristic pattern:
Lag phase
Exponential/ logarithmic phase
Stationary phase
Death phase

Question 59

What is DNA replication?

Why does it occur?

Where does it occur?

Answer 59

DNA replication is the process by which a cell makes an identical copy of its DNA (deoxyribonucleic acid) molecule.

It is a fundamental biological process that occurs before cell division and is crucial for the accurate transmission of genetic information to the next generation of cells.

DNA replication takes place in the nucleus of eukaryotic cells (such as those in humans) and in the cytoplasm of prokaryotic cells (such as bacteria).

Question 60

Describe the process of DNA replication.

Answer 60

1. Initiation:

DNA replication begins at a specific site on the DNA molecule known as the origin of replication.

Enzymes called helicases unwind the double-stranded DNA at the origin, creating two single-stranded DNA templates.

2. Priming:

DNA polymerase, a crucial enzyme, requires a short RNA primer to initiate the synthesis of a new DNA strand.

Primase, a specialized RNA polymerase, synthesizes these RNA primers complementary to the single-stranded DNA templates.

3. Elongation:

DNA polymerase adds complementary deoxyribonucleotides to the growing DNA strand, using the single-stranded DNA template as a guide.

DNA polymerase III is the primary enzyme involved in the elongation process, synthesizing the new DNA strand.

DNA polymerase I, which has both polymerase and exonuclease activities, is responsible for removing the RNA primers and filling the gaps with DNA nucleotides.

4. Complementary Base Pairing:

Adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G), following the base-pairing rules.

5. Directionality:

DNA polymerase synthesizes the new DNA strand in the 5’ to 3’ direction.

Because the DNA double helix is antiparallel, one strand, called the leading strand, can be synthesized continuously in the 5’ to 3’ direction as the replication fork unwinds.

The other strand, called the lagging strand, is synthesized in short fragments called Okazaki fragments in the 3’ to 5’ direction.

DNA ligase then joins these fragments together to form a continuous strand.

6. Proofreading and Repair:

DNA polymerases have proofreading and repair functions to ensure the accuracy of DNA replication.

If an incorrect base is added, the 3’ to 5’ exonuclease activity of the polymerase removes the incorrect nucleotide, and the correct nucleotide is added in its place.

7. Termination:

DNA replication proceeds bidirectionally from the origin of replication until it reaches the termination site, at which point it is completed.
I
n circular DNA, like that found in prokaryotes, replication eventually results in two daughter DNA molecules.

Overall, DNA replication is a highly controlled and complex process that ensures the faithful duplication of genetic information during cell division. Mistakes in DNA replication can lead to mutations, which may have various consequences, including genetic diseases and cancer.

Regenerate

Question 61

State the functions of the following key enzymes in DNA replication.

Helicase:
Topoisomerase II (DNA Gyrase):
Primase:
DNA Polymerase III:
DNA Polymerase I:
DNA Ligase:
Exonuclease:

Answer 61

The key enzymes involved in DNA replication include:

Helicase: Unwinds the DNA double helix.
Topoisomerase II (DNA Gyrase): Regulate supercoiling.
Primase: Synthesizes RNA primers.
DNA Polymerase III: Main enzyme responsible for DNA synthesis.
DNA Polymerase I: Involved in primer removal and gap filling.
DNA Ligase: Joins Okazaki fragments on the lagging strand.
Exonuclease: Removes incorrect nucleotides and damaged DNA segments.

Question 62

Bacteria reproduce by binary fission.

Describe the process of binary fission.

Answer 62

Binary fission (divide into 2) - asexual reproduction (no gametes or partners required)

1st step- chromosome (& other macromolecules) must be duplicated prior to cell division.

2nd step- elongation occurs & septum forms, dividing cell into 2 daughter cells.
1 generation has occurred.

Proteins essential for cell division:
-Filamentous temperature sensitive (Fts) proteins
-FtsZ forms a ring centrally, where the cell division plane will later occur
-Other essential proteins: FtsA, FtsI, ZipA, MinC, D, E

Timing & frequency of cells division essential

Question 63

What is binary fission?

Answer 63

Binary fission:
Asexual reproduction; creates new bacteria but no (or minimal) genetic diversity.

Question 64

How does genetic diversity come about in Bacteria?

Answer 64

Through Bacterial exchange of genetic material.

Bacterial conjugation

Bacterial Transformation

Bacterial Transduction

Bacterial transposition**

Question 65

Describe how bacteria gain diversity via Bacterial conjugation.

Answer 65

Bacteria - single circular chromosome comprising genes essential for growth & reproduction

However, some bacteria may also contain extra chromosomal ‘autonomous’ genetic material termed ‘plasmids.

Plasmids- carry additional ‘’ genes.

Note: not all bacteria carry plasmids, thus some bacteria transfer a copy of their plasmid to another bacterium

*Conjugation not reproduction (no new daughter cells)

*Transfer of genetic material i.e., plasmids, which typically carry antibiotic resistance genes allows genetic diversity.

*Genetic material transferred into recipient slightly different than in donor.

Bacterial conjugation
Transfer of plasmid DNA from donor bacterium to recipient bacterium. Not reproduction but introduces genetic diversity into bacterial population.

Question 66

Describe bacterial transformation.

Answer 66

Transform - ‘to change’

Some bacteria have ability to attain DNA from the environment i.e., post cell death of other bacteria.

Newly attained DNA incorporated into bacterial cell & genes expressed.

During bacterial replication (binary fission) newly attained DNA also replicated & passed on to daughter cells.

Question 67

What happens in bacterial transduction?

Answer 67

Transduction – ‘to move across’

Transfer of bacterial DNA from one bacterium to another via a viral vector (bacteriophage).

Question 68

Describe the process of bacterial transduction.

Answer 68

1ST - Adherence
Penetration- viral DNA injected into bacterial cytoplasm.

Prophage or lytic cycle

Viral DNA excises & replicates entering lytic stage but picks up some bacterial chromosomal DNA.

Viral components assembled; progeny released after lysis of cell.

Viral progeny transduct other bacterial cells

Question 69

Describe the following ways of bacterial reproduction & exchange of genetic material.

Bacterial conjugation

Bacterial Transformation

Bacterial Transduction

Answer 69

Bacterial conjugation
Transfer of plasmid DNA from donor bacterium to recipient bacterium. Not reproduction. Introduces genetic diversity into bacterial population

Bacterial Transformation
Attainment of extra chromosomal DNA from the environment. Not reproduction. Introduces genetic diversity into bacterial population

Bacterial Transduction
DNA is transferred from one bacterium to another by a viral vector. Not reproduction. Introduces genetic diversity into bacterial population.

Question 70

What is bacterial transposition?

Answer 70

Bacterial Transposition
DNA sequences that jump or copy themselves from one location in the DNA chromosome to another. Not reproduction. Introduces genetic diversity

Question 71

State the 4 optimal environmental conditions needed by bacteria for survival.

Answer 71

Optimal environmental conditions i.e.,
-O2concentration
-Temperature
-H2O
-pH

Question 72

Bacteria require essential elements for growth:
State 3.

State Nutritional elements incorporated into structural or functional roles of bacteria.

State Trace elements - typically metal ions (minute concentrations) needed by bacteria.

What are they essential for?

Answer 72

Bacteria require essential elements for growth:
Carbon source
Energy source
Other required nutrients (macronutrients & micronutrients, trace elements)

Nutritional elements incorporated into structural or functional roles:
C, H, O, N, S, P, K, Mg, Fe, Ca & Mn

Trace elements - typically metal ions (minute concentrations)
For instance - Mn, Co, Zn, Cu, & Mo
Usually, cofactors for essential enzymatic reactions in the cell

Question 73

State the 2 main modes of nutrition.

Answer 73

*Autotrophs
*Heterotrophs

Question 74

What are autotrophs?

State the 2 groups of autotrophs.

Answer 74

Autotrophs - manufacture complex organic compounds from simple inorganic sources i.e. CO2, H2O & nitrates.

Definition: Autotrophs are organisms that can produce their own organic molecules, such as glucose, from inorganic sources of carbon and energy. They are “self-feeders.”

Energy Source: Autotrophs capture energy from the environment, typically through processes like photosynthesis or chemosynthesis.

Carbon Source: Autotrophs use inorganic carbon, usually in the form of carbon dioxide (CO2), to synthesize organic compounds.

Examples: Plants, algae, and some bacteria are common examples of autotrophs. They use sunlight and CO2 to produce their own food.

*Further divided: chemo & photo autotrophs

-Photoautotrophs: Get energy from light.

EXAMPLES: Cyanobacteria, some Purple & Green Bacteria.

-Chemoautotrophs: Get energy from inorganic compounds e.g., H2, NH3, NO2, H2S

EXAMPLES: Nitrifying, sulfur oxidizing & iron bacteria.

Question 75

What are heterotrophs?

Answer 75

Definition: Heterotrophs are organisms that obtain organic molecules, such as carbohydrates, proteins, and lipids, from external sources as their primary source of energy and carbon. They are “other feeders.”

Energy and Carbon Source: Heterotrophs obtain energy and carbon from consuming other living or dead organisms, or organic matter, and breaking down the complex organic compounds into simpler molecules.

Examples: Animals, fungi, most bacteria, and many protists are heterotrophs.

They rely on ingesting plants, other animals, or decomposing matter for their energy and carbon needs.

THERE ARE 2 TYPES OF HETEROTROPHS

-PHOTOHETEROTROPHS: Obtain energy from light

EXAMPLES: Some Purple & Green Bacteria

-CHEMOHETEROTROPHS: Obtain energy from Organic compounds e.g., sugars, proteins, lipids

EXAMPLES: Most Bacteria, some Archaea

Question 76

Differentiate between autotrophs and heterotrophs.

Answer 76

To summarize, autotrophs are capable of synthesizing their own organic molecules from inorganic sources, while heterotrophs rely on external sources of organic molecules to meet their energy and carbon requirements.

These two nutritional strategies are essential for the flow of energy and matter in ecosystems, as autotrophs serve as the primary producers that provide the foundation for food chains, while heterotrophs occupy various trophic levels as consumers.

Question 77

Describe the following classification according to environmental O2.

Obligate aerobe

Micro- aerophilic aerobe

Obligate anaerobe

Facultative (aerobe / anaerobe)

Aerotolerant anaerobe

Micro-aerophilic organism

Capnophilic organism

Answer 77

Obligate aerobe; Grows only in the presence of oxygen. Does not grow when oxygen is absent.

Micro aerobe: Growth in low oxygen levels. Does not grow when oxygen is absent.

Obligate anaerobe: Grow when oxygen is absent. Does not grow when oxygen is present.

Facultative (aerobe / anaerobe): Grow when oxygen is both present and absent.

Aerotolerant anaerobe: Anaerobic but can tolerate oxygen.

Capnophilic organism: Requires increased Carbon dioxide levels to grow.

Question 78

Describe the following classification according to Growth temperature.

1. Pathogens that replicate on or in the human body grow within 20-40°C temperature range.
   What are they called?

2.(cold loving): capable of growth in food or pharmaceuticals stored at normal refrigeration temperatures (0-8°C). What are they called?

3. (heat loving) i.e., hot springs. What are they called?
4. most Archaea bacteria): bizarre physical conditions e.g., under enormous pressure (e.g., in ocean floor). What are they called?

Answer 78

Pathogens that replicate on or in the human body grow within 20-40°C temperature range. referred to as’Mesophiles.’

Psychrophiles(cold loving): capable of growth in food or pharmaceuticals stored at normal refrigeration temperatures (0-8°C)

Thermophiles(heat loving) i.e. hot springs

Extremophiles (most Archaea bacteria): bizarre physical conditions e.g., under enormous pressure (e.g., in ocean floor).