BHCS1006 Summary Notes
Physical barriers – 1st line of defence
• Skin
• Mucous membranes – digestive tract, respiratory tract, stomach, nose
Innate immunity – 2nd line of defence
• Non-specific defence that is built-in
• Involves macrophages, neutrophils, eosinophil and phagocytosis
• Non-antigen specific makes it a quick response
• Monocytes mature into macrophages when in tissues
• Macrophages detect foreign substances, engulf it and release cytokines to recruit more WBCs to
fight the foreign cells and increase blood flow to the wound
Adaptive immunity - 3rd line of defence
• How the immune system adapts to specific invaders
• Involves production of antibodies by B cells in response to an unfamiliar antigen the invader
carriers
• Modular design
o Aren’t enough genes in human DNA to code for 100 million different antibodies needed for
all antigens
o Immature B cells, therefore, have 4 DNA modules (gene segments) which are all slightly
different, containing varying amounts of genes
o When mature, B cells select one of each kind of segment from each module randomly (same
idea as 20 amino acids coding for countless proteins)
o Junctional diversity also used when DNA added or deleted when segments join
Macrophages and neutrophils pass information of the pathogen to the dendritic cells which pass
information onto the primary lymphoid organ (red bone marrow and thymus) which deploy T cells and B
cells
Three domains of life
• Bacteria – prokaryotes with peptidoglycan cell wall
• Archaea – prokaryotes without peptidoglycan cell wall
• Eukarya – all eukaryotes
Linnaean taxonomy used to name organism ‘Genus species’
Domain→ Kingdom → Phylum → Class → Order → Family → Genus → Species
Microbes are in the prokaryote domains, viruses don’t fall into a cellular category as aren’t technically alive
(and are too small (nm) to be seen with a microscope).
Microorganisms that cause disease in those with normal host defences are pathogens
Types of microorganisms
• Living (cellular)
o Parasites – organism that grows and feeds on host, detrimentally to host survival (e.g.
Helminth worms)
o Protozoa – single celled eukaryotes, free-living or parasitic (e.g. Plasmodia that causes
malaria)
o Fungi – eukaryotes that attack body surfaces (e.g. Athlete’s Foot)
o Prokaryotes – unicellular cells that reproduce quickly and compete with host cells for space
and nutrition (e.g. leprosy bacteria)
• Non-living (acellular)
o Virus – metabolically inert, reproduction dependant on host machinery (e.g. HIV)
1
,BHCS1006 Summary Notes
o Prions
▪ Infectious, abnormally folded proteins capable of causing disease
▪ Abnormal folding creates holes in tissues
▪ No cure or theory of mechanism – very dangerous and always fatal
▪ E.g. Creutzfeldt-Jakob disease (CJD) – holes in brain
Prokaryotes Eukaryotes
Organism Bacteria Protists, fungi, plants, animals
Cell size 1-10um 1-100um
Metabolism An/aerobic An/aerobic
Cell support External cell wall Internal cytoskeleton
Organelles None Yes
DNA Circular DNA in single Long linear DNA within
compartment membraned nucleus
RNA & protein Synthesised in single RNA in nucleus, proteins in
compartment cytoplasm
Transmembrane movement None Endo/Exocytosis
Cell division Binary fission Chromosomes pulled apart by
cytoskeleton
Cellular Unicellular Uni/multicellular and
differentiated types
Classification of microbes
• Phylogeny – morphology, shape
• Bioinformatics – gene sequencing more accurate
o Sanger sequencing
o Illumina
o New era of personalised genomics-based medicine
• Electron microscope needed to see phylogeny of viruses
Zoonosis – transmittance of pathogen from animal to human
Disease X – disease that causes a pandemic
Bacteria morphology
• Neisseria – coffee bean shaped in pairs (e.g. N. meningitidis and N. gonorrhoeae)
• Acinetobacter – gram negative bacteria
• Staphylococcus – gram positive bacteria, grape-like clusters (e.g. Methicillin-resistance S. aureus
superbug)
• Clostridium – gram positive bacteria, spindle-shaped with bulges at end (e.g. C.difficile infects
bowels causing diarrhoea – very hard to clear so very dangerous)
• Escherichia – gram negative, rod shaped with flagella sometimes (e.g. E. coli exists in gut flora,
there are many different types, E. coli 0157 causes food poisoning)
• Mycobacterium – gram positive, rod-shaped (e.g. M. tuberculosis and M. leprae)
• Streptococcus – gram positive, pairs or chains that appear bent (e.g. S. pneumoniae and S.
pyogenes – Strep throat)
The Gram stain
• Three types of bacteria – gram positive, gram negative and acid fast
• Process of gram staining (aseptic technique)
2
,BHCS1006 Summary Notes
1. Heat fix along slide and flood with crystal violet, leave then wash
2. Flood slide with Gram’s iodine, leave then wash
3. Flood slide with 95% ethanol, leave then wash (ethanol rids any crystal violet than hasn’t
adhered to bacteria)
4. Flood slide with Safranin, leave then wash and dry
• Gram+ bacteria will stain purple (from crystal violet)
• Gram- bacteria will stain pink (from safranin)
• Difference staining due to difference in cell wall structure
o Gram+ bacteria
▪ 90% of cell wall is peptidoglycan which strongly binds to crystal violet therefore
retaining purple colour
▪ Low lipid content
▪ Contains teichoic acid (unique to Gram+) - role unknown
▪ Can form spores
o Gram- bacteria
▪ 10% of cell wall is made up of thin layer of peptidoglycan so doesn’t bind to crystal
violet very well
▪ Lipopolysaccharide (LPS) – endotoxins that cause a lot of diseases
▪ High lipid content
Bacterial replication – binary fission
• Asexual process
• Cell doubles its mass
• Genome DNA replicates
• In ideal conditions, E. coli can undergo 1 cell cycle every 20 minutes
Vegetative bacteria – can reproduce, is alive and active
Spore formers
• Survive in any environment and will activate in right environment
• Can’t replicate in this form (dormant)
• Very difficult to kill (e.g. C. diff resistant to heat, chemicals, depletion and desiccation)
• E.g Bacillus, Clostridia
Food bacteria
• Pathogenic bacteria – food poisoning
o Gram- rods; E. coli, Pseudomonads
o Gram+ rods; Clostridia, Bacillus
• Cultured bacteria
o Gram+ rods – Lactobacilli in yogurt (produces lactase in body)
o Rice
o Raw honey
Microbial nutrition
• Autotrophs
o Synthesis complex organic molecules from simple, non-organic molecules
o Uses light or chemical energy
o E.g. plants are photoautotrophs, iron bacteria are chemoautotrophs
• Heterotrophs
3
, BHCS1006 Summary Notes
o Use organic molecules like carbon
o 2 and 3rd consumers in the food chain (carnivores, herbivores etc)
Growing microbes in the lab
• Culture
o Nutrient source
▪ Carbohydrate – sugar derivatives
▪ Proteins – meat/yeast extracts
▪ Minerals/vitamins
o Broth (liquid) culture – test tubes/bottles
o Solid (agar) media – test tubes/bottles/plates
o Culture media formulated to meet nutritional requirements of certain bacteria, selectively
grow or inhibit certain bacteria and be diagnostic
• Optimal conditions
o Nutrient source
o Temperature (mesophiles)
▪ For every 10C increase, metabolic and growth rate doubles
▪ At high temps; membrane disruption, protein denaturation
▪ At low temps; adapt to maintain membrane fluidity, slow metabolic and growth rate
o Water availability
o pH
o gaseous atmosphere
o no antimicrobials – e.g. naturally occurring polyphenols, preservatives etc
o Oxygen tolerance
▪ Obligate aerobes – love O2
▪ Obligate anaerobes – hate O2
▪ Facultative anaerobes – in between
▪ Aerotolerant anaerobes – in between
▪ Microaerobes – low level of O2 required for survival
Standard pattern on growth shown as a Growth Curve with Set Phases
Viruses
• Genetic elements containing either RNA or DNA that replicate in cells
• Viruses are dormant when they are outside of cells
• Morphology
o Determined using electron microscope, genetic makeup and size
4
Physical barriers – 1st line of defence
• Skin
• Mucous membranes – digestive tract, respiratory tract, stomach, nose
Innate immunity – 2nd line of defence
• Non-specific defence that is built-in
• Involves macrophages, neutrophils, eosinophil and phagocytosis
• Non-antigen specific makes it a quick response
• Monocytes mature into macrophages when in tissues
• Macrophages detect foreign substances, engulf it and release cytokines to recruit more WBCs to
fight the foreign cells and increase blood flow to the wound
Adaptive immunity - 3rd line of defence
• How the immune system adapts to specific invaders
• Involves production of antibodies by B cells in response to an unfamiliar antigen the invader
carriers
• Modular design
o Aren’t enough genes in human DNA to code for 100 million different antibodies needed for
all antigens
o Immature B cells, therefore, have 4 DNA modules (gene segments) which are all slightly
different, containing varying amounts of genes
o When mature, B cells select one of each kind of segment from each module randomly (same
idea as 20 amino acids coding for countless proteins)
o Junctional diversity also used when DNA added or deleted when segments join
Macrophages and neutrophils pass information of the pathogen to the dendritic cells which pass
information onto the primary lymphoid organ (red bone marrow and thymus) which deploy T cells and B
cells
Three domains of life
• Bacteria – prokaryotes with peptidoglycan cell wall
• Archaea – prokaryotes without peptidoglycan cell wall
• Eukarya – all eukaryotes
Linnaean taxonomy used to name organism ‘Genus species’
Domain→ Kingdom → Phylum → Class → Order → Family → Genus → Species
Microbes are in the prokaryote domains, viruses don’t fall into a cellular category as aren’t technically alive
(and are too small (nm) to be seen with a microscope).
Microorganisms that cause disease in those with normal host defences are pathogens
Types of microorganisms
• Living (cellular)
o Parasites – organism that grows and feeds on host, detrimentally to host survival (e.g.
Helminth worms)
o Protozoa – single celled eukaryotes, free-living or parasitic (e.g. Plasmodia that causes
malaria)
o Fungi – eukaryotes that attack body surfaces (e.g. Athlete’s Foot)
o Prokaryotes – unicellular cells that reproduce quickly and compete with host cells for space
and nutrition (e.g. leprosy bacteria)
• Non-living (acellular)
o Virus – metabolically inert, reproduction dependant on host machinery (e.g. HIV)
1
,BHCS1006 Summary Notes
o Prions
▪ Infectious, abnormally folded proteins capable of causing disease
▪ Abnormal folding creates holes in tissues
▪ No cure or theory of mechanism – very dangerous and always fatal
▪ E.g. Creutzfeldt-Jakob disease (CJD) – holes in brain
Prokaryotes Eukaryotes
Organism Bacteria Protists, fungi, plants, animals
Cell size 1-10um 1-100um
Metabolism An/aerobic An/aerobic
Cell support External cell wall Internal cytoskeleton
Organelles None Yes
DNA Circular DNA in single Long linear DNA within
compartment membraned nucleus
RNA & protein Synthesised in single RNA in nucleus, proteins in
compartment cytoplasm
Transmembrane movement None Endo/Exocytosis
Cell division Binary fission Chromosomes pulled apart by
cytoskeleton
Cellular Unicellular Uni/multicellular and
differentiated types
Classification of microbes
• Phylogeny – morphology, shape
• Bioinformatics – gene sequencing more accurate
o Sanger sequencing
o Illumina
o New era of personalised genomics-based medicine
• Electron microscope needed to see phylogeny of viruses
Zoonosis – transmittance of pathogen from animal to human
Disease X – disease that causes a pandemic
Bacteria morphology
• Neisseria – coffee bean shaped in pairs (e.g. N. meningitidis and N. gonorrhoeae)
• Acinetobacter – gram negative bacteria
• Staphylococcus – gram positive bacteria, grape-like clusters (e.g. Methicillin-resistance S. aureus
superbug)
• Clostridium – gram positive bacteria, spindle-shaped with bulges at end (e.g. C.difficile infects
bowels causing diarrhoea – very hard to clear so very dangerous)
• Escherichia – gram negative, rod shaped with flagella sometimes (e.g. E. coli exists in gut flora,
there are many different types, E. coli 0157 causes food poisoning)
• Mycobacterium – gram positive, rod-shaped (e.g. M. tuberculosis and M. leprae)
• Streptococcus – gram positive, pairs or chains that appear bent (e.g. S. pneumoniae and S.
pyogenes – Strep throat)
The Gram stain
• Three types of bacteria – gram positive, gram negative and acid fast
• Process of gram staining (aseptic technique)
2
,BHCS1006 Summary Notes
1. Heat fix along slide and flood with crystal violet, leave then wash
2. Flood slide with Gram’s iodine, leave then wash
3. Flood slide with 95% ethanol, leave then wash (ethanol rids any crystal violet than hasn’t
adhered to bacteria)
4. Flood slide with Safranin, leave then wash and dry
• Gram+ bacteria will stain purple (from crystal violet)
• Gram- bacteria will stain pink (from safranin)
• Difference staining due to difference in cell wall structure
o Gram+ bacteria
▪ 90% of cell wall is peptidoglycan which strongly binds to crystal violet therefore
retaining purple colour
▪ Low lipid content
▪ Contains teichoic acid (unique to Gram+) - role unknown
▪ Can form spores
o Gram- bacteria
▪ 10% of cell wall is made up of thin layer of peptidoglycan so doesn’t bind to crystal
violet very well
▪ Lipopolysaccharide (LPS) – endotoxins that cause a lot of diseases
▪ High lipid content
Bacterial replication – binary fission
• Asexual process
• Cell doubles its mass
• Genome DNA replicates
• In ideal conditions, E. coli can undergo 1 cell cycle every 20 minutes
Vegetative bacteria – can reproduce, is alive and active
Spore formers
• Survive in any environment and will activate in right environment
• Can’t replicate in this form (dormant)
• Very difficult to kill (e.g. C. diff resistant to heat, chemicals, depletion and desiccation)
• E.g Bacillus, Clostridia
Food bacteria
• Pathogenic bacteria – food poisoning
o Gram- rods; E. coli, Pseudomonads
o Gram+ rods; Clostridia, Bacillus
• Cultured bacteria
o Gram+ rods – Lactobacilli in yogurt (produces lactase in body)
o Rice
o Raw honey
Microbial nutrition
• Autotrophs
o Synthesis complex organic molecules from simple, non-organic molecules
o Uses light or chemical energy
o E.g. plants are photoautotrophs, iron bacteria are chemoautotrophs
• Heterotrophs
3
, BHCS1006 Summary Notes
o Use organic molecules like carbon
o 2 and 3rd consumers in the food chain (carnivores, herbivores etc)
Growing microbes in the lab
• Culture
o Nutrient source
▪ Carbohydrate – sugar derivatives
▪ Proteins – meat/yeast extracts
▪ Minerals/vitamins
o Broth (liquid) culture – test tubes/bottles
o Solid (agar) media – test tubes/bottles/plates
o Culture media formulated to meet nutritional requirements of certain bacteria, selectively
grow or inhibit certain bacteria and be diagnostic
• Optimal conditions
o Nutrient source
o Temperature (mesophiles)
▪ For every 10C increase, metabolic and growth rate doubles
▪ At high temps; membrane disruption, protein denaturation
▪ At low temps; adapt to maintain membrane fluidity, slow metabolic and growth rate
o Water availability
o pH
o gaseous atmosphere
o no antimicrobials – e.g. naturally occurring polyphenols, preservatives etc
o Oxygen tolerance
▪ Obligate aerobes – love O2
▪ Obligate anaerobes – hate O2
▪ Facultative anaerobes – in between
▪ Aerotolerant anaerobes – in between
▪ Microaerobes – low level of O2 required for survival
Standard pattern on growth shown as a Growth Curve with Set Phases
Viruses
• Genetic elements containing either RNA or DNA that replicate in cells
• Viruses are dormant when they are outside of cells
• Morphology
o Determined using electron microscope, genetic makeup and size
4
