1
Q
What is microbiology?
A
Microbiology is the study of living organisms (‘microorganisms’ or ‘microbes’); simple in structure and usually small in size (cannot be seen with the naked eye).
2
Q
What does the study of microbiology include?
A
They include bacteria, fungi, protozoa, and viruses.
3
Q
What is the importance of microbiology?
A
Microorganisms cause many diseases and some microorganisms have been used in the manufacture of antibiotics and foodstuffs.
4
Q
What are creatures classified into?
A
- Animalia (Eukaryotic): helminths
- Plantae (Eukaryotic)
- Protista (Eukaryotic): Protozoa
- Fungi (Eukaryotic)
- Monera (Prokaryotic): cellulars like bacteria and acellular like a virus
5
Q
What is another term for prokaryotic?
A
Pre-mature
6
Q
What is the difference between cellular prokaryotic and eukaryotic?
A
Nuclear membrane: absent - present Chromosomal number: haploid - diploid Histones: absent - present Ribosome: 70s - 80s Peptidoglycan: present - absent Mitochondria: absent - present Mitosis: absent - present Cell wall sterols: absent - present Membrane-bounded organelles: absent - present
7
Q
What is the size of bacterial cells?
A
Measured by micron (micron= 1/ 1000 mm).
8
Q
What is the shape of bacterial cells?
A
- Cocci or spherical: e.g. Staphylococci.
- Bacilli or cylindrical: e.g. Diphtheria bacilli.
- Spiral:
ο· One curve: e.g. Vibrio.
ο· More than one: e.g. Spirochetes, Spirillum.
9
Q
What is the habitat of bacterial cells?
A
a. Parasitic (need host): bacterial flora (commensally) and pathogenic bacteria.
b. Saprophytic: free-living in soil, air, and water.
10
Q
What is the structure of bacterial cells?
A
- Surface Structures (bacterial envelope):
β Cell wall.
β Cytoplasmic membrane.
β Capsule or slime layer. - Internal structures:
- Nuclear body
- Flagellae
- Inclusion bodies
- Ribosomes
- Fimbria
- Mesosomes
11
Q
What are the characters of the cell wall?
A
It is the rigid layer outside the cytoplasmic membrane.
12
Q
What is the chemical structure of the cell wall?
A
Composed of peptidoglycan.
13
Q
What are the Differences between Gram-positive and Gram-negative cell walls?
A
Peptydoglycan:
ο· Thick (~ 40 sheets)
ο· Comprising up to 50% of the cell wall.
ο· Thin (One or two sheets)
ο· Comprising only 5β10% of the cell wall.
Special Components:
ο· Teichoicacid:ribitol or glycerol.
ο· Polysaccharides.
- Outer membrane (thick).
ο· Lipoprotein.
ο· Lipopolysaccharide: o Lipid A (the endotoxin). o Polysaccharide (somatic antigen).
2- Periplasmic space
ο· Between cytoplasmic membrane and outer
membrane and contains hydrolytic enzymes and penicillinase.
14
Q
What is the function of the cell wall?
A
SPA GTG
- Preservation of the shape of the cell.
- Protectiveagainst high internal osmotic pressure.
- Antigenic character:
ο§ In Gram-positive: Teichoic acid.
ο§ In Gram-negative: somatic “O” antigen(Polysaccharide). - Toxicity: The lipid A endotoxin of Gram-negative cell wall.
- Cell wall is responsible for Gram staining reaction (Gram-positive bacteria stain violet while Gram-negative bacteria stain pink)
- Cell wall is the target for the action of some antibiotics: penicillin and cephalosporins and vancomycin.
15
Q
What are the enzymes that attack the cell wall?
A
The peptidoglycan is hydrolyzed by lysozyme found in tears, saliva, and nasal secretions.
16
Q
What are the characters of the cell membrane?
A
It is a very thin elastic membrane that lies immediately under the cell wall.
17
Q
What is the chemical structure of the cell membrane?
A
- composed of biphospholipids and proteins.
- prokaryotes have no sterols in the cytoplasmic membrane except for Mycoplasma.
18
Q
What is the function of the cell membrane?
A
- Permeability and transport: transport nutrients into and waste products out of the cell.
- Electron transport and oxidative phosphorylation: for energy production (ATP).
- Excretion of hydrolytic enzymes.
- Biosynthetic function: carries enzymes and molecules for the biosynthesis of the cell wall, DNA, and membrane lipids.
- Chemotactic function: contain receptors of binding and repellents.
19
Q
What are the characters of the capsule?
A
-Some bacteria can produce a gelatinous layer surrounding the cell outside the cell wall.
Capsule: condensed well-fined layer closely surrounds the cell.
Glycocalyx: polysaccharide-containing material lying outside the cell.
Slim layer: if glycocalyx is loosely surrounding the cell.
20
Q
What is the chemical structure of the capsule?
A
Consists of polysaccharides, except in bacillus anthracis(protein polymers).
21
Q
What is the function of the capsule?
A
- Virulence factor as it protects the bacterial cell from phagocytosis.
- Protects the cell wall against attack by bacteriophages, complement, and lysozymes.
- Antigenic (K-antigen): used in serodiagnosis or vaccine preparation.
22
Q
What is the definition of flagella?
A
Long thread-like, helical filaments.
23
Q
What are the types of flagellate?
A
- Monotrichous (single polar flagellum).
- Lophotrichous (multiple polar flagellae).
- Amphitrichous (One flagellum in each pole of the
cell) . - Peritrichous (flagella distributed over the entire
cell) e.g. E.coli.
24
Q
What is the structure of flagella?
A
made up of a contractile protein called flagellin.
25
What are the functions of flagella?
1. It is the organ of Motility:
> Movement toward the optimal nutrients.
> Movement toward optimal oxygen concentration in aerobic bacteria.
> Choosing the locality suitable for colonization.
> Assist pathogenic bacteria in penetration through a viscid mucous secretion.
2. Highly Antigenic (H-antigens).
26
What are viruses?
- Viruses are not cells, i.e. they do not have a nucleus or organelles.
- The smallest infectious agents (20 to 300 nm in diameter).
- They are obligate intracellular parasites (they do not have ribosomes and can't be planted on agar)
- contain one kind of nucleic acid (RNA or DNA)
27
What is the difference between prokaryotes and acellular organisms?
- Prokaryotes: they do not have a membrane-bound nucleus
| - Acellular: do not have a cell membrane
28
What is a virus particle (virion) composed of?
1. Protein coat (capsid)
2. Nucleic acid core
3. Envelope (in some viruses)
29
What are the characters of viral capsid?
o It surrounds viral nucleic acid.
o made up of subunits called capsomers.
o Each capsomer is consisting of one or several proteins.
o The capsid with the enclosed nucleic acid is called the nucleocapsid.
30
What are the functions of the capsid?
a) It protects the viral genome against inactivation by nuclease enzymes.
b) The arrangement of capsomers (symmetry) is either icosahedral, helical, or complex.
c) Participates in adsorption of virions to susceptible cells. It determines the antigenicity
D) has a role in attachment.
31
What is viral symmetry?
1- Icosahedral (enveloped and non enveloped)
2- Helical (enveloped and non enveloped)
3- Complex (rare)
32
What are the characters of viral nucleic acid?
ο DNA (single molecule) or RNA (single or segmented).
ο Single or double-stranded (but one molecule)
ο Linear or circular.
ο It is the infectious part of the virus and codes for viral structure and non-structural proteins.
33
What are the characters of the viral envelopes?
ο Lipoprotein, the lipid from the host cell membranes and protein is virus-specific.
ο Glycoproteins in the form of spike-like projections on the surface attach to the host cell receptors.
ο It determines viral antigenicity and specificity
34
What determines the antigenicity of the virus?
The envelope and the capsid
35
What are the spikes of HIV and the receptor it works on respectively?
Gp120 and cd4
36
What are the steps of the viral replication cycle?
1-Attachment (adsorption by glycoprotein spikes)
2-Penetration
3-Uncoating
4-Viral gene expression (transcription) and protein synthesis (translation for the synthesis of coat)
5-Viral nucleic acid synthesis (replication for the synthesis of more versions)
6. Assembly (reunion)
7. Release
37
Attachment step of virus
ο Attachment of the virus to the host cell
| ο It is receptor-specific
38
Penetration step of the virus
ο In non enveloped viruses penetration occurs by crossing the plasma membrane directly or by receptor-mediated endocytosis.
ο In enveloped viruses penetration occurs by fusion of viral envelope with cell membrane or with the membrane of endosome at the cell surface
39
Uncoating step of the virus
ο It is the release of viral nucleic acid by cellular enzymes.
ο Uncoating renders viral nucleic acid accessible for transcription and replication.
40
Viral nucleic acid synthesis (replication) step of the virus
by using a strand of the parental nucleic acid as a template for the production of progeny DNA or RNA molecules.
41
Assembly step of the virus
Assembly of viral nucleic acid and protein coats to form mature virus particles.
42
Release step of the virus
Virus particles are released from the cell either by:
ο Budding through the outer cell membrane as in enveloped viruses (taking a part of the bilayer)
ο Rupture of the cell membrane and release of the mature particles in unenveloped viruses.
43
How are viruses laboratorally detected?
Direct or indirect (virus isolation) and serologic detection of antiviral antibodies
44
How are viruses directly detected in the laboratory?
1) Detection of Virus particles by (electron microscope), inclusion bodies by (LM) (in cytoplasm and nucleus)
2) Detection of viral antigens by (EIA, RIA...)
3) Detection of the viral nucleic acid by (PCR) and other
molecular techniques.
45
How are viruses indirectly detected in the laboratory?
-Viruses are obligate intracellular parasites and can be cultivated on:
a) Tissue cultures:
ο Pieces of animal or human tissues are trypsinized to get separate cells.
ο Cells are grown in media containing amino acids, vitamins, calf serum, and antibiotics.
ο A monolayer or sheet of cells is formed on the flat side of the container within a few days. Viruses are inoculated on the monolayer (we notice the change on the cells done by the virus)
b) Embryonated egg.
c) Animal inoculation.
46
How are viruses serological detected in the lab?
By serological methods (ELISA, RIA...).
47
How is the prevention of viruses?
Vaccination and public health measures.
48
How are viruses treated?
ο Antiviral drugs are medicines that cure or control virus infections.
ο antiviral agents tend to be narrow in the spectrum and have limited efficacy. (Unlike antibiotics)
49
What are the types of antiviral drugs?
1) Inhibitors of Herpesviruses
2) Inhibitors of Retroviruses
3) Inhibitors of other viruses
4) Interferon
50
What are examples of Inhibitors of Herpes viruses?
Nucleoside analogue : inhibits virus-specific DNA polymerase e.g. Acyclovir, Ganciclovir, and rhindisevir (for covid)
51
What are examples of Inhibitors of Retroviruses?
- Reverse transcriptase inhibitors
- protease inhibitors
- fuzeon
- integrate inhibitors
52
What is the function of reverse transcriptase inhibitors?
- inhibit reverse transcriptase of HIV
| - e.g. Azidothymidine (AZT), dideoxyinosine and bcavar sulfate
53
What is the function of protease inhibitors
- saquinavir and indinavir for treatment of HIV
54
What is the action of fuzeon?
- blocks the viral and cellular membrane fusion step involved in the entry of HIV into the cell
55
What is the action of integrase inhibitors?
- inhibit integrase enzyme of the virus
56
Give examples for inhibitors of other viruses
- amantadine
- zanamivir and oseltamivir
- ribavirin
57
What is the function of amantadine?
inhibits Influenza A virus uncoating
58
What is the function of zanamivir and oseltamivir?
inhibit viral neuraminidase of influenza A and B viruses (inhibit viral release from an infected cell to other cells
59
What is the function of ribavirin?
inhibits both DNA and RNA polymerase enzymes. Used for treatment of HBV, HCV infections, and RSV pneumonitis
60
How are interferons produced?
Infection of cells with viruses induces the production of proteins that are known as interferons because they were found to interfere with viral replication in previously uninfected tissue culture cells.
61
What are the types of interferons?
There are 3 types of interferons:
1. interferon-Ξ± (IFN-Ξ±)
2. interferon -Ξ² (IFN-Ξ²),
3. interferon-Ξ³ (IFN-Ξ³), which is induced by activated T cells.
62
What is the mechanism of action of interferons?
- IFN-Ξ± and IFN-Ξ² are secreted by the infected cell and then bind to a common cell-surface receptor, known as the interferon receptor, on both the infected cell and nearby cells.
- Interferon induces the synthesis of several host cell proteins e.g. RNA dependent protein kinase (PKR) that contributes to the inhibition of viral replication
63
What is the definition of the genome?
It is the total genetic information in an organism.
64
What are the characters of the prokaryotic genome?
ο Consists of a single copy (Haploid) circular DNA molecule.
ο Range from 580-4600 Kbp
ο Many bacteria contain extrachromosomal DNA materials as a part of the genome called plasmids and transposons.
65
What is the definition of bacterial extrachromosomal elements?
- These are the DNA material present in a cell other than chromosomal DNA
- The most famous extrachromosomal DNA are:
A. Plasmid.
B. Transposons.
C. Bacteriophage (virus infecting bacteria)
66
What is the definition of plasmids?
Plasmids are pieces of DNA that exist separate from the chromosome, they contain an origin of replication so they replicate independently.
67
What are plasmids classified according to?
```
1- According to the size of the plasmid
2- According to copy number
3- Shape of plasmid
4- Moving plasmid from cell to cell
5- Artificial and natural plasmids
6- according to host range
7- according to compatibility
```
68
What are plasmids classified according to size?
Starting from a few hundred base pairs up to 3000 Kbp.
69
What are plasmids classified into according to copy number per cell?
1- Stringent plasmids
ο 1-2 copies / cell
ο like F- plasmid and phage β plasmid
hybrid (P1)
2- Low copy number plasmids
ο 10-15/copies/cell
ο such as pSC 101
3- High copy number plasmid
ο up to 50 copies/cell
ο like ColE, plasmid
4- Extremely high copy number plasmid
ο these are specifically engineered to be up to 100-200 copies/cell
70
What are plasmids classified into according to the compatibility of plasmids?
Compatible plasmids:
β’ a cell can maintain more than one plasmid in the same cell (if they carry
different origins of replication).
Incompatible plasmids:
β’ The inability of two plasmids to be maintained in the same cell (if they carry the same origin of replication
71
What are plasmids classified into according to the shape?
The shape of plasmids can be classified into 3 groups
1- Covalently closed circular (CCC) form:
ο The most common form
ο Present as ds completely closed circular forms (as in E.coli).
2- Semicircular form:
ο Transient form
ο Present as one strand is completely closed, the other strand is opened.
3- Linear:
ο unstable because it is attacked by exonucleases.
72
What are plasmids classified into according to host range?
1- Broad host range plasmids:
β’ Can replicate in a wide range of bacteria.
2- Narrow host range plasmids:
β’ only replicate in one or a few closely related bacteria.
73
What are plasmids classified into according to moving from one cell to another?
Conjugative plasmids: which have the tra genes that can mobilize the plasmid from one cell to another by conjugation
Shuttle vectors: plasmids that propagate in 2 diff. Hosts species (yeast and bacteria)
Nonβconjugative plasmids: Cannot be mobilized under any known conditions
74
What are plasmids classified into according to naturallity or artificiality?
1- natural plasmids:
β’ All the above plasmids are present naturally in bacterial and some yeast cells.
2- Artificial plasmids :
β’ are naturally present plasmid but designed artificially
β’ to be used in genetic cloning as vectors
β’ by adding antibiotic-resistant markers or DNA sequences to be the target of
restriction endonucleases.
75
What is the importance of plasmids?
1. Resistance:
ο Antibiotic resistance.
ο Heavy metals (metal reductase).
ο U/V (DNA repair enzymes).
2. Conjugation.
3. Production: Toxins & enzymes and bacteriocin.
4. Biochemical reactions: Sugar fermentation.
5. Molecular biology: As a vector.
ο Cloning vectors
ο Gene therapy: These are plasmids used for the insertion of therapeutic genes to express the protein that is lacking in the cells
76
What are transposons?
Extra-chromosomal small pieces of DNA those are capable of moving themselves from one location in DNA to another, (movable elements or jumping genes).
77
What are the 3 forms of transposons?
(a) Insertion sequence (IS)
(b) Composite transposons (Tn)
(C) Non β composite transposons
78
What are the characters of the insertion sequence?
ο The simplest form.
ο They encode only proteins needed for their own transposition
ο Carry repeated nucleotides at their ends (direct repeats or inverted repeats ~ (15-25).
ο Examples: IS 1, 3, and 10.
79
What are the characters of composite transposons?
Contain 2 IS at both ends and central piece of DNA which encode for antibiotic resistance, virulence factors.
80
What are examples of composite transposons?
- Tn5: encodes for kanamycin resistance.
| - Tn10: encodes for tetracycline resistance.
81
What are the characters of non-composite transposons?
ο Have no IS at their ends but encode for transposition proteins.
ο They carry genes for antibiotic resistance, virulence
factors, and catabolic enzymes.
82
What are the examples of non-composite transposons?
o Tn 3: carry Ampicillin resistance gene.
| o Tn 7: carry streptomycin and trimethoprim resistance
83
What is the definition of gene transfer?
It is the process of moving apiece of DNA (Either chromosomal or plasmid) from one cell to another using different means.
84
What are the types of gene transfer?
Vertical Gene Transfer: The Transfer of genetic material from parental organism to progeny
Horizontal Gene Transfer:
- known as lateral gene transfer,
- organism transfers genetic material to another organism that is not its offspring
85
What are the types of lateral gene transfer?
a) Conjugation.
b) Transduction.
c) Transformation.
86
What is the definition of conjugation?
It is a form of gene transfer in which two cells come in direct contact and DNA is transferred from one cell (donor) to the other (recipient).
87
What are the requirements for conjugation?
ο Donor cells should contain F plasmid, which encodes for F pili needed for conjugation.
ο The donor plasmid should contain tra gene(conjugative type) to mobilize the plasmid.
88
What are the steps of conjugation?
1- Donor Gram-negative bacilli containing F plasmid come in contact with other F-Gram negative bacilli.
2- The F pili of the donor cell (F +) attach to a specific receptor on the recipient cell (F -).
3- The F pili contract the recipient cell to be in close contact and then canalization occurs through the F pili between the two cells.
4- Once the canal is formed, the F plasmid starts to mobilize one strand of its ds DNA to the recipient cell.
5- New ds DNA is formed from the single strand in both donor and recipient cells so the recipient now contains F plasmid and changed to F+ cell which will act as a donor cell.
89
What is the method of conjugation in gram-positive organisms?
mediated by signaling molecules called pheromones.
90
Equation of conjugation
F+ + F- = 2F+
91
What is the HFr and what are its characteristics?
* If the F plasmid integrates into loci in the chromosome, this integrated F factor creates a high frequency of recombination cell (Hfrcell).
* If this integrated plasmid is transferred to another cell by conjugation, it can transfer a segment (locus) of the chromosome during excision and can transfer this locus (gene or genes) from the donor cell (Hfr) to a recipient chromosomal cell
92
Where does conjugation mostly occur?οΏΌ
Conjugation most frequently occurs in Gram-negative bacilli (only gram-negative have pili) but Gram-positive organisms can make conjugation.
93
What is the definition of transduction?
It is a form of gene transfer in which bacteriophage (a virus that infects a bacterial cell) mediate the DNA transfer.
94
What are the types of transduction?
1. Generalized transduction
| 2. Specialized transduction
95
What are the bacteriophage types in transduction?
1- Virulent phage (Lytic cycle)
| 2- Tempratephage (lysogenic cycle)
96
Which type of cycle happens in generalized transduction?
This occurs with the lytic cycle of Bacteriophage (virulent phage).
97
How does generalized transduction take place?
- The phage infects a bacterial cell and replicates, any piece of bacterial DNA can be packaged inside the phage head.
- By cell lysis and release of phages, it can infect another bacterial cell transferring the chromosomal DNA to the recipient cell.
98
Which type of cycle happens in specialized transduction?
This occurs with the temperate or lysogenic bacteriophage
99
How does specialized transduction take place? And why is it called "specialized"?
the phage DNA become integrated inside the bacterial DNA at a specific region, When the integrated phage is excised with a piece of bacterial chromosome and infect another bacterial cell transferring this DNA into the recipient cell.
(so it is called specialized)
100
What is the definition of transformation?
It is a method of gene transfer in which direct uptake of DNA by recipient cell either naturally or artificially in the laboratory
101
What are the methods of transformation?
- Natural transformation
- Laboratory induced competence
- Transformation by electroporation
102
Is natural transformation rare or common and give an example for an organism that works with it?
rare occasion e.g., Streptococcus pneumoniae
103
What are the methods of laboratory-induced competence?
(increasing the permeability of the cell envelopes) by:
ο Electroporation (exposing a mixture of recipient cells and plasmids to the electrical field to form pores in the cell envelopes)
ο Adding calcium chloride solution and chilled on ice then heat-shocked
104
What is the definition of transformation by electroporation?
(by exposing a mixture of recipient cells and plasmids to an electrical field to form pores in the cell envelopes).
105
Equation of HFr cells
HFr cell + F- = HFr cell + F-
106
What are the characters of bacterial endospores?
- Forming endospores under certain unfavorable conditions as starvation, desiccation, heat, and chemical agents in vitro (outside the body).
- Sporulation occurs outside the body Spore has no metabolic activity & can remain dormant for many years.
107
What are examples of bacterial endospores?
ο Clostridium (aerobic)
| ο Bacillus (anerobic)
108
What are the types of bacterial endospores?
```
- According to:
ο² Site:
-central
-subterminal
-terminal
```
ο² Shape: -
rounded
oval
ο² Size:
- bulging
- not bulging
109
What are the functions of bacterial endospores?
Resting cells, highly resistant to desiccation, heat, and chemical agents.
110
What is the mechanism of bacterial endospores?
1) The nuclear material in the cell moves to one pole.
2) Cytoplasmic membrane invaginates to form the forespore.
3) Cytoplasmic membrane grows & engulfs forespore within a second membrane.
4) Cortex formation by deposition of Dipicolinic acid and
calcium.
5) Formation of spore coat.
6) Release of endospores.
7) Rest of bacterial cells undergoes autolysis.
111
Germination of bacterial endospores
- The spore has no metabolic activity and can remain dormant for many years.
- When exposed to water and appropriate nutrients:
β’ Specific enzymes degrade the coat.
β’ Water and nutrients enter.
β’ Germination into a metabolizing, reproducing bacterial cell occurs.
112
What is the spore structure?
```
ο Bacterial DNA.
ο A small amount of cytoplasm.
ο A very little amount of water.
ο Cell membrane.
ο Peptidoglycan.
ο Thick keratin coat with Ca+.
```
113
What are the growth requirements of bacteria?
(1) Bacteria nutrition.
(2) Gases.
(3) Moisture.
(4) Temperature.
(5) Hydrogen ion concentration (pH).
(6) Other factors...
114
What are bacteria classified into according to nutrition?
- Autotrophic bacteria
| - Heterotrophic bacteria
115
Compare between autotrophic and heterotrophic bacteria
Carbon source
Examples
- Autotrophic (environmental) bacteria:
```
Inorganic chemicals(CO2).
Saprophytic bacteria.
```
- Heterotrophic bacteria:
Organic sources
Pathogenic bacteria.
116
What are the nutrients needed by bacteria?
-Basic elements
ο Needed in larger amounts.
ο For structure as basic components.
-Essential metabolites and growth factors
ο Needed in very minute amounts.
ο Used as a catalytic for growth.
117
What are examples of basic elements needed by the bacteria?
Major:
ο Carbon
ο Nitrogen
οwater
Minor: βΨ³Ψ¨ΩΩ
+ phosphorusβ
```
ο Phosphorous
ο Calcium
ο Sulpher
ο Magnesium
ο Potassium
```
118
What are the examples of essential metabolites and growth factors?
Nucleotides, vitamins
119
What are bacteria classified into according to the need for oxygen?
- Obligatory aerobes
- Facultative anaerobes
- Obligatory anaerobes
- Microaerophilic
120
What are obligatory aerobes?
- Grow only in presence of free O2.
Example: TB
121
What are facultative anaerobes?
- Grow well in the presence or absence of O2.
- They have two systems of respiration.
Examples: pathogenic bacteria.
122
What are obligatory aneorobic bacteria?
- Grow in absence of O2 and cannot grow in the presence of oxygen (why):
β’ Due to lack of peroxidase enzyme or catalase enzyme so in presence of O2, peroxides will be formed which is very toxic to the organism.
2O2 + 2H ββsuperoxide dismutase ββ> O2 + H2O2
2H2O2 β-Catalaseβ-> 2H2O + O2
Example: Clostridium
123
What are microaerophilic bacteria?
Grow best in the presence of a minimal amount of oxygen.
Example: Propionibacterium acne.
124
Is carbon dioxide essential for the growth of bacteria?
Yes
125
Is the amount of CO2 in the atmosphere sufficient?
β’ The normal atmospheric CO2 content is usually sufficient.
β’ Some organisms require higher concentrations of CO2 (5-10%) to be provided in the culture media for:
* Stimulation of growth (capnophilic) as in Neisseria & Brucella abortus.
* Formation of capsule as in Pasteurella pestis & Bacillus anthrax.
* Enterotoxin production as in Staph aureus.
126
What is the structure of fungi? And what were they considered before?
* Fungi were formerly considered to be plants. Now has its own kingdom Mycota.
* Fungi are eukaryotic organisms having true nuclei (two or more), nuclear membranes.
* Fungi possess rigid cell walls made of chitin (a polymer of N-acetyl glucosamine), glucans, mannans & complex polysaccharides.
* Cell membrane encloses the cytoplasm, vacuoles, endoplasmic reticulum, and mitochondria. It contains ergosterol.
127
What is the morphology of fungi?
There are three main groups of fungi based on cell morphology:
- Yeast and Yeast-like
- filamentous (hyphae)
- dimorphic fungi
128
What is the definition of Yeast and yeast-like fungi?
* Yeasts are round to oval unicellular fungi which reproduce by budding or fission, a progenitor then detached from the mother cell, e.g. (Cryptococcus neoformans).
* Yeast-like is round to oval multi-cellular fungi reproduce by budding but a progenitor remains attached to the mother cell giving a chain of elongated yeast cells called pseudohyphae. e.g. (Candida).
129
What is the definition of filamentous fungi?
* Filamentous fungi (hyphae) are tubular, branching structures that may or may not be separated by porous cross-walls (septa) forming septated or aseptated hyphae.
* The part of the hyphae that anchor the colony, absorbs nutrients is termed vegetative hyphae.
* The part that projects above & carries the reproductive structure called aerial hyphae.
130
What is the definition of dimorphic fungi?
Dimorphic fungi exist either as yeast or as filaments depending on the condition of growth.
131
What are examples of dimorphic fungi?
Coccidioides immitis
Histoplasma capsulatum
paracoccidioides brasiliensis
lastomisis demesis
132
How do fungi reproduce?
Fungi reproduce by the formation of spores either asexual or sexual
133
What are the types of asexual spores?
There are two general types of asexual spores:
a. Sporangiospore
b. Conidiospore
134
What are sporangiospores? And where does it happen?
ο Some fungi during growth form sac filled with spores.
ο They are mitotic spores produced within a sac termed sporangium often supported by one hyphae termed sporangiophore and this type of spores exists on non-septated fungi.
135
What are the types of conidiospores?
* Arthroconidia (Arthrospores): conidia that result from fragmentation of hyphae cell.
* Blastoconidia (Blastospores): conidial formation through a budding process.
* Phialoconidia: conidia that are produced by a (vase-shaped) conidiogenous cell termed a phialide. These spores formed at the terminal part of fertile hyphae.
* Chlamydoconidia (Chlamydospores): large thick-walled resting spores developed from hyphae for existence during long periods of dormancy.
136
How are sexual spores formed?
During sexual reproduction, haploid cells of compatible strains mate through a process of plasmogamy, karyogamy, and meiosis to form transient diploidββ>ο meiosis of this transient diploid to form sexual spores
137
What are the types of sexual spores?
* Ascospores
* Basidiospores
* Zygospores
* Oospores
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What is the definition of ascospores?
four to eight meiospores form within a sac-shaped structure termed ascus.
139
What is the definition of basidiospores?
four meiospores usually form on the surface of a specialized club-shaped structure termed basidium.
140
What are zygospores?
a large thick-walled zygospore develops between two different hyphae.
141
What are oospores?
a large thick-walled zygospore develops within the same hyphae.
142
What are the harmful effects of fungi?
1. Hypersensitivity reactions due to environmental exposure to fungal spores.
2. Infection results from invasion Of tissue and organs.
3. Toxicosis (With description)
143
What are types of fungal toxicoses?
a) Mycotoxicosis: result from accidental consumption of food products contaminated by toxin-producing fungi e.g β’ Ergot alkaloids toxicosis
β’ Aflatoxicosis
b) Mycetismus: result from ingestion of fungi containing preformed toxin e.g: β’ Mushroom poisoning
144
What is the classification of medically important fungi?
I. Primary pathogenic fungi:
Affect immunocompetent individuals e.g. dimorphic fungi
II. Opportunistic fungi:
Affect immunocompromised individuals e.g. candida (yeast-like)
145
What is mycosis?
Mycosis means diseases caused by fungi.
146
What are fungal infections classified according to?
Fungal infections are classified according to affected tissue or organ
147
What are the types of mycosis?
I) Superficial mycosis
II) Cutaneous mycosis
III) Subcutaneous mycosis
V) Opportunistic mycosis
148
What is superficial mycosis and what is an example for it?
ο Strictly surface infections are limited to the outermost layers of skin and hair.
ο Example:
* Pityriasis versicolor
ο Caused by Malassezia
ο Clinically appear as blotchy hypo or hyperpigmented itchy macular lesions usually on the chest, back, abdomen, upper arm.
149
What is cuteness mycosis and what is an example for it?
ο Fungal infections that extend deeper into the epidermis, hair, and nail.
ο Example:
* Dermatophytosis caused by dermatophytes
There are different clinical forms based on site of involvement:
- Tinea capites
- Tinea Barbae
- Tinea unguim
- Tinea pedis
- Tinea corporis
- Tinea cruris
150
What does Tinea capitis affect? And what are its symptoms?
ο Affecting the scalp & hair.
ο Dull gray circular patches of alopecia with itching broken hair.
151
What does Tinea barbae affect? And what are its symptoms?
ο Affecting the beard hair.
| ο Edematous, erythematous lesion.
152
What does Tinea ungium affect? And what are its symptoms?
ο Affecting the nails.
| ο Thickened, yellow discoloration, lusterless brittle nail.
153
What does Tinea pedis affect? And what are its symptoms?
ο Affecting between toes.
| οItching, development of small vesicles, rupture, toe webs become macerated, and peels.
154
What does Tinea corporis affect? And what are its symptoms?
ο Affecting non-hairy smooth skin.
| ο Advancing rings with scaly center and periphery are inflamed, vesiculated βsite of active fungal growthβ.
155
What does Tinea cruris affect?
Affecting the groin, moist areas.
156
What is subcutaneous mycosis and what is an example for it?
ο Infection involving the dermis, subcutaneous tissue, muscle, and fascia.
ο Example: *Mycetoma
157
What is the definition of myectoma and what is it caused by?
ο Caused by Madurell, Exophiala.
ο The chronic subcutaneous infection progresses slowly and burrows into deeper tissue producing abscess which bursts with the formation of chronic sinuses discharging fluid containing granules.
158
What is systemic mycosis? And what is it caused by?
- Infections involve many organ systems.
ο Caused by primary pathogenic dimorphic fungi.
159
What are examples of systemic mycosis?
Histoplasmosis, Blastomycosis,
| Coccidioidomycosis, Paracoccidioidomycosis
160
What is opportunistic mycosis? And what are examples of it?
ο Group of mycoses caused by saprophytic immunocompromised individuals.
ο e.g. Candidiasis, Aspergillosis, and Cryptococcosis.
161
What are the targets of anti-fungal therapy?
There are drugs that act on:
1. Cell wall synthesis:
ο· Caspofungin: inhibit 1,3- Ξ² glucan synthetase enzymeβββ->Inhibit cell wall synthesis.
2. Ergosterol synthesis:
ο· Polyenes: e.g. Amphotericin B, Nystatin: bind firmly to ergosterol in the fungal cell membrane forming pores--->disrupt membrane function--->cell death.
ο· Azoles: interact with cytochrome P450 dependent 14-Ξ± demethylase to inhibit demethylation of lanosterol to ergosterol.
3. Cytoplasmic membrane function:
ο· Polyenes
ο· Azoles
4. Nuclear division:
ο· Griseofulvin: interact with microtubules--->disrupt mitotic spindle function--->inhibit growth.
5. Nucleic acid synthesis:
ο· 5 fluorocytosine: converted by fungal enzyme cytosine deaminase into 5- fluorouracil which interferes with DNA synthesis.
6. Protein synthesis: Blasticidin
7. Metabolic inhibitors
162
What is a good amount of the body of bacteria made of?
Water
163
Is water essential for bacterial cultivation?
Yes
164
Which type of bacteria needs high conc. Of moisture?
TB
165
What is the optimum temperature for the growth of bacteria?
37
166
What is the range of bacteria in which the bacteria can live?
(10-42)
167
What are psychophilic bacteria?
Growth below the minimum temperature.
168
What are thermophilic bacteria?
growth above the maximum temperature.
169
What is the optimum Ph of the pathogenic bacteria?
Most of the pathogenic bacteria grow at optimum pH of 7.5 (neutral).
170
What are the bacteria that tolerate alkaline media?
alkalophilic bacteria as Vibrio cholera.
171
What are the bacteria that tolerate acidic media?
acidophilic bacteria as Lactobacillus.
172
What are other needs for bacteria?
LOM
As:
β’ Light.
β’ Osmotic pressure.
β’ Mechanical factors.
173
What are the bacterial products?
1) Enzymes
2) Toxins
3) Pigments
4) Other products
174
What are the enzymes of bacteria?
β’ The enzymes may act on:
ο² Protein β proteolytic enzymes.
ο² CHO β saccharolytic enzymes.
ο² lipids β lipolytic enzymes.
β’ Bacteria also have respiratory enzymes as dehydrogenases and oxidases.
175
What do enzymes need for their work?
optimum temperature and pH for its action
176
What are the characters of endopigment bacteria?
ο Remains bound to the body of the organism.
ο Do not diffuse into the surrounding medium.
ο They are demonstrated on solid media.
ο Only colonies are colored.
177
What are the characters of the exopigment?
ο Diffuses into the surrounding medium.
| ο Both colony and medium are colored.
178
What are examples of endopigment?
ο Red pigment: Serratiamarcescens.
ο Golden yellow: Staphylococcus
aureus.
179
What are examples of exopigment?
ο Pseudomonas aeruginosa produces:
β’ Blue pigment called pyocyanin.
β’ Yellow pigment called fluorescens
180
What is the function of endopigment and exopigment?
Play a role in bacterial respiration and also have antibacterial action.
181
Compare between exo and endo toxins Acc to:
AGD PS ASS EFFECT
```
ACTION
GENE THAT CODES IT
DIFFUISBILITY
PREPARATION
SOURCE
ANTIGENICITY AND TOXICITY
STRUCTURE
SPECIFICITY
EFFECT OF HEAT (60-80)
EFFECT OF 0.3% formaline
```
Diffusibility:
ο Diffusible toxins, which diffuse into the surrounding medium.
ο Non-Diffusible toxins, remain bound to the body of the organism and are released only when the organism disintegrates.
Action:
ο On specific organs according to their types.
ο On Interleukin 1 & Tumor necrosis factor.
Antigenicity & toxicity;
ο Highly
ο Less
Gene code it:
ο On plasmid or transferred by Bacteriophage.
ο On chromosome.
Source
ο G + ve mainly & G-ve
ο G β ve
Preparation
ο Growing the organism in fluid media, Then filtrated through a bacterial filter, The filtrate contains the toxin.
ο The disintegration of the organism.
Structure
ο Protein.
ο Lipopolysaccharides
Specificity
ο Specific in action.
ο Nonspecific.
Effect of heat (60-80C)
ο Thermolabile ο Destroyed.
ο Thermostable.
Effect of 0.3%formaline
ο Detoxicated.
ο Not detoxicated.
182
what are other products of bacteria?οΏΌ
1 Lysin - 1 Cidin - 6 ase
β’ Haemolysin: Produced by many bacteria like Staphylococcus aureus.
β’ Leucocidins: Produced by Staphylococci and Streptococci and kill leucocytes.
β’ Hyaluronidase: Dissolving hyaluronic acid (Cement substances between cells).
β’ Coagulase: Produced by Staphylococcus aureus and causes clotting of plasma.
β’ Protease
β’ DNAse
β’ Staphylokinase: lysis of fibrin
β’ Lipase: the destruction of lipids
183
How do bacteria reproduce?
β’ Bacteria multiply by simple binary fission which includes:
1) Growth in size (elongation) of the bacterium.
2) Division of the nuclear bodies.
3) Constriction originating from cell wall inwards.
4) Then the bacterium divides into two daughter cells.
β’ Growth on solid media produce:
β’ Colonies that are specific for each bacterial species.
β’ Growth on fluid media may give:
β’ Uniform turbidity (facultative anaerobic bacteria).
β’ Surface pellicle (aerobic bacteria).
β’ Sediment leaving relatively clear medium (anaerobic bacteria).
184
What is the definition of a growth curve?
Curve demonstrates the relationship between the logarithmic number of living bacteria against the time
185
What are the procedures done to obtain the growth curve?
Bacteria is cultured on a fluid medium & samples are taken at regular intervals to count the number of living bacteria
186
Lag phase
ο No multiplication (Constant number).
ο Bacteria increase in size and prepare for reproduction.
ο Correlate with incubation period in vivo.
```
ο Duration depends on:
1) Nature of organism:
E.coliβshort.
TBβlong.
2) Type of the media:
The more suitable the shorter the lag phase.
```
3) size of inoculum:
The bigger the shorter the lag phase.
4) Stage from which bacteria is taken:
E.g. If from the logarithmic phase the lag phase will be short.
187
Logarithmic (exponential) phase
ο The division occurs at a maximum.
ο Correlate with the invasive period in vivo.
ο In this stage, bacteria could be inhibited efficiently by antibiotics.
ο Duration depends on:
β’ Nature of organism.
β’ Type of the media.
188
Stationary phase
ο The rate of division equals the rate of death
ο The ultimate number of living organisms remains stationary.
ο Correlate with symptoms and signs in vivo.
ο The diminution of the rate of growth due to:
1) Exhaustion of nutrients.
2) O2 Starvation.
3) Accumulation of toxic materials.
189
Phase of decline
ο The number of the organism begins to decrease. And the rate of death more than the rate of growth.
ο Correlate with convalescent period in vivo.
ο Antibiotics should be continued to completely eradicate bacteria to avoid resistance.
ο β death depends on:
β’ Nature of organism.
β’ Effect of temperature.
β’ Accumulation of toxic metabolites.
190
Give example for DNA enveloped viruses
Herpesviruses
Hepatitis
Pox
191
Give examples for DNA non-enveloped viruses
Adenovirus
| Parvovirus
192
Give example for RNA enveloped viruses.
Influenza
| Corona
193
Give example for RNA non-enveloped viruses
Polioviruses
| Reoviruses
194
All DNA viruses are DS except parvovirus.
..
195
All RNA viruses are single-stranded except Reoviruses
..
196
What is the function of drugs that are similar to adenine, guanine, or others in the nucleic acid chain?
Polymerase incorporate them instead of the nucleic acid bases so inhibition of polymerase happens
197
What is the function of interferons?
They stimulate infected cells and nearby cells to produce enzymes as protein kinase which compete with IF2 at the ribosome so it decreases protein synthesis of the virus and replication
Y1B2 (PPMIP & PPP) π
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