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stayMicrobial physiology
Study of normally functioning vital life processes
Microbial nutritional requirements (chemical elements):
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Enzyme
- Biologic catalyst (NOT altered during chemical reaction)
- Protein which either:
➔ 6 major elements: C, H, O, N, P, S ➔ Induces specific chemical reaction to occur
➔ Others (lesser amounts): Na, K, Cl, Mg, Ca, Fe & I ➔ Catalyzes (accelerates or increases) its rate
➔ Some trace elements - Holoenzyme = apoenzyme + coenzyme
- Nutrients serve as:
➔ Sources of energy (breaking their chemical bonds) - Apoenzyme:
➔ Sources of smaller molecules (building blocks) ➔ Protein that can’t catalyze chemical reaction on its own
➔ Sources of C, N, & other elements ➔ Must first link up with:
▪ Cofactor: mineral ion as Ca, Mg, or Fe cations
- Essential nutrients: MO needs them but unable to synthesize them ▪ Coenzyme
- Categories of MOs according to the energy and carbon sources:
- Coenzyme:
Energy source Carbon source
Autotrophs (CO2) Heterotrophs (organic
compounds not CO2)
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➔ Small organic, vitamin-type molecules (FAD & NAD)
➔ Participate in Krebs cycle

Phototroph (sunlight)
Chemotrophs (chemicals):
- Lithotrophs: inorganic
- Organotrophs: organic
Metabolism:
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Photoautotroph Photoheterotroph
Chemoautotroph Chemoheterotroph:
animals, fungi, protozoa &
most pathogenic medically
important bacteria
➔ Do not have to be present in large amounts
➔ NOT altered during chemical reaction
- Metabolic enzyme:
➔ Enhance & regulate metabolic reactions
➔ Cell must have genes which code for their production
➔ Moves from one substrate molecule to another at a rate of

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- All chemical pathways (reactions) within living cell
- Spontaneous energy transformation processes which occur
several hundred each second (quickly)
➔ All enzymes required for certain metabolic pathway need NOT
be present at any particular time
Catabolism (degradation) Anabolism (biosynthesis)
➔ Do not have to be present in large amounts
Breakdown of large macromolecules Building up large macromolecules
➔ NOT altered during chemical reaction
into smaller molecules (hydrolysis) from smaller molecules (dehydration)
➔ Finally degenerate & lose their activity (do NOT last indefinitely)
Breaking of chemical bonds Formation of chemical bonds → must be synthesized & replaced
Releases energy Requires energy
Energy required for anabolic reactions is provided by catabolic reactions
Quite diverse in bacteria Quite similar for all types of cells
Types of enzymes:
- Endoenzymes:
➔ Produced within cell & remain within cell
➔ Catalyze intracellular reactions
➔ Ex: digestive enzymes within phagocytes
- Exoenzymes:
➔ Produced within cell & released outside
➔ Catalyze extracellular reactions
➔ Cellulase & pectinase, by saprophytic fungi
- Hydrolases:
➔ Breakdown macromolecules by addition of water
➔ Enable saprophytes to break down complex materials
- Polymerases:
➔ Involved in formation of large polymers
➔ DNA polymerase is required for DNA replication
➔ RNA polymerase is required for mRNA synthesis
Examples of exoenzymes:
1- Coagulase:
➔ Converts fibrinogen to fibrin
➔ Produced by S.aureus to from fibrin coat:
▪ Protects the bacteria from phagocytes
▪ Protects the bacteria from antibodies
➔ Used in-vitro in clinical microbiology lab for identification of
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S.aureus which is coagulase-positive
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2- Kinases (fibrinloysins):
➔ Opposite effect of coagulase by lysing fibrin clots
➔ Streptococcus:
▪ Produces streptokinase
▪ Streptokinase used in treatment of coronary thrombosis
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➔ Staphylococcus: produces staphylokinase
3- Hemolysins:
➔ Damage host’s RBC
➔ Provide iron to pathogen in-vivo
➔ Used in-vitro in clinical microbiology lab
for identification of Streptococci species
▪ Alpha (α-hemolytic): partial hemolysis (green color)
▪ Beta (β-hemolytic): complete hemolysis (clear zone)
▪ Gamma (γ-hemolytic): non-hemolytic
4- Hyaluronidase:
➔ Breaks down hyaluronic acid (polysaccharide cement of CT)
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➔ Also known as the spreading factor
➔ Allows spreading of certain bacteria: Staph, Strep, Clostridium
5- Collagenase:
➔ Breaks down collagen (tendons, cartilage and bone)
➔ Allows bacterial tissue invasion
➔ Clostridium perfringens:
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▪ Produces both hyaluronidase and collagenase
▪ Can spread very deep in the tissues
6- Lecithinase:
➔ Breaks down lecithin (phospholipid)
➔ Destruction of cell membranes of RBCs & other tissues
➔ Clostridium perfringens: destruction of tissues mainly muscles
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7- Necrotizing enzymes: - Halophiles: MOs that prefer high salt concentration (salinity):
➔ Destroy tissues ▪ Enterococcus

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➔ Flesh-eating strains of Group A streptococcus: ▪ Staphylococcus
▪ Produces necrotizing enzymes like protease ▪ Vibrio parahemolyticus
▪ Very rapid destruction of soft tissues ▪ Vibrio vulnificus
▪ Leads to necrotizing fasciitis
➔ Clostridium:
Campylobacter
▪ Produces both protease and lipase
- The most common cause of gastroenteritis in developed countries
▪ Myonecrosis and gas gangrene - Gram negative bacilli
- Oxidase positive
Factors which affect efficiency of enzymes - Microaerophilic
- Thermophilic (42 °C)
1- Limited range of temp, pH & [substrate]:
➔ If too high or too low → won’t function at peak Vibrio cholera
➔ Extremes: denature enzymes (loss of 3D shape) - The causative agent of cholera
- Requires low salt concentration
2- Some minerals (Ca, Mg, & Fe) serve as cofactors & enhance activity - Alkaliphile (requires high pH)

3- Heavy metal ions (Pb, Zn, Hg, & As) replace cofactors at their
combining sites of enzymes & inhibit activity of enzymes
4- Competitive inhibition by binding to molecule with similar structure
to substrate
Extremophiles
- Thermophiles: MOs that prefer high temperatures (Pseudomonas)
- Psychrophiles (cryophiles): prefer cold temperatures
- Acidophiles: MOs that prefer high acidity: H.pylori & Lactobacillus
- Alkaliphiles: MOs that prefer high alkalinity (high pH)
- Xerophiles: MOs that prefer dryness
- Hygrophiles: MOs that prefer humidity (moisture)
- Barophiles: MOs that prefer high pressure
- Radiophile: MOs that prefer high level of radiation
Listeria monocytogenes
- Common cause of gastroenteritis outbreaks
- Requires low temperature (psychrophile)
- Ready-to-eat (RTE) food: dairy products (soft cheese and ice
creams) and deli meats
- Cook chill food preservation method (in hospitals)
Legionella pneumophila
- Thermophile
- Natural habitat – water:
➔ Warm water in nebulizers and oxygen line humidifiers
➔ Whirlpool spa baths and showers in hotels
- Causes: legionnaire’s disease (atypical pneumonia), & Pontiac fever
 Cellular respiration of one glucose molecule Identification according to respiration in thioglycolate broth

Phase Condition Site ATP

Prokaryote Eukaryote
Glycolysis (9 steps) Anaerobic Cytoplasm 2
Krebs cycle (8 steps) Aerobic Inner cell Mitochondria 2
Electron transport membrane Prok = 34
chain Euk = 32-34

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Cytochrome oxidase (cytochrome C):
- Used in clinical microbiology lab (CML) for diagnostic purposes
- Bacteria that don’t possess this enzyme are oxidase negative
- Bacteria that possess this enzyme are oxidase positive
- Oxidase positive Gram-negative bacilli:

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➔ Pseudomonas
➔ Brucella
➔ Vibrio cholera
➔ Neisseria
➔ Campylobacter
➔ Helicobacter

Anaerobes die in presence of oxygen

Fermentation of glucose
- Reduction of molecular O2 → potent toxic reactive oxygen species
- ROS cause damage to enzymes & cell membranes → death - Usually anaerobic process
- Formation of ROS: - One glucose molecule → very little energy (only 2 ATP)
- Very inefficient energy-yielding system
- Aerobic respiration → 18-19 times as much energy
- Protection is by detoxifying neutralizing enzymes:
➔ Superoxide dismutase Lyme disease
➔ Peroxidase - Caused by the spirochete Borrelia burgdorferi
➔ Catalase - Lyme is a town in Connecticut
- Anaerobes: lack ≥ 1 of the protective enzymes - Tick-borne disease
- Catalase enzyme is used in CML for diagnostic purposes: - Characterized by erythema migrans:

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➔ Catalase positive: Staphylococcus ➔ Bull’s eye skin rash
➔ Catalase negative: Streptococcus ➔ Rash: circular red area with clearing in the middle
 Biochemistry review - Polysaccharides:
➔ For energy storage and structural support in living organisms
Biomolecules
➔ They are further classified into:
- Organic compounds with covalently-bonded carbon backbones
▪ Homopolysaccharides: made of the same monomeric unit:
- Found as essential components of living organisms
✓ Cellulose: cell wall of algae & plants (β glycosidic bond)
- Many are polymers of simple building blocks (monomers)
✓ Chitin:
- There are four main types of polymeric biomolecules:
❖ Cell wall of fungi

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➔ Polysaccharides: the main component of bacterial capsules
➔ Lipids
➔ Proteins
❖ Exoskeleton of insects &crustaceans
É energy storage in plants (α glycosidic bond)
✓ Starch:
✓ Glycogen: energy storage in animals
➔ Nucleic acids
▪ Heteropolysaccharides: made of different monomeric units:
Carbohydrates ✓ Peptidoglycan: cell wall of bacteria
- Monosaccharides (formula: CH2O): ✓ Hyaluronic acid: extracellular matrix in human
➔ The basic monomeric units of all carbohydrates
➔ Classified according to the number of carbon atoms:
▪ Trioses ③ (Glyceraldehyde, Dihydroxyacetone)
▪ Tetroses ④ (Erythrose)
▪ Pentoses ⑤ (Ribose, Deoxyribose, Ribulose, Xylose, Arabinose)
l ▪ Hexoses ⑥ (Glucose, Galactose, Fructose, Mannose)
▪ Heptoses ⑦ (Sedoheptulose, Mannoheptulose)
▪ Octoses ⑧ (Do not occur in nature)
▪ Nonoses ⑨ (Neuraminic acid) Lipids
➔ Fructose is the sweetest monosaccharide - The major unifying characteristic of all lipids is their hydrophobicity
- Display a wide range of structural variations
- Oligosaccharides: - They perform various functions in living cells:
➔ Few monosaccharide units bind to each other ➔ Neutral (completely hydrophobic) lipids:
➔ Linked through the formation of glycosidic bonds ▪ Energy storage: triacylglycerols and waxes
➔ Synthesized by dehydration & cleaved by hydrolysis ▪ Heat insulation: triacylglycerols
➔ Types of oligosaccharides: ▪ Water repulsion: waxes (on plants’ leaves)
▪ Sucrose (Glucose & Fructose): table sugar ▪ Signal transmission: eicosanoids, steroid hormones and
▪ Maltose (Glucose & Glucose) derivatives of fat-soluble vitamins
▪ Lactose (Glucose & Galactose): milk sugar ▪ Enzyme co-factors: derivatives of fat-soluble vitamins
 ➔ Amphipathic (polar) lipids: - Classification of fatty acid-derived membrane lipids:
▪ Structural components of membranes: fatty acid-derived
membrane lipids and sterols Hydrophobic Glycerol Sphingosine
▪ Helping in lipid digestion: bile salts Hydrophilic (glycerolipids) (sphingolipids)
Phosphate group Glycerophospholipids: Sphingophospholipids:
- Classification of lipids according to structure and polarity (phospholipids) Lecithins Sphingomyelin
Sugar (glycolipids) Glyceroglycolipids: Glycosphingolipids:
Monogalactosyl a- Cerebrosides
Fatty acid-derived Isoprene-derived
Diacylglycerol b- Gangliosides
Neutral 1- Triacylglycerols (fats and oils): 1- Steroid hormones:
(MGDG)
glycerol + three fatty acids A- Adrenocortical
hormones:

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▪ Glucocorticoids Proteins:
▪ Mineralcorticoids
B- Sex Hormones: - Proteins are polymers of amino acids (building blocks)
▪ Testosterone - Essential amino acids: must be acquired from the environment
2- Waxes: long-chain alcohol + long- ▪ Estrogen - A major biological activity of proteins is the enzymatic activity
chain fatty acid ▪ Progesterone - Although the majority of enzymes are proteins, some RNA
molecules, called ribozymes, may act as enzymes

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2- Fat-soluble vitamins: - Sometimes, the protein requires non-protein cofactors to function
(A, D, E, K) - Levels of protein architecture:
3- Eicosanoids (arachidonic acid Structure Definition
derivatives [20 carbon atoms]): Primary The sequence of amino acids in the polypeptide chain
prostaglandins, leukotrienes Bound by peptide bonds

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Polar Fatty Acid-Derived Membrane Lipids 1- Sterols:

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Secondary The folding of the polypeptide chain into patterns (α-
a- Cholesterol: animal helices, β-sheets) by nearby amino acid residues

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cell membranes Bound by hydrogen and disulfide bonds
b- Ergosterol: fungal Tertiary The overall 3D arrangement of the polypeptide chain
cell membranes Bound by hydrogen and disulfide bonds
2- Bile salts: lipid Quaternary The binding of more than one polypeptide chain
digestion Bound by hydrogen and disulfide bonds
Form a functional protein (like hemoglobin)
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- Holoenzyme is composed of:
1- Apoenzyme: the polypeptide component
- Genes:
co ➔ Responsible for encoding gene products
➔ Classified according to the nature of their expression into:
▪ Constitutive: expressed all the time

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2- Cofactor, which could be:
▪ Inducible: expressed at certain times
a- Metal ion (inorganic): Mg2+, Ca2+, Fe2+, Cu2+
b- Coenzyme (organic): Vitamin-type compounds
- Types of RNA, according to the function they perform:

Nucleic acids O
1- mRNA (Messenger RNA):

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▪ Synthesized with the DNA acting as template
- The monomer of nucleic acids is the nucleotide: ▪ Transmits the stored information to the ribosome
➔ Pentose: deoxyribose or ribose ▪ Each codon along the strand eventually responsible for
➔ Nitrogenous base: encoding an amino acid

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▪ Purines: Adenine and Guanine 2- tRNA (Transfer RNA):
▪ Pyrimidines: Cytosine, Thymine and Uracil ▪ Carries the individual amino acids to the ribosome
➔ Phosphate group ▪ AAs are polymerized according to the information
stored on mRNA through codon-anticodon pairing
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There are two types of nucleic acids in living organisms:
1- DNA (Deoxyribonucleic Acid): making up the genes containing o
3- rRNA (Ribosomal RNA): enters in the structure of ribosomes

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the genetic code - Central dogma of molecular biology:
2- RNA (Ribonucleic Acid): regulating the flow of genetic ➔ Transcription: DNA → m-RNA
information inside the cell ➔ Translation: m-RNA → Protein
➔ Expression: transcription + translation
- Differences between DNA and RNA:

Pentose Nitrogenous base

DNA Deoxyribose Never contains uracil

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RNA Ribose Never contains thymine
Single or double strandedness is not an absolute
characteristic of either DNA or RNA