Microbiology: Stereoisomers & Enantiomers

• Focus on microbiology related topics in chapter 7
• Enantiomers including glucose and dextrose isomers and their importance specifically thinking about the glucose in TSI and the dextrose in Phenol red broth

Stereoisomers and Enantiomers

• Stereoisomers are isomers differing in the spatial arrangement of atoms.
• Enantiomers are a unique type of stereoisomer.
• Louis Pasteur discovered enantiomer properties in 1848 analyzing crystallized wine fermentation products via microscope.
• Enantiomers possess chirality, meaning nonsuperimposable mirror images of each other.
• Chirality is vital in biologically significant molecules like glucose and alanine.
• Organisms typically utilize only one enantiomeric form of molecules.
• Taste and smell varies among enantiomeric forms of amino acids, such as sweet L-aspartame versus tasteless D-aspartame.
• Drug enantiomers exhibit varied pharmacologic effects; dextromethorphan is an antitussive, while levomethorphan is an analgesic.

Polysaccharides

• Polysaccharides show structural variety, composed of repetitive glucose units.
• Starch, glycogen, and cellulose, are biologically vital polysaccharides.
• Cellulose has linear glucose chains; a component of plant cell walls.
• Glycogen and starch are branched polymers and glycogen stores energy in animals/bacteria, contrasting with starch in plants.
• These polymers' glycosidic linkage orientation influences their differing properties.
• N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM) are modified structural polysaccharides within bacterial cell wall peptidoglycan.
• Chitin, a polymer of NAG, composes fungal cell walls and insect exoskeletons.

Isoprenoids

• Isoprenoids (terpenoids) are modified branched lipids, with roles in plants/animals.
• Isoprenoids include pharmaceuticals (capsaicin), pigments (beta carotene, xanthophylls), and fragrances (menthol, camphor etc).
• Long-chain isoprenoids feature in hydrophobic oils/waxes.
• Sebum, from human skin hair follicle sebaceous glands, comprises triacylglycerol, wax esters, and squalene.
• Sebum is a secreted substance and benefits the normal microbiota
• Propionibacterium acnes is a bacteria that feeds on skin lipids, producing short-chain fatty acids, and its involvement in acne.

Steroids

• Steroids are complex ringed lipids in cell membranes that function as hormones.
• Sterols are steroids with an OH group, mainly hydrophobic, but with hydrophilic hydroxyl groups.
• Cholesterol, a sterol in animal tissues, has a four-ring structure with a double bond and hydroxyl group.
• Cholesterol strengthens eukaryotic cell membranes, and occurs in bacteria without cell walls like Mycoplasma.
• Bacteria produce hopanoids, similar to cholesterol to strengthen bacterial membranes and Fungi/protozoa create ergosterol to strengthen membranes.

Extrinsic and Intrinsic Proteins + Cystic Fibrosis

• Proteins associated with biological membranes are either extrinsic or intrinsic.
• Extrinsic proteins, (peripheral proteins), loosely associate with one membrane side.
• Intrinsic proteins, (integral proteins), are embedded within the membrane and part of transmembrane protein transport systems.
• Cystic fibrosis (CF) results from mutation affecting transmembrane proteins, especially in lungs, and is a genetic disorder.
• Loss of phenylalanine amino acid in cystic fibrosis transmembrane regulator (CFTR) disrupts salt/water transport.
• The primary structure changes from altered protein function results in thick mucus, causing obstruction in the lungs and pancreas.
• Biofilms form in the altered mucus in airways with Pseudomonas aeruginosa and Burkholderia cepacia common pathogens.
• Pseudomonas forms "mucoid" colonies in the lung biofilm, showing unique pigmentation on lab tests, indicating CF.

MALDI-TOF

• Automated systems identify microorganisms identifying mass spectra, which are then correlated with databases.
• MALDI-TOF involves disposable MALDI plates with microorganism/matrix reagent mixture.
• A high-intensity pulsed UV laser irradiates the sample/reagent mixture, ejecting gaseous ions from microorganism's constituents.
• Gaseous ions get accelerated in a mass spectrometer, traveling at speed relevant to mass-to-charge ratio (m/z).
• A detector captures a detector signal (plot of detector signal versus m/z) related to the organism's biochemical composition.
• The mass spectrum gets compared by analyzing the reference spectrum, obtained from known microorganisms which enables unknown microbe identifications.
• MALDI-TOF is now used in clinical microbiology for rapid identification of microorganisms, especially those difficult to identify traditionally.

PHB

• Poly-ẞ-hydroxybutyrate (PHB) is a carbon/energy-storage compound in nonfluorescent bacteria from genus Pseudomonas.

FAME

• Microbes can be identified by unique lipid profiles determined by fatty acids.
• FAME (fatty acid methyl ester) analysis detects fatty acid differences, commonly used in clinical/public health/food labs.
• Fatty acids extracted from microorganism membranes are chemically altered into volatile methyl esters.
• Altered Methyl esters get analyzed using gas chromatography (GC).
• Comparisons of resulting GC chromatograms to databases of reference chromatograms identify unknown microorganisms.

PLFA

• Phospholipid-derived fatty acids (PLFA) analysis identifies microorganisms by saponifying membrane phospholipids releasing fatty acids.
• PLFA analysis follows the same methodology in which FAME analysis occurs and measures lipid profiles compared with known microorganisms.

Proteomic Analysis

• Proteomic analysis identifies bacteria depending on the protein produced in a growth within the human body.
• Proteins from pathogens are isolated via high-Pressure Liquid Chromatography (HPLC).
• Proteins get digested to create small peptide fragments.
• Peptides are identified with mass spectrometry and compared with those of known microorganisms for identification.

Clinical Focus

• Nutrient agar consists of many organic compounds including: protein, vitamins, salts, and carbs.
• Lab medias contain nutrients necessary to successfully cultivate bacteria.
• P. aeruginosa forms a blue-green pigment (pyocyanin) at 42°C inhibiting other microbial flora.
• Tests confirmed presence of P. aeruginosa in Penny’s skin sample, doctor decided not to prescribe antibiotic.
• Skin infections of Pseudomonas are usually self-limiting, usually lasts about 2 weeks that heals within, even with or without treatment.
• Doctor advised patient to wait it out and use corticosteroid cream to calm her rash for treatment of P. aeruginosa.

Chapter 8

• Prokayotes metabolize inorganic and organic molecules, including cellulose, atmospheric nitrogen, molecular hydrogen, sulfide, manganese, ferrous iron, and ferric iron that eurakyotes cannot.

Chemo vs. Phototrophs + Lithotrophs

• Autotrophs convert carbon dioxide (CO2) to organic carbon compounds, plants and cyanobacteria belong to this branch.
• Heterotrophs depends upon more complex organic matter for nutrients as provided initially by the autotrophs, example ranging from humans to prokaryotes/Escherichia coli.
• Phototrophs get energy for electron transfer from light.
• Chemotrophs obtain energy for electron transfer by breaking chemical bonds.
• Lithotrophs are chemotrophs deriving energy from inorganic compounds like hydrogen sulfide or reduced iron.

Aerobic, Anerobic, and Fermentation

• Cytochrome oxidase transferring electrons to oxygen as electron transport system end.
• Genes encoding enzymes that minimize the damaging effects from aerobic respiration, (hydrogen peroxide or superoxide).
• A cell uses Glycolysis - An organic molecule, commonly pyruvate, is a final electron acceptor.
• Fermentation doesn't use an electron transport, and is not directly producting of ATP.
• Homolactic fermentation produces lactic acid.
• Heterolactic fermentation gives a mixture of lactic acid, ethanol, acetic acid, and CO2, using a branched pentose phosphate pathway.
• One heterolactic fermenter is Leuconostoc mesenteroides, uses souring vegetables and respectively producing pickles/sauerkraut.

API + Virulence and other factors related to metabolism

• Analytical Profile Index (API) panel is one of the first rapid identification methods invented in the 70s.
• API test contains biochemistry and tests for differentiation of strains contained in the microbes selected.
• Based on pH, metabolic profile is formed, microbiologists can compare profile database used.
• Virulence for lipases is Staphylococcus auerus, Cryptococcus neoformans, Mycobacterium tuberculosis
• Enzymes that catalyze triglycerides are lipases/phopholipases.
• Gelatinase enzymes is Proteus, Serratia

Photosynthesis & Nitrogen/Carbon Cycle

• Oxygen photosynthesis- by product is referred as oxygenic photosynthesis-H2O is split.
• Anooxygenic photosynthesis- Compounds Serve as electron donors.
• Cyanobacteria in aquatic ecosystems fix nitrogen to ammonia that is easily incorporated into macromolecule.
• Rhizobium* - also fix nitrogen live symbiotically for plant growth.
• Azotobacter*- also able to fix nitrogen.
• Nitrogen converted back to nitrogen gas involving three steps- ammonification, nitrification, and denitrification.

Chapter 9

• Binary fission: is the most common form of replication in bacterial cells, this involves chromosomes and cellular components multiplying.

FtsZ

• Protein that is the protein that initiates cytokinesis and cell division by forming a z ring in the cell. FtsZ is anchored by FtsZ binding proteins.

Lag phase

• There is a small number of cells, inoculums, added to a broth for an culture to support growth
• Cell doesn't change in population but it is actively working metabolically and synthesizing proteins needed for growth of bacterial cells.

Log phase

• Bacterial species and their generation depends on growth rate under the optimum conditions that are given by the temp, PH and the nutrients that bacteria need for nutrition.

Stationary phase

• Stationary phase the culture is constant or stagnant. The new division of bacterial cell is now equivalent to the number of bacteria dying.

Death phase

• As the cells continues to accumulate, they soon exhaust the nutrients, the death cells increase in numbers, which lead. to an exponential decay in cell volume for bacterial cell.

Culture Density

• The number of bacterial cell contained in a volume. Infections in cells don't follow each other, although infections can exist if some bacterial is present in those mediums.

Chemostat

• Used to maintain continuous cultures - a vessel fitted with an opening to add nutrients and an outlet to expel fluids, effectively diluting toxic wastes and bacterial cells.

Cell count

• Direct cell count are used in culture of cells or colony on a plate for counting.

Plating/Serial dilution

• Use of viable plating. The viable plating. is a concept that live cells are replicate and viable to give light of live incubation rate in the medium provided. Colonies use units for milli liter(CFU/ML). It uses methods to dilute the sample. This is used to give a high concentration of cells with the right volume needed.

Turbidity

• Besides direct cell counts, other methods based from cell culture are all used for different. conditions. The foremost of these will be the measure of the turbidity, of a liquid. Cell. The lab instrument used is called a Spectrophotometer

Structure of Biofilms

• Contains polysaccharides, Nucleic Acids and lipids to stay afloat from predation.

O2 Requirements

• Grow bacteria into a thioglycolate tube. Shows types of growth with specific concentrations.
• Aerobes are obligate/strict. Those growing with no oxygen are anaerobes.
• The type with heavy growth at top but throughout tube are facultative anaerobes.

Oxygen level requirements

Aerotolerant stay indifferent. Microaerophiles require level, about about 1% to 10%, what is natural for oxygen.

• Obligate examples include- M. Tuberculosis.
• Meningitis and N honorrhea- obligate aerobes.
• Anoerobic chamber: Organisms found in these types are found soil and still waters were anaerobic conditions exist.

Clostridium

• Clostridium causes health problems which increase with prolonged use of antibiodies.
• C Tetani causes tetnus and C.pferfingens causes gas gangrene- lack of oxygen and blood.

Factors for cell growth concentration levels

• Optimum oxygen concentration.
• Maximum permissive oxygen concentration.
• Minime permissive oxygen concentration.

Catalysis

• Hydrogen peroxide causes damage - the way our body protects ourselves from harmful bacteria
• Aerobic respiration - generate reactive radicals that need to be detoxified.

pH

• The ideal favorable pH is optimum growth, but the highest is maximum growth pH and lowerest is minimum growth pH.
• Neutriophiles- grows in pH with one or two pH. Unit of neutral ph 7.
• Acidophies is optimal growth is in pH less than 5.55.
• **Sulfolubus spp- are extreme acidophiles.

Helicobacter pylori

• H pylori- is commonly found slim cork screw shapes, and causes the disease - Peptic ulcers, or stomach ulcers.
• These survive the stomach by creating a microworld. The Micro world produces heavy amounts of enzymes.

Alkaliphies

• pH values of between 8 and 10. They can be found is V Cholerae- grows best with basic properties.

Factors for cell growth (temp)

• Low amounts= subzeros, and no obvious nutrients.
• High point levels (ex. vents in Ocean, 700f).

Catagories for growth- Thermo, meso, and psychro

Mesophies- temp ranges from temp (20-45C). Ex - E.COLI - and normal human micro. pathogens(

• Psychrotolerant - high temp (5- refridgeration temp. .
• Arctic circle psychrophiles- cold loving , optimal for 15 deg. C.

Thermophile

• Optimal temp growth and can’t multiply beyond this certain amount. Examples would garden compost.

Hypothermophiles

• Highest limit at the high part of temperature and are isolated by from vents with better growth for all temperatures. Examples is Pyrobolus grow 105C.

High Temperatures on Microbes

• The way they will adapt is by using macromolecul.
• Protein rich - flexibility will also decrease bond
• Solvates in the membrane and will tend to be desaturated in the high temperature.

Halophiles-

• The water must high enough percentage so it can grow.

Genome size matters.

• Pathogens for small genome - for example are: myoplasma, chamydias

Bacteria and Growth media in the Lab

• General all purpose medium - TSB are used.
• Enriched media - growth factors are used

Type of Medias that are known

• Chemically medium is when a medium is known. in every way with each other. In example EZ Medium.
• -Complex media- exact amount are not known/ yest ect.

Selctive

• Unwanted microorganisms- the organism and competition, Example: MacConkey Agar. This makes it have better growth

Enrichemnt -

• It’s a fraction of the type found in an inoculum. For example, isolating the bacteria and a medium of crude will enrich the of oil- eating.

Differential-

• Color of organism on the different medium. In exam, the interactions is what creates this, and lysis of cells or medium.

Picnic

• Chicken - signs are always showed quickly - blood will be present from toxins in the body.

Medical care case study

• Medical care study- Listeria will be present, this will the body system, bloods can come back negative- results- and also to treat antibiotic , and the patient has to go through a week for treatment.

Sterptococcus Pneumoniae

• S - is virulence and produces capsule. R is nonvirulence , does not produce or produce.

Chapter 3 in notes.

• DNA- transciption and translation

Griffith

horizontal and transformation

Mac and McCarty

S and and the transformation

Alfred and Martha Chase

Bacteriaphage and the gene type material Enviromental growth.

Table sugar , influences slimy layer of S Mutans

Mutano shows some are to teeth Some can be resistant from high temp.

Chapter 11

• DNA replication replication ( small size- available).
• E.Coli has- single circle for replication and will run on over to 42 minutes.