Microbiology

refers to all of the chemical processes that occur inside living cells.

Enzymes

may be pure proteins or proteins  plus cofactors such as metallic ions or coenzymes, organic group that contain groups derived from vitamins

ES complex

the substrate fits

binding with its substrate, the molecule whose reaction is catalyzed

There is an exact molecular fit between enzyme and substrate.

Some enzymes work with only one substrate, others work with a group of molecules

enzyme A

enzyme B

Energy

ATP

adenosine (adenine + ribose) and a triphosphate group

high energy bonds

reduced. Higher energy.

oxidized. Oxygen is a common electron acceptor.

–One atom loses the electron, the other gains the electron.

redox reactions

the oxidation of food molecules to obtain energy

• 1st: Glycolysis
• 2nd: Aerobic or anaerobic respiration 

in the presence of oxygen

aerobic   respiration. 

in the absence of oxygen

anaerobic process of fermentation.

• harvested, transferred along the electron transport chain
• and eventually donated to O2 gas.

aerobic respiration

• •ATP.
• –Occurs in cytoplasm
• –Doesn’t require O2

• ATP production.
• –Only in mitochondria
• –More powerful

•Occurs in the mitochondria of eukaryotes and cell membrane of bacteria

B. Anaerobic Metabolism

• Glycolisis
• This means that glycolysis is part of aerobic and anaerobic respiration

• Glycolysis
• Fermentation

pyruvate, is used in fermentation.

NAD+  and allows glycolysis to start again

Glycolysis

• alcohol
• Present in wine & beer.
• Alcoholic fermentation

growth of a population (or an increase in the number of cells), not to an increase in the size of the individual cell.

the growth of cells in the population 

• –infection control
• –growth of industrial and biotech organisms

• •Nutrients
• •Environmental conditions: temperature, pH, osmotic pressure
• •Generation time

organic matter of dead organisms

 organic matter of living host = pathogens

• •Temperature
• •O2
• •pH
• •Osmotic Pressure (tonicity)
• •Moisture
• •Hydrostatic pressure
• •Radiation
• •Nutrients

Mesophiles

Optimum growth temperature is usually near the top of the growth range

enzyme inactivation 

• Many industrial processes involve high heat
• –450C (113F) is a problem for most enzymes
• –First Extremophile found in 1972

• •Efficient enzymes to work in the cold
• –Enzymes to work on foods that need to be refrigerated
• –Perfumes - most don’t tolerate high temperatures
• –Cold-wash detergents

oxygen kills the bacteria; ex. Clostridium tetani

lack of oxygen kills the bacteria; ex. Pserdomonas

•can shift their metabolism (anaerobic if oxygen is absent or aerobic if oxygen is present); ex. E.coli, Staphylococcus

the bacteria don’t use oxygen, but oxygen doesn’t harm them; ex. Lactobacillus

•like low oxygen concentrations and higher carbon dioxide concentrations; ex. Campylobacter

(acid-loving) – grow best at a  pH of 1 to 5.4; Ex. Lactobacilllus (ferments milk)

exist from pH to 5.4 to 8.5; most bacteria that cause human disease are in this category.

•(base loving) – exist from pH to 7.0 to 11.5; ex. Vibrio cholerae (causes cholera)

Acidophiles

–Alkaliphilic enzymes soften fabric and release some of the dyes, giving worn look & feel

• –Enzymes dissolve proteins or fats
• –Detergents do not inhibit alkaliphilic enzymes

salt lovers inhabit the oceans.

protective substances and enzymes

cell wall

The extraction of carotene from carotene rich halobacteria and halophilic algae 

Spores of sport-forming bacteria 

•Pressure exerted by standing water (ex. lakes, oceans, etc.)

• Binary fission 
• Budding
• see pg 69

bacteria and some eukaryotes (including yeasts) may also replicate by budding, forming a bubble-like growth that enlarges and separates from the parent cell

• A.    Lag Phase
• B.    Log Phase
• C.   Stationary Phase
• D.   Death Phase 

• •The number of cells doesn't increase.
• •However, considerable metabolic activity is occurring as the cells prepare to grow.   
• •This phase may not occur, if the cells used to inoculate a new culture are in the log phase & provided conditions are the same.

• •Cell numbers increase exponentially
• •During each generation time, the number of cells in the population increases by a factor of two. 
• •The number of microbes in an exponentially increasing population increases slowly at first, then extremely rapidly. 
• •Organisms in a tube of culture medium can maintain log growth for only a limited time, as nutrients are used up, metabolic wastes accumulate, microobes suffer from oxygen depletion.

• •The number of cells doesn't increase, but changes in cells occur
• •Cell become smaller and synthesize components to help them survive longer periods without growing (some may even produce endospores)
• •The signal to enter this phase may have to do with overcrowding (accumulation of metabolic byproducts, depletion of nutrients, etc.).

• •In this phase, cells begin to die out. 
• •Death occurs exponentially, but at a low rate. 
• •Death occurs because cell have depleted intracellular ATP reserves. 
• •Not all cells necessarily die during this phase!

–Adapt to nutrients

Active Growth 

Death = Growth rate

• Nutrients consumed 
• ph too low

Measures a property of the mass of cells and then ESTIMATE the number of microbes

much light a solution of microbial cell transmits; the greater the mass of cells in the culture, the greater its turbidity (cloudiness) and the less light that will be transmitted.

• •The rate of utilization of a substrate, such as oxygen or glucose.
• •The rate of formation of metabolic products, such as gases or acids, that a culture produces.

•The rate of reduction of certain dyes.

Give more accurate measurements of numbers of microbes.

• •electronic counter
• • rapid & accurate only if bacterial cells are the only particles present in the solution.
• •[gives a total count - live & dead cells].

• Quebec colony counter 
• [gives a viable count]

rapidly increase the concentration of the organism or when you want to grow motile cells

• (1) antibiotic sensitivity
• (2) estimate culture concentrations from environmental samples
• (3) isolate individual colonies from environmental
• samples. 

agar (agarose) and poured as a thin layer in the bottom of a culture dish (also sometimes called petri plate)

has an ingredient that causes an observable change in the medium when a particular biochemical reaction occurs (ex. a color or pH change).

•oxygen-binding agent added to the medium to prevent oxygen from exerting toxic effects on anaerobes

• •Alteration of membrane permeability
• •Damage to proteins and nucleic acids
• •Mutation

• •Temperature
• •Desiccation
• •Osmotic pressure
• •Radiation

The removal of water

• •Coagulates proteins by breaking hydrogenbonds
• •Boiling: 10 minutes kills most pathogens (hepatitis
• virus needs 30 minutes and spores need 20 hours!)
• •Autoclave: 15 psi for 15 minutes (121° C)

• •Used when taste of product would be damaged by longer heating: lowers numbers of pathogens (63°C for 30 minutes)
• •High-temperature short-term (HTST) pasteurization (72°C for 15 seconds)

frezze druing

• gamma rays,
• X rays,
• high energy electron beams – most energetic

• •Thymine dimers in DNA
• •Germicidal lamps, vaccine disinfection
• •Not penetrating
• •Can damage eyes

• •Very little effect on microbes
• •Microwave ovens kill vegetative pathogens by heating
• •Solid foods heat unevenly

• •Disinfectants and antiseptics
• •Surface-active agents (surfactants)
• •Chemical food preservatives
• •Aldehydes
• •Gas sterilization
• •Oxidizing agents
• •[Antibiotics]

• •Kill/inhibit growth of  microbes on surfaces
• •Phenols and phenolics: damage lipid membranes
• –Active in presence of organic matter
• –Stable
• –Persist for long periods after application

OH also called carbolic acid

• •protein denaturation and membrane damage
• – evaporate quickly
• – ethanol and isopropanol
• – [not effective if taken internally]

• silver nitrate (topical cream)
• mercuric chloride (paint)
• copper sulfate (algaecide)
• zinc (mouthwash, paints

• •Decrease surface tension
• •Soaps and detergents
• – Quaternary ammonium compounds : microbicidal

• •Formaldehyde (formalin) and glutaraldehyde
• –Disinfect instruments
• –Used to preserve tissues for pathology
• –Cross-link protein molecules

• •Ozone
• •Hydrogen peroxide
• •Benzoyl peroxide
• •Peracetic acid
• – Interfere with metabolism (especially of
• anaerobes)

• •Genetic recombination
• •Genetic engineering
• •Microbial genomics

• •The genetic compliment of an organism
• •Types of genotypic changes
• –Mutation
• –Conjugation
• –Transduction
• –Transformation

• •The genetic expression of an organism
• •Types of phenotypic expressions
• –Morphology
• –Cultural
• –Physiological

•DNA is arranged as a single molecule with no histones present, and with no dominance or recessiveness in the genes.

are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes

• •Fragments of DNA in the cytoplasm
• •R Factors - confer drug resistance
• •Bacteriocins -proteins toxic to other bacteria and human cell
• •Many plasmids are found in Gram-Negative bacteria

• Spontaneous mutations = Example: Salmonella
• strains antibiotic resistance
• Induced mutations = Chemical
• or Physical agents enhance mutation rate

• –Mismatch repair “proofreads”
• –Damage repair
• »Excision repair
• »Dimer repair (UV light)

DNA transformation involves the transfer of naked DNA into a recipient cell

Thetransfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells

Is the process by which DNA is transferred from one bacterium to another by a virus.

main method of viral replication, since it results in the destruction of the infected cell. 

separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA

Genetic regulatory system found in bacteria and their viruses

• •Genetic engineering involves changing the genetic material in an organism to alter its traits or products
• •A recombinant DNA molecule contains DNA fragments spliced together from 2 or more organisms 

• •Pharmaceutical production
• –Insulin, interferon, hormones, vaccines etc.
• •Genetically engineered plants 
• •Animal gene alterations
• •Gene probes
• •DNA fingerprinting
• •The human genome initiative

metabolism

physical and chemical environment

•DNA to produce what we want