Microbiology Midterm Study Guide Covers Chapters 1-13 /Week 1 (Chapters 1-3), Exams of Microbiology

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Covers Chapters 1-13 /Week 1 (Chapters 1-3)

1. Pasteur - Final disproof spontaneous generation
2. Hook - Saw first microbes
3. Lister -Aseptic techniques during surgery
4. Semmelweis - Dr. had to wash hands in maternity ward
5. Schultze & Schwann - Chemical treatment of air stops ability to produce life
6. Koch - Developed postulates for disease microbe connection
7. Redi - Maggot-meat experiment
8. Leeuwenhoek - Made first microscope Fundamental of cells: Unicellular (Bacteria, Archaea, Protozoa, some fungi) and multicellular organisms (animals and plants)  All cells (prokaryotes + eukaryotes) have in common: Cell membrane DNA that holds genetic information Ribosomes for protein synthesis Cytoplasm Eukaryotes are more complex with DNA enclosed in nucleus and membrane enclosed organelles Bacterial shapes: Cocci Rods. Vibrio Spirillum Spirochete Branching Filaments

The 5 Is: Inoculation - Purposely moving something from 1 place to another. starts with specimen collection; lesion, draw blood, bird droppings, etc.

• introducing a tiny sample into a medium to provide an env't where they multiply. Incubation - To hear bacteria to make it grow (usually body temp). maintaining something at the most favorable temperature for its development. 20 deg C & 40 deg. C02 may be required.
• promotes multiplication of microbes over period of hours.
• produces a culture Isolation - Separate from each other separation of a strain from a natural, mixed population of living microbes, spreading bacteria apart as far as possible.
• isolated microbes takes the form of separate colonies on solid media or turbidity (free floating cells) on broth. Inspection - Doing tests on the bug appearance, cells, colony (red? shape, gram stain, sugar, etc.). Identification - determine type of microbe
• specialized tests; biochemical test to determine metabolic activities specific to microbes
• immunologic tests, genetic analysis. Microscopy Basics / Types of microscopes :
  1. Bright field microscope - Most widely used microscope image is darker than illuminated field made by putting light through specimen
  2. Dark field microscope- similar to bright field image is lighter than illuminated field bright field microscope is changed to dark field microscope by adding a condenser to the light
  3. Phase contrast microscope- used with live specimen produces image with specimen against gray background can see internal cells
  4. Differential interreference microscope- produces colorful 3D image 2 prisms which add contrasting colors to image

Macromolecule Basic Formula, key features Monomer^ Examples^ Uses Proteins

CHON

−NH 2 + −COOH +R

group Amino acids Enzymes, some hormones Storage; Signals; Structural; Contractile; Defensive; Enzyme; Transport; Receptors Lipids

C:H:O

Greater than 2:1 H:O (carboxyl group) Fatty acid and glycerol Butter, oil, cholesterol, beeswax Energy storage; Protection; Chemical messengers; Repel water Carbohydrates

C:H:O

Monosaccharides Glucose, Fructose, Starch, Glycogen, Cellulose Energy storage; Structure Nucleic Acids

CHONP

pentose, nitrogenous base, phosphate Nucleotides DNA, RNA Genetic information Phospholipids, mycolic acid, enzymes, etc. Week 2 (Chapters 4-6) Phospholipids – has 2 fatty acids, plasma membrane made out of phospholipids. Class of lipids that are similar to triglycerides, but each has a phosphorus-containing acid in place of one of the fatty acids; present in all cell membranes Mycolic acid or cord factor:

• Very-long-chain fatty acid components in mycobacterium cells walls-waxy nature
• Contributes to pathogenicity of these organisms
• Makes them resistant to certain chemicals and dyes
• Acid-fast stain used to diagnose tuberculosis and leprosy Cellular structures in each type of microorganism / Reproductive strategies for Bacteria and Archaea vs Eukaryotes (protozoa, algae, fungus):

 Bacteria - Small, simple, single celled organisms that have prokaryotic cell structure. Most have peptidoglycan cells walls, while few lacks any cell wall  Protozoa - unicellular organisms that have eukaryotic cell structure, lack cell walls, require an organic source of carbon and do not carry out photosynthesis  Archea - Small, simple, single celled organisms that have a prokaryotic cell structure.  Fungi - unicellular or multicellular organisms that have eukaryotic cell structure, cells walls composed of cellulose or chitin, a plant-like absorptive metabolism, require an organic source of carbon and do not carry out photosynthesis.  Algae - Unicellular and multicellular organisms that have a eukaryotic cell structure, carry out photosynthesis, have cell walls compose of a polysaccharide and other substances Bacteria and Archaea vs. Eukaryotes: Packaging of DNA:

• Bacteria and archaea have nuclear material that is free in the cytoplasm
• Eukaryotes have a nucleus Cell wall makeup:
• Bacteria: cell wall made of peptidoglycan
• Archaea: cell wall distinct from bacteria and eukaryotes Internal structures:
• Bacteria and archaea: no membrane-bound organelles Basic structural differences between prokaryotes and eukaryotes: Prokaryotes:
• Prokaryotes found in bacteria
• Much smaller
• Less complex
• unicellular, but can make multicellular groups/clusters
• No true nucleus
• Circular DNA that is found in the cytoplasm
• No organelles found in the cytoplasm
• Surrounded by a cell wall
• No nucleus
• DNA Prokaryotic Cells – Single circular of DNA
• No membrane Eukaryotes:
• Eukaryotes found in protists, fungi, plants, and animals
• Are Much larger
• Much more complex
• Mostly multicellular but can be unicellular (fungi and protists)
• Contain a true nucleus to house the genetic material (DNA)
• Linear DNA packaged into chromatin found inside the nucleus
• Contains specialized structures in the cytoplasm called organelles to carry out various functions
• Not all have a cell wall

Spikes:

• Found on both naked and enveloped viruses
• Project from either the nucleocapsid or envelope
• Allow viruses to dock with their host cells Virion:
• Fully formed virus able to establish infection in a host Virus vs Virion: Virus- acellular structures composed of nucleic acid enclosed by a protein coat and sometimes an envelope Virion - A complete, fully developed, infectious viral particle composed of nucleic acid and surrounded by a protein coat outside of the host cell, and is a vehicle of transmission from one host cell to another
• Fully formed virus able to establish infection in a host Intracellular vs extracellular forms: extracellular state: outside of a cell a virus is called a virion -virion consists of a protein coat, called a capsid, surrounding a nucleic acid core. intracellular state: virus is inside
• has no capsid Obligate intracellular parasites:
• Cannot multiply unless they invade a specific host cell
• Must instruct the genetic and metabolic machinery of the host cell to make and release new viruses Viral life cycle: Lytic - conversion- bacteriophage genes can change a bacterium from a nonvirulent cell to a virulent cell, it can pass genes for virulence factors.

Lysogenic - conversion- bacteriophage genes can change a bacterium from a nonvirulent cell to a virulent cell, it can pass genes for virulence factors.

• Lysogenic cycle: bacteriophage becomes incorporated into the host cell DNA Chronic latent state: periodic activation after a period of viral inactivity Prions- "proteinaceous infective particles" that lack any nucleic acid are not considered viruses because they do not have any DNA or RNA Prions:
• Common feature of spongiform encephalopathies
• Distinct protein fibrils deposited in brain tissue of affected animals Prion infection:
• Exact mode of infection is unknown
• Protein composition of prions has revolutionized ideas of what can constitute an infectious agent
• Questions about how prions replicate given that they have no nucleic acid Viroid’s - extremely small, circular pieces of infections RNA. Only pathogenic in plants. Causes stunting in potatoes. Viroid’s:
• Virus-like agent that parasitizes plants
• About one-tenth the size of an average virus
• Composed only of naked strands of RNA—lack a capsid or other type of coating
• Significant pathogens in economically important plants: tomatoes, potatoes, cucumbers, citrus trees, and chrysanthemums Satellite viruses:
• Dependent on other viruses for replication
• Adeno-associated virus (AAV)
• Originally thought that it could only replicate in cells infected with the adenovirus
• Now found to infect cells infected with other viruses or that have had their DNA disrupted through other means Week 3 (Chapters 7-9, 10.4) Classification of microbes based on energy and carbon sources of Photo-chemotrophs:  Phototrophs - Uses light as main energy source  Chemotroph - Uses oxidation-reduction of inorganic or organic compounds as main energy source  Autotroph - Uses carbon dioxide as main carbon source  Heterotroph - Uses organic carbon source  Photoautotroph - Uses light for energy, carbon dioxide for carbon  Photoheterotroph - Uses light for energy, organic carbon source

Terms for temperature preference, pH preference, oxygen preference etc.: Temperature preference: Psychrophile - Optimum temperature: 15 C Psuedomonas fluorescens psychrotroph - Optimum temperature: 20-30 C Psuedomonas fluorescen mesophile - Optimum temperature:37 C Escherichia coli thermophile - Optimum temperature:55-65 C Thermus aquatics hyperthermophile - Optimum temperature: 85-113 C Sulfobolus Oxygen preference: Obligate aerobe – micrococcus luteus Obligate anaerobic – Clostridium tetani (tetanus) Facultative anaerobe – Escherichia Coli Aerotolerant anaerobe – streptococcus pyogens (sore throat) Microaerophile – campylobacter jejuni Ph:  Neutrophiles (pH 5-8)

- Acidophiles (pH below 5.5)  Alkaliphiles (pH over 8.5) Central dogma of biology (DNA→RNA→Protein):  One of the "unifying" theories of biology. -Information coded in molecules is stored, replicated, transcribed and translated for cellular machinery. -It describes a process of using "instructions" encoded in DNA to replicate itself for cell division, and express itself to produce machinery for cell functioning. DNA-->mRNA-->Protein  The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein. Transcription is the synthesis of an RNA copy of a segment of DNA.

Steps of the central Dogma: Replication

• copy both strands of the DNA for cell division in the nucleus tools: DNA polymerase Transcription
• transcribe one strand of the DNA as a message -in the nucleus -tools: RNA polymerase Translation
• -translate the mRNA message into a protein sequence -in the cytoplasm (on ribosomes) -tools: ribosomes and other "factors" Positive-sense RNA:
• Single-stranded RNA genomes ready for immediate translation into proteins Negative-sense RNA:
• RNA genomes that need to be converted into the proper form to be made into proteins Types of mutations (Point, frame shift, missense, etc.)  mutations - changes in genetic material  chromosomal mutations - mutations that produce changes in whole chromosomes  gene mutations - mutations that produce changes in a single gene  missense mutation - point mutation in which a single nucleotide is changed (replaced) resulting in a codon that codes for a different amino acid, results in an altered protein  silent mutation - point mutation where a single nucleotide is (replaced) but the change does not result in a different amino acid, therefore a normal protein is formed  Point mutations - gene mutations involving a change in one or a few nucleotides are known as...

1. Frameshift mutations - additions or deletions of a nucleotide that cause a shift in the grouping of codons
2. Spontaneous Mutations -that occur naturally (i.e. sickle cell mutation)

1. Oxidoreductases transfer electrons from one substrate to another, and
2. dehydrogenases transfer a hydrogen from one compound to another.
3. Transferases transfer functional groups from one substrate to another.
4. Hydrolases cleave bonds on molecules with the addition of water.
5. Lyases add groups to or remove groups from double-bonded substrates.

6. Isomerases change a substrate into its isomeric^1 form.

7. Ligases catalyze the formation of bonds with the input of ATP and the removal of water. Metabolic pathways (inputs, outputs and when they are used)  Glycolysis: This series of reactions, which takes place in the cytosol, splits one molecule of glucose into two molecules of pyruvic acid. In the process, the cell produces a total of two ATP molecules and one NADH If oxygen is present, the resulting pyruvic acid is converted to acetyl CoA, a molecule that can then enter the Krebs’s cycle, which occurs in the lumen of the mitochondria. This is considered the preparation for the Krebs’s cycle.  Krebs’s cycle: This series of reactions completes the breakdown of acetyl CoA into carbon dioxide within the mitochondria. In the process, they generate two molecules of ATP and, more importantly, six molecules of the electron carrier NADH and two molecules of the electron carrier FADH 2 , which are then used in the electron transport chain.  Electron transport chain: This occurs in the inner membrane of the mitochondria, using the energy of the donated electrons from NADH and FADH 2 to pump H+ions across the membrane, creating a concentration gradient across the membrane. The H+^ ions seek to return to the area of lower concentration (remember diffusion!) and rush through a channel created by a protein called ATP synthase. The movement of the H+^ ions powers the regeneration of ATP from ADP. The electron transport chain results in 34 ATP molecules for each molecule of glucose.
8. Process Location Main substrates Main products Glycolysis Cytosol

ADP

NAD

Glucose

2 ATP

2 NADH

2 pyruvate Krebs’s Cycle Mitochondria 2 pyruvate à 2 Acetyl CoA

2 ATP

6 NADH

2 FADH 2

Electron Transport Chain Inner membrane of Electrons from NADH and

34 ATP

mitochondria

FADH 2

O 2 (oxygen, final electron acceptor) H 2 O (water, formed when oxygen gains electrons) Total ATP from one glucose molecule: ~38 ATP Fermentation:  known as another process that can catabolize glucose.  This occurs when oxygen is not present and starts with glycolysis.  The pyruvate formed in glycolysis is then converted to organic acids or alcohols, and sometimes produces CO 2.  This entire process occurs in the cytosol and produces only 2 ATP. a) Fermentation - incomplete oxidation of glucose, organic molecule is final electron acceptor, does not require oxygen b) Fermentation Pathway - glycolysis (net gain of 2 ATP via SLP and 2 NADH), oxidize reduce coenzymes to produce gas, acid, or alcohol Fermentation:

• Uses organic compounds as terminal electron acceptor
• Much less energy gain
• from fermentation (net 2 ATP per glucose molecule)
• Reason for fermentation:
• to oxidize NADH to NAD+ (needed for glycolysis) Aerobic vs anaerobic: Bacteria can be anaerobic or aerobic. Aerobic means involving oxygen, so anaerobic bacteria can survive without oxygen. ... All organisms make energy through cellular respiration, but they do this differently depending on if they are anaerobic or aerobic. Anaerobes- Organisms do not require gaseous oxygen and grow best in its absence. Two subcategories:

1. Aerotolerant
2. Strict anaerobes All lack the enzymes catalase or peroxidase needed to breakdown hydrogen peroxide, a toxic substance that forms in the presence of oxygen. Many are fermenters which use organic substances as electron acceptors. Aerobes- Organisms that absolutely require oxygen which is used as the final electron acceptor of their metabolism Aerobic respiration: Glycolysis: converts 1 glucose to 2 pyruvate molecules yet yield: 2 ATP, 2 NADH

 The same as disinfection, but on a living surface Sepsis: the growth of microorganisms in blood and other tissues Asepsis: any practice that prevents the entry of infectious agents into sterile tissues and prevents infection Aseptic techniques:

• Sterile methods that exclude all microbes
• Antisepsis: application of chemical agents (antiseptics) to exposed body surfaces, wounds, and surgical incisions to destroy or inhibit vegetative pathogens Decontamination:
• Also called sanitization
• The mechanical removal of most microbes from an animate or inanimate surface
• Any cleansing technique that mechanically removes microbes and debris
• Reduces contamination to safe levels
• Sanitizer: a soap or detergent used to sanitize
• Reduction of the number of microbes on the skin
• Involves scrubbing the skin or immersing it in chemicals, or both
• Emulsifies oils on the outer cutaneous layer
• Mechanically removes potential pathogens on the outer layers of the skin

Physical methods of microbial control: Heat is the most widely used method of microbial control Radiation:  Energy emitted from atomic activities and dispersed at high velocity through matter or space  Electromagnetic radiation travels in waves (form of energy)  Shorter wavelengths have higher energy Radiation suitable for microbial control:

• Gamma rays
• X rays
• Ultraviolet radiation Filtration:
• Used in liquids that cannot withstand heat
• Alternative method for decontaminating milk and beer
• Important step in water purification
• Efficient means of removing airborne contaminants Ultraviolet (UV) radiation:

• Those that do not touch the patient or are only expected to touch intact skin What is microbial death? Death of microscopic organisms:
• Harder to detect than in macroscopic organisms
• No conspicuous vital signs
• Lethal agents do not alter the overt appearance of microbial cells
• Loss of movement cannot be used to indicate death
• Special qualifications are needed to define and delineate microbial death Heat methods (e.g. autoclave, incineration) Autoclave: Sterilizes heat- and moist- tolerant items  Uses pressured steam  Steam at normal pressure = 100°C but with additional pressure steam = 121°C  Kills even endospores Incineration: Incineration is a waste treatment process that involves the combustion of organic substances contained in waste materials. Incineration and other high-temperature waste treatment systems are described as "thermal treatment". Incineration of waste materials converts the waste into ash, flue gas and heat. Chemical methods of microbial control: Halogens:
• Fluorine, bromine, chlorine, iodine
• Microbicidal and sporicidal
• Active ingredients in

of all antimicrobial chemicals

• Chlorine can kill all microbes and is used for
• swimming pools
• Diluting bleach (sodium hypo-chloride) 1:100 or 1:10 gives effective chlorine solution.
• Chlorine is corrosive and toxic; regular fresh solutions of bleach necessary
• Effective also against endospores and viruses Phenolics:
• Destroy vegetative bacteria, fungi, and most viruses
• Able to act in the presence of organic matter

• Detergent action
• Too toxic to use as antiseptics Phenol Compound:
• was one of the first disinfectants
• Phenolics are derivatives and more effective,
• thus can be used in higher dilution which causes less skin irritation (e.g. Lysol)
• Destroys plasma membrane and denature proteins
• Kills most vegetative bacteria Alcohols: - Only ethyl and isopropyl alcohol are appropriate for microbial control
• Greater efficacy at 70%
• Destroys vegetative microbial forms but not endospores
• More effective against enveloped viruses than nonenveloped viruses
• Ethyl alcohol (70 to 95 %):
• Skin degerming and disinfection of some types of medical equipment
• Evaporation rate limits effectiveness Isopropyl alcohol:
• More microbicidal and less expensive than ethanol
• Evaporation rate also limits efficacy
• Vapors can adversely affect the nervous system

Hydrogen peroxide ( H 2 O 2 ) :

• Germicidal effects are due to toxic reactive oxygen
• Bactericidal, viricidal, fungicidal, and sporicidal at high concentrations Detergents and soaps:
• Act as surfactant
• Hydrophilic and hydrophobic region
• Household soaps and detergents are negatively charged and repelled by cells
• Quaternary ammonium compounds (Quats) are positively charged
• Quats are attracted to cells and destroy membrane