How to Print Outlines
Sometimes when I copy and paste the outlines into the blog, the tabbing does not transfer. My suggestion to you is to copy the blog into Microsoft Word and then add the tabs yourself. Hopefully I can figure out how to overcome this glitch...but I don't have the time right now with exams coming up.
Tab 1x before every capital letter. Tab 2x before every numeral. Tab 3x before every lower case letter. Tab 4x before every lower case Roman numeral.
Thursday, April 17, 2008
Friday, April 11, 2008
Chpt 20 Antimicrobial Drugs
Antimicrobial Drugs
Chapter 20
I History of Chemotherapy
II Spectrum of Antimicrobial Activity
III Action of Antimicrobial Drugs
A. Bactericidal
B. Bacteriostatic
C. Inhibition of Cell wall synthesis
1. Peptidoglycan: alternating NAM and NAG subunit chains that are held together by peptide bridges.
a. When reproducing and growing, bacteria must synthesize more NAG/NAM units to add.
2. Antibiotic types ( Natural Beta – lactams): Prevent cross-linkage of NAM subunits
a. penicillin: narrow spectrum, kills only gram +
b. methicillin: works on some gram -
c. cephalosporin: works on some gram -
d. vancomycin: works on gram +
e. bacitracin: works on gram +
f. isoniazid: block mycolic acid addition to cell walls as well as peptidoglycan production
D. Inhibition of Protein synthesis
1. Ribosomes: The major structure of a cell that caries out protein synthesis
a. eukaryotic: 80s ribosomes
b. prokaryotic: 30s + 50s ribosomes = 70s
2. Antibiotic types
a. aminoglycosides:
i. streptomycin: change the shape of the 30s subunit
ii. gentomycin: change the shape of the 30s subunit
iii. tetracycline: prevent amino acids from entering the ribosome at the 30s subunit
b. chloramphenicol: blocks 50s ribosome, preventing peptide bond formation
c. macrolides:
i. bind to 50s ribosome
ii. prevent movement from one codon to the next, halting translation
iii. ex: erythromycin
E. Injury to the Plasma Membrane (Disruption of cytoplasmic membranes)
1. plasma membranes: phospholipids bi-layers that contain sterols (lipids)
a. polymyxin: disturbs phospholipids bi-layers
i. effective against gram – (Pseudomonas)
ii. toxic to kidneys and is usually used for external pathogens
2. Fungi contain a sterol called ergosterol, humans = cholesterol
3. Antifungal drugs:
a. polyenes: attach to ergosterol in the membrane
b. azoles: inhibit ergosterol synthesis
F. Inhibition of Nucleic Acid (DNA/RNA) Synthesis 21, 22, 23
G. Inhibiting the Synthesis of essential metabolites (anti-metabolic agents/inhibit metabolism) 17
1. Metabolism: all of the chemical reactions within a cell used to store or release energy
a. organisms often have unique metabolic pathways
b. most narrow antibiotic
2. Sulfonamides
a. Para-Aminobenzoic acid (PABA) 18, 19
H. Block attachment
I. Antifungal Drugs
J. Antiviral Drugs 20, 24
K. Antiprotozoan and Antihelminthic Drugs
IV Tests to Guide Chemotherapy
V Effectiveness of chemotherapeutic agents
VI Clinical considerations
Definitions:
Chemotherapy: the treatment of disease with chemicals (drugs) taken into the body.
Chemotherapeutic agents: drugs used for chemotherapy
Antimicrobial drugs: The class of chemotherapeutic agents used to treat infectious diseases.
Selective toxicity: killing the harmful organism without harming the host
1. The drug must be more toxic to a pathogen than a pathogen’s host.
2. possible due to difference in structure or metabolism between the pathogen and the host.
Synthetic drugs: synthesized in the laboratory
Antibiotics: produced by microorganisms, and in small amounts, inhibit another mo.
1. naturally occurring (Penicillin)
2. Semi-synthetic: slight alterations to naturally occurring agents
Chapter 20
I History of Chemotherapy
II Spectrum of Antimicrobial Activity
III Action of Antimicrobial Drugs
A. Bactericidal
B. Bacteriostatic
C. Inhibition of Cell wall synthesis
1. Peptidoglycan: alternating NAM and NAG subunit chains that are held together by peptide bridges.
a. When reproducing and growing, bacteria must synthesize more NAG/NAM units to add.
2. Antibiotic types ( Natural Beta – lactams): Prevent cross-linkage of NAM subunits
a. penicillin: narrow spectrum, kills only gram +
b. methicillin: works on some gram -
c. cephalosporin: works on some gram -
d. vancomycin: works on gram +
e. bacitracin: works on gram +
f. isoniazid: block mycolic acid addition to cell walls as well as peptidoglycan production
D. Inhibition of Protein synthesis
1. Ribosomes: The major structure of a cell that caries out protein synthesis
a. eukaryotic: 80s ribosomes
b. prokaryotic: 30s + 50s ribosomes = 70s
2. Antibiotic types
a. aminoglycosides:
i. streptomycin: change the shape of the 30s subunit
ii. gentomycin: change the shape of the 30s subunit
iii. tetracycline: prevent amino acids from entering the ribosome at the 30s subunit
b. chloramphenicol: blocks 50s ribosome, preventing peptide bond formation
c. macrolides:
i. bind to 50s ribosome
ii. prevent movement from one codon to the next, halting translation
iii. ex: erythromycin
E. Injury to the Plasma Membrane (Disruption of cytoplasmic membranes)
1. plasma membranes: phospholipids bi-layers that contain sterols (lipids)
a. polymyxin: disturbs phospholipids bi-layers
i. effective against gram – (Pseudomonas)
ii. toxic to kidneys and is usually used for external pathogens
2. Fungi contain a sterol called ergosterol, humans = cholesterol
3. Antifungal drugs:
a. polyenes: attach to ergosterol in the membrane
b. azoles: inhibit ergosterol synthesis
F. Inhibition of Nucleic Acid (DNA/RNA) Synthesis 21, 22, 23
G. Inhibiting the Synthesis of essential metabolites (anti-metabolic agents/inhibit metabolism) 17
1. Metabolism: all of the chemical reactions within a cell used to store or release energy
a. organisms often have unique metabolic pathways
b. most narrow antibiotic
2. Sulfonamides
a. Para-Aminobenzoic acid (PABA) 18, 19
H. Block attachment
I. Antifungal Drugs
J. Antiviral Drugs 20, 24
K. Antiprotozoan and Antihelminthic Drugs
IV Tests to Guide Chemotherapy
V Effectiveness of chemotherapeutic agents
VI Clinical considerations
Definitions:
Chemotherapy: the treatment of disease with chemicals (drugs) taken into the body.
Chemotherapeutic agents: drugs used for chemotherapy
Antimicrobial drugs: The class of chemotherapeutic agents used to treat infectious diseases.
Selective toxicity: killing the harmful organism without harming the host
1. The drug must be more toxic to a pathogen than a pathogen’s host.
2. possible due to difference in structure or metabolism between the pathogen and the host.
Synthetic drugs: synthesized in the laboratory
Antibiotics: produced by microorganisms, and in small amounts, inhibit another mo.
1. naturally occurring (Penicillin)
2. Semi-synthetic: slight alterations to naturally occurring agents
Chpt 19 Disorders Associated with the Immune System
Disorders Associated with the Immune System
Chapter 19
Hypersenstivity: sensitivity beyond what is considred normal. It occurs in people who have been previously sensitized by exposure to an antigen (allergen). Once sensitized, another exposure to the antigen triggers an immune response that damages host tissue. Based on mechanism and time, there are 4 types of hypersensitivity reactions:
I Type I (Anaphylaxis) Reactions
A. Mechanisms:
1. Involve IgE and the release of mediators such as histamine by mast cells and basophils (granulated cells)
2. involve allergens, sensitization and triggering
B. Time course: rapid, usually within 30 minutes
C. Clinical manifestations
1. Systemic anaphylaxis: System wide dramatic response to an allergen. Treated with epinephrine.
a. causes:
i. hormones: insulin, vasopressin
ii. antibiotics: penicillin, amphotericin B
iii. other: diazepam (valium), barbiturates
2. Localized anaphylaxis (atopic diseases): usually associated with antigens that are ingested or inhaled. Antihistamines to treat.
a. causes
i. peanuts
ii. tree nuts
iii. shellfish
iv. dairy
v. egg whites
vi. wasp or bee stings
vii. inhalants such as: pollen, fungal spores, animal dander, house dust mites
b. Allergic rhinitis symptoms
i. itchy, teary eyes
ii. congested nasal passages
iii. sneezing
3. Asthma
a. causes
i. allergens, irritants, exertion, stress
ii. triggers airway narrowing and mucus production
b. incidence
i. number of cases and deaths has increased significantly
c. symptoms
i. cough, wheezing, difficulty breathing
ii. reversible airway obstruction
d. treatment
i. smooth muscle relaxants
ii. corticosteroids
4. Hives (Urticaria)
a. cause: usually food or drugs
b. symptoms: swollen plaques on the skin
5. Food allergies
a. most common causes: wheat, eggs, milk, fish, peanuts, strawberries, tomatoes, crustaceans, nuts
b. symptoms: hives, itching, swollen lips, nausea, vomiting
c. treatment: antihistamines, avoiding contact of sensitizing agents
D. Prevention
1. desensitization: consists of a series of injections with a small dose of the antigen.
II Type 2 (Cytotoxic) Reactions
A. Mechanisms
1. involve antibodies (IgG, IgM) and causing cell damage
B. Time course: variable, usually 5 – 12 hours
1. ex: transfusion reactions
a. ABO
b. Rh
c. Target is donor RBCs
d. Hemolytic disease of the newborn (Rh disease)
i. Rh – mother
ii. Rh+ fetus, or ABO incompatible
III Type 3 (Immune Complex) Reactions
A. Mechanisms
1. involve antibodies (IgG or IgM) forming immune complexes and triggering local tissue damage
2. antigen: exogenous or endogenous
B. Time Course: variable, usually 3 – 8 hours
IV Type 4 (Delayed) Reactions (Delayed Cell-Mediated Reactions/Hypersensitivity)
A. Mechanisms
1. involve T cells and macrophages triggering inflammation
B. Time Course: slow, usually 24 – 48 hours
C. Clinical manifestations
1. Contact dermatitis
a. localized to the skin
b. maximum response 24 – 48 hours after exposure
c. symptoms: erythema, induration, sometimes blistering
d. triggered by certain materials: metals, clothing, rubber, leather, cosmetics, plants (poison ivy)
e. TB test: intentionally trigger a type 4 reaction for diagnosis
**** Only hypersensitivity is being covered in this chapter, not autoimmunity. That is why I did not outline the rest of the chapter.
Chapter 19
Hypersenstivity: sensitivity beyond what is considred normal. It occurs in people who have been previously sensitized by exposure to an antigen (allergen). Once sensitized, another exposure to the antigen triggers an immune response that damages host tissue. Based on mechanism and time, there are 4 types of hypersensitivity reactions:
I Type I (Anaphylaxis) Reactions
A. Mechanisms:
1. Involve IgE and the release of mediators such as histamine by mast cells and basophils (granulated cells)
2. involve allergens, sensitization and triggering
B. Time course: rapid, usually within 30 minutes
C. Clinical manifestations
1. Systemic anaphylaxis: System wide dramatic response to an allergen. Treated with epinephrine.
a. causes:
i. hormones: insulin, vasopressin
ii. antibiotics: penicillin, amphotericin B
iii. other: diazepam (valium), barbiturates
2. Localized anaphylaxis (atopic diseases): usually associated with antigens that are ingested or inhaled. Antihistamines to treat.
a. causes
i. peanuts
ii. tree nuts
iii. shellfish
iv. dairy
v. egg whites
vi. wasp or bee stings
vii. inhalants such as: pollen, fungal spores, animal dander, house dust mites
b. Allergic rhinitis symptoms
i. itchy, teary eyes
ii. congested nasal passages
iii. sneezing
3. Asthma
a. causes
i. allergens, irritants, exertion, stress
ii. triggers airway narrowing and mucus production
b. incidence
i. number of cases and deaths has increased significantly
c. symptoms
i. cough, wheezing, difficulty breathing
ii. reversible airway obstruction
d. treatment
i. smooth muscle relaxants
ii. corticosteroids
4. Hives (Urticaria)
a. cause: usually food or drugs
b. symptoms: swollen plaques on the skin
5. Food allergies
a. most common causes: wheat, eggs, milk, fish, peanuts, strawberries, tomatoes, crustaceans, nuts
b. symptoms: hives, itching, swollen lips, nausea, vomiting
c. treatment: antihistamines, avoiding contact of sensitizing agents
D. Prevention
1. desensitization: consists of a series of injections with a small dose of the antigen.
II Type 2 (Cytotoxic) Reactions
A. Mechanisms
1. involve antibodies (IgG, IgM) and causing cell damage
B. Time course: variable, usually 5 – 12 hours
1. ex: transfusion reactions
a. ABO
b. Rh
c. Target is donor RBCs
d. Hemolytic disease of the newborn (Rh disease)
i. Rh – mother
ii. Rh+ fetus, or ABO incompatible
III Type 3 (Immune Complex) Reactions
A. Mechanisms
1. involve antibodies (IgG or IgM) forming immune complexes and triggering local tissue damage
2. antigen: exogenous or endogenous
B. Time Course: variable, usually 3 – 8 hours
IV Type 4 (Delayed) Reactions (Delayed Cell-Mediated Reactions/Hypersensitivity)
A. Mechanisms
1. involve T cells and macrophages triggering inflammation
B. Time Course: slow, usually 24 – 48 hours
C. Clinical manifestations
1. Contact dermatitis
a. localized to the skin
b. maximum response 24 – 48 hours after exposure
c. symptoms: erythema, induration, sometimes blistering
d. triggered by certain materials: metals, clothing, rubber, leather, cosmetics, plants (poison ivy)
e. TB test: intentionally trigger a type 4 reaction for diagnosis
**** Only hypersensitivity is being covered in this chapter, not autoimmunity. That is why I did not outline the rest of the chapter.
Chpt 18 Practical Applications of Immunology
Practical Applications of Immunology
Chapter 18
I Vaccines (injection of antigens)
A. Principles and Effects of Vaccination
1. vaccine: a suspension of microorganisms, or some part or product of them, that will induce immunity when it is administered to the host.
2. herd immunity: when most, but not all, of the population is immune
B. Types of Vaccines and their characteristics
1. Inactivated (killed) Organism Vaccines: injection of killed mo
a. killed by:
i. phenol
ii. formalin
b. examples:
i. influenza: inactivated influenza virus
ii. rabies: inactivated rabies virus
2. whole agent
3. attenuated (weakened) whole agent: mimic actual infection and usually provide better immunity.
a. injection of weakened strain of mo
b. disadvantage: organism can become virulent
c. examples:
i. measles (MMR) attenuated measles virus
ii. TB (BCG) Mycobacterium bovis
4. Subunit (Component)Vaccines: uses only those antigenic fragments of a mo that are best suited to stimulate an immune response.
a. injection of part of microorganism
b. advantages: safe
c. examples:
i. tetanus: toxoid of Clostridium tetani (toxoid: inactivated bacterial virus)
ii. HIB: polysaccharide of Haemophilus influenzae
iii. Hepatitis B: HBV surface antigen (HBsAg)
5. Carrier Vaccines: injection of harmless organism
a. containing/expressing gene from disease causing organism
6. DNA vaccines
a. injection of DNA from mo
b. new technology
7. Passive immunization
a. injection of antibodies
b. instant immunity
c. protection lasts 5-6 months
d. examples
i. antivenom (antivenin)
II Diagnostic Immunology
A. Essential diagnostic tests for determining immunity:
1. sensitivity: the probability that the test is reactive if the specimen is a true positive
2. specificity: the probability that a positive test will not be reactive if a specimen is a true negative
A. Monoclonal Antibodies and their uses
B. Precipitation Reactions: involve the reaction of soluble antigens with IgG or IgM antibodies to form large lattices.
1. Ag - IgM or IgG react to form a complex
2. Ag – Ab complex form lattices and precipitate from solution
3. Ag – Ab ratio is optimal
4. Antigens – soluble
5. Immunoprecipitation: antigens and antibodies precipitate in agarose
6. Remember these test from lab.
C. Agglutination Reactions: involve particulate antigens that can be linked together by antibodies.
1. Direct agglutination
a. cells to be identified are agglutinated by antibodies.
b. titer: concentration of antibody in a serum
2. Indirect (passive) agglutination
a. antibodies or antigens are attached to plastic beads
b. beads clump
c. easy to do
D. Neutralization Reactions
1. antitoxin
2. viral hemagglutination inhibition test
E. Complement-fixation reactions
F. Fluorescent-antibody techniques (immunofluorescence)
1. antibodies labeled with a fluorescent dye
2. can look for antigens or antibodies
3. dyes are combined with antibodies to make them fluoresce when exposed to ultraviolet light.
4. methods:
a. direct
b. indirect
G. Enzyme-Linked Immunosorbent Assay (ELISA)
1. antibodies are labeled with an enzyme in a micro titer plate
2. enzyme causes color change for positive result
3. flexible, sensitive
4. home tests: early pregnancy tests
5. methods:
a. direct: goal is to identify an unknown antigen such as a drug in a serum sample
b. indirect: object is to determine the presence of certain antibodies in the serum. (AIDS virus)
Chapter 18
I Vaccines (injection of antigens)
A. Principles and Effects of Vaccination
1. vaccine: a suspension of microorganisms, or some part or product of them, that will induce immunity when it is administered to the host.
2. herd immunity: when most, but not all, of the population is immune
B. Types of Vaccines and their characteristics
1. Inactivated (killed) Organism Vaccines: injection of killed mo
a. killed by:
i. phenol
ii. formalin
b. examples:
i. influenza: inactivated influenza virus
ii. rabies: inactivated rabies virus
2. whole agent
3. attenuated (weakened) whole agent: mimic actual infection and usually provide better immunity.
a. injection of weakened strain of mo
b. disadvantage: organism can become virulent
c. examples:
i. measles (MMR) attenuated measles virus
ii. TB (BCG) Mycobacterium bovis
4. Subunit (Component)Vaccines: uses only those antigenic fragments of a mo that are best suited to stimulate an immune response.
a. injection of part of microorganism
b. advantages: safe
c. examples:
i. tetanus: toxoid of Clostridium tetani (toxoid: inactivated bacterial virus)
ii. HIB: polysaccharide of Haemophilus influenzae
iii. Hepatitis B: HBV surface antigen (HBsAg)
5. Carrier Vaccines: injection of harmless organism
a. containing/expressing gene from disease causing organism
6. DNA vaccines
a. injection of DNA from mo
b. new technology
7. Passive immunization
a. injection of antibodies
b. instant immunity
c. protection lasts 5-6 months
d. examples
i. antivenom (antivenin)
II Diagnostic Immunology
A. Essential diagnostic tests for determining immunity:
1. sensitivity: the probability that the test is reactive if the specimen is a true positive
2. specificity: the probability that a positive test will not be reactive if a specimen is a true negative
A. Monoclonal Antibodies and their uses
B. Precipitation Reactions: involve the reaction of soluble antigens with IgG or IgM antibodies to form large lattices.
1. Ag - IgM or IgG react to form a complex
2. Ag – Ab complex form lattices and precipitate from solution
3. Ag – Ab ratio is optimal
4. Antigens – soluble
5. Immunoprecipitation: antigens and antibodies precipitate in agarose
6. Remember these test from lab.
C. Agglutination Reactions: involve particulate antigens that can be linked together by antibodies.
1. Direct agglutination
a. cells to be identified are agglutinated by antibodies.
b. titer: concentration of antibody in a serum
2. Indirect (passive) agglutination
a. antibodies or antigens are attached to plastic beads
b. beads clump
c. easy to do
D. Neutralization Reactions
1. antitoxin
2. viral hemagglutination inhibition test
E. Complement-fixation reactions
F. Fluorescent-antibody techniques (immunofluorescence)
1. antibodies labeled with a fluorescent dye
2. can look for antigens or antibodies
3. dyes are combined with antibodies to make them fluoresce when exposed to ultraviolet light.
4. methods:
a. direct
b. indirect
G. Enzyme-Linked Immunosorbent Assay (ELISA)
1. antibodies are labeled with an enzyme in a micro titer plate
2. enzyme causes color change for positive result
3. flexible, sensitive
4. home tests: early pregnancy tests
5. methods:
a. direct: goal is to identify an unknown antigen such as a drug in a serum sample
b. indirect: object is to determine the presence of certain antibodies in the serum. (AIDS virus)
Chpt 17 Specific Defenses of the Host: Adaptive Immunity
Specific Defenses of the Host: Adaptive Immunity
Chapter 17
Functional divisions of immunity:
Nonspecific immunity
Specific immunity
Specific immunity usually functions when organisms get past nonspecific defenses. Involves recognition and memory. It is slower to respond and uses antibodies and lymphocytes. (Immunity: specific antibody and lymphocyte response to an antigen)
I The adaptive immune system: so called because it adapts to conditions
II Dual nature of the adaptive immune system
A. Humoral immunity: brought about by antibodies (antibody mediated immunity)
1. antibodies (Ab) *antibodies = B cells
a. Proteins made in response to an antigen.
b. involves antibodies made by B cells (made in the bone marrow)
2. Defends primarily against bacteria, bacterial toxins, and freely circulating viruses.
B. Cellular immunity (cell mediated immunity) *Cellular imm = t cells
1. T cells: involves T lymphocytes that act directly against foreign organisms.
a. T cell receptors
2. Activates other immune cells like macrophages
3. Effective against bacteria/viruses within host cells, also against eukaryotic infections.
III Antigens and Antibodies
A. The nature of Antigens (immunogens) Ag: A substance that causes the body to produce specific antibodies or sensitized T cells. (The nature of an antigen is a protein or carbohydrate. A foreign substance to which our bodies produce antibodies.)
1. Antigenic Determinants (epitopes)
a. antibodies recognize and react with specific antigenic determinates.
2. Haptens: low –molecular weight antigens that are not antigenic unless first attached to a carrier molecule.
a. Can bind with a protein or a carb.
b. inflammation starts when phagocytes start to attack it because it sees it as a foreign substance.
c. penicillin
B. The nature of Antibodies (Immunoglobulins Ig): Antibodies are proteins made in response to an antigen.
1. Globulins: proteins of a certain solubility characteristic
2. Antigen bonding sites: each antibody has at least two antigen bonding sites.
a. Binding of antibody to antigen does not destroy the antigen. Instead, the antibody tags foreign cells and molecules for destruction by phagocytes and complement.
b. Valence: the number of antigen bonding sites on the antibody
4. Antibody structure
a. light (L) chains
b. heavy (H) chains
c. variable (V) regions: the end of the Y shaped antibody. V region joins to the epitope.
d. antigen-binding sites
C. Immunogloblulin classes:
1. IgG
a. most abundant
b. crosses placenta to give immunity to the fetus
c. protect against circulating bacteria and viruses
d. neutralize bacterial toxins
e. trigger the complement system
f. bind to antigens to enhance action of phagocytic cells.
g. long lived: its presence may indicate immunity against a past disease.
2. IgM
a. first to appear in response to an antigen, but their concentration declines rapidly.
b. predominant antibody in the ABO blood group antigen reactions.
3. IgA
a. main function is preventing attachment of viruses and certain bacteria to mucosal surfaces.
4. IgD: unknown
5. IgE
a. releases histamine
IV B Cells and Humoral Immunity
A. B cells: A special group of lymphocytes which develop from stem cell precursors. (made and matured in bone marrow)
B. B cells and T cells have specific antigen receptors.
1. A mature B cell recognizes antigen receptors using IgM and IgD antibodies.
2. The intensity of a humoral response is reflected by the antibody titer. (the amount of antibody in the serum)
C. Clonal selection of antibody-producing cells involve T-dependent antigens. (an antigen that requires a Th cell for antibody production)
1. Out of 5 B cells only 1 recognizes the antigen and creates antibodies.
2. It gets divided into:
a. plasma cells: get turned into antibodies
b. memory cells
2. T-independent antigen
D. Diversity of antibodies
V Antigen-antibody binding and its results
A. Antigen-antibody complex
1. affinity
2. specificity
B. Antibody function
1. agglutination
a. hinder pathogenic activity
b. increase chances of phagocytosis
2. neutralization
a. binding and neutralizing toxins
b. block adherence to host cell
3. opsonization
a. stimulate phagocytosis
4. antibody-dependent cell mediated toxicity
5. activation of the complement system
a. non-specific chemical defense against pathogens
b. uses a series of blood serum proteins to destroy invading microbes.
c. Effects of complement activation: See chapter 16 for cascade
i. opsonization or immune adherence: enhanced phagocytosis
ii. membrane attack complex: cytolysis
iii. attract phagocytes.
VI T cells and cellular immunity (Cell mediated Immunity)
A. Intracellular antigens stimulate cell-mediated immunity
B. Specialized lymphocytes, mostly T cells, respond to intracellular antigens
C. T cells differentiate into effector T cells when stimulated by an antigen
D. Some effector T cells become memory cells
E. Classes of T cells
1. Helper T Cells (TH): CD4 adhesion molecule
a. TH1: activate cells related to cell-mediated immunity
b. TH2: activated B cells to produce eosinophils, IgM, and IgE
2. Cytotoxic T cells (TC): CD8 adhesion molecule, attack any cell which is altered
3. Delayed Hypersensitivity T cells (TD)
4. Suppressor T cells
a. turn off immune response when Ag no longer present
VII Antigen-presenting cells (APCs): antigens should be processed to be recognized by T cells.
VIII Extracellular killing by the immune system (did not go over)
IX Antibody-dependent cell mediated cytotoxicity (did not go over)
X Cytokines
A. Chemical messengers
B. Produced mainly by T helper cells
C. Induces the migration of leukocytes on to area of infection: chemotaxis
XI Immunological memory (did not go over)
XII Types of adaptive immunity: Active and Passive Immunity
A. Acquired Immunity
1. Naturally acquired
a. active: antigens enter the body naturally; body produces antibodies and specialized lymphocytes.
b. passive: antibodies pass from mother to fetus via placenta or to infant in the mother’s milk.
2. Artificially acquired
a. active: antigens are introduced in vaccines; body produces antibodies and specialized lymphocytes.
b. passive: preformed antibodies in immune serum introduced in body by injection. (snake venom….when we need it fast)
Various notes:
Sushma likes the term antigenic determinants instead of the term epitopes. Make sure you remember that they mean the same thing.
All enzymes are proteins. If a mo is making an enzyme, we will produce an antibody.
Look at charts in textbook
TC cell = killer cell
Need a lot of T cells to trigger others
I may go blind trying to read the last slide that summarized everything. If I can enlarge it I will.
Study pages: 504-516
Cytokines 518
Immunological memory 519
Types of adaptive immunity 520 – 521
The extra credit III questions are below:
1. Define epitopes and give two characteristics about ideal anitgen. (****she said it should be a protein or a carb with a molecular weight higher than 10, 000)
2. Describe 5 different kinds of immunoglobulins. (so name and characteristics)
3. Name at least three different kinds of anitgen-antibody complexes.
4. What are two major types of T cells and explain the differences among them.
5. List four major differences between Humoral and Cellular immunity. (KNOW THIS QUESTION AS IT ACCOUNTS FOR 15% OF NEXT EXAM QUESTIONS.)
Chapter 17
Functional divisions of immunity:
Nonspecific immunity
Specific immunity
Specific immunity usually functions when organisms get past nonspecific defenses. Involves recognition and memory. It is slower to respond and uses antibodies and lymphocytes. (Immunity: specific antibody and lymphocyte response to an antigen)
I The adaptive immune system: so called because it adapts to conditions
II Dual nature of the adaptive immune system
A. Humoral immunity: brought about by antibodies (antibody mediated immunity)
1. antibodies (Ab) *antibodies = B cells
a. Proteins made in response to an antigen.
b. involves antibodies made by B cells (made in the bone marrow)
2. Defends primarily against bacteria, bacterial toxins, and freely circulating viruses.
B. Cellular immunity (cell mediated immunity) *Cellular imm = t cells
1. T cells: involves T lymphocytes that act directly against foreign organisms.
a. T cell receptors
2. Activates other immune cells like macrophages
3. Effective against bacteria/viruses within host cells, also against eukaryotic infections.
III Antigens and Antibodies
A. The nature of Antigens (immunogens) Ag: A substance that causes the body to produce specific antibodies or sensitized T cells. (The nature of an antigen is a protein or carbohydrate. A foreign substance to which our bodies produce antibodies.)
1. Antigenic Determinants (epitopes)
a. antibodies recognize and react with specific antigenic determinates.
2. Haptens: low –molecular weight antigens that are not antigenic unless first attached to a carrier molecule.
a. Can bind with a protein or a carb.
b. inflammation starts when phagocytes start to attack it because it sees it as a foreign substance.
c. penicillin
B. The nature of Antibodies (Immunoglobulins Ig): Antibodies are proteins made in response to an antigen.
1. Globulins: proteins of a certain solubility characteristic
2. Antigen bonding sites: each antibody has at least two antigen bonding sites.
a. Binding of antibody to antigen does not destroy the antigen. Instead, the antibody tags foreign cells and molecules for destruction by phagocytes and complement.
b. Valence: the number of antigen bonding sites on the antibody
4. Antibody structure
a. light (L) chains
b. heavy (H) chains
c. variable (V) regions: the end of the Y shaped antibody. V region joins to the epitope.
d. antigen-binding sites
C. Immunogloblulin classes:
1. IgG
a. most abundant
b. crosses placenta to give immunity to the fetus
c. protect against circulating bacteria and viruses
d. neutralize bacterial toxins
e. trigger the complement system
f. bind to antigens to enhance action of phagocytic cells.
g. long lived: its presence may indicate immunity against a past disease.
2. IgM
a. first to appear in response to an antigen, but their concentration declines rapidly.
b. predominant antibody in the ABO blood group antigen reactions.
3. IgA
a. main function is preventing attachment of viruses and certain bacteria to mucosal surfaces.
4. IgD: unknown
5. IgE
a. releases histamine
IV B Cells and Humoral Immunity
A. B cells: A special group of lymphocytes which develop from stem cell precursors. (made and matured in bone marrow)
B. B cells and T cells have specific antigen receptors.
1. A mature B cell recognizes antigen receptors using IgM and IgD antibodies.
2. The intensity of a humoral response is reflected by the antibody titer. (the amount of antibody in the serum)
C. Clonal selection of antibody-producing cells involve T-dependent antigens. (an antigen that requires a Th cell for antibody production)
1. Out of 5 B cells only 1 recognizes the antigen and creates antibodies.
2. It gets divided into:
a. plasma cells: get turned into antibodies
b. memory cells
2. T-independent antigen
D. Diversity of antibodies
V Antigen-antibody binding and its results
A. Antigen-antibody complex
1. affinity
2. specificity
B. Antibody function
1. agglutination
a. hinder pathogenic activity
b. increase chances of phagocytosis
2. neutralization
a. binding and neutralizing toxins
b. block adherence to host cell
3. opsonization
a. stimulate phagocytosis
4. antibody-dependent cell mediated toxicity
5. activation of the complement system
a. non-specific chemical defense against pathogens
b. uses a series of blood serum proteins to destroy invading microbes.
c. Effects of complement activation: See chapter 16 for cascade
i. opsonization or immune adherence: enhanced phagocytosis
ii. membrane attack complex: cytolysis
iii. attract phagocytes.
VI T cells and cellular immunity (Cell mediated Immunity)
A. Intracellular antigens stimulate cell-mediated immunity
B. Specialized lymphocytes, mostly T cells, respond to intracellular antigens
C. T cells differentiate into effector T cells when stimulated by an antigen
D. Some effector T cells become memory cells
E. Classes of T cells
1. Helper T Cells (TH): CD4 adhesion molecule
a. TH1: activate cells related to cell-mediated immunity
b. TH2: activated B cells to produce eosinophils, IgM, and IgE
2. Cytotoxic T cells (TC): CD8 adhesion molecule, attack any cell which is altered
3. Delayed Hypersensitivity T cells (TD)
4. Suppressor T cells
a. turn off immune response when Ag no longer present
VII Antigen-presenting cells (APCs): antigens should be processed to be recognized by T cells.
VIII Extracellular killing by the immune system (did not go over)
IX Antibody-dependent cell mediated cytotoxicity (did not go over)
X Cytokines
A. Chemical messengers
B. Produced mainly by T helper cells
C. Induces the migration of leukocytes on to area of infection: chemotaxis
XI Immunological memory (did not go over)
XII Types of adaptive immunity: Active and Passive Immunity
A. Acquired Immunity
1. Naturally acquired
a. active: antigens enter the body naturally; body produces antibodies and specialized lymphocytes.
b. passive: antibodies pass from mother to fetus via placenta or to infant in the mother’s milk.
2. Artificially acquired
a. active: antigens are introduced in vaccines; body produces antibodies and specialized lymphocytes.
b. passive: preformed antibodies in immune serum introduced in body by injection. (snake venom….when we need it fast)
Various notes:
Sushma likes the term antigenic determinants instead of the term epitopes. Make sure you remember that they mean the same thing.
All enzymes are proteins. If a mo is making an enzyme, we will produce an antibody.
Look at charts in textbook
TC cell = killer cell
Need a lot of T cells to trigger others
I may go blind trying to read the last slide that summarized everything. If I can enlarge it I will.
Study pages: 504-516
Cytokines 518
Immunological memory 519
Types of adaptive immunity 520 – 521
The extra credit III questions are below:
1. Define epitopes and give two characteristics about ideal anitgen. (****she said it should be a protein or a carb with a molecular weight higher than 10, 000)
2. Describe 5 different kinds of immunoglobulins. (so name and characteristics)
3. Name at least three different kinds of anitgen-antibody complexes.
4. What are two major types of T cells and explain the differences among them.
5. List four major differences between Humoral and Cellular immunity. (KNOW THIS QUESTION AS IT ACCOUNTS FOR 15% OF NEXT EXAM QUESTIONS.)
Chpt 15 Innate Immunity, etc
Innate Immunity: Nonspecific Defenses of the Host
Nonspecific Immunity
Chapter 16
Functional divisions of immunity:
Nonspecific immunity
Specific immunity
Nonspecific immunity is our first line of defense. It stops most potential pathogens and prevents them from entering the body. It involves various barriers and mechanisms.
I Skin and Mucous Membranes
A. Mechanical factors
1. Skin
a. effective barrier
b. dry, low pH. (stops bacteria, but fungi like low pH)
c. has antimicrobial secretions
d. hard for bacteria to penetrate
e. skin layers
i. dermis
ii. epidermis: contains keratin
2. Mucous membranes: line the body cavities
a. barrier, protects underlying cells
b. traps organisms in mucous. (mucous also keeps the cavities from drying out)
c. offers less protection than skin
d. Eyes
i. lacrimal apparatus: manufactures and drains away tears.
e. Oral cavity:
i. saliva: produced by salivary glands washes microorganisms from the surfaces of the teeth and mucous membranes of the mouth. Prevents colonization.
f. Respiratory tract:
i. Cilia in the respiratory tract move trapped mo’s out
ii. epiglottis cover the larynx during swallowing
iii. Ciliary (mucociliary) elevator: move and propel mo’s trapped in mucous out of the respiratory system
iv. alveolar macrophages
v. coughing and sneezing
h. Digestive tract
1. defecation and vomiting
2. mucous lining
i. urination
1. urinary pH
2. production of urine
3. normal flora
B. Chemical factors
1. sebum: sebaceous oil glands in the skin which form a protective film over the skin surface
2. sweat glands: produce perspiration which flushes mo’s from the skin surface Sweat contains lysozyme which breaks down cell walls of gram + bacteria.
3. Eye: tears contain lysozyme
4. Oral Cavity:
a. saliva: contains lysozyme and salivary enzymes
5. Digestive tract:
a. stomach acid: (gastric juice) Low pH destroys most organisms.
i. Helicobacter can grow in the low pH of the stomach
b. enzymes
c. bile
d. normal flora
C. Normal microbiota (flora) and nonspecific resistance
1. Compete with disease causing organisms (competitive exclusion)
2. inhibit disease causing organisms
3.
II Phagocytosis: the ingestion of solids by eukaryotic cells
A. Formed elements in blood: cells and cell fragments.
1. Plasma: blood fluid
2. Leukocytes: white blood cells.
a. leukocytosis: an increase of white blood cells during infection
b. leucopenia: decreased white blood cells
3. Types of leukocytes:
a. neutrophils (nonspecific): a phagocyte
b. eosinophiles (nonspecific)
c. basophiles (nonspecific)
d. monocytes (become macrophages which are phagocytes)
e. lyphocytes (specific)
i. T cell
ii. B cell
iii. NK cell
B. Actions of phagocytic cells. (did not go over)
C. Mechanism of phagocytosis
1. Chemotaxis: the attraction of mo’s to chemicals
2. Adherence: (attachment) between the cell membrane of the phagocyte and the organism. Facilitated by chemotaxis.
3. Ingestion: the process of a phagocyte folding inward and forming a sac around a mo.
4. Digestion
D. Microbial evasion of phagocytosis (did not go over)
III Inflammation: a host response to tissue damage, characterized by redness, pain, heat, swelling, and perhaps loss of function. A major protective mechanism in response to injury or infection. Activated in multiple ways:
A. Vasodilation: The first stage of inflammation; involving an increase in blood vessel diameter thereby causing more blood flow to the injured area.
1. responsible for the redness, heat, edema and pain of inflammation
B. Permeability: (swelling/edema) allows defense substances in the blood to pass through the walls of the blood vessels.
1. histamine can increase permeability
C. Phagocyte migration and phagocytosis (did not call it that… called it) Leukocyte accumulation/chemotaxis
D. Tissue repair: the final stage of inflammation (connective tissue)
E. Fever
1. Temp can be altered by the ingestion of gram – bacteria by phagocytes.
2. protective mechanism
3. inhibits growth of bacteria and viruses
4. enhances immune response
F. Pus: The last step of inflammation. (according to Sushma) Sign that inflammation has ended.
IV Antimicrobial Substances
A. The complement system
1. Complement: consist of a group of over 20 different proteins found in blood serum. (30 proteins produced by the liver)
a. blood serum: the liquid portion of blood that remains after it is drawn and clotting proteins for a clot with the formed elements.
2. Complements participate in:
a. lysis of foreign cells
b. inflammation
c. phagocytosis
3. Can be activatied by:
a. classical pathway: initiated when antibody molecules bind to the antigen (ex: bacterial cell)
b. alternative pathway: (Does not involve antibodies) Complement proteins, and proteins called factors B, D and P, combine with certain microbial polysaccharides. Especially affected are the lopopolysaccharade cell wall portions (endotoxins) of gram – enteric bacteria.
c. lectin pathway: macrophage stimulate the liver to release lectins which enhance opsonization by binding to cell carbohydrates.
4. Complement proteins act in an ordered sequence, or cascade. (one protein activates another)
a. Designated by “C” numbered 1 through 9
b. Inactive state is denoted by “C”
c. Upon activation they split into Ca; Cb; etc
d. C3 plays a central role in both the classical and alternative pathways.
B. The Result of Complement Activation:
1. Cytolysis: complement protein then binds to 2 adjacent antibodies and initiates a sequence known as the membrane attack complex.
2. transmembrane channels (membrane pores): circular lesions that cause the eventual lysis of the cell to which the antibodies are attached.
3. Inflammation
4. opsonization (immune adherence) promotes attachment of a phagocyte to the microbe.
5. Attract pahgocytes
C. Interferons (IFNs): proteins produced in response to viruses.
1. inhibit viral replication inside cells
2. activates NK cells and macrophages
*********************************************************
Extra Stuff
Definitions:
Immunity: (resistance) Our ability to ward off disease through our defenses.
Susceptibility: Our vulnerability or lack of resistance to disease
Innate (nonspecific) immunity: defenses that tend to protect us from any kind of pathogen.
Adaptive (specific) immunity: is based on antibody production and is a defense against a particular organism.
Immunology: the study of a host’s defense to a pathogen.
Phagocytes: blood cells or derivatives of blood cells that ingest mo’s or a particulate matter.
Immunology is complicated because there are many different enemies out to get you.
3 steps of defense (what I wrote down from lecture, but isn’t inflammation and fever the same thing?)
1. inflammation
2. phagocytosis
3. fever
Ok, the lines of defense: (according to the study guide)
First: skin and mucous membranes
Second: phagocytosis
Signs of inflammation: Pa, He Reads Swell
Pain
Heat
Redness
Swelling
There is a slide from the second handout that discusses ways of preventing phagocytosis. It is not in my study guide:
Inhibit adherence capsules K. ?
Kill phagocytes S. aureus
Escape phagosome Shigella
Prevent phagosome-lysozome fusion HIV and ?
C3 and C5 are major in the complement system
Study pages:
474-484
486-488
Fever 489
Complement system 490-494
Nonspecific Immunity
Chapter 16
Functional divisions of immunity:
Nonspecific immunity
Specific immunity
Nonspecific immunity is our first line of defense. It stops most potential pathogens and prevents them from entering the body. It involves various barriers and mechanisms.
I Skin and Mucous Membranes
A. Mechanical factors
1. Skin
a. effective barrier
b. dry, low pH. (stops bacteria, but fungi like low pH)
c. has antimicrobial secretions
d. hard for bacteria to penetrate
e. skin layers
i. dermis
ii. epidermis: contains keratin
2. Mucous membranes: line the body cavities
a. barrier, protects underlying cells
b. traps organisms in mucous. (mucous also keeps the cavities from drying out)
c. offers less protection than skin
d. Eyes
i. lacrimal apparatus: manufactures and drains away tears.
e. Oral cavity:
i. saliva: produced by salivary glands washes microorganisms from the surfaces of the teeth and mucous membranes of the mouth. Prevents colonization.
f. Respiratory tract:
i. Cilia in the respiratory tract move trapped mo’s out
ii. epiglottis cover the larynx during swallowing
iii. Ciliary (mucociliary) elevator: move and propel mo’s trapped in mucous out of the respiratory system
iv. alveolar macrophages
v. coughing and sneezing
h. Digestive tract
1. defecation and vomiting
2. mucous lining
i. urination
1. urinary pH
2. production of urine
3. normal flora
B. Chemical factors
1. sebum: sebaceous oil glands in the skin which form a protective film over the skin surface
2. sweat glands: produce perspiration which flushes mo’s from the skin surface Sweat contains lysozyme which breaks down cell walls of gram + bacteria.
3. Eye: tears contain lysozyme
4. Oral Cavity:
a. saliva: contains lysozyme and salivary enzymes
5. Digestive tract:
a. stomach acid: (gastric juice) Low pH destroys most organisms.
i. Helicobacter can grow in the low pH of the stomach
b. enzymes
c. bile
d. normal flora
C. Normal microbiota (flora) and nonspecific resistance
1. Compete with disease causing organisms (competitive exclusion)
2. inhibit disease causing organisms
3.
II Phagocytosis: the ingestion of solids by eukaryotic cells
A. Formed elements in blood: cells and cell fragments.
1. Plasma: blood fluid
2. Leukocytes: white blood cells.
a. leukocytosis: an increase of white blood cells during infection
b. leucopenia: decreased white blood cells
3. Types of leukocytes:
a. neutrophils (nonspecific): a phagocyte
b. eosinophiles (nonspecific)
c. basophiles (nonspecific)
d. monocytes (become macrophages which are phagocytes)
e. lyphocytes (specific)
i. T cell
ii. B cell
iii. NK cell
B. Actions of phagocytic cells. (did not go over)
C. Mechanism of phagocytosis
1. Chemotaxis: the attraction of mo’s to chemicals
2. Adherence: (attachment) between the cell membrane of the phagocyte and the organism. Facilitated by chemotaxis.
3. Ingestion: the process of a phagocyte folding inward and forming a sac around a mo.
4. Digestion
D. Microbial evasion of phagocytosis (did not go over)
III Inflammation: a host response to tissue damage, characterized by redness, pain, heat, swelling, and perhaps loss of function. A major protective mechanism in response to injury or infection. Activated in multiple ways:
A. Vasodilation: The first stage of inflammation; involving an increase in blood vessel diameter thereby causing more blood flow to the injured area.
1. responsible for the redness, heat, edema and pain of inflammation
B. Permeability: (swelling/edema) allows defense substances in the blood to pass through the walls of the blood vessels.
1. histamine can increase permeability
C. Phagocyte migration and phagocytosis (did not call it that… called it) Leukocyte accumulation/chemotaxis
D. Tissue repair: the final stage of inflammation (connective tissue)
E. Fever
1. Temp can be altered by the ingestion of gram – bacteria by phagocytes.
2. protective mechanism
3. inhibits growth of bacteria and viruses
4. enhances immune response
F. Pus: The last step of inflammation. (according to Sushma) Sign that inflammation has ended.
IV Antimicrobial Substances
A. The complement system
1. Complement: consist of a group of over 20 different proteins found in blood serum. (30 proteins produced by the liver)
a. blood serum: the liquid portion of blood that remains after it is drawn and clotting proteins for a clot with the formed elements.
2. Complements participate in:
a. lysis of foreign cells
b. inflammation
c. phagocytosis
3. Can be activatied by:
a. classical pathway: initiated when antibody molecules bind to the antigen (ex: bacterial cell)
b. alternative pathway: (Does not involve antibodies) Complement proteins, and proteins called factors B, D and P, combine with certain microbial polysaccharides. Especially affected are the lopopolysaccharade cell wall portions (endotoxins) of gram – enteric bacteria.
c. lectin pathway: macrophage stimulate the liver to release lectins which enhance opsonization by binding to cell carbohydrates.
4. Complement proteins act in an ordered sequence, or cascade. (one protein activates another)
a. Designated by “C” numbered 1 through 9
b. Inactive state is denoted by “C”
c. Upon activation they split into Ca; Cb; etc
d. C3 plays a central role in both the classical and alternative pathways.
B. The Result of Complement Activation:
1. Cytolysis: complement protein then binds to 2 adjacent antibodies and initiates a sequence known as the membrane attack complex.
2. transmembrane channels (membrane pores): circular lesions that cause the eventual lysis of the cell to which the antibodies are attached.
3. Inflammation
4. opsonization (immune adherence) promotes attachment of a phagocyte to the microbe.
5. Attract pahgocytes
C. Interferons (IFNs): proteins produced in response to viruses.
1. inhibit viral replication inside cells
2. activates NK cells and macrophages
*********************************************************
Extra Stuff
Definitions:
Immunity: (resistance) Our ability to ward off disease through our defenses.
Susceptibility: Our vulnerability or lack of resistance to disease
Innate (nonspecific) immunity: defenses that tend to protect us from any kind of pathogen.
Adaptive (specific) immunity: is based on antibody production and is a defense against a particular organism.
Immunology: the study of a host’s defense to a pathogen.
Phagocytes: blood cells or derivatives of blood cells that ingest mo’s or a particulate matter.
Immunology is complicated because there are many different enemies out to get you.
3 steps of defense (what I wrote down from lecture, but isn’t inflammation and fever the same thing?)
1. inflammation
2. phagocytosis
3. fever
Ok, the lines of defense: (according to the study guide)
First: skin and mucous membranes
Second: phagocytosis
Signs of inflammation: Pa, He Reads Swell
Pain
Heat
Redness
Swelling
There is a slide from the second handout that discusses ways of preventing phagocytosis. It is not in my study guide:
Inhibit adherence capsules K. ?
Kill phagocytes S. aureus
Escape phagosome Shigella
Prevent phagosome-lysozome fusion HIV and ?
C3 and C5 are major in the complement system
Study pages:
474-484
486-488
Fever 489
Complement system 490-494
Chpt 15 Microbial Mechanisms of Pathogenicity
Microbial Mechanisms of Pathogenicity
Chapter 15
Pathogenicity: the ability to cause disease in a host.
Virulence: the degree of pathogenicity. A measure of pathogenicity.
I. Portal of entry: the avenue by which a microbe gains access to the body. (There is also a portal of exit, which like portal of entry is often a characteristic of a disease.)
A. Mucous membranes: unlike skin, mucous membranes are warm, moist, thin living cells.
1. respiratory tract: the easiest, most frequently used route of entry for infectious microorganisms. (Sushma said best portal is broken skin)
a. common cold
b. pneumonia
c. TB
d. influenza
e. measles
f. small pox
2. gastrointestinal tract: microorganisms enter by contact with food, water, or fingers
a. poliomyelitis
b. hepatitis A
c. typhoid fever
d. amoebic dysentery
e. shigellosis
f. cholera
3. genitourinary tract
a. HIV/AIDS
b. Chlamydia
c. syphilis
d. gonorrhea
4. conjunctiva (eyes)
B. Skin
1. sweat glands
2. cuts (broken skin is the best portal of entry * according to Sushma)
C. Parenteral route: microorganisms entering through skin or mucous membranes that are punctured or injured (traumatized).
D. Preferred portal of entry (did not go over)
E. Numbers of invading microbes (did not go over)
F. Adherence: attachment between pathogen and host by the use of surface adhesions.
1. Suckers and hooks (helminthes)
2. Ligands: proteins on surface of bacteria and viruses found on fimbraie, flagella and glycocalyces.
a. adhesions: proteins on surface of bacteria
b. attachment proteins: proteins on surfaces of viruses.
3. Surface receptors: complementary receptors on host cells to which ligands attach.
II How bacterial pathogens penetrate host defenses.
A. Capsules: resist phagocytosis
1. Streptococcus pneumoniae
2. Haemophilus influenzae
B. Cell wall components: waxes in cell walls resist digestion by macrophages.
1. Mycobacterium tuberculosis
C. Enzymes
1. Extracellular enzymes: dissolve structural components/chemicals
a. Hyaluronidase and collagenase allow bacteria to invade deeper tissues
b. Coagulase: coagulates blood clot proteins, “hiding” the bacteria protecting it from phagocytosis. (produced by S. aureus)
c. Kinase: dissolves clots, releases bacteria from clots. A modified version can be used to dissolve blood clots.
i. Streptokinase
ii. Staphylokinase
D. Antigenic variation (did not go over)
E. Penetration into host cell cytoskeleton
1. Adhesins: microbes attach to host cells by adhesions.
III How bacterial pathogens damage host cells
A. Siderophores (did not go over)
B. Toxins: poisonous substance produced by certain microorganisms. Chemicals that harm tissue or elicit host immune response, damaging tissue.
1. Definitions:
a. Toxigenicity: the capacity to produce toxins.
b. Toxemia: the presence of toxins in the blood and lymph. Toxins enter the bloodstream and are carried to other parts of the body.
2. Types:
a. Exotoxins: proteins secreted by the bacterium, mostly gram +, into the surrounding medium or released following lysis. Destroy host cells or interfere with host cell metabolism by secreting toxin from cell.
i. highly specific
ii. among the most lethal substances known
iii. antitoxins: antibodies (produced by the body) that provide immunity to exotoxins.
iv. both gram + and gram – but mostly gram +
v. types of exotoxins
a. cytotoxins: attack any type of cell
b. neurotoxins: attack nerves. Cause paralysis, stiff muscles. (Clostridium gram +)
c. enterotoxins:attack the stomach (E coli gram -)
vi. hemolysins: toxins that target red blood cells. Streptococci
vii. representative extoxins (did not go over): named for the tissues they affect, such as neurotoxins, cardiotoxins, etc.
b. Endotoxins: not secreted by bacteria, but are part of the outer portion of the cell wall of gram – bacteria.
i. gram – cell wall
ii. have lipopolysaccharide layer on outer membrane (LPS)
iii. lipid A: the lipid part of LPS
a. released upon bacterial cell death often causing fever and inflammation. Also can be released during bacterial multiplication.
iv. at high levels can cause hemorrhaging and septic shock
v. released only after bacteria have died. (therefore to give antibiotics is wrong in this case because the dead bacteria would release all of the endotoxins. Hydrate patient.)
C. Anti-phagocytic factors: (whenever you see this term you should remember macrophages)
1. macrophages: white blood cells that engulf and remove invading pathogens.
a. capsules
i. made up of chemicals normally found in a host
ii. slippery glycocalyx blocks phagocytosis
b. antiphgocytic chemicals: chemicals that prevent the fusionof lysosomes with phagocytic vesicles.
i. M protein: protein produced on its cell wall by Streptococcus pyogenes
ii. Leudocidins: kill white blood cells
iii. Mycolic acid: lysozomes cannot enter. Mycobacterium
IV Plasmids, Lysogeny, and Pathogenicity (did not go over)
V Pathogenic properties of nonbacterial microorganisms (did not go over)
A. Viruses
1. Cytopathic effects of viruses:
B. Fungi
C. Protozoa
D. Helminths
E. Algae
Extra
This outline follows the book format which is different from Sushma’s format. All of the information that Sushma discussed is included on this outline, just in a way that is easier for me to understand. I hope it helps. :0)
Virulence: a measure of pathogenicity (the ability of an organism to cause disease)
Viurlence factors: (besides adhesions these can be classified into three categories)
I Adhesins
II Extracellular enzymes
II IToxins
IV Anti-phagocytic factors
Possible questions:
Which produces an endotoxin? Gram – (neg)
Need to know which bacteria are gram – for above question.
See table 15.3 page 464
Denatured proteins can renature when cooled causing food poisoning.
Protein in endotoxins are lipids
Damage to host cells occur in the Log phase.
Chapter 15
Pathogenicity: the ability to cause disease in a host.
Virulence: the degree of pathogenicity. A measure of pathogenicity.
I. Portal of entry: the avenue by which a microbe gains access to the body. (There is also a portal of exit, which like portal of entry is often a characteristic of a disease.)
A. Mucous membranes: unlike skin, mucous membranes are warm, moist, thin living cells.
1. respiratory tract: the easiest, most frequently used route of entry for infectious microorganisms. (Sushma said best portal is broken skin)
a. common cold
b. pneumonia
c. TB
d. influenza
e. measles
f. small pox
2. gastrointestinal tract: microorganisms enter by contact with food, water, or fingers
a. poliomyelitis
b. hepatitis A
c. typhoid fever
d. amoebic dysentery
e. shigellosis
f. cholera
3. genitourinary tract
a. HIV/AIDS
b. Chlamydia
c. syphilis
d. gonorrhea
4. conjunctiva (eyes)
B. Skin
1. sweat glands
2. cuts (broken skin is the best portal of entry * according to Sushma)
C. Parenteral route: microorganisms entering through skin or mucous membranes that are punctured or injured (traumatized).
D. Preferred portal of entry (did not go over)
E. Numbers of invading microbes (did not go over)
F. Adherence: attachment between pathogen and host by the use of surface adhesions.
1. Suckers and hooks (helminthes)
2. Ligands: proteins on surface of bacteria and viruses found on fimbraie, flagella and glycocalyces.
a. adhesions: proteins on surface of bacteria
b. attachment proteins: proteins on surfaces of viruses.
3. Surface receptors: complementary receptors on host cells to which ligands attach.
II How bacterial pathogens penetrate host defenses.
A. Capsules: resist phagocytosis
1. Streptococcus pneumoniae
2. Haemophilus influenzae
B. Cell wall components: waxes in cell walls resist digestion by macrophages.
1. Mycobacterium tuberculosis
C. Enzymes
1. Extracellular enzymes: dissolve structural components/chemicals
a. Hyaluronidase and collagenase allow bacteria to invade deeper tissues
b. Coagulase: coagulates blood clot proteins, “hiding” the bacteria protecting it from phagocytosis. (produced by S. aureus)
c. Kinase: dissolves clots, releases bacteria from clots. A modified version can be used to dissolve blood clots.
i. Streptokinase
ii. Staphylokinase
D. Antigenic variation (did not go over)
E. Penetration into host cell cytoskeleton
1. Adhesins: microbes attach to host cells by adhesions.
III How bacterial pathogens damage host cells
A. Siderophores (did not go over)
B. Toxins: poisonous substance produced by certain microorganisms. Chemicals that harm tissue or elicit host immune response, damaging tissue.
1. Definitions:
a. Toxigenicity: the capacity to produce toxins.
b. Toxemia: the presence of toxins in the blood and lymph. Toxins enter the bloodstream and are carried to other parts of the body.
2. Types:
a. Exotoxins: proteins secreted by the bacterium, mostly gram +, into the surrounding medium or released following lysis. Destroy host cells or interfere with host cell metabolism by secreting toxin from cell.
i. highly specific
ii. among the most lethal substances known
iii. antitoxins: antibodies (produced by the body) that provide immunity to exotoxins.
iv. both gram + and gram – but mostly gram +
v. types of exotoxins
a. cytotoxins: attack any type of cell
b. neurotoxins: attack nerves. Cause paralysis, stiff muscles. (Clostridium gram +)
c. enterotoxins:attack the stomach (E coli gram -)
vi. hemolysins: toxins that target red blood cells. Streptococci
vii. representative extoxins (did not go over): named for the tissues they affect, such as neurotoxins, cardiotoxins, etc.
b. Endotoxins: not secreted by bacteria, but are part of the outer portion of the cell wall of gram – bacteria.
i. gram – cell wall
ii. have lipopolysaccharide layer on outer membrane (LPS)
iii. lipid A: the lipid part of LPS
a. released upon bacterial cell death often causing fever and inflammation. Also can be released during bacterial multiplication.
iv. at high levels can cause hemorrhaging and septic shock
v. released only after bacteria have died. (therefore to give antibiotics is wrong in this case because the dead bacteria would release all of the endotoxins. Hydrate patient.)
C. Anti-phagocytic factors: (whenever you see this term you should remember macrophages)
1. macrophages: white blood cells that engulf and remove invading pathogens.
a. capsules
i. made up of chemicals normally found in a host
ii. slippery glycocalyx blocks phagocytosis
b. antiphgocytic chemicals: chemicals that prevent the fusionof lysosomes with phagocytic vesicles.
i. M protein: protein produced on its cell wall by Streptococcus pyogenes
ii. Leudocidins: kill white blood cells
iii. Mycolic acid: lysozomes cannot enter. Mycobacterium
IV Plasmids, Lysogeny, and Pathogenicity (did not go over)
V Pathogenic properties of nonbacterial microorganisms (did not go over)
A. Viruses
1. Cytopathic effects of viruses:
B. Fungi
C. Protozoa
D. Helminths
E. Algae
Extra
This outline follows the book format which is different from Sushma’s format. All of the information that Sushma discussed is included on this outline, just in a way that is easier for me to understand. I hope it helps. :0)
Virulence: a measure of pathogenicity (the ability of an organism to cause disease)
Viurlence factors: (besides adhesions these can be classified into three categories)
I Adhesins
II Extracellular enzymes
II IToxins
IV Anti-phagocytic factors
Possible questions:
Which produces an endotoxin? Gram – (neg)
Need to know which bacteria are gram – for above question.
See table 15.3 page 464
Denatured proteins can renature when cooled causing food poisoning.
Protein in endotoxins are lipids
Damage to host cells occur in the Log phase.
Chpt 14 Principles of Disease and Epidemiology
Principles of Disease and Epidemiology
Chapter 14
I Pathology, Infection, and Disease
A. Pathology: the scientific study of disease
1. etiology: the cause of disease
2. pathogenesis: the manner in which a disease develops
B. Infection: invasion or colonization of the body (host) by potentially pathogenic microorganisms.
C. Disease: any change from a state of health. An abnormal state in which the body is not properly adjusted or capable of performing its normal functions.
II Normal Microbiota (flora): the microorganisms that establish permanent residence (colonize) but that do not produce disease under normal conditions.
A. Protect the host by:
1. occupying niches that pathogens might occupy.
2. producing acids
3. Microbial antagonism (competitive exclusion): A phenomenon in which normal microbiota can benefit the host by preventing the overgrowth of harmful microorganisms.
a. Example: bacteriocins by E. coli dells in the large intestine, which inhibits pathogens such as Salmonella and Shigella.
b. symbiosis: the relationship between normal microbiota of a healthy person and the person.
i. commensalism: one organism benefiting, the other unaffected.
ii. mutualism: both parties benefiting
iii. parasitism: one organism benefited a the expense of the other.
B. Types:
1. gram + (aerobe)
a. Staphylococcus
b. Streptococcus
c. Candida
2. gram – (facultative anaerobe)
a. E. coli
b. Klebsiella
c. Proteus
d. Lactobacillus
e. Candida (listed under positive and negative)
C. Opportunistic Microorganisms (pathogens): They ordinarily do not cause disease in the normal habitat of a healthy person, but may do so in a different environment.
1. in the immunocompromised cell
2. as a result of a reduction in microbial microflora (as in broad spectrum antibiotics)
3. when introduced into an abnormal area of the body
4. Types:
a. E. coli.
D. Synergism: two microbes acting together have a greater effect than either acting alone.
1. probiotics: live bacterial cultures administered for beneficial effects.
2. prebiotics: chemicals administered to promote their growth.
III Etiology of Infectious Disease (did not cover this)
IV Classifying Infectious Diseases
A. Symptoms (did not cover)
B. Communicable Disease: spread directly or indirectly from one host to another.
1. contagious disease: easily spread
C. Noncommunicable diseases: not spread between hosts
D. Occurrence of a disease:
1. Endemic: disease constantly present in a population
2. Epidemic: Disease acquired by many hosts in a given area in a short time
3. Pandemic: worldwide epidemic
4. Sporadic: occurs only occasionally
E. Severity or duration (did not cover)
F. Extent of Host Involvement
1. Local infection: one in which the invading microorganisms are limited to a relatively small area of the body. (boil)
2. Systemic infection (generalized): spread throughout the body by the blood or lymphatic system.
3. Sepsis: toxic, inflammatory condition arising from the spread of bacteria or bacterial toxins from a focus of infection.
a. Septicemia: pathogens in the blood stream
i. bacteremia: bacteria pathogens in the blood
b. Toxemia: presence of toxins in the blood
V Patterns of Disease (did not cover)
VI Spread of Infection
A. Resevoirs of infection: a continual source of the pathogen
1. Human (carriers) AIDS
2. Animal (zoonoses) Rabies
3. Nonliving: soil, water. Botulism
B. Transmission of disease
1. Contact
a. direct: kissing, intercourse. Requires close association between carrier and host.
b. droplet: less than a meter (airborne)
c. indirect: involves a nonliving object such as a cup. (fomite) Syringe
2. Vehicle: inanimate reservoirs such as food, water or blood.
a. Oral-fecal
b. foodborn
c. airborne: when droplets or dust travel distance of more than a meter.
d. waterborne
3. Vectors: animals that carry pathogens from one host to another.
a. mechanical transmission: vectors carry pathogens on their bodies to food that is later swallowed by the host.
b. biological transmission: passed in a bite, or feces which later enter the wound caused by the vector.
VII Nococomial (hospital acquired) infections: one not evident or present at admission to a hospital but acquired as a result of a hospital stay.
A. 5 – 15% of all hospital patients acquire nosocomial infections.
B. Reasons:
1. Microorganisms in hospital environment
2. Compromised host
a. poor immunity
b. antibiotic resisitant drugs
3. Chain of transmission
VIII Emerging Infectious Diseases: new or changing diseases showing an increase of incidence in the recent past or a potential for increase in the near future.
A. Contributing factors:
1. evolution of new strains
2. changes in weather patterns
a. Malaria
3. Modern transportation
a. West Nile Virus
4. Ecological disaster
5. Animal control measures
a. Lyme disease
6. Public health failure
IX Epidemiology: the science that deals with the transmission of diseases in the human population, and where and when they occur. (did not cover different kinds)
Chapter 14
I Pathology, Infection, and Disease
A. Pathology: the scientific study of disease
1. etiology: the cause of disease
2. pathogenesis: the manner in which a disease develops
B. Infection: invasion or colonization of the body (host) by potentially pathogenic microorganisms.
C. Disease: any change from a state of health. An abnormal state in which the body is not properly adjusted or capable of performing its normal functions.
II Normal Microbiota (flora): the microorganisms that establish permanent residence (colonize) but that do not produce disease under normal conditions.
A. Protect the host by:
1. occupying niches that pathogens might occupy.
2. producing acids
3. Microbial antagonism (competitive exclusion): A phenomenon in which normal microbiota can benefit the host by preventing the overgrowth of harmful microorganisms.
a. Example: bacteriocins by E. coli dells in the large intestine, which inhibits pathogens such as Salmonella and Shigella.
b. symbiosis: the relationship between normal microbiota of a healthy person and the person.
i. commensalism: one organism benefiting, the other unaffected.
ii. mutualism: both parties benefiting
iii. parasitism: one organism benefited a the expense of the other.
B. Types:
1. gram + (aerobe)
a. Staphylococcus
b. Streptococcus
c. Candida
2. gram – (facultative anaerobe)
a. E. coli
b. Klebsiella
c. Proteus
d. Lactobacillus
e. Candida (listed under positive and negative)
C. Opportunistic Microorganisms (pathogens): They ordinarily do not cause disease in the normal habitat of a healthy person, but may do so in a different environment.
1. in the immunocompromised cell
2. as a result of a reduction in microbial microflora (as in broad spectrum antibiotics)
3. when introduced into an abnormal area of the body
4. Types:
a. E. coli.
D. Synergism: two microbes acting together have a greater effect than either acting alone.
1. probiotics: live bacterial cultures administered for beneficial effects.
2. prebiotics: chemicals administered to promote their growth.
III Etiology of Infectious Disease (did not cover this)
IV Classifying Infectious Diseases
A. Symptoms (did not cover)
B. Communicable Disease: spread directly or indirectly from one host to another.
1. contagious disease: easily spread
C. Noncommunicable diseases: not spread between hosts
D. Occurrence of a disease:
1. Endemic: disease constantly present in a population
2. Epidemic: Disease acquired by many hosts in a given area in a short time
3. Pandemic: worldwide epidemic
4. Sporadic: occurs only occasionally
E. Severity or duration (did not cover)
F. Extent of Host Involvement
1. Local infection: one in which the invading microorganisms are limited to a relatively small area of the body. (boil)
2. Systemic infection (generalized): spread throughout the body by the blood or lymphatic system.
3. Sepsis: toxic, inflammatory condition arising from the spread of bacteria or bacterial toxins from a focus of infection.
a. Septicemia: pathogens in the blood stream
i. bacteremia: bacteria pathogens in the blood
b. Toxemia: presence of toxins in the blood
V Patterns of Disease (did not cover)
VI Spread of Infection
A. Resevoirs of infection: a continual source of the pathogen
1. Human (carriers) AIDS
2. Animal (zoonoses) Rabies
3. Nonliving: soil, water. Botulism
B. Transmission of disease
1. Contact
a. direct: kissing, intercourse. Requires close association between carrier and host.
b. droplet: less than a meter (airborne)
c. indirect: involves a nonliving object such as a cup. (fomite) Syringe
2. Vehicle: inanimate reservoirs such as food, water or blood.
a. Oral-fecal
b. foodborn
c. airborne: when droplets or dust travel distance of more than a meter.
d. waterborne
3. Vectors: animals that carry pathogens from one host to another.
a. mechanical transmission: vectors carry pathogens on their bodies to food that is later swallowed by the host.
b. biological transmission: passed in a bite, or feces which later enter the wound caused by the vector.
VII Nococomial (hospital acquired) infections: one not evident or present at admission to a hospital but acquired as a result of a hospital stay.
A. 5 – 15% of all hospital patients acquire nosocomial infections.
B. Reasons:
1. Microorganisms in hospital environment
2. Compromised host
a. poor immunity
b. antibiotic resisitant drugs
3. Chain of transmission
VIII Emerging Infectious Diseases: new or changing diseases showing an increase of incidence in the recent past or a potential for increase in the near future.
A. Contributing factors:
1. evolution of new strains
2. changes in weather patterns
a. Malaria
3. Modern transportation
a. West Nile Virus
4. Ecological disaster
5. Animal control measures
a. Lyme disease
6. Public health failure
IX Epidemiology: the science that deals with the transmission of diseases in the human population, and where and when they occur. (did not cover different kinds)
Chapter 8 Microbial Genetics
Microbial Genetics Chapter 8
I Structure and function of genetic material
A. DNA is composed of repeating nucleotides
1. Base pairs (the hydrogen bonds from which DNA is connected)
a. Adenine & Thymine
b. Cystosine & Guanine
2. Deoxyribose sugar & Phosphate group
a. The “backbone” or basis of DNA is deoxyribose.
b. Phosphate is held together by hydrogen bonds between AT & CG.
II DNA replication (Reproduction)
(see next page for steps)
A. Bacteria replication begins at the origin of replication.
B. Circular molecule
C. DNA polymerase
III RNA and Protein Synthesis (Regulation)
A. Transcription: a strand of mRNA is synthesized from the genetic info of DNA.
1. Uracil replaces Thymine. (AT becomes AU)
2. promoter site: the region where RNA polymerase binds to DNA and transcription begins.
3. terminator site: where RNA polymerase and newly formed mRNA are released from the DNA, signaling the end point for transcription of the gene.
B. Translation: translates the language of nucleic acids into the language of proteins.
1. codons: (the language of mRNA) groups of 3 nucleotides that “code” for a particular amino acid.
a. 64 possible codons
b. 20 amino acids (therefore amino acids have more than one codon)
c. degeneracy of the code: 20 amino acids/64 codons
d. sense codons: code for amino acids
e. nonsense codons: signal the end of the synthesis of protein.
i. UAA, UGA, UAG
f. Met/start codon
i. AUG
2. Ribosomes: the sites of translation that move along mRNA.
a. Transfer (t)RNA: transports amino acids to the ribosome.
b. anticodon: a complimentary tRNA molecule made for a specific amino acid. (3 nucleotides by which a tRNA recognizes an mRNA codon.) AUG for mRNA meets UAC for tRNA.
IV Mutations: a change in the base sequence (genetic material) of DNA. Carcinogenic and can be genetic.
A. Types
1. base substitution
2. nonsense mutation
3. Spontaneous: occurs without known intervention of mutation causing agents.
B. Mutagens: chemicals and radiation that bring about mutations.
1. Chemical mutagens
2. Radiation
a. ionizing
b. nonionizing
i. UV light
3. Viruses
V Genetic transfer and recombination
A. Recombination, general overview:
1. Donor cell gives a portion of its total DNA to a different recipient cell.
2. Recipient cell (aka recombinant) DNA from donor is added to its own DNA.
3. Vertical gene transfer: DNA passed from an organism to its offspring.
4. horizontal gene transfer: DNA passed laterally to other microbes of the same generation.
B. Recombination: the rearrangement of genes to form new combinations. Types:
1. Transformation
a. DNA released when donor cell dies.
b. DNA taken up by adjacent cells.
c. competence: the ability to take up foreign DNA.
i. ex: antibiotic resistance
d. Gram + that can take up outside DNA (exogenous)
i. Streptococcus pneumoniae
ii. Staphylococcus aureus
iii. Bacillus subtilis
e. Gram – (neg) that can take up exogenous DNA
i. Neisseria meningitis
ii. Neisseria gonorrhea
iii. Haemophilus influenzae
iv. E. coli
2. Conjugation: transfer of a plasmid (F- Factor) DNA from one bacterium to another. (page 243)
a. Plasmid transfer in gram – bacteria occurs only between strains of the same species or closely related species.
b. Need cell to cell contact. With a sex pilus. (This is how we get a double coil plasmid.)
c. Usually only occurs in gram – bacteria. The exceptions are gram +:
i. Bacillus subtilis
ii. some Streptococcus
iii. Enterococcus faecalis
3. Transduction: A virus carries DNA from one bacteria to another.
(pg 244)
a. Generalized, not specific.
b. Occurs between unrelated species.
c. Can often lead to changes in microbial pathogenicity.
i. Botulism toxin of Clostridium botulinum
ii. Capsule of Streptococcus pneumoniae
iii. E. coli 0157.H7 toxin. (pathogenic)
VI Plasmids and transposons (only went over plasmids)
A. Plasmids: circular pieces of DNA that replicate independently from the cell’s chromosome.
1. Plasmids usually carry only genes that are not essential for growth of the cell.
2. Types
a. dissimilation plasmids: code for enzymes to utilize unusual sugars and hydrocarbons. (Pseudomonas)
b. bacteriocins: toxic proteins that kill other bacteria.
i. plasmids cause the synthesis of bacteriocins
c. resistance (R)factors: carry genes for antibiotic resistance and other antimicrobial factors.
i. encode antibiotic resistance in gram negative bacteria.
d. other plasmids contribute to the pathogenicity of microbes.
i. S. mutans, the cause of cavities.
I Structure and function of genetic material
A. DNA is composed of repeating nucleotides
1. Base pairs (the hydrogen bonds from which DNA is connected)
a. Adenine & Thymine
b. Cystosine & Guanine
2. Deoxyribose sugar & Phosphate group
a. The “backbone” or basis of DNA is deoxyribose.
b. Phosphate is held together by hydrogen bonds between AT & CG.
II DNA replication (Reproduction)
(see next page for steps)
A. Bacteria replication begins at the origin of replication.
B. Circular molecule
C. DNA polymerase
III RNA and Protein Synthesis (Regulation)
A. Transcription: a strand of mRNA is synthesized from the genetic info of DNA.
1. Uracil replaces Thymine. (AT becomes AU)
2. promoter site: the region where RNA polymerase binds to DNA and transcription begins.
3. terminator site: where RNA polymerase and newly formed mRNA are released from the DNA, signaling the end point for transcription of the gene.
B. Translation: translates the language of nucleic acids into the language of proteins.
1. codons: (the language of mRNA) groups of 3 nucleotides that “code” for a particular amino acid.
a. 64 possible codons
b. 20 amino acids (therefore amino acids have more than one codon)
c. degeneracy of the code: 20 amino acids/64 codons
d. sense codons: code for amino acids
e. nonsense codons: signal the end of the synthesis of protein.
i. UAA, UGA, UAG
f. Met/start codon
i. AUG
2. Ribosomes: the sites of translation that move along mRNA.
a. Transfer (t)RNA: transports amino acids to the ribosome.
b. anticodon: a complimentary tRNA molecule made for a specific amino acid. (3 nucleotides by which a tRNA recognizes an mRNA codon.) AUG for mRNA meets UAC for tRNA.
IV Mutations: a change in the base sequence (genetic material) of DNA. Carcinogenic and can be genetic.
A. Types
1. base substitution
2. nonsense mutation
3. Spontaneous: occurs without known intervention of mutation causing agents.
B. Mutagens: chemicals and radiation that bring about mutations.
1. Chemical mutagens
2. Radiation
a. ionizing
b. nonionizing
i. UV light
3. Viruses
V Genetic transfer and recombination
A. Recombination, general overview:
1. Donor cell gives a portion of its total DNA to a different recipient cell.
2. Recipient cell (aka recombinant) DNA from donor is added to its own DNA.
3. Vertical gene transfer: DNA passed from an organism to its offspring.
4. horizontal gene transfer: DNA passed laterally to other microbes of the same generation.
B. Recombination: the rearrangement of genes to form new combinations. Types:
1. Transformation
a. DNA released when donor cell dies.
b. DNA taken up by adjacent cells.
c. competence: the ability to take up foreign DNA.
i. ex: antibiotic resistance
d. Gram + that can take up outside DNA (exogenous)
i. Streptococcus pneumoniae
ii. Staphylococcus aureus
iii. Bacillus subtilis
e. Gram – (neg) that can take up exogenous DNA
i. Neisseria meningitis
ii. Neisseria gonorrhea
iii. Haemophilus influenzae
iv. E. coli
2. Conjugation: transfer of a plasmid (F- Factor) DNA from one bacterium to another. (page 243)
a. Plasmid transfer in gram – bacteria occurs only between strains of the same species or closely related species.
b. Need cell to cell contact. With a sex pilus. (This is how we get a double coil plasmid.)
c. Usually only occurs in gram – bacteria. The exceptions are gram +:
i. Bacillus subtilis
ii. some Streptococcus
iii. Enterococcus faecalis
3. Transduction: A virus carries DNA from one bacteria to another.
(pg 244)
a. Generalized, not specific.
b. Occurs between unrelated species.
c. Can often lead to changes in microbial pathogenicity.
i. Botulism toxin of Clostridium botulinum
ii. Capsule of Streptococcus pneumoniae
iii. E. coli 0157.H7 toxin. (pathogenic)
VI Plasmids and transposons (only went over plasmids)
A. Plasmids: circular pieces of DNA that replicate independently from the cell’s chromosome.
1. Plasmids usually carry only genes that are not essential for growth of the cell.
2. Types
a. dissimilation plasmids: code for enzymes to utilize unusual sugars and hydrocarbons. (Pseudomonas)
b. bacteriocins: toxic proteins that kill other bacteria.
i. plasmids cause the synthesis of bacteriocins
c. resistance (R)factors: carry genes for antibiotic resistance and other antimicrobial factors.
i. encode antibiotic resistance in gram negative bacteria.
d. other plasmids contribute to the pathogenicity of microbes.
i. S. mutans, the cause of cavities.
Chapter 8 DNA Replication
DNA Replication
1. Two helical strands unravel and separate from each other at a replication fork.
2. Synthesis of new strand begins.
3. Complementary base pairing yields a complementary copy of the original DNA. (AT, CG)
4. Segments of new nucleotides are joined to form short strands of DNA by DNA polymerase enzymes.
5. Short strands are joined into continuous DNA by action of DNA ligase enzymes.
(skipped some enzyme steps here)
6. Called semi conservative replication because each new double stranded DNA molecule has one original strand and one new strand.
Protein Synthesis
1. DNA gets a signal we need more proteins. Sends a message to mRNA.
2. mRNA carries the message DNA to protein transcriber.
1. mRNA is translated in codons. (three mRNA nucleotides = one amino acid)
2. codons “encode” for each amino acid in a protein (see degeneracy, sense, nonsense)
3. codes until it gets a stop codon because there is no tRNA to stop it. Has a start and an end because they don’t want the entire DNA transcribed.
DNA Polymerase reads it in:
E: placing (empty site)
P: reading (where the peptide bond happens. Peptide bond joins two amino acids)
A: attachment
(another way to look at it)
Transcription: In transcription, a strand of messenger RNA (mRNA) is synthesized from the genetic information in DNA. The region where RNA polymerase (needed for synthesis) binds to DNA and transcription begins is known as the promoter site. The terminator site is whereENA polymerase and newly formed mRNA are released from the DNA, signaling the endpoint for transcription of the gene.
Translation: Protein synthesis is called translation because it translates the language of nucleic acids into the language of proteins. The language of mRNA is in codons, groups of three nucleotides such as AUG. Each codon “codes” for a particular amino acid. The sites of translation are ribosomes that move along mRNA. The amino acids are transported to the ribosome by transfer RNA (tRNA). Each tRNA molecule is made specifice for an amino acid by an anticodon that is complementary to a codon. The codon AUG would be complementary to the anticodon UAC. (see 8.9 fig)
Various facts
mRNA is the transcriber
rRNA on ribosomes
tRNA translator
RNA polymerase is in transcription.
The “ladder” sides of DNA are made up of phosphate and carbon.
Most bacteria have only one chromosome.
Circular molecule
DNA polymerase: enzyme that replicates DNA
There are two major steps for expressing any enzyme:
1. transcription
2. translation
Proteins are composed of amino acids. (GCAT)
DNA is made up of nucleotides
Reproduction = DNA replication
Regulation = protein synthesis
Ribosome carry out protein synthesis. 50s and 30s = 70s
Protein synthesis starts at AUG.
AUG may be the start of a new amino acid or the middle of another.
Protein synthesis ends at UAA, UAG, UGA. (nonsense codons)
You do not need a live cell for recombination, only a piece of DNA is transferred. Host may take 2 genes and leave 8. The rest will degrade. That is why it is so scary, bacteria dies, but the DNA lives. (I think in this case she was talking about TRANSFORMATION)
Definitions
RNA primer: a short strand of RNA used to start synthesis of the lagging strand of DNA, and to start the polymerase chain reaction.
mRNA: (messenger RNA) the type of RNA molecule that directs the incorporation of amino acids into proteins.
tRNA: (transfer RNA) the type of RNA molecule that brings amino acid to the ribosomal site where they are incorporated into proteins.
Anticodon: the three nucleotides by which a tRNA recognizes an mRNA codon.
Bacteriocin: An antimicrobial peptide produced by bacteria that kills other bacteria.
Chromosomes: The structure that carries hereditary information; chromosomes contain genes.
Codon: a sequence of three nucleotides in mRNA that specifies the insertion of an amino acid into a polypeptide.
Degeneracy: Redundancy of the genetic code; that is, most of the amino acids are encoded by several codons.
Genetic code: the mRNA codons and the amino acids they encode.
Genetic recombination: the process of joining pieces of DNA from different sources.
Genome: One complete copy of the genetic information in a cell.
Genotype: The genetic makeup of an organism.
Lagging strand: During DNA replication, the daughter strand that is synthesized discontinuously.
Leading strand: During DNA replication, the daughter strand that is synthesized continuously.
Nonsense codon: a condon that does not encode any amino acid.
Phenotype: the external manifestations of an organism’s genotype (genetic makeup)
Replication fork: The point where DNA strands separate and new strands will be synthesized.
Semiconservative replication: The process of DNA replication in which each double-stranded DNA molecule contains one original strand and one new one.
Spontaneous mutation: a mutation that occurs without a mutagen.
Transcription: The process of synthesizing RNA from a DNA template.
Translation: the mRNA as a template in the synthesis of protein.
1. Two helical strands unravel and separate from each other at a replication fork.
2. Synthesis of new strand begins.
3. Complementary base pairing yields a complementary copy of the original DNA. (AT, CG)
4. Segments of new nucleotides are joined to form short strands of DNA by DNA polymerase enzymes.
5. Short strands are joined into continuous DNA by action of DNA ligase enzymes.
(skipped some enzyme steps here)
6. Called semi conservative replication because each new double stranded DNA molecule has one original strand and one new strand.
Protein Synthesis
1. DNA gets a signal we need more proteins. Sends a message to mRNA.
2. mRNA carries the message DNA to protein transcriber.
1. mRNA is translated in codons. (three mRNA nucleotides = one amino acid)
2. codons “encode” for each amino acid in a protein (see degeneracy, sense, nonsense)
3. codes until it gets a stop codon because there is no tRNA to stop it. Has a start and an end because they don’t want the entire DNA transcribed.
DNA Polymerase reads it in:
E: placing (empty site)
P: reading (where the peptide bond happens. Peptide bond joins two amino acids)
A: attachment
(another way to look at it)
Transcription: In transcription, a strand of messenger RNA (mRNA) is synthesized from the genetic information in DNA. The region where RNA polymerase (needed for synthesis) binds to DNA and transcription begins is known as the promoter site. The terminator site is whereENA polymerase and newly formed mRNA are released from the DNA, signaling the endpoint for transcription of the gene.
Translation: Protein synthesis is called translation because it translates the language of nucleic acids into the language of proteins. The language of mRNA is in codons, groups of three nucleotides such as AUG. Each codon “codes” for a particular amino acid. The sites of translation are ribosomes that move along mRNA. The amino acids are transported to the ribosome by transfer RNA (tRNA). Each tRNA molecule is made specifice for an amino acid by an anticodon that is complementary to a codon. The codon AUG would be complementary to the anticodon UAC. (see 8.9 fig)
Various facts
mRNA is the transcriber
rRNA on ribosomes
tRNA translator
RNA polymerase is in transcription.
The “ladder” sides of DNA are made up of phosphate and carbon.
Most bacteria have only one chromosome.
Circular molecule
DNA polymerase: enzyme that replicates DNA
There are two major steps for expressing any enzyme:
1. transcription
2. translation
Proteins are composed of amino acids. (GCAT)
DNA is made up of nucleotides
Reproduction = DNA replication
Regulation = protein synthesis
Ribosome carry out protein synthesis. 50s and 30s = 70s
Protein synthesis starts at AUG.
AUG may be the start of a new amino acid or the middle of another.
Protein synthesis ends at UAA, UAG, UGA. (nonsense codons)
You do not need a live cell for recombination, only a piece of DNA is transferred. Host may take 2 genes and leave 8. The rest will degrade. That is why it is so scary, bacteria dies, but the DNA lives. (I think in this case she was talking about TRANSFORMATION)
Definitions
RNA primer: a short strand of RNA used to start synthesis of the lagging strand of DNA, and to start the polymerase chain reaction.
mRNA: (messenger RNA) the type of RNA molecule that directs the incorporation of amino acids into proteins.
tRNA: (transfer RNA) the type of RNA molecule that brings amino acid to the ribosomal site where they are incorporated into proteins.
Anticodon: the three nucleotides by which a tRNA recognizes an mRNA codon.
Bacteriocin: An antimicrobial peptide produced by bacteria that kills other bacteria.
Chromosomes: The structure that carries hereditary information; chromosomes contain genes.
Codon: a sequence of three nucleotides in mRNA that specifies the insertion of an amino acid into a polypeptide.
Degeneracy: Redundancy of the genetic code; that is, most of the amino acids are encoded by several codons.
Genetic code: the mRNA codons and the amino acids they encode.
Genetic recombination: the process of joining pieces of DNA from different sources.
Genome: One complete copy of the genetic information in a cell.
Genotype: The genetic makeup of an organism.
Lagging strand: During DNA replication, the daughter strand that is synthesized discontinuously.
Leading strand: During DNA replication, the daughter strand that is synthesized continuously.
Nonsense codon: a condon that does not encode any amino acid.
Phenotype: the external manifestations of an organism’s genotype (genetic makeup)
Replication fork: The point where DNA strands separate and new strands will be synthesized.
Semiconservative replication: The process of DNA replication in which each double-stranded DNA molecule contains one original strand and one new one.
Spontaneous mutation: a mutation that occurs without a mutagen.
Transcription: The process of synthesizing RNA from a DNA template.
Translation: the mRNA as a template in the synthesis of protein.
Microbial Control Chpt 7 Physical Methods
Microbial Control Chapter 7
Physical Methods
I Disinfection: for inanimate objects. Reduces the amount of bacteria. (decreases, not eliminate)
II Sterilization: for animate objects. Kills all cells.
A. cidal: kills bacteria and endospores
B. static: upon usage killed, but when removed they regrow. (refrigeration)
C. order of death:
1. gram +
2. lipid virus
3. gram –
4. endospore
III Heat: structural proteins and enzymes damaged (denatured). Water is lost.
A. Dry heat: kills all forms of life.
1. hot air: 2 hours at 170 C. (baking) requires a long time.
2. direct flame/incineration
B. Moist heat
1. boiling: 10 minutes at 100 C. Used for food and water.
a. Will not kill Clostridium.
b. Kills 95% of bacteria.
c. for disinfection of food and water.
2. autoclaving: 15psi @ 121 C for 20 minutes.
a. kills all organisms and spores
b. widely used in medical applications.
3. Pasteurization: 15 seconds @ 72 C
a. milder process
b. makes materials (wine, milk) safe
c. aka: intermediated (intermittent) heating
4. UHT (ultra high temperature) 5 seconds @ 140 C
a. short time at high temp
b. “flash” sterilization
c. Ex: start at 74 C, heat at 5 seconds @ 140 C, back to 74 C.
IV Filtration
A. Membrane filters for fluids
B. HEPA filters for air
V Radiation
A. Ionizing radiation (x-ray, gamma ray)
1. highly penetrating
2. generate free radicals inside cells
3. used for certain medical products
4. use on food being explored. (don’t want humans creating free radicals)
B. Non-ionizing radiation (UV)
1. damages DNA
2. poor penetration
3. used primarily for surface sterilization (germicidal lamps)
VI Drying: creates a hypertonic situation
A. Salting
B. Sugaring
VII Low Temperature
A. Refrigeration is bacteriostatic
************************************************************************
Various notes
Microwaving does not kill endospores
Antibiotics are ingested to kill bacteria.
Clostridium = endospores
Order of death:
1. gram +
2. lipid virus (b/c easily soluble in disinfectant)
3. gram - (b/c of polylipid layer)
4. endospore
Physical Methods
I Disinfection: for inanimate objects. Reduces the amount of bacteria. (decreases, not eliminate)
II Sterilization: for animate objects. Kills all cells.
A. cidal: kills bacteria and endospores
B. static: upon usage killed, but when removed they regrow. (refrigeration)
C. order of death:
1. gram +
2. lipid virus
3. gram –
4. endospore
III Heat: structural proteins and enzymes damaged (denatured). Water is lost.
A. Dry heat: kills all forms of life.
1. hot air: 2 hours at 170 C. (baking) requires a long time.
2. direct flame/incineration
B. Moist heat
1. boiling: 10 minutes at 100 C. Used for food and water.
a. Will not kill Clostridium.
b. Kills 95% of bacteria.
c. for disinfection of food and water.
2. autoclaving: 15psi @ 121 C for 20 minutes.
a. kills all organisms and spores
b. widely used in medical applications.
3. Pasteurization: 15 seconds @ 72 C
a. milder process
b. makes materials (wine, milk) safe
c. aka: intermediated (intermittent) heating
4. UHT (ultra high temperature) 5 seconds @ 140 C
a. short time at high temp
b. “flash” sterilization
c. Ex: start at 74 C, heat at 5 seconds @ 140 C, back to 74 C.
IV Filtration
A. Membrane filters for fluids
B. HEPA filters for air
V Radiation
A. Ionizing radiation (x-ray, gamma ray)
1. highly penetrating
2. generate free radicals inside cells
3. used for certain medical products
4. use on food being explored. (don’t want humans creating free radicals)
B. Non-ionizing radiation (UV)
1. damages DNA
2. poor penetration
3. used primarily for surface sterilization (germicidal lamps)
VI Drying: creates a hypertonic situation
A. Salting
B. Sugaring
VII Low Temperature
A. Refrigeration is bacteriostatic
************************************************************************
Various notes
Microwaving does not kill endospores
Antibiotics are ingested to kill bacteria.
Clostridium = endospores
Order of death:
1. gram +
2. lipid virus (b/c easily soluble in disinfectant)
3. gram - (b/c of polylipid layer)
4. endospore
Chapter 7 Microbial Control Chemical Methods
Microbial Control Chapter 7
Chemical Methods
Fall into two categories:
Antiseptics: reduce the number of microbes and viruses on living tissue
Disinfectants: destruction of most microorganisms and viruses on non-living tissue
I Alcohol
A. Isopropanol (rubbing alcohol) 70%
B. Ethanol 90% alcohol
C. denatures proteins and disrupt cell membranes
D. Kills most microbes (not spores)
E. Used as antiseptic or disinfectant
II Chlorine: denatures proteins
A. Hypochlorite (Bleach)
B. Chloramine (Cl & NH3)
C. Gas
D. Widely used as disinfectant, antiseptic, and water purification
III Phenols: denatures proteins and disrupts cell membranes
A. Examples: Lysol, hibiclens, phisohex, triclosan
B. Widely used as skin antiseptic and disinfectant, but harsh on skin
IV Iodine: denatures proteins
A. tincture (mixed with alcohol)
B. iodophors (betadine)
C. widely used as a skin antiseptic
V QUATS (quanternary ammonium compound): disrupt cell membranes
A. surface active chemicals (surfactants)
B. detergents: zepharin & cepacol
C. Antiseptic: mill many microbes, but spores and others are resistant.
D. works effectively against gram + bacteria
VI Hydrogen Peroxide: denatures proteins
A. used as antiseptic or disinfectant for deep wounds
B. a catalyst enzyme (by product of aerobic respiration….oxidation)
VII Formaldehyde & Gluteraldehyde: denatures proteins and inactivating nucleic acids
A. kills all microbes and spores
B. toxic and irritating
C. used as preservative and for vaccine production
VIII Ethylene Oxide: denatures proteins
A. gas
B. kills all microbes and spores
C. Sterilization of heat and water-sensitive objects
D. widely used on medical supplies and equipment
E. may be carcinogenic
Chemical Methods
Fall into two categories:
Antiseptics: reduce the number of microbes and viruses on living tissue
Disinfectants: destruction of most microorganisms and viruses on non-living tissue
I Alcohol
A. Isopropanol (rubbing alcohol) 70%
B. Ethanol 90% alcohol
C. denatures proteins and disrupt cell membranes
D. Kills most microbes (not spores)
E. Used as antiseptic or disinfectant
II Chlorine: denatures proteins
A. Hypochlorite (Bleach)
B. Chloramine (Cl & NH3)
C. Gas
D. Widely used as disinfectant, antiseptic, and water purification
III Phenols: denatures proteins and disrupts cell membranes
A. Examples: Lysol, hibiclens, phisohex, triclosan
B. Widely used as skin antiseptic and disinfectant, but harsh on skin
IV Iodine: denatures proteins
A. tincture (mixed with alcohol)
B. iodophors (betadine)
C. widely used as a skin antiseptic
V QUATS (quanternary ammonium compound): disrupt cell membranes
A. surface active chemicals (surfactants)
B. detergents: zepharin & cepacol
C. Antiseptic: mill many microbes, but spores and others are resistant.
D. works effectively against gram + bacteria
VI Hydrogen Peroxide: denatures proteins
A. used as antiseptic or disinfectant for deep wounds
B. a catalyst enzyme (by product of aerobic respiration….oxidation)
VII Formaldehyde & Gluteraldehyde: denatures proteins and inactivating nucleic acids
A. kills all microbes and spores
B. toxic and irritating
C. used as preservative and for vaccine production
VIII Ethylene Oxide: denatures proteins
A. gas
B. kills all microbes and spores
C. Sterilization of heat and water-sensitive objects
D. widely used on medical supplies and equipment
E. may be carcinogenic
Glycolosis Preparatory Stage
Glycolysis Preparatory Stage
In this stage, 2 molecules of atp are used to phosphorylate a molecule of glucose. The resultant phosphorylated sugar is then split into two 3-carbon molecules.
Glucose enters the cell and is phosphorylated 000000
A molecule of atp is invested ATP
The product is glucose 6 phosphate 000000p
Enzyme
000000p (fructose 6)
ATP
p000000p (1,6 diphosphate)
enzyme
p000 000p
Next an enzyme rearranges glucose 6 phosphate to create fructose 6 phosphate
The phosphate from another atp is used to produce fructose 1,6 diphosphate
Note that 2 atp molecules have been invested up to this point
Next an enzyme splits the sugar into 2 three carbon molecules and the preparatory stage of glycolysis is completed.
2 molecules of ATP used so far. Created two 3 carbon units.
In this stage, 2 molecules of atp are used to phosphorylate a molecule of glucose. The resultant phosphorylated sugar is then split into two 3-carbon molecules.
Glucose enters the cell and is phosphorylated 000000
A molecule of atp is invested ATP
The product is glucose 6 phosphate 000000p
Enzyme
000000p (fructose 6)
ATP
p000000p (1,6 diphosphate)
enzyme
p000 000p
Next an enzyme rearranges glucose 6 phosphate to create fructose 6 phosphate
The phosphate from another atp is used to produce fructose 1,6 diphosphate
Note that 2 atp molecules have been invested up to this point
Next an enzyme splits the sugar into 2 three carbon molecules and the preparatory stage of glycolysis is completed.
2 molecules of ATP used so far. Created two 3 carbon units.
Exam 2 Various Notes
Exam 2
Various Notes
44 multiple choice
6 fill in the blanks/short answer. May be write the difference between 2 cycles, or describe a cycle.
Chapter 5
115
119
121-125
125-131
133-136
137-143
Chapter 6
Complete chapter
161-163 carbon and nitrogen
Know range, mesophiles etc
166 not enzymes
Know pic @ top and definition
167 not mechanisms
168 chemic def media
Fastidious
Complex
Omit anaerobic growth media and methods
171 selective and differential media
172, not 17
Chapter 13
387-393
400-410
411-412: latent and persistent viral infections
Various Notes
44 multiple choice
6 fill in the blanks/short answer. May be write the difference between 2 cycles, or describe a cycle.
Chapter 5
115
119
121-125
125-131
133-136
137-143
Chapter 6
Complete chapter
161-163 carbon and nitrogen
Know range, mesophiles etc
166 not enzymes
Know pic @ top and definition
167 not mechanisms
168 chemic def media
Fastidious
Complex
Omit anaerobic growth media and methods
171 selective and differential media
172, not 17
Chapter 13
387-393
400-410
411-412: latent and persistent viral infections
Chapter 13 Viruses, Viroids, and Prions
Chapter 13
Viruses, Viroids, and Prions
VIRUSES
I General Characteristics
A. Virus definition: viruses are obligatory intracellular parasites that require a living host in order to multiply. Latin for “poison”.
1. host range: the spectrum of host cells the virus can infect
2. bacteriophages (phages): viruses that infect bacteria.
B. A filterable agent: passes through filters that retain bacteria.
1. range in size from 20 to 1000 nanometers in length.
II Viral Structure
A. Viron: a complete, fully developed, infectious viral particle composed of nucleic acid and surrounded by a protein coat that protects it from the environment and is a vehicle of transmission from one host cell to another. A virion is an infectious stage. Protein and nucleic acid make a viron that is infectious.
B. Nucleic Acid: May either be DNA or RNA in a double stranded or single stranded form. Can be linear or several separate segments.
C. Capsid and envelope
1. capsid: protein coat made up of protein subunits (capsomeres)
2. envelope: may cover a capsid
a. made up of some combination of lipids, proteins, and carbohydrates.
b. may be covered with spikes (most envelopes are covered with spikes)
i. spikes: carbohydrate-protein complexes that project from the surface of the envelope
ii. can be used as a means of identification
iii. influenza virus is spiked to attach to red blood cells
i. hemagglutination: when viruses use spikes to adhere to red blood cells. Causes clumping. Useful for lab tests.
c. Nonenveloped virus: not covered by an envelope. (never have spikes.
D. General morphology
1. Helical viruses: resemble long rods. Their capsids a hollow cylinder with a helical structure. (tobacco mosaic virus or bacteriophage M13, ebola)
2. Polyhedral viruses(icosohedral): usually have a capsid in the shape of an icosahedron. (adenovirus and poliovirus)
3. Enveloped viruses: have their capsid covered by an envelope.
a. roughly spherical but pleomorphic
b. enveloped helical (influenza)
c. enveloped polyhedral (herpes simplex) with a capsule.
4. Complex viruses: (poxviruses ex: small pox and cow pox. *chicken pox is a herpes virus not a pox virus)
a. bacteriophage: looks like a spaceship
b. pox viruses: do not contain clearly identifiable capsids, but have several coats around the nucleic acid.
III Taxonomy of Viruses
A. family: -viridae
B. genus: -virus
C. viral species: a group of viruses sharing the same genetic information and ecological niche.
1. Specific epithets are not used
2. Designated by descriptive common names.
a. ex: HIV-1, HIV-2
D. Herpesviridae simplex virus. Human herpes virus 2
IV Isolation, Cultivation, and Identification of viruses (omit except for highlighted, just need to identify these three) Three ways of culturing:
A. Growing bacteriophages in the lab
B. Growing animal viruses in the lab. In live animals.
1. embryonated eggs
C. In cell cultures
1. monolayer: describes growth characteristics of normal cell cultures in glass or plastic containers.
2. cytopathic effects (CPE)
3. primary cell line: derived from tissue slices, tend to die out after only a few generations.
4. diploid cell line: developed from human embryos can be maintained for about 100 generations and are widedly used for culturing viruses that require a human host.
5. continuous cell line: transformed cancerous cells that can be maintained throught an indefinite number of generations. (aka immortal) HeLa.
C. Identification
V Viral Multiplication (omit)
A. Multiplication of bacteriophages
1. lytic cycle of T-even phages
a. phage lysozyme
b. eclipse period
c. maturation period
i. lyses
ii. releases
d. burst time
e. burst size: the number of bacteriophages produced by one bacterial host cell.
f. one-step growth experiment (13.11)
2. Lysogeny
a. prophage: phage DNA inserted into a host’s DNA
b. lysogenic (temperate) phages
c. lysogenic cells
d. phage conversion
e. specialized transduction
B. Multiplication of Animal Viruses
1. Attachment
a. endocytosis
b. receptor site
2. Entry
a. Non-enveloped virions:
i. direct penetration
b. Enveloped virions:
i. membrane fusion: a method of entry for enveloped viruses in which the viral envelope fuses with the plasma membrane and releases the capsid into the cell’s cytoplasm. (HIV)
ii. membrane fusion and endocytosis (together)
iii. pinocytosis: an active cellular process by which nutrients and other molecules are brought into a cell. The plasma membrane folds inward to form vesicles.
3. Uncoating: the separation of the viral nucleic acid from its protein coat once the virion is enclosed within the vesicle.
a. the capsid is digested when the cell attempts to digest the vesicle’s contents, or the nonenveloped capsid may be released into the cytoplasm of the host cell.
4. Biosynthesis of DNA containing viruses:
a. Adenoviridae (common cold)
b. Poxviridae (small pox and cow pox)
c. Herpesviridae
d. Papovaviridae (papillomas)
e. Hepadnaviridae (hepatitis)
5. Biosynthesis of RNA containing viruses
a. Picornaviridae (pico=small RNA) (polio)
b. Togaviridae (toga=covering)
c. Rhabdoviridae (rhabdo=rod) (rabies)
d. Reoviridae (respiratory, enteric, orphan)
e. Retroviridae
i. AIDS
ii. reverse transcriptase
iii. provirus
6. Maturation and release: the time during which the capsids and DNA of a phage, already formed, are now assembled into complete viruses.
a. Enveloped viruses released by
i. budding: the envelope develops around the capsid
b. Non-enveloped viruses released by:
i. lysis: cell bursts, viruses released, cell dies
VI Viruses and Cancer (omit)
A. Cancer
1. tumor
a. malignant
i. leukemias
ii. sarcoma
iii. adenocarcinoma
b. benign
B. Transformation of normal cells into tumor cells
1. oncogenes
2. transformation
3. oncogenic viruses (oncoviruses)
4. TSTA: tumor specific transplantation antigens (T-antigens)
C. DNA oncogenic viruses
D. RNA Oncogenic viruses
VII Latent Viral Infections
A. Latent infection: Virus remains in asymptomatic host cell for long periods. (inactive)
1. shingles, HIV, Herpes
2. often the viral DNA is integrated into the host DNA
3. This is termed a provirus.
4. Can be reactivated to cause disease.
VIII Persistent Viral Infections
A. Persistent (chronic) viral infection: a disease process that occurs gradually over a long period.
1. aka: slow viral infection
2. budding viruses often cause persistent infections
PRIONS (omit)
I Prion
A. proteinaceous infectious particle.
1. scrapie
2. mad cow disease
3. CJD
VIROIDS (omit)
I Viroid
A. Short pieces of naked RNA with no protein coat
B. causes plant disease
NOTES
Rickettsias and Chlamydias are bacteria NOT viruses. But all 3 are intracellular parasites.
Page 401 table 13.3
Biosynthesis of DNA containing viruses:
I. Following attachment, entry and uncoating, the viral DNA is released into the nucleus of the host cell.
II Transcription of a portion of the viral DNA occurs, then translation.
III Remaining late viral genes occur.
IV Synthesis of capsid proteins in the cytoplasm of the host cell.
V After the capsid proteins migrate into the nucleus of the host cell, maturation occurs. The viral DNA and capsid proteins assemble to form complete viruses.
VI The viruses are then released from the host cell.
Biosynthesis of RNA containing viruses:
Essential the same as DNA viruses.
Multiply in the host cell’s cytoplasm.
Wendell Stanley, an American chemist isolated tobacco mosaic virus in 1935.
Viruses are harder to kill because they use the host’s own cells. Killing the virus may kill the host.
*Know the 4 major virus types and an example of each one. See general morphology above.
Helical: Ebola
Polyhedral: Adenovirus, Polio
Enveloped : Influenza, Herpes simplex
Complex: Small pox, bacteriophages
*Know 5 stages of viral replication and what happens at each stage. Focus on animal viruses.
Page 400.
1. attachment
2. penetration
3. uncoating
4. synthesis and maturation
5. release or budding
All of our major viral diseases are enveloped. (HIV)
Capsules mutate, that is another reason that it is hard to treat viruses.
Provirus definition: Viral DNA integrated into a host cell chromosome. It never comes out of the chromosome.
Viruses use the least number of enzymes. Humans use many.
Recognize shape, picture of Ebola. A helical virus in our PowerPoint notes. Pg 390
Poxvirus’s synthesize DNA in the cytoplasm.
Herpes, papo, adeno, hepadna synthesize in the nucleus.
Reverse transcription: RNA to DNA
Transduction: the capacity for lysogenic bacteriophages to transfer a piece of cell DNA to the prophage of an adjacent cell.
See slides on Herpesvirus, Picornavirus, and Retrovirus Families. Pg 383 & 404
Herpesviridae:
Large
Enveloped icosehedral
DNA virus
Often establish latent infections
Picornaviridae:
Small
Non enveloped Icosohedral
RNA virus
Environmentally resistant
Many different types
Common cold, poliomyelitis, Hepatitis A
Retroviridae:
Enveloved icosohedral
RNA virus
Reverse transcriptase
HIV 1 & 2
Viruses, Viroids, and Prions
VIRUSES
I General Characteristics
A. Virus definition: viruses are obligatory intracellular parasites that require a living host in order to multiply. Latin for “poison”.
1. host range: the spectrum of host cells the virus can infect
2. bacteriophages (phages): viruses that infect bacteria.
B. A filterable agent: passes through filters that retain bacteria.
1. range in size from 20 to 1000 nanometers in length.
II Viral Structure
A. Viron: a complete, fully developed, infectious viral particle composed of nucleic acid and surrounded by a protein coat that protects it from the environment and is a vehicle of transmission from one host cell to another. A virion is an infectious stage. Protein and nucleic acid make a viron that is infectious.
B. Nucleic Acid: May either be DNA or RNA in a double stranded or single stranded form. Can be linear or several separate segments.
C. Capsid and envelope
1. capsid: protein coat made up of protein subunits (capsomeres)
2. envelope: may cover a capsid
a. made up of some combination of lipids, proteins, and carbohydrates.
b. may be covered with spikes (most envelopes are covered with spikes)
i. spikes: carbohydrate-protein complexes that project from the surface of the envelope
ii. can be used as a means of identification
iii. influenza virus is spiked to attach to red blood cells
i. hemagglutination: when viruses use spikes to adhere to red blood cells. Causes clumping. Useful for lab tests.
c. Nonenveloped virus: not covered by an envelope. (never have spikes.
D. General morphology
1. Helical viruses: resemble long rods. Their capsids a hollow cylinder with a helical structure. (tobacco mosaic virus or bacteriophage M13, ebola)
2. Polyhedral viruses(icosohedral): usually have a capsid in the shape of an icosahedron. (adenovirus and poliovirus)
3. Enveloped viruses: have their capsid covered by an envelope.
a. roughly spherical but pleomorphic
b. enveloped helical (influenza)
c. enveloped polyhedral (herpes simplex) with a capsule.
4. Complex viruses: (poxviruses ex: small pox and cow pox. *chicken pox is a herpes virus not a pox virus)
a. bacteriophage: looks like a spaceship
b. pox viruses: do not contain clearly identifiable capsids, but have several coats around the nucleic acid.
III Taxonomy of Viruses
A. family: -viridae
B. genus: -virus
C. viral species: a group of viruses sharing the same genetic information and ecological niche.
1. Specific epithets are not used
2. Designated by descriptive common names.
a. ex: HIV-1, HIV-2
D. Herpesviridae simplex virus. Human herpes virus 2
IV Isolation, Cultivation, and Identification of viruses (omit except for highlighted, just need to identify these three) Three ways of culturing:
A. Growing bacteriophages in the lab
B. Growing animal viruses in the lab. In live animals.
1. embryonated eggs
C. In cell cultures
1. monolayer: describes growth characteristics of normal cell cultures in glass or plastic containers.
2. cytopathic effects (CPE)
3. primary cell line: derived from tissue slices, tend to die out after only a few generations.
4. diploid cell line: developed from human embryos can be maintained for about 100 generations and are widedly used for culturing viruses that require a human host.
5. continuous cell line: transformed cancerous cells that can be maintained throught an indefinite number of generations. (aka immortal) HeLa.
C. Identification
V Viral Multiplication (omit)
A. Multiplication of bacteriophages
1. lytic cycle of T-even phages
a. phage lysozyme
b. eclipse period
c. maturation period
i. lyses
ii. releases
d. burst time
e. burst size: the number of bacteriophages produced by one bacterial host cell.
f. one-step growth experiment (13.11)
2. Lysogeny
a. prophage: phage DNA inserted into a host’s DNA
b. lysogenic (temperate) phages
c. lysogenic cells
d. phage conversion
e. specialized transduction
B. Multiplication of Animal Viruses
1. Attachment
a. endocytosis
b. receptor site
2. Entry
a. Non-enveloped virions:
i. direct penetration
b. Enveloped virions:
i. membrane fusion: a method of entry for enveloped viruses in which the viral envelope fuses with the plasma membrane and releases the capsid into the cell’s cytoplasm. (HIV)
ii. membrane fusion and endocytosis (together)
iii. pinocytosis: an active cellular process by which nutrients and other molecules are brought into a cell. The plasma membrane folds inward to form vesicles.
3. Uncoating: the separation of the viral nucleic acid from its protein coat once the virion is enclosed within the vesicle.
a. the capsid is digested when the cell attempts to digest the vesicle’s contents, or the nonenveloped capsid may be released into the cytoplasm of the host cell.
4. Biosynthesis of DNA containing viruses:
a. Adenoviridae (common cold)
b. Poxviridae (small pox and cow pox)
c. Herpesviridae
d. Papovaviridae (papillomas)
e. Hepadnaviridae (hepatitis)
5. Biosynthesis of RNA containing viruses
a. Picornaviridae (pico=small RNA) (polio)
b. Togaviridae (toga=covering)
c. Rhabdoviridae (rhabdo=rod) (rabies)
d. Reoviridae (respiratory, enteric, orphan)
e. Retroviridae
i. AIDS
ii. reverse transcriptase
iii. provirus
6. Maturation and release: the time during which the capsids and DNA of a phage, already formed, are now assembled into complete viruses.
a. Enveloped viruses released by
i. budding: the envelope develops around the capsid
b. Non-enveloped viruses released by:
i. lysis: cell bursts, viruses released, cell dies
VI Viruses and Cancer (omit)
A. Cancer
1. tumor
a. malignant
i. leukemias
ii. sarcoma
iii. adenocarcinoma
b. benign
B. Transformation of normal cells into tumor cells
1. oncogenes
2. transformation
3. oncogenic viruses (oncoviruses)
4. TSTA: tumor specific transplantation antigens (T-antigens)
C. DNA oncogenic viruses
D. RNA Oncogenic viruses
VII Latent Viral Infections
A. Latent infection: Virus remains in asymptomatic host cell for long periods. (inactive)
1. shingles, HIV, Herpes
2. often the viral DNA is integrated into the host DNA
3. This is termed a provirus.
4. Can be reactivated to cause disease.
VIII Persistent Viral Infections
A. Persistent (chronic) viral infection: a disease process that occurs gradually over a long period.
1. aka: slow viral infection
2. budding viruses often cause persistent infections
PRIONS (omit)
I Prion
A. proteinaceous infectious particle.
1. scrapie
2. mad cow disease
3. CJD
VIROIDS (omit)
I Viroid
A. Short pieces of naked RNA with no protein coat
B. causes plant disease
NOTES
Rickettsias and Chlamydias are bacteria NOT viruses. But all 3 are intracellular parasites.
Page 401 table 13.3
Biosynthesis of DNA containing viruses:
I. Following attachment, entry and uncoating, the viral DNA is released into the nucleus of the host cell.
II Transcription of a portion of the viral DNA occurs, then translation.
III Remaining late viral genes occur.
IV Synthesis of capsid proteins in the cytoplasm of the host cell.
V After the capsid proteins migrate into the nucleus of the host cell, maturation occurs. The viral DNA and capsid proteins assemble to form complete viruses.
VI The viruses are then released from the host cell.
Biosynthesis of RNA containing viruses:
Essential the same as DNA viruses.
Multiply in the host cell’s cytoplasm.
Wendell Stanley, an American chemist isolated tobacco mosaic virus in 1935.
Viruses are harder to kill because they use the host’s own cells. Killing the virus may kill the host.
*Know the 4 major virus types and an example of each one. See general morphology above.
Helical: Ebola
Polyhedral: Adenovirus, Polio
Enveloped : Influenza, Herpes simplex
Complex: Small pox, bacteriophages
*Know 5 stages of viral replication and what happens at each stage. Focus on animal viruses.
Page 400.
1. attachment
2. penetration
3. uncoating
4. synthesis and maturation
5. release or budding
All of our major viral diseases are enveloped. (HIV)
Capsules mutate, that is another reason that it is hard to treat viruses.
Provirus definition: Viral DNA integrated into a host cell chromosome. It never comes out of the chromosome.
Viruses use the least number of enzymes. Humans use many.
Recognize shape, picture of Ebola. A helical virus in our PowerPoint notes. Pg 390
Poxvirus’s synthesize DNA in the cytoplasm.
Herpes, papo, adeno, hepadna synthesize in the nucleus.
Reverse transcription: RNA to DNA
Transduction: the capacity for lysogenic bacteriophages to transfer a piece of cell DNA to the prophage of an adjacent cell.
See slides on Herpesvirus, Picornavirus, and Retrovirus Families. Pg 383 & 404
Herpesviridae:
Large
Enveloped icosehedral
DNA virus
Often establish latent infections
Picornaviridae:
Small
Non enveloped Icosohedral
RNA virus
Environmentally resistant
Many different types
Common cold, poliomyelitis, Hepatitis A
Retroviridae:
Enveloved icosohedral
RNA virus
Reverse transcriptase
HIV 1 & 2
Chapter 6 Microbial Growth
Chapter 6
Microbial Growth
I Physical requirements
A. Temperature *Know ranges
1. psychrophiles: an organism that grows best at about 15 C and does not grow at over 20 C.
a. A cold loving microbe.
b. psychrotrophs: an organism capable of growth between 0 and 30 C
1. moderate psychrotrophs
2. facultative psychrotrophs
3. mesophiles: an organism that grows between 10 and 50 C; 35
a. a moderate temperature loving microbe.
b. most common type of microbe
c. includes most common spoilage and disease organisms
4. thermophiles: an organism whose optimum growth temperature is between 50 and 60 C. 40 , 60, 70
a. A heat loving microbe.
b. create endospores
c. Important for compost piles
d. not considered a public health problem.
e. hyperthermophiles: an organism whose optimum growth temperature is at least 80 C. Also called an extreme thermophile. 65, 95, 110
i. Archaea
ii. need sulfur
5. Extremophile: a microorganism that lives in environmental extremes of temperature, acidity, alkalinity, salinity or pressure.
6. Minimum growth temperature: The lowest temperature at which a species can grow.
8. Maximum growth temperature: The highest temperature at which a species can grow.
9. Optimum growth temperature: the temperature at which a species grows best.
B. pH
1. most bacteria grow best near neutrality at 6.5 to 7.5 pH (Sushma 6.3 – 7.3)
2. acidophiles: a bacterium that grows below pH 4
3. buffer: peptones and amino acids which help maintain the proper pH in a growth medium. See page 162 last paragraph, left column.
C. Osmotic pressure
1. plasmolysis: loss of water from a cell in a hypertonic environment Shrinking of the cell.
a. best example: Staphylococcus aureus = halophile
2. Importance: the growth of the cell is inhibited as the plasma membrane pulls away from the cell wall. Thus, the addition of salts can be used to preserve food. The salt keeps the microbes from growing because of plasmolysis. The high salt or sugar concentrations draw water out of the cell and prevent their growth. Effects of osmotic pressure are roughly related to the number of dissolved molecules and ions in a volume of solution.
3. extreme halophiles (obligate halophiles): an organism that requires a high salt concentration for growth
a. add salt to the inoculating loop and medium if growing organisms from the ocean (halophiles)
4. facultative halophiles: a organism capable of growth in, but not requiring, salt. 2% to 15%
5. hypotonic solutions cause swelling of the cell or lysis
6. hypertonic solutions cause plasmolysis
II Chemical requirements
A. Carbon: besides water this is one of the most important microbial requirements for growth
1. structural backbone of living matter
2. needed for all organic compounds that make up a living cell
3. half the dry weight of a typical bacterial cell is carbon
4. don’t know if we need to know about chemo, photo trophs, etc.
B. Nitrogen
1. nitrogen fixation: the conversion of nitrogen (N2) into ammonia.
a. Symbiosis: the living together of two different organisms or populations
2. DNA and RNA synthesis requires nitrogen
3. ATP requires nitrogen
4. used to form the amino group of the amino acid of proteins
C. Sulfur
D. Phosphorus
E. Trace element: a chemical element required in small amounts for growth.
F. Oxygen see table 6.1 page 166
1. aerobes
a. obligate aerobes: an organism that requires molecular oxygen to live. (grow at top of tube)
b. catalase
c. microaerophile: an organism that grows best in an environment with less molecular oxygen than is normally found in air.
d. Microbes that use molecular O2 produce more energy from nutrients than microbes that do not use O2.
2. anaerobes
a. facultative anaerobes: an organism that can live with or without molecular oxygen. (mostly at top of tube, and throughout)
i. use fermentation or anaerobic respiration when O2 not available.
ii. E. coli
b. obligate anaerobes: an organism that does not use molecular oxygen and is killed in its presence. (bottom of tube)
i. Clostridium
c. aerotolerant anaerobes: cannot use oxygen for growth, but they tolerate fairly well. (throughout tube evenly)
d. microaerophiles: aerobic (requires O2) only grow in oxygen concentrations lower than that in air. (middle of tube)
3. toxic forms of O2
a. singlet: highly reactive molecular oxygen
b. superoxide free radical: a toxic form of oxygen formed during aerobic respiration.
i. superoxide dismutase: an enzyme that destroys superoxide free radicals
c. hydroxyl radical: a toxic form of oxygen formed in cytoplasm by ionizing radiation and aerobic respiration.
d. peroxide anion
i. Catalase: an enzyme that catalyzes the breakdown of hydrogen peroxide to water and oxygen.
G. Organic growth factor: an essential organic compound that an organism is unable to synthesize.
1. must be obtained from the environment (ex: vitamins for humans)
III Culture Media
A. culture medium: the nutrient material prepared for growth of microorganisms in a laboratory.
1. Sterile: free of microorganisms
B. culture: microorganisms that grow and multiply in a container of culture medium.
C. inoculum: a culture medium in which microorganisms are implanted
D. agar: a complex polysaccharide derived from a marine alga and used as a solidifying agent in culture media.
E. chemically defined medium: a culture medium in which the exact chemical composition is known
1. fastidious: organisms that require many growth factors pg. 168
a. Lactobacillus
2. for growth of chemoautotrophs and photoautotrophs
F. Complex media: a culture medium in which the exact chemical composition is not known. Undefined.
1. nutrient broth: A complex medium made of beef extract and peptone. (can be yeast extract)
2. nutrient agar: Nutrient broth containing agar.
3. Major components for growth are carbon and nitrogen. Nitrogen for protein synthesis.
4. for growth of most chemoteterotrophic organisms
G. anaerobic growth media and methods (told to omit this)
1. Reducing: growth of obligate anaerobes
H. special culture techniques (omit)
I. Selective and differential media
1. selective: A culture medium designed to suppress the growth of unwanted microorganisms and encourage the growth of desired ones
a. media that targets only one group
b. Example: add salt for Staphylococcus or increase pH to 5 for fungi.
2. differential: A solid culture medium that makes it easier to distinguish colonies of the desired organism.
a. pH indicators are added to the media.
i. Yellow = acid, pink = base
ii. example: blood agar with alpha, beta, gamma, etc. Differentiated between 3 different Staphylococcus.
J. Enrichment culture (media): a culture medium used for preliminary isolation
that favors the growth of a particular microorganism.
1. similar to selective media but designed to increase numbers of desired microbes to detectable levels.
K. Obtaining pure cultures
1. streak plate method: (omit)
2. Colony: a visible mass of microbial cells arising from one cell or from a group of the same microbes.
IV Preserving bacterial cultures
A. deep freezing: preservation of bacterial cultures at 250 C to 295 C
B. lyophilization: freeze drying. -54 through -72C. water removed by vacuum
V Growth of Bacterial cultures 6.11, 6.12, 6.14
A. bacterial division
1. binary fission
a. cell elongates and dna is replicated
b. cell wall and plasma membrane begin to grow inward
c. cross-wall forms completely around divide dna
d. cells separate
2. budding: asexual reproduction
3. reproductive spores
4. fragment
B. Generation Time
1. generation (doubling) time: the time required for a cell population to divide and double in number.
a. E. coli takes 20 minutes to double in number
b. logarithmically
c. arithmetically
C. Phases of growth (Bacterial growth curve: a graph plotting the growth of cells over a period of time.)
1. lag phase: the time interval in bacterial growth curve during which there is no growth. (0-1 hr)
a. The microbial population is undergoing a period of intense metabolic activity.
2. log phase: the period of bacterial growth or logarithmic increase in cell numbers; also called exponential growth phase. (1-4 hr)
a. microorganisms are particularly sensitive during this time as medications can interfere with an important step in the growth process and are thereby harmful to cells during this phase.
b. chemostat: an apparatus that allows this phase to last indefinitely. (continuous culture)
3. Stationary phase: the period in a bacterial growth curve when the number of cells dividing equals the number dying. (4-5 hr)
a. Not dormant during this time, using up all of the nutrients.
b. once nutrients are gone, they start death phase
4. Death phase (logarithmic decline): the period of logarithmic decrease in a bacterial population. (5-10 hr)
D. Measurement of microbial growth
1. Direct
a. plate count: a method of determining the number of bacteria in a sample by counting the number of CFU’s on a solid culture medium.
i. serial dilution: the process of diluting a sample several times
ii. colony forming units (CFU) b/c one bacterium or a chain of bacteria may start a colony.
iii. disadvantages: takes 24 hours for results
iv. advantages: measures number of viable cells
v. Pour plate method: a method of inoculating a solid nutrient medium by mixing bacteria in the melted medium and pouring the medium into a Petri dish to solidify. Disadvantages: melted agar may kill mo’s. Colonies that form best on surfaces are not forming well.
vi. Spread plate method: a plate count method in which inoculum is spread over the surface of a solid culture medium.
b. filtration: 100 ml of water are passed through a thin membrane filter whose pores are too small to allow bacteria to pass. The bacteria remaining on the filter and the filter are transferred to a Petri dish containing a pad soaked in liquid nutrient medium, where colonies arise from the bacteria on the filter’s surface.
i. for E. coli and Klebsiella (coliform bacteria – fecal pollution)
ii. where bacteria quantity is very small such as relatively pure bodies of water
c. most probable number (MPN)
d. direct microscopic count: enumeration of cells by observation through a microscope.
i. disadvantages: cannot tell if alive or dead, must count at least 5 chambers, a high number of cells must be available in order to be counted (10 million per mL)
ii. advantages: no incubation time required
iii. grided slides
iv. uses microscope with a counting chamber.
v. must count at least five chambers
vi. used for milk
2. Indirect
a. turbidity: the cloudiness of a suspension. Measure absorbance in a spectrophotometer. (colorimeter)
i. disadvantages: can’t use in the milk industry, can’t tell if alive or dead. More than 1 million cells per mL. Not a useful measure of contamination by liquids with a small amt of bacteria.
b. metabolic activity
c. dry weight
Definitions:
Minimal bactericidal concentration (MBC): The lowest concentration of chemotherapeutic agent that will kill test organisms.
Aerotolerant anaerobe: an organism that does not use molecular oxygen, but is not affected by its presence.
Peroxide anion: an oxygen anion consisting of two atoms of oxygen
Capnophile: an organism that grows best at relatively high CO2 concentrations
Minimal inhibitory concentration (MIC): the lowest concentration of a chemotherapeutic agent that will prevent growth of the test organisms.
Most probable number method (MPN): a statistical determination of the number of coliforms per 100 ml of water or 100 g of food.
Note on refrigeration: preservation of food based on the principle that microbial reproductive rates decrease at low temperatures. Psychrotrophs do not grow well in low temps, but over time they are slowly able to degrade food. A fridge will greatly slow the growth of most spoilage organisms and will entirely prevent the growth (not kill) of all but a few pathogenic bacteria.
Obligate: requires
Facultative: capable of growth in, but not requiring
Chemoautotrophs: an organism that uses an inorganic chemical as an energy source and CO2 as a carbon source
Photoautotrophs: an organism that uses light as its energy source and CO2 as its carbon source
Chemoheterotrophic: an organism that uses organic molecules as a source of carbon and energy.
autotroph: cell feeders. Carbon is the source. CO2 the end product. Sole carbon source.
heterotroph: saprophytes. Sources other than CO2. sodium citrate.
Microbial Growth
I Physical requirements
A. Temperature *Know ranges
1. psychrophiles: an organism that grows best at about 15 C and does not grow at over 20 C.
a. A cold loving microbe.
b. psychrotrophs: an organism capable of growth between 0 and 30 C
1. moderate psychrotrophs
2. facultative psychrotrophs
3. mesophiles: an organism that grows between 10 and 50 C; 35
a. a moderate temperature loving microbe.
b. most common type of microbe
c. includes most common spoilage and disease organisms
4. thermophiles: an organism whose optimum growth temperature is between 50 and 60 C. 40 , 60, 70
a. A heat loving microbe.
b. create endospores
c. Important for compost piles
d. not considered a public health problem.
e. hyperthermophiles: an organism whose optimum growth temperature is at least 80 C. Also called an extreme thermophile. 65, 95, 110
i. Archaea
ii. need sulfur
5. Extremophile: a microorganism that lives in environmental extremes of temperature, acidity, alkalinity, salinity or pressure.
6. Minimum growth temperature: The lowest temperature at which a species can grow.
8. Maximum growth temperature: The highest temperature at which a species can grow.
9. Optimum growth temperature: the temperature at which a species grows best.
B. pH
1. most bacteria grow best near neutrality at 6.5 to 7.5 pH (Sushma 6.3 – 7.3)
2. acidophiles: a bacterium that grows below pH 4
3. buffer: peptones and amino acids which help maintain the proper pH in a growth medium. See page 162 last paragraph, left column.
C. Osmotic pressure
1. plasmolysis: loss of water from a cell in a hypertonic environment Shrinking of the cell.
a. best example: Staphylococcus aureus = halophile
2. Importance: the growth of the cell is inhibited as the plasma membrane pulls away from the cell wall. Thus, the addition of salts can be used to preserve food. The salt keeps the microbes from growing because of plasmolysis. The high salt or sugar concentrations draw water out of the cell and prevent their growth. Effects of osmotic pressure are roughly related to the number of dissolved molecules and ions in a volume of solution.
3. extreme halophiles (obligate halophiles): an organism that requires a high salt concentration for growth
a. add salt to the inoculating loop and medium if growing organisms from the ocean (halophiles)
4. facultative halophiles: a organism capable of growth in, but not requiring, salt. 2% to 15%
5. hypotonic solutions cause swelling of the cell or lysis
6. hypertonic solutions cause plasmolysis
II Chemical requirements
A. Carbon: besides water this is one of the most important microbial requirements for growth
1. structural backbone of living matter
2. needed for all organic compounds that make up a living cell
3. half the dry weight of a typical bacterial cell is carbon
4. don’t know if we need to know about chemo, photo trophs, etc.
B. Nitrogen
1. nitrogen fixation: the conversion of nitrogen (N2) into ammonia.
a. Symbiosis: the living together of two different organisms or populations
2. DNA and RNA synthesis requires nitrogen
3. ATP requires nitrogen
4. used to form the amino group of the amino acid of proteins
C. Sulfur
D. Phosphorus
E. Trace element: a chemical element required in small amounts for growth.
F. Oxygen see table 6.1 page 166
1. aerobes
a. obligate aerobes: an organism that requires molecular oxygen to live. (grow at top of tube)
b. catalase
c. microaerophile: an organism that grows best in an environment with less molecular oxygen than is normally found in air.
d. Microbes that use molecular O2 produce more energy from nutrients than microbes that do not use O2.
2. anaerobes
a. facultative anaerobes: an organism that can live with or without molecular oxygen. (mostly at top of tube, and throughout)
i. use fermentation or anaerobic respiration when O2 not available.
ii. E. coli
b. obligate anaerobes: an organism that does not use molecular oxygen and is killed in its presence. (bottom of tube)
i. Clostridium
c. aerotolerant anaerobes: cannot use oxygen for growth, but they tolerate fairly well. (throughout tube evenly)
d. microaerophiles: aerobic (requires O2) only grow in oxygen concentrations lower than that in air. (middle of tube)
3. toxic forms of O2
a. singlet: highly reactive molecular oxygen
b. superoxide free radical: a toxic form of oxygen formed during aerobic respiration.
i. superoxide dismutase: an enzyme that destroys superoxide free radicals
c. hydroxyl radical: a toxic form of oxygen formed in cytoplasm by ionizing radiation and aerobic respiration.
d. peroxide anion
i. Catalase: an enzyme that catalyzes the breakdown of hydrogen peroxide to water and oxygen.
G. Organic growth factor: an essential organic compound that an organism is unable to synthesize.
1. must be obtained from the environment (ex: vitamins for humans)
III Culture Media
A. culture medium: the nutrient material prepared for growth of microorganisms in a laboratory.
1. Sterile: free of microorganisms
B. culture: microorganisms that grow and multiply in a container of culture medium.
C. inoculum: a culture medium in which microorganisms are implanted
D. agar: a complex polysaccharide derived from a marine alga and used as a solidifying agent in culture media.
E. chemically defined medium: a culture medium in which the exact chemical composition is known
1. fastidious: organisms that require many growth factors pg. 168
a. Lactobacillus
2. for growth of chemoautotrophs and photoautotrophs
F. Complex media: a culture medium in which the exact chemical composition is not known. Undefined.
1. nutrient broth: A complex medium made of beef extract and peptone. (can be yeast extract)
2. nutrient agar: Nutrient broth containing agar.
3. Major components for growth are carbon and nitrogen. Nitrogen for protein synthesis.
4. for growth of most chemoteterotrophic organisms
G. anaerobic growth media and methods (told to omit this)
1. Reducing: growth of obligate anaerobes
H. special culture techniques (omit)
I. Selective and differential media
1. selective: A culture medium designed to suppress the growth of unwanted microorganisms and encourage the growth of desired ones
a. media that targets only one group
b. Example: add salt for Staphylococcus or increase pH to 5 for fungi.
2. differential: A solid culture medium that makes it easier to distinguish colonies of the desired organism.
a. pH indicators are added to the media.
i. Yellow = acid, pink = base
ii. example: blood agar with alpha, beta, gamma, etc. Differentiated between 3 different Staphylococcus.
J. Enrichment culture (media): a culture medium used for preliminary isolation
that favors the growth of a particular microorganism.
1. similar to selective media but designed to increase numbers of desired microbes to detectable levels.
K. Obtaining pure cultures
1. streak plate method: (omit)
2. Colony: a visible mass of microbial cells arising from one cell or from a group of the same microbes.
IV Preserving bacterial cultures
A. deep freezing: preservation of bacterial cultures at 250 C to 295 C
B. lyophilization: freeze drying. -54 through -72C. water removed by vacuum
V Growth of Bacterial cultures 6.11, 6.12, 6.14
A. bacterial division
1. binary fission
a. cell elongates and dna is replicated
b. cell wall and plasma membrane begin to grow inward
c. cross-wall forms completely around divide dna
d. cells separate
2. budding: asexual reproduction
3. reproductive spores
4. fragment
B. Generation Time
1. generation (doubling) time: the time required for a cell population to divide and double in number.
a. E. coli takes 20 minutes to double in number
b. logarithmically
c. arithmetically
C. Phases of growth (Bacterial growth curve: a graph plotting the growth of cells over a period of time.)
1. lag phase: the time interval in bacterial growth curve during which there is no growth. (0-1 hr)
a. The microbial population is undergoing a period of intense metabolic activity.
2. log phase: the period of bacterial growth or logarithmic increase in cell numbers; also called exponential growth phase. (1-4 hr)
a. microorganisms are particularly sensitive during this time as medications can interfere with an important step in the growth process and are thereby harmful to cells during this phase.
b. chemostat: an apparatus that allows this phase to last indefinitely. (continuous culture)
3. Stationary phase: the period in a bacterial growth curve when the number of cells dividing equals the number dying. (4-5 hr)
a. Not dormant during this time, using up all of the nutrients.
b. once nutrients are gone, they start death phase
4. Death phase (logarithmic decline): the period of logarithmic decrease in a bacterial population. (5-10 hr)
D. Measurement of microbial growth
1. Direct
a. plate count: a method of determining the number of bacteria in a sample by counting the number of CFU’s on a solid culture medium.
i. serial dilution: the process of diluting a sample several times
ii. colony forming units (CFU) b/c one bacterium or a chain of bacteria may start a colony.
iii. disadvantages: takes 24 hours for results
iv. advantages: measures number of viable cells
v. Pour plate method: a method of inoculating a solid nutrient medium by mixing bacteria in the melted medium and pouring the medium into a Petri dish to solidify. Disadvantages: melted agar may kill mo’s. Colonies that form best on surfaces are not forming well.
vi. Spread plate method: a plate count method in which inoculum is spread over the surface of a solid culture medium.
b. filtration: 100 ml of water are passed through a thin membrane filter whose pores are too small to allow bacteria to pass. The bacteria remaining on the filter and the filter are transferred to a Petri dish containing a pad soaked in liquid nutrient medium, where colonies arise from the bacteria on the filter’s surface.
i. for E. coli and Klebsiella (coliform bacteria – fecal pollution)
ii. where bacteria quantity is very small such as relatively pure bodies of water
c. most probable number (MPN)
d. direct microscopic count: enumeration of cells by observation through a microscope.
i. disadvantages: cannot tell if alive or dead, must count at least 5 chambers, a high number of cells must be available in order to be counted (10 million per mL)
ii. advantages: no incubation time required
iii. grided slides
iv. uses microscope with a counting chamber.
v. must count at least five chambers
vi. used for milk
2. Indirect
a. turbidity: the cloudiness of a suspension. Measure absorbance in a spectrophotometer. (colorimeter)
i. disadvantages: can’t use in the milk industry, can’t tell if alive or dead. More than 1 million cells per mL. Not a useful measure of contamination by liquids with a small amt of bacteria.
b. metabolic activity
c. dry weight
Definitions:
Minimal bactericidal concentration (MBC): The lowest concentration of chemotherapeutic agent that will kill test organisms.
Aerotolerant anaerobe: an organism that does not use molecular oxygen, but is not affected by its presence.
Peroxide anion: an oxygen anion consisting of two atoms of oxygen
Capnophile: an organism that grows best at relatively high CO2 concentrations
Minimal inhibitory concentration (MIC): the lowest concentration of a chemotherapeutic agent that will prevent growth of the test organisms.
Most probable number method (MPN): a statistical determination of the number of coliforms per 100 ml of water or 100 g of food.
Note on refrigeration: preservation of food based on the principle that microbial reproductive rates decrease at low temperatures. Psychrotrophs do not grow well in low temps, but over time they are slowly able to degrade food. A fridge will greatly slow the growth of most spoilage organisms and will entirely prevent the growth (not kill) of all but a few pathogenic bacteria.
Obligate: requires
Facultative: capable of growth in, but not requiring
Chemoautotrophs: an organism that uses an inorganic chemical as an energy source and CO2 as a carbon source
Photoautotrophs: an organism that uses light as its energy source and CO2 as its carbon source
Chemoheterotrophic: an organism that uses organic molecules as a source of carbon and energy.
autotroph: cell feeders. Carbon is the source. CO2 the end product. Sole carbon source.
heterotroph: saprophytes. Sources other than CO2. sodium citrate.
Chapter 5 Microbial Metabolism
Chapter 5
Microbial Metabolism
Metabolism: the sum of all chemical reactions within a living organism.
A. anabolic: (biosynthetic reactions) The combination of simpler substances into complex substances. Requires energy.
B. catabolic: (degradative reactions) Releases energy stored in organic molecules. Yields energy. Energy liberated by catabolism is stored in energy rich bonds of adenosine triphosphate. (ATP)
I Enzymes
A. Collision Theory
B. Enzymes and Chemical Reactions
C. Enzyme specificity and efficiency
D. Naming enzymes
F. Factors influencing enzymatic activity
1. temperature
a. reaction rate
b. denaturation
2. pH
a. pH optimum
3. substrate concentration
a. saturated
G. Feedback inhibition
H. Ribozymes
II Energy production (Nutrient molecules have energy stored in bonds that can be concentrated into the “high energy” [or “unstable”] bonds of ATP)
A. Oxidation – Reduction
1. dehydrogenation
2. oxidation-reduction
a. NAD
b. NADP
B. Generation of ATP
1. phosphorylation
2. oxidative phosphorylation
3. electron transport chain
4. substrate-level phosphorylation
5. photophosphorylation
III Metabolic Pathways of Energy Production
A. metabolic pathway
IV Carbohydrate Catabolism *************
A. glycolysis:
1. Pyruvic acid
2.
B. Cellular respiration
1. aerobic
2. anaerobic
C. Krebs cycle
1. decarboxylation
D. Electron transport chain
1. flavoproteins
2. cytochromes
3. ubiquinones (coenzyme Q)
E. Chemiosmotic Mechanism of ATP Generation
1. chemiosmosis
F. Summary of Aerobic Respiration: Prokaryotes generate 38 molecules of ATP aerobically for each molecule of glucose; eukaryotes produce only 36.
G. Anaerobic respiration:
H. Fermentation
1. lactic acid
2. ethanol
3. homolactic
4. heterolactic
I. Lipid catabolism
1. beta oxidation
J. Protein catabolism
1. deaminated: NH2 removed
2. decarboxylated: COOH removed
V Photosynthesis
A. photosynthesis
1. photophosphorylation
2. cyclic photophosphorylation
3. noncyclic photophosphorylation
4. Calvin-Benson cycle
B. metabolic diversity among organisms
1. phototrophs
2. chemotrophs
3. autotrophs
4. heterotrophs
5. photoautotrophs
a. green sulfur bacteria
b. purple sulfur bacteria
c. anoxygenic
d. oxygenic
6. photoheterotrophs
a. green nonsulfur bacteria
b. purple nonsulfur bacteria
7. chemoautotrophs
8. chemoheterotrophs
a. saprophytes
b. parasites
VI Metabolic pathways of energy use
A. polysaccharides
B. lipids
C. amino acids
D. amination
E. transamination
F. nucleotides
1. purine
2. pyrimidine
VII Integration of metabolism
A. Amphibolic pathways
Microbial Metabolism
Metabolism: the sum of all chemical reactions within a living organism.
A. anabolic: (biosynthetic reactions) The combination of simpler substances into complex substances. Requires energy.
B. catabolic: (degradative reactions) Releases energy stored in organic molecules. Yields energy. Energy liberated by catabolism is stored in energy rich bonds of adenosine triphosphate. (ATP)
I Enzymes
A. Collision Theory
B. Enzymes and Chemical Reactions
C. Enzyme specificity and efficiency
D. Naming enzymes
F. Factors influencing enzymatic activity
1. temperature
a. reaction rate
b. denaturation
2. pH
a. pH optimum
3. substrate concentration
a. saturated
G. Feedback inhibition
H. Ribozymes
II Energy production (Nutrient molecules have energy stored in bonds that can be concentrated into the “high energy” [or “unstable”] bonds of ATP)
A. Oxidation – Reduction
1. dehydrogenation
2. oxidation-reduction
a. NAD
b. NADP
B. Generation of ATP
1. phosphorylation
2. oxidative phosphorylation
3. electron transport chain
4. substrate-level phosphorylation
5. photophosphorylation
III Metabolic Pathways of Energy Production
A. metabolic pathway
IV Carbohydrate Catabolism *************
A. glycolysis:
1. Pyruvic acid
2.
B. Cellular respiration
1. aerobic
2. anaerobic
C. Krebs cycle
1. decarboxylation
D. Electron transport chain
1. flavoproteins
2. cytochromes
3. ubiquinones (coenzyme Q)
E. Chemiosmotic Mechanism of ATP Generation
1. chemiosmosis
F. Summary of Aerobic Respiration: Prokaryotes generate 38 molecules of ATP aerobically for each molecule of glucose; eukaryotes produce only 36.
G. Anaerobic respiration:
H. Fermentation
1. lactic acid
2. ethanol
3. homolactic
4. heterolactic
I. Lipid catabolism
1. beta oxidation
J. Protein catabolism
1. deaminated: NH2 removed
2. decarboxylated: COOH removed
V Photosynthesis
A. photosynthesis
1. photophosphorylation
2. cyclic photophosphorylation
3. noncyclic photophosphorylation
4. Calvin-Benson cycle
B. metabolic diversity among organisms
1. phototrophs
2. chemotrophs
3. autotrophs
4. heterotrophs
5. photoautotrophs
a. green sulfur bacteria
b. purple sulfur bacteria
c. anoxygenic
d. oxygenic
6. photoheterotrophs
a. green nonsulfur bacteria
b. purple nonsulfur bacteria
7. chemoautotrophs
8. chemoheterotrophs
a. saprophytes
b. parasites
VI Metabolic pathways of energy use
A. polysaccharides
B. lipids
C. amino acids
D. amination
E. transamination
F. nucleotides
1. purine
2. pyrimidine
VII Integration of metabolism
A. Amphibolic pathways
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