Exam Review 4
Chapters 28
• Know the difference between resident, transient, and opportunistic members, and all other definitions in presentation
• Identify the portals through which pathogens invade the body.
• Know how extracellular enzymes, toxins, and antiphagocytic factors affect virulence. Know 3 types of toxins. Know list of steps of how organism infects cell
• Know non-specific lines of defense in the human body. (
• Explain non-specific lines of defense. Identify physical and chemical factors that inhibit pathogens.
Chapter 29-31
•Know the components of blood and their functions. Be able to ID the different types of white blood cells.
• Know the 2 types of macrophages
• Know the process of phagocytosis.
• Describe the role of eosinophils and NK cells in extracellular killing.
• Describe the complement system, including its classical and alternate pathways. How are they different? How are they the same?
• Know the process of inflammation.
• Define antigen
• What is the lymphatic system. .
• What are B lymphocytes.
• Describe the basic structure of an antibody (immunoglobulin) molecule.
• Contrast the structure and function of the five classes of immunoglobulins.
• Describe five functions of antibodies.
• Know the three types of T lymphocytes covered in lecture/text.
• What are cytokines.
• Describe the two classes of major histocompatibility complex (MHC) proteins.
• Describe antigen processing.
• Describe the functions of plasma cells and memory B cells.
• Describe cytotoxic T-cell action.
• Describe the establishment of B and T-cell memory.
• Describe the three types of vaccines.
• Compare active immunization versus passive immunization.
• Describe the four types of hypersensitivity.
• What cells and antibody are involved in allergic response.
• Describe immune complex disease.
• What is type IV hypersensitivity.
• Define autoimmunity.
Chapter 33
• Know the Keywords for Chapter 33
• Differentiate between the terms endemic, sporadic, epidemic, and pandemic.
• List and describe the five stages of the disease process.
• Define nosocomial infection.
Chapter 34
• Organisms Disease(s)
• Strep Strep throat, Rheumatic Fever, Toxic Shock, • Corynebacterium Diphtheria
• Bordetella Whooping Cough
• Mycobacterium TB and Leprosy
• Neisseria Gonorrhea and Meningitis
• Virus Measles
• Virus Mumps
• Rubella German Measles
• Varicella Chickenpox/Shingles
• Rhinovirus, Coronovirus Colds
• Influenza Flu
• Staphylococcus Skin Infections, Toxic Shock, Food-borne illness,
• Helicobacter Ulcers
• Hepatitis A-E
• Gonorrhea STI
• Treponema pallidum Syphilis
• Chlamydia STI and Blindness
• Herpes STI and Cold Sores
• Trichomonas STI
• HIV STI
Chapter 35
• Rabies Zoonosis
• Hantavirus Pulmonary Syndrome
• Rickettsia Rocky Mountain Spotted Fever, Typhus
• Ehrlichia Ehrlichiosis
• Borrelia Lyme Disease
• West Nile Meningitis, systemic infection
• Yersinia pestis Plague
• Fungi
• Clostridium tetanus Tetanus
Saturday, April 25, 2009
Chapter 33-Epidemiology
Principles of Epidemiology
Epidemiology
Epidemiology is the study of disease in populations.
Includes the study of the interactions of the pathogen with the host population.
Pathogens can be selective forces in the evolution of the host and visa versa.
Etiology
Study of the cause of disease
Germ theory of disease- disease caused by infections of pathogenic microorganisms
Robert Koch developed a set of postulates one must satisfy to prove a particular pathogen causes a particular disease
Infection
Chronic (long-term) infection
Lives in balance with the host
Minimum harm
Acute infections
Characterized by rapid onset and, often, rapid recovery.
Mortality: death
Morbidity: Infection/Disease
Symptoms
Symptoms: subjective characteristic of a disease. A symptom perceived by the patient but not by the examiner
Signs: objective characteristics of disease (verifiable).
Syndrome: group of symptoms and signs that collectively characterizes a particular disease
Asymtomatic or subclinal: No observable symptoms.
Pathogenicity
Pathogenicity: the ability of a microorganism to cause disease
Virulence: the degree of pathogenicity
Virulence Factors: traits that enable pathogens to cause infections.
The Vocabulary of Epidemiology
Prevalence: the proportion of diseased individuals in a population in a given time period.
Incidence: the number of cases of an individual disease in a population in a given time period.
Definitions
Endemic disease: constantly present at low incidence in a specific population.
Epidemic: an unusually high incidence of disease which occurs in a specific population.
Pandemic: A worldwide epidemic.
Reservoirs of Infection
Most pathogens cannot survive long outside of their host
Reservoirs of infection
pathogens that are maintained as a source of infection are termed reservoirs. 3 types of reservoirs:
Animal reservoir
Human carriers
Nonliving reservoir
Opportunistic Pathogens
Normal microbiota that cause disease
Conditions that provide opportunities for pathogens
Immune suppression
Changes in the normal microbiota- changes in relative abundance of normal microbiota may allow opportunity for a member to thrive and cause disease
Introduction of normal microbiota into unusual site in the body
Animal Reservoirs
Zoonoses- diseases that are naturally spread from their usual animal host to humans
Acquire zoonoses through various routes
Direct contact with animal or its waste
Eating animals
Bloodsucking arthropods
Humans are usually dead end host to zoonotic pathogens
Vectors
Biological vectors: hosts for the multiplication of the pathogen during some stage of the pathogen’s life. Plague: Rodents: Fleas
Mechanical: passively carry pathogens to new hosts (fomites)
Some pathogens exist in soil, water, or animals.
Others exist only in humans and are maintained solely by person-to-person contact.
Severe Acute Respiratory Syndrome
Zoonosis: an infection that occurs primarily in animals and is transferred to humans.
SARS-CoV: zoonotic virus that causes severe acute respiratory syndrome (SARS).
Person-to-person spread is by respiratory means.
Infectious Disease Transmission
Transmission: A pathogen spread directly from one host to another, or indirectly by living vectors or
Fomites: inanimate objects.
Vehicles: food and water.
AIDS
AIDS is one of the most studied disease pandemics.
AIDS will continue to be a major public health problem, especially in developing countries.
There is no effective cure or immunization to prevent AIDS
Nosocomial Infections
Infections acquired while in a health care facility
Types of nosocomial infections
Exogenous- pathogen acquired from the health care environment
Endogenous- pathogen arise from normal microbiota due to factors within the health care setting
Iatrogenic- results from modern medical procedures
Control of Nosocomial Infections
Involves precautions designed to reduce the factors that result in disease
Universal (Standard) Precautions instituted by the CDC to limit exposure to pathogens
Hand washing is the most effective way to reduce nosocomial infections
Control of Disease
Public health measures that play a major role in reduction of disease incidence:
Food and water purity regulations, vector control
immunization
quarantine
disease surveillance
pathogen eradication
Virulence-enhancing Mechanisms
Virulence-enhancing mechanisms:
include the mobile genetic elements-
bacteriophages
plasmids
transposons.
Biological Warfare and Biological Weapons
Biological warfare: the use of biological agents to incapacitate or kill a military or civilian population in an act of war or terrorism.
Mode of inoculation:common sources such as food and water are the most likely
Anthrax as a Biological Weapon
Bacillus anthracis has emerged as an important pathogen because of its use as a bioweapon.
Endospores are form of transmission
> 90% mortality rate in untreated individuals
Effective treatment relies on timely observation and diagnosis of symptoms
Epidemiology
Epidemiology is the study of disease in populations.
Includes the study of the interactions of the pathogen with the host population.
Pathogens can be selective forces in the evolution of the host and visa versa.
Etiology
Study of the cause of disease
Germ theory of disease- disease caused by infections of pathogenic microorganisms
Robert Koch developed a set of postulates one must satisfy to prove a particular pathogen causes a particular disease
Infection
Chronic (long-term) infection
Lives in balance with the host
Minimum harm
Acute infections
Characterized by rapid onset and, often, rapid recovery.
Mortality: death
Morbidity: Infection/Disease
Symptoms
Symptoms: subjective characteristic of a disease. A symptom perceived by the patient but not by the examiner
Signs: objective characteristics of disease (verifiable).
Syndrome: group of symptoms and signs that collectively characterizes a particular disease
Asymtomatic or subclinal: No observable symptoms.
Pathogenicity
Pathogenicity: the ability of a microorganism to cause disease
Virulence: the degree of pathogenicity
Virulence Factors: traits that enable pathogens to cause infections.
The Vocabulary of Epidemiology
Prevalence: the proportion of diseased individuals in a population in a given time period.
Incidence: the number of cases of an individual disease in a population in a given time period.
Definitions
Endemic disease: constantly present at low incidence in a specific population.
Epidemic: an unusually high incidence of disease which occurs in a specific population.
Pandemic: A worldwide epidemic.
Reservoirs of Infection
Most pathogens cannot survive long outside of their host
Reservoirs of infection
pathogens that are maintained as a source of infection are termed reservoirs. 3 types of reservoirs:
Animal reservoir
Human carriers
Nonliving reservoir
Opportunistic Pathogens
Normal microbiota that cause disease
Conditions that provide opportunities for pathogens
Immune suppression
Changes in the normal microbiota- changes in relative abundance of normal microbiota may allow opportunity for a member to thrive and cause disease
Introduction of normal microbiota into unusual site in the body
Animal Reservoirs
Zoonoses- diseases that are naturally spread from their usual animal host to humans
Acquire zoonoses through various routes
Direct contact with animal or its waste
Eating animals
Bloodsucking arthropods
Humans are usually dead end host to zoonotic pathogens
Vectors
Biological vectors: hosts for the multiplication of the pathogen during some stage of the pathogen’s life. Plague: Rodents: Fleas
Mechanical: passively carry pathogens to new hosts (fomites)
Some pathogens exist in soil, water, or animals.
Others exist only in humans and are maintained solely by person-to-person contact.
Severe Acute Respiratory Syndrome
Zoonosis: an infection that occurs primarily in animals and is transferred to humans.
SARS-CoV: zoonotic virus that causes severe acute respiratory syndrome (SARS).
Person-to-person spread is by respiratory means.
Infectious Disease Transmission
Transmission: A pathogen spread directly from one host to another, or indirectly by living vectors or
Fomites: inanimate objects.
Vehicles: food and water.
AIDS
AIDS is one of the most studied disease pandemics.
AIDS will continue to be a major public health problem, especially in developing countries.
There is no effective cure or immunization to prevent AIDS
Nosocomial Infections
Infections acquired while in a health care facility
Types of nosocomial infections
Exogenous- pathogen acquired from the health care environment
Endogenous- pathogen arise from normal microbiota due to factors within the health care setting
Iatrogenic- results from modern medical procedures
Control of Nosocomial Infections
Involves precautions designed to reduce the factors that result in disease
Universal (Standard) Precautions instituted by the CDC to limit exposure to pathogens
Hand washing is the most effective way to reduce nosocomial infections
Control of Disease
Public health measures that play a major role in reduction of disease incidence:
Food and water purity regulations, vector control
immunization
quarantine
disease surveillance
pathogen eradication
Virulence-enhancing Mechanisms
Virulence-enhancing mechanisms:
include the mobile genetic elements-
bacteriophages
plasmids
transposons.
Biological Warfare and Biological Weapons
Biological warfare: the use of biological agents to incapacitate or kill a military or civilian population in an act of war or terrorism.
Mode of inoculation:common sources such as food and water are the most likely
Anthrax as a Biological Weapon
Bacillus anthracis has emerged as an important pathogen because of its use as a bioweapon.
Endospores are form of transmission
> 90% mortality rate in untreated individuals
Effective treatment relies on timely observation and diagnosis of symptoms
Chapter 29,30,31-Immunology
Whole blood is composed of plasma, a liquid containing proteins ,other solutes and suspended cells.
Outside the body, plasma forms an insoluble clot. Plasma remains liquid only when an anticoagulant (anticlotting agent) is added.
After clotting, the remaining fluid, called serum, contains no cells or clotting proteins. Serum does, however, contain a high concentration of other proteins, including soluble antibody proteins, and is widely used in immunological investigations.
The Innate Immune Response
Not antibody mediated
Innate immunity is mediated by phagocytes.
Phagocytes recognize pathogen-associated molecular patterns (PAMPs) via a family of membrane-bound pattern-recognition molecules (PRMs)
Cytokines participate in cellular signals
Leukocytes
A variety of leukocytes participate in immune responses. Be able to name and recognize. Neutrophils, Eosinophils, Basophils, Monocytes/Macrophages, Lymphocytes
Phagocytosis-Ingestion and killing of invader by phagocytic cells (neutrophil)
Inflammation, Fever, and Septic Shock
Inflammation is characterized by pain, swelling (edema), redness (erythema), and heat. The inflammatory response is a normal and generally desirable outcome of an immune response.
Uncontrolled systemic inflammation, called septic shock, can lead to serious illness and death.
Adaptive Immune Response
In adaptive immunity, nonspecific phagocytes present antigen to specific T cells, triggering the production of effector T cells and antibodies. Immune T cells and antibodies react directly or indirectly to neutralize or destroy the antigen.
The adaptive immune response is characterized by
Specificity for the antigen
Memory-the ability to respond more vigorously when reexposed to the same antigen
Tolerance- the ability to discriminate self antigens from nonself antigens
B Cell Receptor (BCR)
B lymphocytes have multiple copies of a BCR type
BCR is identical to that of the secreted antibody for that particular cell
The randomly generated antibody variable region determines the BCR (not in response to antigens)
Each BCR is complementary to one antigen
Specific-Adaptive Immunity
Cell-mediated immunity leads to killing of pathogen-infected cells through recognition of pathogen antigens found on infected host cells.
Humoral immunity –killing of cells by antibodies and complement
Immunogens
Immunogens are foreign molecules that induce an immune response. Molecular size, complexity, and physical form are intrinsic properties of immunogens.
Antigens are molecules recognized by antibodies or by T-cell receptors (TCRs).
Presentation of Antigen to T Lymphocytes
T cells recognize antigens presented by antigen-presenting cells (APCs) or by pathogen-infected cells.
At the molecular level, TCRs bind peptide antigens presented by major histocompatibility complex (MHC) proteins. Class I MHC proteins are found on the surfaces of all nucleated cells.
Class II MHC proteins are found only on the surface of B lymphocytes, macrophages, and dendritic cells, all of which are APCs
Cytokines
These molecular interactions stimulate T cells to kill antigen-bearing cells or to produce cell-stimulating proteins known as cytokines.
Natural Killer Cells
Natural killer (NK) cells use the same effectors to kill virus-infected cells and tumors. However, NK cells do not require stimulation, nor do they exhibit memory. NK cells respond in the absence of MHC proteins.
T-Helper Cells: Activating the Immune Response
TH1 and TH2 cells play pivotal roles in cell-mediated and antibody-mediated immune responses.
Following the initial antigen exposure, each antigen-stimulated B cell multiplies and differentiates to form both antibody-secreting plasma cells and memory cells . TH1 inflammatory and TH2 helper cells each stimulate effector cells through the action of cytokines.
Antibody
The amino-terminal region is a variable domain, meaning that the amino acid sequence in this structural region differs in each different antibody.
The antigen-binding site is formed by the interaction of variable regions of heavy and light chains
Antibody Production
Antibody production is initiated by antigen contact with an antigen-specific B cell that processes the antigen and presents it to an antigen-specific TH2 cell.
The activated TH2 cell then signals the antigen-specific B cell to produce antibody.
Plasma Cells
Plasma cells are relatively short-lived (less than 1 week), but produce and secrete large amounts of IgM antibody in this primary antibody response.
Memory B Cells
The memory B cells generated by the initial exposure to antigen may live for years. If reexposure to the immunizing antigen occurs at a later time, memory cells need no T-cell activation; they quickly transform to plasma cells and begin producing IgG.
Secondary Antibody Response
Upon reexposure, the antibody titer rises rapidly to a level 10–100 times greater than the titer achieved following the first exposure. This rise in antibody titer is referred to as the secondary antibody response.
Complement, Antibodies, and Pathogen Destruction-Know complement and alternate pathways
Passive Immunity
Occurs naturally during pregnancy
IgG from mother crosses placenta
Infers protection to the baby
Occurs naturally as result of breast feeding
IgA antibodies in breast milk given to child
Artificial passive immunity involves transfer of antibodies produced by another person or animal
Can be used to prevent disease before or after likely exposure
Vaccines and Immunization
Attenuated vaccines
Weakened form of pathogen
Generally unable to cause disease
Strain replicates in vaccine recipient
Causes infection with undetectable or mild symptoms
Results in long lasting immunity
Vaccines and Immunization
Inactivated vaccines
Unable to replicate in vaccinated individual
Retains immunogenicity of infectious agent
Immunogenic not pathogenic
Inactivated vaccines fall into two categories
Whole agents
Contain killed organisms of inactivated virus
Fragments
Portions of organisms or agents including toxins proteins and cell wall components
Hypersensitivity Reactions
Hypersensitivity results when foreign antigens induce cellular or antibody immune responses, leading to host tissue damage.
Type I-IgE allergic response
Type II-Cytotoxic-complement and antibodies
Type III-Immune Complexes
Type IV-Cell-mediated-Delayed response
Type II (Cytotoxic) Hypersensitivity
Results when cells are destroyed by an immune response, often due to the combined activities of complement and antibodies
Component of many autoimmune diseases
2 examples
Destruction of blood cells following an incompatible blood transfusion
Destruction of fetal red blood cells in hemolytic disease of the newborn
Type III (Immune-Complex Mediated) Hypersensitivity
Due to the formation of antigen-antibody complexes, also called immune-complexes
Can cause systemic or localized reactions
Systemic
Systemic lupus erythematosus
Rhematoid arthritis
Localized
Hypersensitivity pneumonitis
Glomerulonephritis
Type IV Hypersensitivity
Type IV hypersensitivity, or delayed-type hypersensitivity (DTH), is cell-mediated hypersensitivity characterized by tissue damage due to inflammatory responses produced by TH1 inflammatory cells.
Autoimmune Diseases
Body usually recognizes self antigens
Destroys cells that would destroy self
Malfunction in immune recognition basis for autoimmunity
Autoimmune diseases may result from reactions to antigens that are similar to MHC self antigens
Autoimmunity may occur after tissue injury
Self antigens released from injured organ
Autoantibodies form and interact with injured tissues
Outside the body, plasma forms an insoluble clot. Plasma remains liquid only when an anticoagulant (anticlotting agent) is added.
After clotting, the remaining fluid, called serum, contains no cells or clotting proteins. Serum does, however, contain a high concentration of other proteins, including soluble antibody proteins, and is widely used in immunological investigations.
The Innate Immune Response
Not antibody mediated
Innate immunity is mediated by phagocytes.
Phagocytes recognize pathogen-associated molecular patterns (PAMPs) via a family of membrane-bound pattern-recognition molecules (PRMs)
Cytokines participate in cellular signals
Leukocytes
A variety of leukocytes participate in immune responses. Be able to name and recognize. Neutrophils, Eosinophils, Basophils, Monocytes/Macrophages, Lymphocytes
Phagocytosis-Ingestion and killing of invader by phagocytic cells (neutrophil)
Inflammation, Fever, and Septic Shock
Inflammation is characterized by pain, swelling (edema), redness (erythema), and heat. The inflammatory response is a normal and generally desirable outcome of an immune response.
Uncontrolled systemic inflammation, called septic shock, can lead to serious illness and death.
Adaptive Immune Response
In adaptive immunity, nonspecific phagocytes present antigen to specific T cells, triggering the production of effector T cells and antibodies. Immune T cells and antibodies react directly or indirectly to neutralize or destroy the antigen.
The adaptive immune response is characterized by
Specificity for the antigen
Memory-the ability to respond more vigorously when reexposed to the same antigen
Tolerance- the ability to discriminate self antigens from nonself antigens
B Cell Receptor (BCR)
B lymphocytes have multiple copies of a BCR type
BCR is identical to that of the secreted antibody for that particular cell
The randomly generated antibody variable region determines the BCR (not in response to antigens)
Each BCR is complementary to one antigen
Specific-Adaptive Immunity
Cell-mediated immunity leads to killing of pathogen-infected cells through recognition of pathogen antigens found on infected host cells.
Humoral immunity –killing of cells by antibodies and complement
Immunogens
Immunogens are foreign molecules that induce an immune response. Molecular size, complexity, and physical form are intrinsic properties of immunogens.
Antigens are molecules recognized by antibodies or by T-cell receptors (TCRs).
Presentation of Antigen to T Lymphocytes
T cells recognize antigens presented by antigen-presenting cells (APCs) or by pathogen-infected cells.
At the molecular level, TCRs bind peptide antigens presented by major histocompatibility complex (MHC) proteins. Class I MHC proteins are found on the surfaces of all nucleated cells.
Class II MHC proteins are found only on the surface of B lymphocytes, macrophages, and dendritic cells, all of which are APCs
Cytokines
These molecular interactions stimulate T cells to kill antigen-bearing cells or to produce cell-stimulating proteins known as cytokines.
Natural Killer Cells
Natural killer (NK) cells use the same effectors to kill virus-infected cells and tumors. However, NK cells do not require stimulation, nor do they exhibit memory. NK cells respond in the absence of MHC proteins.
T-Helper Cells: Activating the Immune Response
TH1 and TH2 cells play pivotal roles in cell-mediated and antibody-mediated immune responses.
Following the initial antigen exposure, each antigen-stimulated B cell multiplies and differentiates to form both antibody-secreting plasma cells and memory cells . TH1 inflammatory and TH2 helper cells each stimulate effector cells through the action of cytokines.
Antibody
The amino-terminal region is a variable domain, meaning that the amino acid sequence in this structural region differs in each different antibody.
The antigen-binding site is formed by the interaction of variable regions of heavy and light chains
Antibody Production
Antibody production is initiated by antigen contact with an antigen-specific B cell that processes the antigen and presents it to an antigen-specific TH2 cell.
The activated TH2 cell then signals the antigen-specific B cell to produce antibody.
Plasma Cells
Plasma cells are relatively short-lived (less than 1 week), but produce and secrete large amounts of IgM antibody in this primary antibody response.
Memory B Cells
The memory B cells generated by the initial exposure to antigen may live for years. If reexposure to the immunizing antigen occurs at a later time, memory cells need no T-cell activation; they quickly transform to plasma cells and begin producing IgG.
Secondary Antibody Response
Upon reexposure, the antibody titer rises rapidly to a level 10–100 times greater than the titer achieved following the first exposure. This rise in antibody titer is referred to as the secondary antibody response.
Complement, Antibodies, and Pathogen Destruction-Know complement and alternate pathways
Passive Immunity
Occurs naturally during pregnancy
IgG from mother crosses placenta
Infers protection to the baby
Occurs naturally as result of breast feeding
IgA antibodies in breast milk given to child
Artificial passive immunity involves transfer of antibodies produced by another person or animal
Can be used to prevent disease before or after likely exposure
Vaccines and Immunization
Attenuated vaccines
Weakened form of pathogen
Generally unable to cause disease
Strain replicates in vaccine recipient
Causes infection with undetectable or mild symptoms
Results in long lasting immunity
Vaccines and Immunization
Inactivated vaccines
Unable to replicate in vaccinated individual
Retains immunogenicity of infectious agent
Immunogenic not pathogenic
Inactivated vaccines fall into two categories
Whole agents
Contain killed organisms of inactivated virus
Fragments
Portions of organisms or agents including toxins proteins and cell wall components
Hypersensitivity Reactions
Hypersensitivity results when foreign antigens induce cellular or antibody immune responses, leading to host tissue damage.
Type I-IgE allergic response
Type II-Cytotoxic-complement and antibodies
Type III-Immune Complexes
Type IV-Cell-mediated-Delayed response
Type II (Cytotoxic) Hypersensitivity
Results when cells are destroyed by an immune response, often due to the combined activities of complement and antibodies
Component of many autoimmune diseases
2 examples
Destruction of blood cells following an incompatible blood transfusion
Destruction of fetal red blood cells in hemolytic disease of the newborn
Type III (Immune-Complex Mediated) Hypersensitivity
Due to the formation of antigen-antibody complexes, also called immune-complexes
Can cause systemic or localized reactions
Systemic
Systemic lupus erythematosus
Rhematoid arthritis
Localized
Hypersensitivity pneumonitis
Glomerulonephritis
Type IV Hypersensitivity
Type IV hypersensitivity, or delayed-type hypersensitivity (DTH), is cell-mediated hypersensitivity characterized by tissue damage due to inflammatory responses produced by TH1 inflammatory cells.
Autoimmune Diseases
Body usually recognizes self antigens
Destroys cells that would destroy self
Malfunction in immune recognition basis for autoimmunity
Autoimmune diseases may result from reactions to antigens that are similar to MHC self antigens
Autoimmunity may occur after tissue injury
Self antigens released from injured organ
Autoantibodies form and interact with injured tissues
Tuesday, April 21, 2009
Chapter 28 Host Microbe Interactions
Microbial Interactions with Humans
Pathogenicity
Pathogens: Microorganisms that cause harm.
Pathogenicity: the ability of a pathogen to cause disease.
Opportunistic : causes disease only in the absence of normal host resistance.
Host-parasite interactions: The ability of a microorganism to cause or prevent disease is influenced by complex
Wound
Normal Flora
Moist areas, especially around sweat glands, are colonized by gram-positive Bacteria and other members of the skin normal flora.
Environmental and host factors influence the quantity and quality of the normal skin microflora.
Normal Flora
Influences on composition:
Weather
Age
Personal Hygiene
Antibiotic Therapy
Transient
Colonizers/Residents
Bacteremia
Normal Flora
Chemoorganotrophs
Fermenters/Non-fermenters
Methanogenic
Pathogenesis
Exposure
Adherence
Invasion
Colonization/growth
Toxicity or Invasion
Damage and Disease
Dental Caries
Plaque microorganisms produce adherent substances.
Acid produced by microorganisms in plaque damages tooth surfaces, and dental caries result.
A variety of microorganisms contribute to caries and periodontal disease.
Intestinal Tract
The stomach is very acidic and is a barrier to most microbial growth.
The intestinal tract is slightly acidic to neutral and supports a diverse population of microorganisms in a variety of nutritional and environmental conditions.
Upper Respiratory Tract
In the upper respiratory tract (nasopharynx, oral cavity, and throat), microorganisms live in areas bathed with the secretions of the mucous membranes.
The normal lower respiratory tract (trachea, bronchi, and lungs) has no resident microflora, despite the large numbers of organisms potentially able to reach this region during breathing.
Adherence
Pathogen invasion starts at the site of adherence and may spread throughout the host via the circulatory systems.
Capsule: A polymer coat consisting of a dense, well-defined layer surrounding the cell.
Slime Layer: A loose network of polymer fibers extending outward from a cell
Fimbriae and pili
Colonization factors
Colonization and Growth
A pathogen must gain access to nutrients and appropriate growth conditions before colonization in host tissue can occur.
Organisms may grow locally at the site of invasion or may spread through the body.
If extensive bacterial growth in tissues occurs, some of the organisms are usually shed into the bloodstream in large numbers, a condition called bacteremia
Virulence
Virulence is determined by invasiveness, toxicity, and other factors produced by a pathogen.
Various pathogens produce proteins that damage the host cytoplasmic membrane, causing cell lysis and death.
Because the activity of these toxins is most easily detected with red blood cells (erythrocytes), they are called hemolysins.
In most pathogens, a number of factors contribute to virulence.
Attenuation is loss of virulence
Virulence
Pathogens produce a variety of enzymes that enhance virulence by breaking down or altering host tissue to provide access and nutrients.
Still other pathogen-produced virulence factors provide protection to the pathogen by interfering with normal host defense mechanisms. These factors enhance colonization and growth of the pathogen
Clots, enzymes, Toxins
Exotoxins
Toxicity: ability to casue disease by preformed toxin that inhibits or kills cells.
Invasiveness: ability of an organism to grow in host tissue
The most potent biological toxins are the exotoxins produced by microorganisms.
Each exotoxin affects specific host cells, causing specific impairment of a major host cell function.
Enterotoxins
Enterotoxins: toxins that specifically affect the small intestine, causing changes in intestinal permeability that lead to diarrhea.
Many enteric pathogens colonize the small intestine and produce A-B enterotoxins.
Food-poisoning bacteria often produce cytotoxins or superantigens.
Endotoxins
Endotoxins are lipopolysaccharides derived from the outer membrane of gram-negative Bacteria.
Released upon lysis of the Bacteria, endotoxins cause fever and other systemic toxic effects in the host.
Endotoxins are generally less toxic than exotoxins
Limulus amebocyte lysate assay
The presence of endotoxin detected by the Limulus amebocyte lysate assay indicates contamination of a substance by gram-negative Bacteria.
White blood cells of Horseshoe Crab
Debilitation
Conditions of age, stress, diet, general health, lifestyle, prior or concurrent disease, and genetic makeup may compromise the host's ability to resist infection.
Many hospital patients with noninfectious diseases (for example, cancer and heart disease) acquire microbial infections because they are compromised hosts.
Nosocomial Infections: hospital-acquired infections are called
Innate Resistance to Infection
Nonspecific physical, anatomical, and chemical barriers prevent colonization of the host by most pathogens.
Lack of these defenses results in susceptibility to infection and colonization by a pathogen.
Definitions
Parasites: organisms on or in a host that cause damage
Opportunistic pathogen: causes disease only in absence of normal resistance
Infection: when a microbe lives and grows in a host.
Disease: damage to the host that impairs body function.
Definitions
Mucous membranes: epithelial cells that line the lumen(opening) of various tissues
Mucus: glycoproteins
Digestive tract: stomach, small intestine (duodenum, ileum and jejunum)
Methane producers: H2 + CO2=CH4
Upper Respiratory tract: nasopharynx, oral cavity and throat
Lower Respiratory tract: trachea, bonchi and lungs
Ciliated epithelial cells: have cilia on surface/line upper respiratory tract
Pathogenicity
Pathogens: Microorganisms that cause harm.
Pathogenicity: the ability of a pathogen to cause disease.
Opportunistic : causes disease only in the absence of normal host resistance.
Host-parasite interactions: The ability of a microorganism to cause or prevent disease is influenced by complex
Wound
Normal Flora
Moist areas, especially around sweat glands, are colonized by gram-positive Bacteria and other members of the skin normal flora.
Environmental and host factors influence the quantity and quality of the normal skin microflora.
Normal Flora
Influences on composition:
Weather
Age
Personal Hygiene
Antibiotic Therapy
Transient
Colonizers/Residents
Bacteremia
Normal Flora
Chemoorganotrophs
Fermenters/Non-fermenters
Methanogenic
Pathogenesis
Exposure
Adherence
Invasion
Colonization/growth
Toxicity or Invasion
Damage and Disease
Dental Caries
Plaque microorganisms produce adherent substances.
Acid produced by microorganisms in plaque damages tooth surfaces, and dental caries result.
A variety of microorganisms contribute to caries and periodontal disease.
Intestinal Tract
The stomach is very acidic and is a barrier to most microbial growth.
The intestinal tract is slightly acidic to neutral and supports a diverse population of microorganisms in a variety of nutritional and environmental conditions.
Upper Respiratory Tract
In the upper respiratory tract (nasopharynx, oral cavity, and throat), microorganisms live in areas bathed with the secretions of the mucous membranes.
The normal lower respiratory tract (trachea, bronchi, and lungs) has no resident microflora, despite the large numbers of organisms potentially able to reach this region during breathing.
Adherence
Pathogen invasion starts at the site of adherence and may spread throughout the host via the circulatory systems.
Capsule: A polymer coat consisting of a dense, well-defined layer surrounding the cell.
Slime Layer: A loose network of polymer fibers extending outward from a cell
Fimbriae and pili
Colonization factors
Colonization and Growth
A pathogen must gain access to nutrients and appropriate growth conditions before colonization in host tissue can occur.
Organisms may grow locally at the site of invasion or may spread through the body.
If extensive bacterial growth in tissues occurs, some of the organisms are usually shed into the bloodstream in large numbers, a condition called bacteremia
Virulence
Virulence is determined by invasiveness, toxicity, and other factors produced by a pathogen.
Various pathogens produce proteins that damage the host cytoplasmic membrane, causing cell lysis and death.
Because the activity of these toxins is most easily detected with red blood cells (erythrocytes), they are called hemolysins.
In most pathogens, a number of factors contribute to virulence.
Attenuation is loss of virulence
Virulence
Pathogens produce a variety of enzymes that enhance virulence by breaking down or altering host tissue to provide access and nutrients.
Still other pathogen-produced virulence factors provide protection to the pathogen by interfering with normal host defense mechanisms. These factors enhance colonization and growth of the pathogen
Clots, enzymes, Toxins
Exotoxins
Toxicity: ability to casue disease by preformed toxin that inhibits or kills cells.
Invasiveness: ability of an organism to grow in host tissue
The most potent biological toxins are the exotoxins produced by microorganisms.
Each exotoxin affects specific host cells, causing specific impairment of a major host cell function.
Enterotoxins
Enterotoxins: toxins that specifically affect the small intestine, causing changes in intestinal permeability that lead to diarrhea.
Many enteric pathogens colonize the small intestine and produce A-B enterotoxins.
Food-poisoning bacteria often produce cytotoxins or superantigens.
Endotoxins
Endotoxins are lipopolysaccharides derived from the outer membrane of gram-negative Bacteria.
Released upon lysis of the Bacteria, endotoxins cause fever and other systemic toxic effects in the host.
Endotoxins are generally less toxic than exotoxins
Limulus amebocyte lysate assay
The presence of endotoxin detected by the Limulus amebocyte lysate assay indicates contamination of a substance by gram-negative Bacteria.
White blood cells of Horseshoe Crab
Debilitation
Conditions of age, stress, diet, general health, lifestyle, prior or concurrent disease, and genetic makeup may compromise the host's ability to resist infection.
Many hospital patients with noninfectious diseases (for example, cancer and heart disease) acquire microbial infections because they are compromised hosts.
Nosocomial Infections: hospital-acquired infections are called
Innate Resistance to Infection
Nonspecific physical, anatomical, and chemical barriers prevent colonization of the host by most pathogens.
Lack of these defenses results in susceptibility to infection and colonization by a pathogen.
Definitions
Parasites: organisms on or in a host that cause damage
Opportunistic pathogen: causes disease only in absence of normal resistance
Infection: when a microbe lives and grows in a host.
Disease: damage to the host that impairs body function.
Definitions
Mucous membranes: epithelial cells that line the lumen(opening) of various tissues
Mucus: glycoproteins
Digestive tract: stomach, small intestine (duodenum, ileum and jejunum)
Methane producers: H2 + CO2=CH4
Upper Respiratory tract: nasopharynx, oral cavity and throat
Lower Respiratory tract: trachea, bonchi and lungs
Ciliated epithelial cells: have cilia on surface/line upper respiratory tract
Wednesday, April 15, 2009
Homework assignments until end of term
Assignments are due as you finish them or by last lab or the term.
Tuesday, April 14, 2009
Unknown Info and Example
Unknown Paper: At least (minimum) one page on why you came to the conclusion that your organism was of a particular identification based on the reactions you did and did not get. Give the reactions that supported what it was and the reactions that told you what it was not. Also give brief description of the organism and the potential diseases it causes. The more complete the paper, the better the grade. DUE on last day of LAB CLASS.
Example
Proteus vulgaris is a rod-shaped, Gram negative bacterium that inhabits the intestinal tracts of humans and animals. It can be found in soil, water and faecal matter. It is grouped with the enterobacteriaceae and is an opportunistic pathogen of humans. It is known to cause urinary tract infections and wound infections.
When P. vulgaris is tested using standard biochemical assays, it is discovered that it provides a positive result for: sulfur reduction, urease production, tryptophan deaminase production, and indole production. I identified my unknown as P. vulgaris because it presented with a ……..and negative reactions for.
The optimal growing conditions of this organism is in a facultative anaerobic environment with an average temperature of about 23-37 degrees Celsius .
Example
Proteus vulgaris is a rod-shaped, Gram negative bacterium that inhabits the intestinal tracts of humans and animals. It can be found in soil, water and faecal matter. It is grouped with the enterobacteriaceae and is an opportunistic pathogen of humans. It is known to cause urinary tract infections and wound infections.
When P. vulgaris is tested using standard biochemical assays, it is discovered that it provides a positive result for: sulfur reduction, urease production, tryptophan deaminase production, and indole production. I identified my unknown as P. vulgaris because it presented with a ……..and negative reactions for.
The optimal growing conditions of this organism is in a facultative anaerobic environment with an average temperature of about 23-37 degrees Celsius .
Sunday, April 5, 2009
Exam Review 3: Exam April 21/ Review April 16
Exam 3 Review
Know the Following:
Prokaryotes/Archaea/Eukaryotes
Anoxic- anaerobic and much hotter than the present Earth
Abiotic non-living syntheses that set the stage for the origin of life.
The first life forms may have been self-replicating RNAs (RNA life).
Autotrophy-Use of CO2 for metabolite
Chemolithotrophic-use of inorganic compounds for metabolites
The phylogeny of microorganisms is their evolutionary relationships
SSU (small subunit) RNA sequencing is synonymous with 16S or 18S sequencing.
Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups. The amplification of the gene encoding 16S ribosomal RNA, sequencing it, and analyzing the sequence in reference to other sequences.
Bacterial taxonomy places emphasis on analyses of phenotypic properties of the organism.
Taxonomy: The science of classification.. Consists of two major subdisciplines, identification and nomenclature
Horizontal/Lateral Gene flow: Transduction, Conjugation, Transformation
Largest group: The Proteobacteria
Phenotypic
Gram stain
Morphology
Metabolism
Biochemical reactions
Genotypic
16rRNA:genes for 16S rRNA and related molecules are amplified, treated with one or more restriction enzymes, separated by electrophoresis and then probed with complementary rRNA.
The Archaea can be divided into four groups: the methanogens, the halophiles, the hyperthermophiles and the genus Thermoplasma
Found in: Soil, Mineral deposits, Aquatic areas, Volcanic areas, Animals
Archaeal cell walls do not contain muramic acid and D-amino acids, the building blocks of peptidoglycan.
The Archaeal membranes differ from Bacterial membranes in that they contain ether-linked lipids bonded to glycerol
The eukaryotic microbes: algae, fungi, slime moulds and protozoa.
Eukaryotic microorganisms differ from Bacteria and Archaea.
These differences include:
cell size
internal structure
genetic arrangement
evolutionary history.
Know Eukaryotic organelles
The endoplasmic reticulum
The golgi apparatus
Lysosomes
The peroxisome
3 energy organelles: mitochondria, hydrogenosome, chloroplast
The chloroplast is the site of photosynthetic energy production and CO2 fixation in eukaryotic phototrophs (algae).
Instead, chlorophyll and all other components needed for photosynthesis are located in a series of flattened membrane discs called thylakoids
Endosymbiosis
Microbiological Eukaryotes: Protozoa, flagellates, ciliates, sporozoa, fungi, slime moulds, algae
Genomics
Genes: A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism.
Genome: entire complement of genes
Sequencing: determining the total bases - that make up the DNA
Cloning vectors: A carrier, such as a bacterial plasmid or bacteriophage.
Genomic sequencing:
Reveals genes
Reveals functions of organism
Evolutionary history
Transcription and translation of genetic
information in the genome
An open reading frame or ORF is a portion of a prokaryotic organism's genome which contains a sequence of bases that could potentially encode a protein.
Bacterial Artificial Chromosomes
The use of the F plasmid to carry large amounts of chromosomal DNA
Yeast Artificial Chromosomes
Vectors which replicate in yeast like normal chromosomes but can carry large fragments of DNA
Shotgun techniques use random cloning and sequencing of relatively small genome fragments
Annotation: conversion of raw sequence data into a list of the genes present in the genome.
Bioinformatics: the use of computer tools to acquire, analyze, store, and access DNA and protein sequences
The purpose of genomics is to determine the number, sequence and function of genes in an organism
Gene families: genes that are related to other genes within the organism
Microarrays are genes or gene fragments attached to a solid support in a known pattern
Diversity
Photoautotrophs
Carbon source is carbon dioxide
Energy source is sunlight
Reduction of CO2 to organic compounds
Photoheterotrophs: Use organic carbon as their carbon source
Light-Dependent Reactions-Purpose: to produce ATP from light energy
Pigments:
Chlorophylls a and b
Bacteriochlorophyll
Carotenoids
Chlorophyll Pigment of oxygenic phototrophs.
Bacteriochlorophyll: the chlorophyll pigment of anoxygenic phototrophs.
Prokaryotes-No chloroplasts
Pigments are integrated into the internal membrane system
Carotenoids:
Most widespread accessory pigments
Hydrophobic pigments embedded in membrane
Photoprotective role: Quench toxic oxygen
Transfers energy to the reaction center which is used to make ATP
Antenna: chlorophyll molecules harvest light energy and transfer it on to reaction center of the pigments.
Exciton: mobile forms of energy (photons)
Pigments absorb light energy, give up electron, which enter electron transfer chains.
Water molecules split, ATP and NADH form, and oxygen is released
Anoxygenic Photosynthesis: Photosynthesis in which O2 is not produced
In oxygenic photosynthesis, water donates electrons to drive CO2 production, and oxygen is produced as a by-product.
Two separate light reaction center are involved, photosystems I and II.
Photosystem I resembles the system in anoxygenic photosynthesis. Photosystem II splits H2O to yield O2
Light Independent reactions:
Synthesis part of photosynthesis
Can proceed in the dark
Calvin-Benson cycle
Most phototrophic and other autotrophic organisms accomplish fixation of CO2 via the Calvin cycle, in which the enzyme ribulose bisphosphate carboxylase (RubisCO) plays a key role
Assimilative Metabolism: When an inorganic compound such as NO3, SO4 or CO2 is reduced for biosynthesis
Dissimilative metabolism : The reduced product is excreted into the environment
Phototrophic: obtains energy from light
Chemolithotrophic: oxidize inorganic compounds for energy(some facultative)
Chemoorganotrophic: obtains energy from the oxidation of organic compounds.
Autotrophic: use CO2 as nutrient source
Methanotrophs: use methane for energy
Decomposition: the breakdown of organisms, and the release of nutrients back into the environment.
Nitrogen Cycling: Plants rely on nitrogen from the soil and cannot acquire it from the gaseous nitrogen in the atmosphere.
Under anoxic conditions, organic matter is degraded principally to methane and carbon dioxide by syntrophic bacteria
The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.
Nitrogen fixation: the microbiological reduction of nitrogen to ammonia
Ammonia produced by nitrogen fixation or by ammonification from organic nitrogen compounds can be assimilated into organic matter.
Nitrification: The process by which ammonia is oxidized to nitrate
Denitrification: the microbial process by which nitrate is reduced to gaseous nitrogenous compounds (N2)
Methane is decomposed to ammonia
Utilization of sulfur and Iron as electron donors. Changes in soil or water content.
Microbial decomposition is the single largest source of CO2 released to the atmosphere.
Syntrophy: a metabolic process in which two or more organisms cooperate in the degradation of some compound.
The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.
Sulfate reduction is an important biogeochemical process
Bacterial reduction of ferric iron occurs in anoxic environments causes acid mine drainage.
Methods:
Enrichment culture: technique is a means of obtaining microorganisms from natural samples.
The Winogradsky column is a miniature anoxic ecosystem that can be used as a long-term source of bacteria for enrichment culture purposes
A pure culture can be obtained by conventional microbiological procedures, including streak plates, agar shakes, and dilution methods.
MPN: Most probable number: method of measuring the numbers of microbes in different media and conditions
DAPI is a general stain for identifying microorganisms in natural samples
The green fluorescent protein makes cells autofluorescent and is a means for tracking cells introduced into the environment.
Some stains can differentiate live versus dead cells-Viability stains.
Fluorescent antibodies that are specific for one or a small group of related cells can be prepared
Nucleic acid probes and PCR=highly specific
Microbial Ecology
Microbial ecology: how microorganisms interact with one another and their environment.
Guild: A microbial community which consist of metabolically related organisms.
Ecosystem: a community of organisms and their natural environment.
Biogeochemistry: the study of microbial energy transformations and biogeochemical processes that result in the recycling of elements.
Microenvironment: the place where the microorganism actually lives.
Oxic: the outer zones of a small soil particle containing O2
Anoxic: the center of a soil particle only a very short distance away which is completely anoxic (O2-free)
Biofilms are bacterial colonies, encased in slime, that form on surfaces. Biofilms can lead to damage as a result of the products excreted by the cells. Biofilm involves cell-to-cell communication (quorum sensing) COOPERATION
“A” horizon of soil : where most microbes exist.
The most important factor influencing microbial activity in surface soil is the availability of water
In deep soil (the subsurface environment), nutrient availability plays a major role.
Primary producers: Phototrophs in aquatic ecosystems
Marine waters have less nutrients for bacteria. Many use light to drive ATP synthesis.
Proteorhodopsin
Bacteria -oceanic surface waters
Archaea - deeper waters
Barophiles grow best under pressure.
Barotolerants can grow under elevated pressures but grow best at atmospheric pressures
Extreme barophiles: obtained from the greatest depths, require high pressure for growth.
Bioremediation: the cleanup of oil, toxic chemicals and pollutants by microbes.
Key microbial habitats on plants include the rhizoplane/rhizosphere(root) and the phyllosphere.
The plant provides the energy source needed by the root nodule bacteria, and the bacteria provide fixed nitrogen for the growth of the plant. The bacteria induce the formation of root nodules within which the nitrogen-fixing process occurs.
Know the Following:
Prokaryotes/Archaea/Eukaryotes
Anoxic- anaerobic and much hotter than the present Earth
Abiotic non-living syntheses that set the stage for the origin of life.
The first life forms may have been self-replicating RNAs (RNA life).
Autotrophy-Use of CO2 for metabolite
Chemolithotrophic-use of inorganic compounds for metabolites
The phylogeny of microorganisms is their evolutionary relationships
SSU (small subunit) RNA sequencing is synonymous with 16S or 18S sequencing.
Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups. The amplification of the gene encoding 16S ribosomal RNA, sequencing it, and analyzing the sequence in reference to other sequences.
Bacterial taxonomy places emphasis on analyses of phenotypic properties of the organism.
Taxonomy: The science of classification.. Consists of two major subdisciplines, identification and nomenclature
Horizontal/Lateral Gene flow: Transduction, Conjugation, Transformation
Largest group: The Proteobacteria
Phenotypic
Gram stain
Morphology
Metabolism
Biochemical reactions
Genotypic
16rRNA:genes for 16S rRNA and related molecules are amplified, treated with one or more restriction enzymes, separated by electrophoresis and then probed with complementary rRNA.
The Archaea can be divided into four groups: the methanogens, the halophiles, the hyperthermophiles and the genus Thermoplasma
Found in: Soil, Mineral deposits, Aquatic areas, Volcanic areas, Animals
Archaeal cell walls do not contain muramic acid and D-amino acids, the building blocks of peptidoglycan.
The Archaeal membranes differ from Bacterial membranes in that they contain ether-linked lipids bonded to glycerol
The eukaryotic microbes: algae, fungi, slime moulds and protozoa.
Eukaryotic microorganisms differ from Bacteria and Archaea.
These differences include:
cell size
internal structure
genetic arrangement
evolutionary history.
Know Eukaryotic organelles
The endoplasmic reticulum
The golgi apparatus
Lysosomes
The peroxisome
3 energy organelles: mitochondria, hydrogenosome, chloroplast
The chloroplast is the site of photosynthetic energy production and CO2 fixation in eukaryotic phototrophs (algae).
Instead, chlorophyll and all other components needed for photosynthesis are located in a series of flattened membrane discs called thylakoids
Endosymbiosis
Microbiological Eukaryotes: Protozoa, flagellates, ciliates, sporozoa, fungi, slime moulds, algae
Genomics
Genes: A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism.
Genome: entire complement of genes
Sequencing: determining the total bases - that make up the DNA
Cloning vectors: A carrier, such as a bacterial plasmid or bacteriophage.
Genomic sequencing:
Reveals genes
Reveals functions of organism
Evolutionary history
Transcription and translation of genetic
information in the genome
An open reading frame or ORF is a portion of a prokaryotic organism's genome which contains a sequence of bases that could potentially encode a protein.
Bacterial Artificial Chromosomes
The use of the F plasmid to carry large amounts of chromosomal DNA
Yeast Artificial Chromosomes
Vectors which replicate in yeast like normal chromosomes but can carry large fragments of DNA
Shotgun techniques use random cloning and sequencing of relatively small genome fragments
Annotation: conversion of raw sequence data into a list of the genes present in the genome.
Bioinformatics: the use of computer tools to acquire, analyze, store, and access DNA and protein sequences
The purpose of genomics is to determine the number, sequence and function of genes in an organism
Gene families: genes that are related to other genes within the organism
Microarrays are genes or gene fragments attached to a solid support in a known pattern
Diversity
Photoautotrophs
Carbon source is carbon dioxide
Energy source is sunlight
Reduction of CO2 to organic compounds
Photoheterotrophs: Use organic carbon as their carbon source
Light-Dependent Reactions-Purpose: to produce ATP from light energy
Pigments:
Chlorophylls a and b
Bacteriochlorophyll
Carotenoids
Chlorophyll Pigment of oxygenic phototrophs.
Bacteriochlorophyll: the chlorophyll pigment of anoxygenic phototrophs.
Prokaryotes-No chloroplasts
Pigments are integrated into the internal membrane system
Carotenoids:
Most widespread accessory pigments
Hydrophobic pigments embedded in membrane
Photoprotective role: Quench toxic oxygen
Transfers energy to the reaction center which is used to make ATP
Antenna: chlorophyll molecules harvest light energy and transfer it on to reaction center of the pigments.
Exciton: mobile forms of energy (photons)
Pigments absorb light energy, give up electron, which enter electron transfer chains.
Water molecules split, ATP and NADH form, and oxygen is released
Anoxygenic Photosynthesis: Photosynthesis in which O2 is not produced
In oxygenic photosynthesis, water donates electrons to drive CO2 production, and oxygen is produced as a by-product.
Two separate light reaction center are involved, photosystems I and II.
Photosystem I resembles the system in anoxygenic photosynthesis. Photosystem II splits H2O to yield O2
Light Independent reactions:
Synthesis part of photosynthesis
Can proceed in the dark
Calvin-Benson cycle
Most phototrophic and other autotrophic organisms accomplish fixation of CO2 via the Calvin cycle, in which the enzyme ribulose bisphosphate carboxylase (RubisCO) plays a key role
Assimilative Metabolism: When an inorganic compound such as NO3, SO4 or CO2 is reduced for biosynthesis
Dissimilative metabolism : The reduced product is excreted into the environment
Phototrophic: obtains energy from light
Chemolithotrophic: oxidize inorganic compounds for energy(some facultative)
Chemoorganotrophic: obtains energy from the oxidation of organic compounds.
Autotrophic: use CO2 as nutrient source
Methanotrophs: use methane for energy
Decomposition: the breakdown of organisms, and the release of nutrients back into the environment.
Nitrogen Cycling: Plants rely on nitrogen from the soil and cannot acquire it from the gaseous nitrogen in the atmosphere.
Under anoxic conditions, organic matter is degraded principally to methane and carbon dioxide by syntrophic bacteria
The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.
Nitrogen fixation: the microbiological reduction of nitrogen to ammonia
Ammonia produced by nitrogen fixation or by ammonification from organic nitrogen compounds can be assimilated into organic matter.
Nitrification: The process by which ammonia is oxidized to nitrate
Denitrification: the microbial process by which nitrate is reduced to gaseous nitrogenous compounds (N2)
Methane is decomposed to ammonia
Utilization of sulfur and Iron as electron donors. Changes in soil or water content.
Microbial decomposition is the single largest source of CO2 released to the atmosphere.
Syntrophy: a metabolic process in which two or more organisms cooperate in the degradation of some compound.
The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria.
Sulfate reduction is an important biogeochemical process
Bacterial reduction of ferric iron occurs in anoxic environments causes acid mine drainage.
Methods:
Enrichment culture: technique is a means of obtaining microorganisms from natural samples.
The Winogradsky column is a miniature anoxic ecosystem that can be used as a long-term source of bacteria for enrichment culture purposes
A pure culture can be obtained by conventional microbiological procedures, including streak plates, agar shakes, and dilution methods.
MPN: Most probable number: method of measuring the numbers of microbes in different media and conditions
DAPI is a general stain for identifying microorganisms in natural samples
The green fluorescent protein makes cells autofluorescent and is a means for tracking cells introduced into the environment.
Some stains can differentiate live versus dead cells-Viability stains.
Fluorescent antibodies that are specific for one or a small group of related cells can be prepared
Nucleic acid probes and PCR=highly specific
Microbial Ecology
Microbial ecology: how microorganisms interact with one another and their environment.
Guild: A microbial community which consist of metabolically related organisms.
Ecosystem: a community of organisms and their natural environment.
Biogeochemistry: the study of microbial energy transformations and biogeochemical processes that result in the recycling of elements.
Microenvironment: the place where the microorganism actually lives.
Oxic: the outer zones of a small soil particle containing O2
Anoxic: the center of a soil particle only a very short distance away which is completely anoxic (O2-free)
Biofilms are bacterial colonies, encased in slime, that form on surfaces. Biofilms can lead to damage as a result of the products excreted by the cells. Biofilm involves cell-to-cell communication (quorum sensing) COOPERATION
“A” horizon of soil : where most microbes exist.
The most important factor influencing microbial activity in surface soil is the availability of water
In deep soil (the subsurface environment), nutrient availability plays a major role.
Primary producers: Phototrophs in aquatic ecosystems
Marine waters have less nutrients for bacteria. Many use light to drive ATP synthesis.
Proteorhodopsin
Bacteria -oceanic surface waters
Archaea - deeper waters
Barophiles grow best under pressure.
Barotolerants can grow under elevated pressures but grow best at atmospheric pressures
Extreme barophiles: obtained from the greatest depths, require high pressure for growth.
Bioremediation: the cleanup of oil, toxic chemicals and pollutants by microbes.
Key microbial habitats on plants include the rhizoplane/rhizosphere(root) and the phyllosphere.
The plant provides the energy source needed by the root nodule bacteria, and the bacteria provide fixed nitrogen for the growth of the plant. The bacteria induce the formation of root nodules within which the nitrogen-fixing process occurs.
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