Microbiology Chapter 13-15

What is the difference between the innate immunity and the adaptive immunity?

*Innate immunity*- routine protection, non-specific and involves pattern recognition of specific molecules *Adaptive immunity*- develops through out life, antigens cause response, system produces antibodies to bind and can also destroy host cells

Contrast between acute and chronic inflammation

-Acute: Short term, mainly neutrophils; macrophages clean up damage by ingesting dead cells and debris. -Chronic: results in macrophages, giant cells accumulate, granulomas form

Give the composition and the function of the first line of defenses.

-All exposed surfaces are lined with epithelium. -Outside borders: skin -Inside borders: digestive tract and respiratory tract. -Function: to prevent microbial entry.

Contrast between macrophages and neutrophils

-Macrophages- kill by phagocytosis, are the everyday protectors, live for weeks or months -Neutrophils- kill in three different ways, can be compared to a SWAT team, have a short life span

What was the first virus to be discovered? What organism does it infect?

-Mosaic disease -Tobacco plants

Replication of RNA viruses

-Most are single stranded -Require virally encoded RNA polymerase (replicase)

What are the secretions of mucous membranes called? What is their function?

-Mucus -Mucus coating and movement of cilia trap and remove foreign particles and bacteria form internal surfaces of body

Contrast between a naïve lymphocyte and an activated lymphocyte

-Naïve lymphocyte: never encountered antigen. -Activated antigen: received specific signals, proliferates, and produces

List some protective outcomes of antibody-antigen binding

-Opsonization -Complement system activation -Immobilization and prevention of adherence -Cross linking(aggregation)-Antibody-dependent cellular cytotoxicity -Neutralization

Animal virus life cycle

1. Adsorption/Attachment 2. Penetration 3. Uncoating 4. Synthesis 5. Assembly 6. Release

What are the five steps of the lytic cycle?

1. Attachment- phage attaches to specific receptors of cell wall 2. Genome entry- the tail contracts and phage DNA is injected into the bacterial cell, leaving the coat outside 3. Synthesis- phage genome is transcribed and phage proteins synthesized. phage DNA is replicated, other virion components are made, and host DNA is degraded 4. Assembly- phage components are assembled into mature virions 5. Release- the bacterial lyses and many new infectious virions are released

What cytokine is responsible for the multiplication of leukocytes?

Colony-stimulating factors

Lysogens are immune to superinfection. Explain

The repressor that maintains the prophage in the integrated state will also bind to the operator on incoming phage DNA -Regulates the expression of genes that direct a lytic infection

Latent infections

The viral genome (provirus) remains silent in host cell; can reactivate -Chickenpox and shingles

What is the central dogma of biology?

The way information flows DNA-Transcription-RNA-Translation-Protein

Activated B cells will develop into what type of cells. What proteins do these cells produce?

They develop into plasma cells and produce y shaped proteins called antibodies

What are retroviruses? Give an example

(+) strand RNA genome and carry reverse transcriptase within the virion -HIV

Benign tumor

Non-cancerous and do not have the potential to spread (metastasize)

What molecules make up the envelop of some viruses?

Nucleic acid- DNA or RNA

Where (in the cell) do animal DNA viruses multiply?

Nucleus

Enteric virus

Oral-fecal route

Viruses are not considered organisms, explain why?

Outside of a cell they are inert, but inside a cell they direct activities that have a large impact on that cell

Define diapedesis

Phagocytes squeezing between cells of vessel

What method is used to study phages in the laboratory?

Plaque assay- used to quantitate phage particles in samples

Repressor

Prevents expression of the gene required for excision and is essential for maintaining a lysogenic state

Contrast between the antibody production during the primary response vs the secondary response

Primary: - Person may be sick, possibly seriously so, although immune system is actively responding -Some activated B cells continue dividing, others differentiate to form antibody-secreting plasma cells -Some B cells differentiate to form plasma cells • Plasma cells generate antibodies • Undergo apoptosis after a few days • Activated B cells continue proliferating and differentiating in presence of antigen, so titer steadily increases Secondary: -Additional exposure to antigen yields much faster secondary response. Significantly faster, more effective than primary • Pathogens usually eliminated before causing harm • Vaccination exploits this natural phenomenon -Memory B cells responsible: greater numbers present

What causes the prion diseases?

Prion proteins accumulate in the neural tissue -Neurons die -Tissues develop holes -Brain function deteriorates

What is apoptosis?

Programmed cell death

What is the function of Restriction-Modification systems? What two enzymes are used for this?

Protect bacteria from phage infection by quickly degrading incoming foreign bacteria -Restriction enzymes recognize short nucleotide sequences in foreign DNA then cuts the DNA -Modification enzymes methylate host sequences that are normally recognized by RE

Capsomere

Protein subunits

Respiratory virus

Respiratory route

How do you define the strandness of a virus?

Single or double-stranded

What organism was Ilya Metchinkoff studying when he discovered phagocytes?

Studied water fleas

Acute infections

Sudden onset of symptoms in a short duration of time -Flu

Reverse transcriptase

Synthesizes single DNA strands

How long does it take to get a primary response?

Takes 10-14 days for substantial antibody accumulation

Chronic infections

The *continuous* production of low levels of virus particles -Hepatitis

Lytic cycle

The destruction of the infected cell and its membrane

What is Crohn's disease?

The inability to tolerate harmless microbes (E. coli)

Burst size

The number of phage particles released- typically 200

Lysogenic cycle

The phage DNA exists within the cell without causing any damage -The integrated phage DNA is called prophage

Describe the 3 pathways activate that complement system?

-Alternative pathway: triggered when C3b binds to foreign cell surfaces (C3 unstable, so some C3b always present) -Lectin pathway: pattern recognition molecules (mannose-binding lectins, or MBLs) bind to mannose of microbial cells, interact with complement system components -Classical pathway: activated by antibodies bound to antigen, which interact with complement system

Contrast between apoptosis and pyroptosis

-Apoptosis is programmed cell death; does not trigger inflammatory response -Pyroptosis is if pattern recognition receptors are triggered, cell may undergo cell death with inflammatory response

Describe the structure of antibody molecules?

-Arms: Bind specific antigen; amino acid sequence of end of arms varies among antibodies, yields specificity -Stem: Functions as "red flag" to tag antigen, enlist other immune system components to eliminate

What are the three types of lymphocytes and what is their function?

-B cells and T cells- highly specific in recognition of antigens -Nature killer cells- destroys certain types of cells

Where do B cells develop? Where do T cells develop?

-B cells develop in bone marrow -T cells develop in thymus

List some examples of cytokines and give their functions

-Chemokines: chemotaxis of immune cells -Colony-stimulating factors (CSFs): multiplication and differentiation of leukocytes -Interferons (IFNs): control of viral infections, regulation of inflammatory response -Interleukins (ILs): produced by leukocytes; important in innate and adaptive immunity -Tumor necrosis factor (TNF): inflammation, apoptosis and act together to promote response

What are monocytes? What two cell types do they differentiate into? Where do you find them?

-Circulate in blood -Cell types develop as they leave the blood stream -Differentiate into Dendritic cells and Macrophages

What is the function of the complement system? What is the function of C3 convertase?

-Complement- proteins circulate in blood and bathing tissues and proteins named in order discovered: C1 through C9- can split into fragments -C3 splits to C3a and C3b -C3 convertase- splits C3

What are granulocytes? What are the three categories?

-Contain cytoplasmic granules filled with biologically active chemicals 1. Neutrophils- phagocytosis, trap and destroy microbial invaders 2. Eosinophils- releases chemicals to destroy eukaryotic parasites 3. Basophils- involved in allergic reactions, releases histamine

What are synonyms of cytotoxic T cells? Helper T cells?

-Cytotoxic T cells: killer t cell -Helper T cells: CD4 cell

What are the two biological molecules that make up most viruses?

-DNA or RNA -Protein

Describe the different structures of viral genomes

-DNA or RNA- never both -Genome is linear or circular

Replication of Reverse-Transcribing viruses

-Encode reverse transcriptase (makes DNA from RNA) -Reverse transcriptase synthesizes single DNA strands -Retroviruses have ss RNA genome (HIV)

Replication of DNA viruses

-Encode their own DNA polymerase -Follows the central dogma -Double strand and single strand

What are several ways taxonomy names viruses?

-End in suffix -viridae -Genus ends in -virus -Species name is often the name for the disease

What is the difference between enveloped virus and non-enveloped viruses?

-Enveloped virus- have a lipid bilayer outside the capsid -Non-enveloped virus- does not have an envelop (naked virus)

Which granulocytes are involved in allergic reactions?

-Eosinophils -Basophils

What two types of make up the skin? Why is it difficult for microbes to penetrate the skin?

-Epidermis- many layers of epithelial cells. outermost are dead, filled with keratin. repels water and maintains a dry environment. continually slough off along with and attached microbes. -Dermis- tightly woven fibrous connective tissue making hard to penetrate

What are three parts of the innate defenses?

-First line defenses- barriers blocking entry. Physical barriers are skin and mucous membrane. -Sensory systems: Sentinel cells use PRR (Pattern Recognition Receptors) in cell membrane and cytoplasm. Complement system. -Innate defense: Work to destroy invaders. Interferons, phagocytosis, and fever.

What method do enveloped viruses use to penetrate the bacterial membrane?

-Fusion with the host membrane -Endocytosis

What are the four types of leukocytes? (WBC)

-Granulocytes -Mononuclear Phagocytes -Dendritic Cells -Lymphocytes

List two viruses that cause cancers in humans

-HPV -Hepatitis B

Contrast between humoral immunity and cell-mediated immunity. Which type of leukocytes are involved in each?

-Humoral immunity: works to eliminate extracellular antigens, involves B lymphocytes (B cells) -Cell-mediated immunity (cellular immunity): deals with antigens residing within a host cell, involves T lymphocytes (T-cells)

List the four different viral shapes

-Icosahedral -Helical or rod -Complex -Spherical

What is the consequence of a ligand binding to a surface receptor?

-Induces response -The internal portion of the receptor is modified

Contrast between the innate immune response and the adaptive immune response

-Innate: always ready to respond to patterns that signify invasion or damage -Adaptive: improves as a result of exposure to microbial invaders or other foreign material (develops throughout life)

Integrase

-Inserts DNA at specific sites -Site specific recombination

What are MAMPs, PAMPs, and DAMPs? Where are they located?

-MAMPS: Microbe-Associated Molecular Patterns, found on all microbes -PAMPS: Pathogen-Associated Molecular Patterns, only found on pathogens -DAMPS: Danger-Associated Molecular Patterns, which indicate host cell damage (released by our cells) -Cell wall components (lipopolysaccharide, peptidoglycan, lipoteichoic acid, lipoproteins)

Describe the three major outcomes of activating the complement

-Opsonization: C3b binds to bacterial cells and foreign particles, promotes engulfment by phagocytes -Inflammatory Response: C5a attracts phagocytes to area; C3a /C5a increase permeability of blood vessels, induce mast cells to release cytokines -Lysis of Foreign Cells: Membrane attack complexes (MACs) formed by C5b, C6, C7, C8, and C9 molecules assembling in cell membranes of Gram negatives

What happens when a PRR bind recognizes a PAMP, DAMP or MAMP? (activation of PRRs)

-PAMPs, DAMPs are detected from microbes or tissue damage -Host cells release inflammatory mediators a. cytokines, b. histamine, c. TNF acts on liver to release acute-phase proteins

What are the sensor systems of the innate immunity? What do they do?

-PRRs and complement system -Detect damage and microbial invasion

List are some of the protein components of viruses and their functions

-Phages have tail fibers -Animal viruses have spikes (these allow viruses to attach)

What are the three mechanisms used my neutrophils to kill microbes?

-Phagocytosis -Degranulation -Neutrophil extracellular traps(NETS)

What happens to plasma cells after they produce antibodies?

-Plasma cells generate antibodies -Undergo apoptosis after a few days -Activated B cells continue proliferating and differentiating in presence of antigen, so titer steadily increases

Bacterial defense mechanisms against phages

-Preventing bacterial attachment -Restriction enzymes -Modification enzymes

Contrast between primary response and secondary response.

-Primary: first adaptive response to a particular antigen. The adaptive immune system "remembers" the mechanism that was effective against that specific antigen. -Secondary: if the same antigen is encountered later in life, there is a stronger antigen-specific adaptive immune response

What is a prion? Give two examples of diseases caused by prions

-Proteinaceous infectious agents -Composed solely of protein -Mad cow disease -Kuru

What are epitopes? Where do you find them?

-Recognized distinct regions.of macromolecules -Bacteria carry multitude of different epitopes

List the three categories of blood cells and give their function

-Red blood cells (erythrocytes) carry O2 -Platelets (from megakaryocytes) involved in clotting -White blood cells (leukocytes) important in host defenses

What are the five signs of inflammation? What process causes each of these signs?

-Redness (greater blood flow to the area) -Heat (greater blood flow to the area) -Pain (increase of fluid) -Swelling (increase of fluid) -Loss of function

Prophage

-Replicates with host chromosome -When the cell divides, this is passed onto the cell's progeny

List the different antimicrobial substances found in the human body and give their functions

-Salt: Accumulates from perspiration -Lysozyme: degrades peptidoglycan (tears, saliva, mucous) -Peroxidase enzymes: Break down hydrogen peroxide (saliva, milk, body tissues, and phagocytes) -Lactoferrin: Binds iron (saliva, mucous, phagocytes) -AMPS (antimicrobial peptides):Defensins form pores in microbial membranes and protect epithelium border

What is a viroid?

-Small, single-stranded RNA molecules that form a closed ring -Only infect plants

What is a fever and why is it an important host defense mechanism?

-Strong indicator of infectious disease, especially bacterial -Temperature-regulation center in brain normally holds at 37°C but raises during infection in response to pyrogens -Growth rates of bacteria optimized for 37°C typically drop sharply above optimum, allows more time for defenses -Enhances inflammatory response, phagocytic killing, multiplication of lymphocytes, release of attractants for neutrophils, production of interferons and antibodies, release of leukocytes from bone marrow.

What are the late proteins and when are they synthesized?

-Structural proteins (capsid and tail) -Produced towards the end of the cycle

List three requirements for cell communication and their functions

-Surface Receptors: Serve as "eyes" and "ears" of cell. Usually span membrane, connect outside to inside. Binding to specific ligand induces response -Cell adhesion molecules (CAM): Allow cells to adhere to other cells. Animal cells are bound together through cell-cell and cell-matrix adhesion molecules -Cytokines: "Voices" of cell. Produced by cells, diffuse to other cells. Bind to appropriate receptors to induce changes: growth, differentiation, movement, cell death

What is hematopoiesis? Where does it occur?

-The formation and development of blood cells -It occurs in hematopoietic stem cells found in bone marrow

What is the normal microbiota? Give examples

-The population of microorganisms that routinely grow on the body surfaces of a healthy organism •Propionibacterium degrade lipids, produce fatty acids •E. coli synthesizes colicins in intestinal tract (toxic to some bacteria) •Lactobacillus in vagina produce low pH (lactic acid)

What are PRRs? List the different types and their functions and locations

-They detect pathogen-associated molecular patterns (signs of microbial invasion) -Cell surface-toll-like receptors (TLR) -Endosomes/phagosomes-TLR -Any cell that do phagocytosis: -Neutrophils -Macrophages -Monocytes or DCs -Cytoplasm: -Nod-Like Receptors (NLR): Detect bacteria -RIG-Like Receptors (RLR): Detect viruses

What is the purpose of inflammation?

-To contain site of damage -Localize response -Eliminate invader -Restore tissue function

What is a synonym for white blood cells & red blood cells?

-WBC- leukocyte -RBC- erythrocyte

What could initiate phage induction?

-When phages escape the damage host -When protease destroys the repressor

Describe the 6 steps of phagocytosis

1. Chemotaxis: phagocytes recruited by chemoattractants (products of microorganisms, phospholipids from injured host cells, chemokines, C5a) 2. Recognition and Attachment: direct (receptors bind mannose) and indirect (binding to opsonins) 3. Engulfment: pseudopods surround, forms a phagosome 4. Phagosome Maturation and Phagolysosome Formation: endosomes fuse, lower pH; lysosomes bring enzymes 5. Destruction and Digestion: toxic ROS and nitric oxide produced; pH decreases; enzymes degrade; defensins damage membrane of invader; lactoferrin ties up iron 6. Exocytosis: vesicle fuses with cytoplasmic membrane, expels remains

What is the relative size of a virus?

10nm-800nm

Lysogen

A bacterium that carries phage DNA (a prophage) integrated into its genome

Nucleocapsid

A capsid together with nucleic acid

What is lysogenic conversion?

A change in the phenotype of a lysogen as a consequence of a specific prophage it carries

Virion

A complete virus in its inert non-replicating form

What is a tumor suppressor gene?

A gene that inhibits cell growth

What is a proto-oncogene?

A gene that stimulates cell growth

Capsid

A protein coat

What are antigens?

A toxin or other foreign substance that induces an immune response in the body, especially the production of antibodies

Replicase (RNA dependent RNA polymerase)

A virally encoded RNA polymerase

Vaccination relies on the abilities of which type of immunity?

Active immunity

What are some methods of preventing phage attachment used by some bacteria?

Alter or cover specific receptors on the cell surface

Tumor

An abnormal growth of tissue resulting from a malfunction in the normally highly regulated process of cell growth

Arbovirus

Are spread by arthropods

Matrix protein

Between the nucleocapsid and envelope

During the cold sore episode, in what tissue does the virus become latent?

Brain/spinal tissue

How are most animal viruses released?

Budding

Which two complement proteins are involved in the inflammatory response?

C3a and C5a

Which complement protein is involved in opsonization?

C3b

Malignant tumor

Cancerous and have the potential to spread (metastasize)

Zoonotic viruses

Causes zoonoses (passes from animal to human)

What microbes do you normally find in the digestive tract?

Clostridium difficile and E. coli

Persistent infections

Continue with or without symptoms for years -HIV

Where do you find surface receptors?

Cytoplasmic membrane

What are the functions of the three different T cells?

Cytotoxic T cells -TC induces apoptosis: proteases, cytotoxins (perforin) -Releases cytokines to alert other cells -CD8 Helper T cells -Activates macrophages- giant cells -Activate B cells -Produce cytokines to direct and support T cells -CD4 Natural Killer Cells Killing of infected cells tagged with antibodies Secrete IFN-gamma that stimulates macrophages

List the two types of T cells

Cytotoxic T cells and Helper T cells

What cells do you find in pus?

Dead neutrophils

What is the function of the T4 lyzozyme?

Degrades cell walls

What is the function of the nuclease?

Degrades the host cell's DNA

Protease

Destroys repressor and allows prophage to be excised- enters lytic cycle

Where do you find mucous membranes on the human body?

Digestive, respiratory, urinary and reproductive tracts

What disease was being studied when antibodies (antitoxins) were discovered?

Diphtheria

Contrast between an effector lymphocyte and a memory lymphocyte

Effector lymphocyte: short lived, primary response. Memory lymphocyte: secondary response

What method do non- enveloped viruses use to penetrate the bacterial membrane?

Endocytosis

What tissue lines all exposed surfaces of the human body?

Epithelium

Lytic (Virulent) phage

Exit the host at the end of the infection cycle by lysing the cell

Explain why the influenza virus always goes through antigenic drift

Mutations accumulate in genes encoding key viral surface proteins that are recognized by the immune by the immune system

What is a pyrogen?

Fever inducing substances

Temperate phage

Have the option of either directing a lytic infection or incorporating their DNA into the host cell genome

What is a synonym of antibodies?

Immunoglobulins

Viruses are said to be inert. Explain

Incapable of metabolism, replication, or motility

What cytokine is responsible for controlling viral infections?

Interferons

How can the excessive/misuse of antibiotics cause infection?

It can predispose a person to infections

What is the consequence of cytokines binding to appropriate receptors?

It induces changes in growth, differentiation, movement and cell death

What two microbes do you normally find in the vagina?

Lactobacillus and Candida albicans

What causes most tumors?

Mutations

Which granulocytes are involved in phagocytosis?

Neutrophils

Why do people get recurrent cold sores?

They get the HSV-1 virus which causes an acute infection in the mucosal epithelial cells. From there, the virus spreads to sensory nerve cells where it remains latent

What is the function of B and T cell receptors (BCR and TCR)

To recognize specific antigens

What do viruses produce during the synthesis step?

Viral particles in an infected cell

Bacteriophage

Viruses that infect bacteria