Microbiology Basics

Microbiology

• Microbiology studies microorganisms, which are extremely small life forms often too small for the naked eye to see.
• A pathogen is an invading microorganism that causes disease.
• Microorganisms are classified into two major types based on their cells.
• Eukaryotes have a nucleus and membrane-bound organelles.
• Prokaryotes do not have a nucleus or membrane-bound organelles.

Five Types of Microorganisms

• Bacteria and Archaea are prokaryotes.
• Fungi and Protists are eukaryotes.
• Viruses are not cells, they are acellular agents.

Bacteria

• Bacteria is a diverse group with many sizes (spherical, rod-shaped, spiral).
• Bacteria is located in many places, including soil, rock, oceans, snow, and organisms.
• Bacteria has many food sources, including starch, sunlight, sulfur, and iron.
• Some bacteria can cause diseases, such as strep throat, UTIs, pneumonia, tuberculosis, gonorrhea, bubonic plague, and tetanus.
• Bacterial infections are treated with antibiotics.

Archaea

• Archaea was once classified as bacteria, but it is now considered to be a distinct group.
• Archaea is extremely diverse, it is adapted to extreme environments such as extreme temperatures, acidity, and salinity.
• Archaea survives off a variety of unusual sources like H₂, sulfur, ammonia, metal ions, and salt.
• Archaea is not known to be pathogenic.

Fungi

• Fungi range from single-celled microorganisms to massive structures, such as yeast, mushrooms, mould, and mildew.
• Fungi does not often cause severe infection in humans unless the immune system is suppressed or normal bacteria are suppressed after antibiotics.
• Fungi causes diseases such as athlete's foot, ringworm, and vaginal yeast infections.
• Fungal infections are treated with antifungal drugs, either orally or topically.

Protists

• Protists are a diverse group including any eukaryote that is not an animal, plant, or fungus.
• Some protists are helpful, like photosynthetic plankton.
• Some protists are parasites, organisms that live on or in another organism and get food at the host's expense.
• Protists cause diseases such as malaria, dysentery, and toxoplasmosis.
• Diseases caused by protists are treated with antiparasitic medications and medications to help relieve symptoms.

Viruses

• Viruses are acellular agents (non-living) which cannot reproduce on their own.
• Viruses are made of nucleic acid (DNA or RNA), surrounded by a capsid called a protein coat.
• Viruses infect other cells and use host cells to make copies of themselves.

How Viruses Invade A Cell

• First, a virus enters a cell.
• Next, the cell begins to strip off the virus's outer coat of protein.
• The nucleic acid in the center of the virus gets released.
• Nucleic acid gets into the cell's chemical manufacturing system.
• The cell ignores its own chemical needs and switches to making new viruses.
• The cell is sometimes destroyed in the process; many of the new viruses are released to infect other cells.

Diseases Caused by Viruses

• Common viral diseases include the common cold, influenza, chicken pox, shingles, and genital herpes.
• More serious viral diseases include meningitis, hepatitis, HPV, and HIV.
• Most viral infections require waiting until the immune system fights off the virus, but symptoms can be treated using antiviral medications as needed.
• Vaccines are the best way to avoid viral infections.

Communicability

• Communicability is the ability of a disease to be passed from one person to another.
• Microorganisms can invade the body through openings with mucous membranes, such as the mouth, eyes, nose, and urogenital openings.
• Microorganisms can invade the body through wounds that breach the skin barrier.

Methods of Infection

• One-to-one contact infections are Direct and Indirect.
• Direct contact involves microorganisms passing from body surface to body surface.
• Direct contact could include touching (shaking hands, kissing, hugging, high-fiving, etc.).
• Indirect contact involves microorganisms being deposited onto an object and shared.
• Indirect contact could include not washing hands and sharing contaminated surfaces or objects.
• Droplet can include contact through air, with sizable transmission of mucous or saliva contaminated with microorganism (e.g. sneezing, coughing).
• Non-contact infections are Airborne, Vehicle, and Vector-borne
• Airborne infections involve the transmission of microorganisms via airborne particles (e.g. ventilation system)
• Vehicle infections occur when a single contaminated source spreads the microorganism (e.g. food recalls, food-borne outbreaks, and medical equipment)
• Vector-borne infections include transmission of microorganisms by an insect or animal, where the animal is called the vector (e.g. mosquitoes transmitting lime disease or malaria)

The Lymphatic System

• Consists of two semi-independent parts: lymphatic vessels and lymphoid tissues and organs.
• Lymphatic vessels are similar to blood vessels and carry fluid (lymph).
• Lymphatic vessels transport lymph into the blood.
• Lymphoid tissues and organs play roles in body defense and resistance to disease.

Lymph

• Lymph is "clear water".
• Lymph is the fluid that accumulates during blood and tissue exchanges in spaces between tissue cells (interstitial fluid).
• Lymphatic vessels carry excess interstitial fluid back to the blood.
• Interstitial fluid is called lymph upon entering the lymphatic vessels.

Properties of Lymphatic Vessels

• The lymphatic system has a one-way system that moves lymph toward the heart.
• The lymphatic system does not use a pump, It relies on skeletal muscle.
• Lymph moves using the milking action of skeletal muscle.
• Lymph moves using peristalsis of smooth muscle in vessel walls, which plays a role in guiding the fluid.
• Lymph capillaries collect lymph from tissues through minivalves.
• Lymph moves through larger lymphatic collecting vessels.
• Lymph passes through lymph nodes along the way.

Lymphatic Vessels Types

• Right Lymphatic Duct drains the right arm and right side of head and thorax.
• Thoracic Duct drains rest of the body.
• Both ducts empty into subclavian veins (Right and Left).

Lymph Materials

• Useful materials returned to the blood in lymph include water, white blood cells, and proteins.
• Protein is something that the body needs.
• Harmful materials that enter lymph vessels include cell debris, bacteria, viruses, and cancer cells.

Lymphatic system (again)

• Lymphatic vessels transport fluids (lymph) back to blood.
• Lymphoid tissues and organs play essential roles in body defense and resistance to disease.

Leukocytes (White Blood Cells)

• Leukocytes are crucial in the body's defense against disease.
• Leukocytes are an army against bacteria, viruses, parasites, and tumor cells.
• Leukocytes are able to move into and out of blood vessels via diapedesis.
• There are two groups of leukocytes that are called granulocytes and agranulocytes.

Granulocytes vs. Agranulocytes

• Neutrophils phagocytize sites of infection to neutralize targets.
• Eosinophils respond to allergens.
• Basophils initiate inflammation.
• Lymphocytes generate immune response.
• Monocytes fight chronic infection and become macrophages outside of blood.

Lymphoid Tissues and Organs

• Lymph Nodes
• Spleen
• Thymus Gland
• Tonsils
• Peyer's Patches
• Appendix

Lymph Nodes

• Lymph Nodes are found in clusters along lymphatic vessels.
• Lymph Nodes filter lymph before it is returned to blood.
• Lymph Nodes contain defense cells.
• Macrophages engulf and destroy foreign substances (phagocytosis).
• Lymphocytes provide immune response to foreign substances.

Lymph Node Structure

• Most are kidney-shaped.
• They are less than 1 inch long.
• Cortex is the outer part with follicles (collections of lymphocytes).
• Medulla is the inner part and contains phagocytic macrophages.

Flow of Lymph Through Nodes

• Lymph enters convex side through afferent lymphatic collecting vessels and then flows through sinuses.
• Lymph exits through efferent lymphatic collecting vessels.
• Fewer efferent than afferent vessels make the flow slowed down so nodes can filter and clean lymph.

Other Lymphoid Organs

• Other organs contributes to lymphatic function.
• Spleen is a lymphoid organ.
• Thymus Gland is a lymphoid organ.
• Tonsils are lymphoid organs.
• Peyer's patches are lymphoid organs.
• Appendix is a lymphoid organ.

The Spleen

• The spleen is located on the left side of the abdomen.
• The spleen filters blood of bacteria, viruses, and debris.
• The spleen destroys worn out blood cells.
• The spleen acts as a blood reservoir.
• The spleen also forms blood cells in a fetus.

The Thymus

• The thymus is located low in the throat, behind the sternum.
• The thymus functions at peak levels only during childhood.
• The thymus produces thymosin to program lymphocytes (white blood cells).

Tonsils

• Tonsils are small masses of lymphoid tissue around the pharynx.
• Tonsils have macrophages (eat stuff) to trap and destroy bacteria, as well as other foreign materials entering throat.
• Palatine tonsils are 2 at the back of the oral cavity, on sides.
• Lingual tonsil is at the back of the tongue.
• Pharyngeal tonsil (adenoid) is at the roof of nasopharynx.
• Tubal tonsils are at the opening of the auditory tubes into pharynx.

Peyer's Patches

• Peyer's patches are found in the wall of the distal part of small intestine.
• Peyer's patches resemble tonsils in structure.
• Peyer's patches have macrophages to trap and destroy foreign invaders in the intestine.

Appendix

• The appendix is found hanging from the cecum.
• Tissue in appendix wall is similar to Peyer's patches.
• The appendix has macrophages to trap and destroy foreign invaders in the intestine.

Body Defenses

• The body is constantly in contact with microorganisms (e.g. bacteria, fungi, and viruses).
• There are two massive defense systems against these foreign invaders: Innate (Nonspecific) defense system & Adaptive (Specific) defense system.

Innate Defense System

• Innate (Nonspecific) defense system responds immediately to protect body from all foreign substances (whatever they are).
• The point of the Innate Defense System is to lower the workload of Adaptive (Specific) Defense System by preventing entry and spread.
• Includes Surface membrane barriers and Cellular & chemical defenses (2nd line of defense).

Surface Membrane Barriers

• Skin and mucous membranes serve as the first line of defense.
• Intact skin is a physical barrier to foreign materials.
• The pH of skin is acidic to inhibit bacterial growth.
• Sebum (oil) is toxic to bacteria.
• Mucous traps microorganisms in digestive and respiratory pathways.
• Vaginal secretions are acidic.
• Saliva and lacrimal fluid contain lysozyme, which kills bacteria.

Cellular & Chemical Defenses

• Cellular Defenses: Phagocytes & Natural Killer Cells
• Chemical Defenses: Inflammatory response, Complement, Interferon, Fever.

Phagocytes

• neutrophils and macrophages
• Engulf foreign material and digests via phagocytosis

Natural Killer Cells

• Can lyse and kill cancer cells and virus-infected cells.
• Cause membrane and nucleus to disintegrate using a chemical called perforin.
• Perforin pokes holes in cells.

Inflammatory Response

• Injured tissues release inflammatory chemicals.
• The inflammatory chemicals attract phagocytes and white blood cells to the area via chemotaxis.
• The inflammatory chemicals dilates local blood vessels.
• The inflammatory chemicals make capillaries leaky.
• Inflammatory Response produces four signs: Redness, Heat, Swelling, Pain.
• Redness and heat are caused by increased blood flow.
• Swelling (edema) and pain are caused by leaky capillaries.

Complement

• The complement system has a group of 20 plasma proteins in the blood.
• Complement is activated when they become attached to foreign cells.
• Complement lyse (burst) cells by creating pores in membrane.

Interferon

• Interferon is secreted proteins of virus-infected cells.
• Interferon binds to healthy cell surfaces.
• Interferon stimulates synthesis of proteins that block the virus from multiplying inside the healthy cell.

Fever

• A fever is an abnormally high body temperature.
• Temperature regulation by the hypothalamus can be reset by pyrogens.
• Pyrogens are molecules secreted by white blood cells.
• High temperatures inhibit the release of iron and zinc from the liver and spleen, which is needed by bacteria.
• Fever also increases metabolic rate, speeding up tissue repair.

Adaptive (Specific) Body Defenses

• Adaptive Body Defense is the third line of defense & is known as the immune system
• The immune system has three characteristics.
• Antigen specificity: recognizes and acts against particular foreign substances.
• Systemic: Body wide and is not restricted to initial infection site.
• Has memory: Recognizes & mounts a stronger attack on previously encountered pathogens.

Antigens (Self)

• Human cells have many surface molecules (proteins and carbohydrates) that identify our cells as ours.
• Immune cells take inventory of these molecules and do not attack our own, because they have a name tag.
• These are "self antigens" which are antigens that belong to you.

Non-Self Antigens

• Non-self antigens are any substances that are not part of the body and provoke an immune response.
• Proteins are the strongest antigens.

Cells of the Immune System: Lymphocytes

• Lymphocytes are programed and matured by thymosin
• There are two types of lymphocytes: B Lymphocyte (B cell) & T Lymphocyte (T cell)

Types of Immunity

• Humoral immunity is an anti-body mediated immunity where B-lymphocytes produce antibodies that target antigens
• Cellular immunity is a cell-mediated immunity where T-Lymphocytes directly target antigens.

Humoral (Antibody-Mediated) Immunity

• Humoral immunity has two stages: primary and secondary.
• Primary humoral response is the first exposure.
• Secondary humoral response is the second exposure.

Primary Humoral Response

• Specific receptors on B lymphocytes (B cells) bind to an antigen.
• This binding activates the lymphocyte to undergo "clonal selection."

Clonal Selection

• Clonal selection is when many identical B cells are made.
• Two types of B cells are produced.
• Plasma cells produce antibodies, they are the vast majority.
• Memory cells.

Antibodies

• Antibodies are proteins secreted by B cells and carried in blood plasma (also known as Immunoglobulins).
• Antibodies have two identical halves with two specific antigen-binding sites.
• Each antibody is uniquely shaped to bind with its specific antigen to inactivate it.

Secondary Humoral Response

• Memory B cells are long-lived and remember the antigen.
• This is more powerful and longer lasting than the primary humoral response.
• Responsible for secondary humoral response:
• Second exposure to same antigen causes a rapid release of antibodies.

Antibody Function

• Antibodies inactivate antigens in four ways: Neutralization, Agglutination, Precipitation, and Complement fixation.
• Neutralization blocks a harmful part of invader.
• Agglutination is clumping of antigens for easy destruction.
• Precipitation is clumping where clumps fall out of solution.
• Complement fixation activates complement.

Adaptive (Specific) Body Defenses

• There are two forms of Humoral immunity: active and passive.

Active Immunity

• Active immunity is when B cells encounter the antigens and produce antibodies against them.
• Active immunity is naturally acquired during infections
• Active immunity is artificially acquired via vaccines.

Passive Immunity

• Passive immunity is immune protection provided by borrowed antibodies obtained from outside one's own body.
• Antibodies are not made by one's own plasma cells.
• Passive immunity is naturally acquired when passed from mother to fetus.
• Passive immunity is artificially acquired via immune sera.
• Memory does not occur with passive immunity.

Types of Immunity (again)

• Humoral immunity is anti-body mediated immunity where B-lymphocytes produce antibodies that target antigens.
• Cellular immunity is a cell-mediated immunity where T-Lymphocytes directly target antigens.

Cellular (Cell-Mediated) Immunity

• Cellular immunity uses T lymphocytes (T cells).
• T-cells do not bind to free antigens like B cells.
• Antigens must be presented by macrophages to the T-cell (called antigen presentation).

Cell-Mediated Immune Response

• Macrophage engulfs an antigen and processes it internally, displaying parts of it on its external surface with one of its own (self) proteins.
• T cells must recognize non-self (antigen) and self parts (called double recognition).
• Macrophage also secretes interleukin-1.
• Antigen binding and interleukin-1 stimulate the T cell to undergo clonal selection.
• Four classes of T cells are produced that promote or stop the immune response.

Types of T Cell Clones

• Cytotoxic T cells specialize in killing infected cells by inserting toxic chemicals to disintegrate them.
• Perforins create pores in the cell membrane and Granzymes are protein digesting, inserted enzymes.
• Helper T cells recruit other cells to fight invaders using interleukin-2.
• Helper T cells stimulates other helper T cells, cytotoxic T cells and interacts directly with B cells.
• Memory cells are a few members of each clone that remain in body for a long time in case of a second exposure.
• Suppressor T cells release chemicals to suppress activity of T and B cells.
• Suppressor T cells stops immune response to prevent uncontrolled activity.