BIOLOGY II NOTES

Louis Pasteur (1822-1895)

  • French chemist, microbiologist during period of inquiry into the origin of microbial life.

  • 1859: Experiments to disprove spontaneous generation.

    • First Experiment:

      • Flasks opened briefly outside, showing 89% growth.

    • Second Experiment:

      • Swan neck flask design.

      • Boiling broth to sterilize.

      • Flask open to air, but spores collect in the neck, preventing growth.

      • 32% growth in flasks inside the building.

      • 100% no growth.

  • Convinced something smaller than bacteria was the cause of rabies.

  • Coined the term "virus" (Latin = poison).

  • Developed rabies vaccine, saving the life of a French boy bitten by a rabid dog.

Prevalence of Microbes

  • Single spoonful of soil contains 101010^{10} bacteria.

  • Total number of bacteria on earth estimated at 103010^{30} (most of all living, except for viruses).

Why Study Microbes (Specifically: Bacteria)?

  • Pathogen: Most bacterial species are not harmful.

    • About 101410^{14} bacteria in the human body, mostly normal microflora.

      • Normal gut E. coli: Prevent growth, digest foods we can't, make Vitamins K and B12.

      • Normal bacteria on skin, nasal passages, mouth, vagina: Inhibit harmful bacteria.

    • Some bacteria do cause disease.

      • E. coli strain O157:H7:

        • Produces shiga toxin, damages intestinal lining, leading to bleeding sores.

        • Causes cramping, diarrhea, then bloody diarrhea, dehydration, and fever.

        • Young and old are more susceptible.

        • Complications can lead to HUS (Hemolytic Uremic Syndrome).

          • RBC lysis leads to renal failure.

Antibiotic Producers

  • Most antibacterial antibiotics are produced by other strains of bacteria (some exceptions, e.g., penicillin family produced by fungi).

  • Antibiotics kill microbes or inhibit their growth.

  • Huge pharmaceutical industry involved.

  • Examples:

    • Streptomycin

    • Erythromycin

    • Kanamycin

    • Tetracycline

    • Cephalosporins

  • Continuous need to find new antibiotics due to resistance.

Decomposers

  • Bacteria, fungi.

  • Produce and secrete enzymes that digest organic material.

    • Absorption of nutrients for themselves and other organisms (recycling of organic material).

    • Can also breakdown some inorganic materials.

  • 1971: Dr. Anantha Chakrabarty genetically crossed bacterial strains to break down hydrocarbons in oil (patent).

    • Such organisms were used for:

      • 1989 Exxon Valdez oil spill

      • 1991 cleanup of Kuwait

Nitrogen Fixation

  • Taking atmospheric N2N_2.

  • Cyanobacteria (a.k.a. blue-green algae) - distinct from most bacteria.

    • Can perform N2N_2 fixation.

    • Also produced atmospheric O2O_2 (2.4 billion years ago).

Food Production

  • As decomposers, bacteria are part of the food chain.

  • Bacteria are also used in the food industry:

    • Fermentation:

      • Milk → yogurt (lactobacillus, bifidobacteria); cheese (fungus and bacteria).

      • Grapes → wine (yeast).

      • Grains → beer, spirits (yeast).

Research/Biotechnology

  • Study prokaryotic life forms.

  • Plasmid DNA production.

  • Protein production.

    • Ex: Insulin gene for insulin.

  • Ex: Bacterial enzyme modifies Type A or Type B blood to Type O.

Environmental Cleanup

  • Oil/hydrocarbon digestion.

  • Neutralize copper, mercury → bioinert forms.

  • Sewage treatment.

Killing Tumors

  • Engineering Salmonella to swim to tumor cells to deliver drugs → apoptosis.

Other Uses

  • Botulinum toxin in improperly canned foods.

    • Clostridium botulinum bacteria.

    • Even small amounts are poisonous (paralysis, respiratory failure).

    • No honey or corn syrup to infants because of this bacteria.

Emerging Diseases

  • Bacterial strains can develop drug resistance.

  • MDR (Multidrug resistance) – mutations and/or acquisition of genes conferring resistance to one or more drugs used to stop strain.

Antibiotics Widely Used; Necessary for Healthcare

  • Most antibiotics kill bacteria (-cidal) or inhibit their growth (-static).

  • Interfere with biochemical/metabolic pathways unique to bacteria.

    • Therefore, ideally, should not harm human cells, but side effects exist (some mild, some severe).

Overuse

  • Sometimes in humans → prescriptions written even when not necessary.

  • Livestock → antibiotics used to make animals bigger → more food.

    • At what cost? Resistance is building.

Need to Understand Strains

  • Better match antibiotic to the strain that is infecting a person.

  • If antibiotic is 99% effective, then 1% of target microorganism survives, then thrives with little to no competition.

Consider MRSA (Methicillin-resistant Staphylococcus Aureus)

  • Staphylococcus aureus - strain of bacteria normally found on skin & nasal passages of ~30% people (no problems).

  • ~2% carry strain resistant to: methicillin, penicillin, oxacillin, amoxicillin.

  • Some infections from S. aureus occur in the community → often skin (e.g., boil).

  • Many infections are nosocomial – occur in hospital → often far worse (infect respiratory system, urinary system, blood).

Clostridium difficile

  • Bacteria spread through improper handwashing (hospital-acquired infection - nosocomial).

  • Antibiotics.

  • Fecal transplants (providing 'good' enteric bacteria).

How Identify Bacteria?

  • Anatomy

  • Biochemistry

Anatomy of Bacteria

  • Shape

    1. Bacillus/Bacilli (rod)

    2. Coccus/Cocci (spherical)

    3. Spirillum/Spirila (spiral or helical)

    4. Vibrio (comma-shaped)

  • Size: 0.22 μm - 5 μm (often, about the size of mitochondria or chloroplast).

  • Grouping

    1. Single-cell / Separate

    2. Clustered:

      • Chains

      • Diplococcus

      • Streptococcus

      • Staphylococcus

  • Structures of bacterium

    • Plasma membrane → outward

      1. Plasma Membrane: Lipid bilayer

      2. Cell Wall: Contains peptidoglycan molecules → stain with certain dyes (Gram Stain)

        • 'Gram-positive' vs 'Gram-negative' helps determine which antibiotic

      3. Capsule: Polysaccharide layer outside cell wall; helps protect from dehydration & immune system

      4. Fimbrae: Bristle-like appendages; allow adherence to surfaces

      5. Flagellum: Stiff filament, rotates like propeller; Placement? (one end, both ends, even??)

Focus on Cell Wall and Gram Staining

  • Gram-positive:

    • Have a uniformly dense cell wall consisting primarily of peptidoglycan.

    • Gram-stain: violet dye + iodine.

      • Mordant.

      • Alcohol wash removes some peptidoglycan.

      • Counterstain with red dye.

    • Thick peptidoglycan wall retains violet dye.

    • Pink & Purple, typically see purple.

  • Gram-negative:

    • Have a very thin peptidoglycan layer and an outer membrane.

    • Thin peptidoglycan layer → no violet dye, but bind red counterstain

    • Extra outer membrane makes more pathogenic, releases LPS; resists immune system & antibiotics

Inside Plasma Membrane

  • Cytoplasm: Contains water & solutes, ribosomes, granules, nucleoid region, plasmids.

  • Chromosome: Single circular strand of DNA; contains bacterial genome.

  • Plasmids: Small circular pieces of DNA.

    • May contain 1 or few genes.

    • Self-replicating within cell.

Pilus/Pili

  • Extension of cell surface.

  • Hair-like extension from bacterial cell surface.

  • Longer than fimbrae, shorter than flagella.

  • Involved in bacterial adherence to surfaces and to other cells.

  • Special 'sex pilus' allows for bacterial conjugation.

  • Importance of Pili: Colitis - inflammation of colon.

    • Normally, beneficial bacteria colonize the large intestine, preventing bad bacteria from colonizing.

    • What about infants?

      • Initially sterile from placenta.

      • Colonized during birth process.

      • Feeding baby can have a major influence on what bacteria colonize baby - by passing things across.

        • Breast milk: proteins (and antibodies), fats, carbohydrates: lactose, oligosaccharides (oligosaccharides compete binding to certain bad bacteria).

        • Skin to Skin (DNA of parents to babies)

Biochemistry to Characterize Bacteria

  • Staining

    • Hundreds of different dyes

    • Ex: methylene blue (pos. charged) → stains neg. charges (nucleus, cell wall).

    • Ex: Gram stain.

  • Metabolism

    • Ex: aerobic vs. anaerobic (O2O_2 can be toxic for some bacteria: Clostridium).

  • Absorptive Nutrition

    • Take directly from environment → no digestive system within cell

    • Secrete enzymes to degrade protein, fat, polysaccharides).

  • Asexual Reproduction

    • Binary fission → all daughter cells identical to original cell.

      • Reproduction can determine how harmful bacteria are when they infect (most are innocuous).

Bacterial Action

Lactose Intolerance

  • Gradual loss of lactase enzyme - Breaking Gal-Glu glycosidic bond.

    • Normal aging.

    • Sickness/ damage to intestines.

    • Autosomal recessive alleles → not produce lactase.

  • Process

    • Undigested sugars that go to large intestine.

    • Malabsorbed lactose, fructose get fermented by the colonic microbiota.

    • Produces Hydrogen, Methane, CO₂.

  • Test for: Hydrogen, CH₄ methane, CO₂ as they grow produce this.

  • Treatment:

    • Lactase enzyme.

    • Lactose-free dairy.

Necrotizing Fasciitis

  • Flesh-eating Bacteria → release enzymes that digest tissue.

    • U.K. case of man working in garden - the man died losing limbs, bacteria consumed him

  • Rapidly progressive and often fatal infection of the subcutaneous tissue and fascia.

  • Risk factors include diabetes, alcoholism, IV drug use, and immunosuppression.

  • Imaging studies may demonstrate soft tissue gas.

  • Intense pain, erythema, tissue crepitus, and systemic toxicity.

  • May be caused by a polymicrobial infection consisting of both aerobic and anaerobic organisms or by a single organism such as Group A Streptococci.

  • Surgical emergency that requires aggressive surgical debridement and IV antibiotics.

Antibiotics - Bacteria specific

Requirements

  • Toxic to target

  • Specific for target (minimize side effects).

What is good target?

  • Biochemical/Metabolic target (usually a protein).

  • Consider:

    1. DNA replication proteins?

    2. RNA synthesis proteins?

    3. Translation machinery?

    4. Cell wall production?

      • Cell wall synthesis target:

        • Cycloserine

        • Vancomycin

        • Bacitracin

        • Penicillins

        • Cephalosporins

        • Monobactams

        • Carbapenems

      • Folic acid metabolism:

        • Trimethoprim

        • Sulfonamides

      • Cytoplasmic membrane structure:

        • Polymyxins

        • Daptomycin

      • DNA gyrase:

        • Nalidixic acid

        • Ciprofloxacin

        • Novobiocin

      • Cytoplasmic membrane

      • DNA-directed RNA polymerase:

        • Rifampin

        • Streptovaricins

      • Protein synthesis (50S inhibitors):

        • Erythromycin (macrolides)

        • Chloramphenicol

        • Clindamycin

        • Lincomycin

      • Protein synthesis (30s inhibitors):

        • Tetracyclines

        • Spectinomycin

        • Streptomycin

        • Gentamicin

        • Kanamycin

        • Amikacin

      • Protein synthesis (tRNA):

        • Mupirocin

        • Puromycin

GI Tract Ulcers

  • Prior to the early 80s, ulcers were believed to be caused by overproduction of stomach acid, largely due to stress.

  • Prescribed bland diet and stomach acid inhibitors.

  • Early 80s: Helicobacter pylori was suspected to be the cause/trigger.

    • Australian doctors Barry Marshall and Robin Warren Nobel Prize 2005.

    • Studied patients with inflamed epithelial cells.

    • Theory: H. pylori stimulates overproduction of acid, kills stomach-lining cells, and causes inflammation; possible links to (rare cancer of GI mucosa lymphoid tissue).

    • Now treat with amoxicillin, tetracycline, metronidazole (combo of any 2).

      • Side effects! Antibiotics also kill beneficial bacteria of gut, vagina → consume probiotics (e.g., yogurt).

Problems with Antibiotic Therapy

*If someone does not take the full course of antibiotics, they can come back.

  • Allergic reactions to antibiotics (some could be fatal).

  • Killing off 'good' bacteria along with 'bad' → may allow overgrowth of certain harmful bacteria or yeast.

  • Increasing incidences of Antibiotic Resistance

    • Killing of susceptible bacteria → selecting for non-susceptible.

    • Bacteria can mutate → antibiotic no longer works.

    • Bacteria can transfer drug-resistance genes to other bacteria → leads to MDR (multidrug-resistance) "superbugs".

Multidrug Resistance (MDR)

What makes bacteria resistant?

Genetic change - change in bacterial DNA → change conformation of target
Mutation

  • Error in DNA replication.

Conjugation

  • Exchange of genetic material (sex pilus).

Transformation

  • Bacteria take up DNA from environment.

    • Ex: O157:H7 (bad E. coli) transformed with Shigella toxin gene.

Transduction

  • Virus introduces genetic material into bacteria

Viruses

Intro to virus world and scale

  • Difficult to classify: Living or Non-living?

  • Extremely small (25-250 nm).

  • Obligate parasites → metabolically active only inside living cells; no metab. on own

Structure of Virion/Virus Particle

Capsid

  • Protein coat made of many subunits.

  • a) containment and physical interaction

  • b) molecular recognition

  • c) redirects host cell activity.
    Example: Adenovirus (DNA) and Influenza (RNA)

Genome

  • DNA or RNA, but not a mix of both.

  • Can be single-stranded or double-stranded.

  • Instructions for making more virions/particles → possibly causing host cell death

Envelope

  • Not all viruses have protein coat. Just Genomes.

Baltimore classification of Viruses

  • +(positive) = sense

  • - (negative) = anti-sense
    [David Baltimore, PhD - 1975 Nobel Prize Medicine]
    *7 kinds of virus genomes

  1. Double Stranded DNA

  2. Single Strand DNA

  3. Double Stranded RNA

  4. Positive Single Strand RNA

  5. Negative Single Strand RNA

  6. Positive stranded RNA with reverse transcriptase

  7. Double Stranded DNA with reverse transcriptase

Stages of Virus Infection Cycle

Recognition/Binding

  • Utilize Unique receptors

Entry

  • Viral spike protein binds host cell surface protein (lock & key).

  • Endocytosis (whole virus).

  • Membrane Fusion

  • Nucleic acid injection (protein coat remains outside)

Uncoating

  • Viral coat proteins separate (often due to cytoplasmic pH disrupting weak bonds)

Replication

  • Of viral nucleic acids and proteins.

Assembly

  • Often self-assembly.

Exit

  • Early/Mid/Late
    *a) viral enzyme ruptures cell membrane-Lytic (Pop and spread everything at once)
    *b)Exocytosis-little at a time; cell lives (Little bit at a time)

Lytic Cycle vs Lysogenic Cycle (phages or some dsDNA/retroviruses)

Lytic Cycle

  • Proceeds Stages 1-6 without stopping.

  • Done by most virulent virions/viruses.

  • Robbery: get in, get out.

Lysogenic Cycle

  • Done by particular viruses.

  • Has latent stage between uncoating and replication.

  • Viral DNA integrates into host cell DNA.
    *
    *Change in bacterial environment → stimulates viral progression into Stage 4 → and onward

Transduction

  • Movement of DNA from one bacterial cell to another via virus (phage).

  • Virus behaves as a vector → doesn't cause disease, but transmits the agent that causes disease.

  • Popping out: integrated viral DNA plus piece of host/bacterial DNA transmit to new bact. cell

RNA Virus: Production Problem

  • Sense RNA if used by ribosome can't be replicated.

  • Complementary RNA (antisense/ -RNA) cannot be used by ribosome

RNA-dependent RNA polymerase (RdRp)

  • Brought in by virus (released during uncoating).

  • Transcribes RNA sense strand from RNA template

  • Viral only protein good target for drugs.

Reverse Transcriptase (RT)

  • Used by retroviruses (e.g., HIV-1).

  • A.k.a. RNA-dependent DNA polymerase (RdDp).

  • Transcribes complementary ssDNA from ssRNA template
    Host DNA-dependent RNA polymerase (RNA Pol or DdRp) makes mRNA

Retrovirus

  • Single-stranded RNA virus.

  • RT generates DNA copy.

  • DNA copy integrates into Host genome.

Retroviral (HIV) Reproductive Life Cycle

Attachment to CD4 or CXCR2
Entry
Uncoating

*Reverse transcriptase

  • Integrase (allows it to go into Host DNA).
    *i) Provirus state.
    *ii) Activation

Host transcription, Host translation
Assembly
Exit

Life-long Infection

*HIV (retrovirus)

Herpes family viruses (group I DNA viruses)

*8 herpes viruses infect humans
1) Herpes simplex virus type 1 (HSV-1; Oral Herpes)
2) Herpes simplex virus type 2 (HSV-2; Genital Herpes)
3) Varicella-zoster Virus (Chickenpox) -Reacts after symptoms pass.
4) Esptein-Barr Virus - Infectious Mononucleosis

Influenza/Flu Virus (Group V antisense RNA)

classifications by H# N#

Hemagglutinin

  • Viral surface protein.

  • Used to enter host cell
    *H1N1 → swine flu

Neuraminidase

  • Viral surface protein.

  • Used to exit from host cell
    *H5N1 → avian flu *

  • Antigenetic Drift - little changes.

  • Antigenetic shift-rearrangement (happens every decade)

Coronaviruses

Group 4 RNA sense virus

S-Protein

route1-membrance
route2-endocytosis

ACE-2- Strokes in sleepMutation to help suvive

-D614G (Triad)
*Upper respritory so lower lung issues don’t happen+

*Omicron Family
*BA.1
*BA.2
*BA.3

Antivirals

  • Not as successful as antibiotics against bacteria.

  • Must target virus but not eukaryotic cells.
    *Targets
    Host or Virus

  • Integrase (viral)

  • Protease (viral)

  • Reverse transcriptase

  • Capsid / Spike proteins

  • Hemagglutinin

  • Neuraminidase
    Protease Inhibitor

RTIs (Reverse Transcription Inhibitors)

1) AZT (Azidothymidine) - thymidine nucleotide analog
2) Acyclovir - guanosine analog - inhibits viral polymerase

HAART - Highly Active Antiretroviral Therapy

  • Prevent Viral Entry at CD4 receptors

  • Prevent Reverse Transcriptase

  • Prevent Integrase

  • Prevent Protease activity
    HAART reduces viral numbers for Chronic Disease

Viroids

  • Naked viral RNA, about 1/10th the size of normal viral RNA

  • Do not code for proteins themselves.

  • Infects plants

Prions

  • Proteins that abnormally fold then induce other proteins to abnormally fold.

  • Destroys nerve cells b/c too much bad protein

  • Break from convention that DNA or RNA is required for infection

  • 1st noticed in sheep → "scrapie"

  • Also found in cows → "mad cow disease" (Bovine Spongiform Encephalopathy)

  • In deer, elk → "chronic wasting disease"

  • In humans → Creutzfeldt-Jacob Disease

Immune System

  • Protection against pathogens - harmful organisms
    *toll likereceptors (TRLs)- recognise nonself
    *Spleen filters circulating blood
    *Multiple systems and organs
    *T cells mature in the thymus
    *B cells mature in the bone marrow
    *Transcription factor NF-kB- damage stimulus from cytokines. Heavy metals, radiation and viral antigens
    *Lymph acts as filtration and white blood cells inspect it

Two Major Types of Defense Systems

Innate/Non-specific

  • Old, mostly bacteria

  • Symptoms
    *Primary bacteria starts cells to fight cancer

Adaptive/Specific

*Evolving and precise hits viruses
Attacks and locks
*Evolving system

Innate/Non-specific Defense System

Surface barriers

  • Skin, mucous membranes

Internal defenses

  • WBCs (phagocytes, NK cells), antimicrobial proteins, inflammation, fever

Surface Barriers

*Generalized Protein/Ex Compliment/juntions
*multilayered skin=normal bacterial flora
*mucus, lysozyme, HCl (stomach) DNase, RNase

White blood cells (leukocytes):
Granuolcytes
   *Basophils- release hestermine
    *Eosinophils- Kills aintidbody covered parasite(worms)
    *Neutrophils- stimulate inflammation
   Mast Cells release hestermine when cells damaged. They cells communicate and work together and developed

from a hematopieis

Monocyte-derived cells.

*Monocytes
*Macrophages.
*Dendritlic cells Phagocytosis. All Engulf microbial particles

Lymphocytes: T cells, B cells

T cells-Kill virus infected and cancer cells activate or inactivate others
B cells differentiate for Anitibodies
*Toll Proteins recognise microbes on the white blood cells.

Antibodies:

Part of Adaptive Humoral Immunity, made by B Cells

Cytokines:

Part of Systemic, signal proteins to tell cells they will alter other cells behavoir

Major histocompatibility complex

(MHC 1 or MHC2)- Tells us what codes our body can show and recognise
*T cell receptors recognise and binds Antigens from 2MHC and antigen cells.

Internal Defenses

  • Complement System: circulating liver proteins

Phagocytes

*Taxis to chase Adhere Engulf Digest Lysozyme Exocytose, season lyme

AP-Antigien Presenting cell

Natural Killer (NK) Cells

*Check is cell heathy? Induce death on virus/cancer infected cells

  • Apoptosis

Eosinophils

*Worm or parasite releases enzymes out and kills
*Helminths worms kill them

Inflammation *Spot Tender to tell you not to touch it!

Cytokines release and attack WBC to take out area.
*Anuploid or stress will occur
*Sequesters iron and sync needed to start. Bacteria is stop from getting resources by a reaction.

Adaptive/Specific Immune System

  • specific, looking for unique targets (Antigens/Epitope)- Look at anti bodies and blood system, subcelluar and Cellular
    *Two Arms Humoral and Celluar work in Adaptive
    *Memory is the reaction

B-cells (bone) called B-cells because they mature in Bone Marrow 1. Cyto Toxic 1. Celluar Recuit and Phagyocytes
T Cells- Coordinate innate attacks CD-4

Antigen

*Foreign object
*A Fragment of an invader (Peptide/protein)

  • RNA vacine from PHzer, moderna or Astraza, J&J and Novas from sinopharm

Generation of Immune System Cells

*Phagocytosis to get bacteris that are seasoned Macrophage/Dendric cells
*APC- Antigien Presenting cell eat season and break it down
*Stem adapt and cell become froms- RBC's(others)
*Bone Marrow- Lymphocyctes- Progenitor N cells
*Plasma cells
#T Cells (4main types)
1)CD8+ - Kill Cytoxic cells. *kill your self* Apoptosis
2)CD4+ - help the cells and learn of machophages. Activate the B cells.
3) suppressor T or regulatory cell block
4) Memory T React Fast- On and turn it into necessary auttoimmune disease

 ###Hematoporesis

Has all the steps of bone and what come from the thymus and adaptive to stop from cancer

##Humoral Responsibility Anitgen Challenege

  1. Anitgen detecing

  2. TH replicate w/Cytokines
    3.Memory
    4 Somatic
    5Fallomes


Louis Pasteur (1822-1895)

  • French chemist, microbiologist during period of inquiry into the origin of microbial life.

  • 1859: Experiments to disprove spontaneous generation.- First Experiment:- Flasks opened briefly outside, showing 89% growth.

    <!-- -->

    • Second Experiment:- Swan neck flask design.

      • Boiling broth to sterilize.

      • Flask open to air, but spores collect in the neck, preventing growth.

      • 32% growth in flasks inside the building.

      • 100% no growth.

  • Convinced something smaller than bacteria was the cause of rabies.

  • Coined the term "virus" (Latin = poison).

  • Developed rabies vaccine, saving the life of a French boy bitten by a rabid dog.

Prevalence of Microbes

  • Single spoonful of soil contains 101010^{10} bacteria.

  • Total number of bacteria on earth estimated at 103010^{30} (most of all living, except for viruses).

Why Study Microbes (Specifically: Bacteria)?

  • Pathogen: Most bacterial species are not harmful.- About 101410^{14} bacteria in the human body, mostly normal microflora.- Normal gut E. coli: Prevent growth, digest foods we can't, make Vitamins K and B12.
    - Normal bacteria on skin, nasal passages, mouth, vagina: Inhibit harmful bacteria.

    <!-- -->

    • Some bacteria do cause disease.- E. coli strain O157:H7:- Produces shiga toxin, damages intestinal lining, leading to bleeding sores.
      - Causes cramping, diarrhea, then bloody diarrhea, dehydration, and fever.
      - Young and old are more susceptible.
      - Complications can lead to HUS (Hemolytic Uremic Syndrome).- RBC lysis leads to renal failure.

          <!-- -->

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Antibiotic Producers

  • Most antibacterial antibiotics are produced by other strains of bacteria (some exceptions, e.g., penicillin family produced by fungi).

  • Antibiotics kill microbes or inhibit their growth.

  • Huge pharmaceutical industry involved.

  • Examples:- Streptomycin

    • Erythromycin

    • Kanamycin

    • Tetracycline

    • Cephalosporins

  • Continuous need to find new antibiotics due to resistance.

Decomposers

  • Bacteria, fungi.

  • Produce and secrete enzymes that digest organic material.- Absorption of nutrients for themselves and other organisms (recycling of organic material).

    • Can also breakdown some inorganic materials.

  • 1971: Dr. Anantha Chakrabarty genetically crossed bacterial strains to break down hydrocarbons in oil (patent).- Such organisms were used for:- 1989 Exxon Valdez oil spill
    - 1991 cleanup of Kuwait

    <!-- -->

Nitrogen Fixation

  • Taking atmospheric N2N_2.

  • Cyanobacteria (a.k.a. blue-green algae) - distinct from most bacteria.- Can perform N2N_2 fixation.

    • Also produced atmospheric O2O_2 (2.4 billion years ago).

Food Production

  • As decomposers, bacteria are part of the food chain.

  • Bacteria are also used in the food industry:- Fermentation:- Milk → yogurt (lactobacillus, bifidobacteria); cheese (fungus and bacteria).
    - Grapes → wine (yeast).
    - Grains → beer, spirits (yeast).

    <!-- -->

Research/Biotechnology

  • Study prokaryotic life forms.

  • Plasmid DNA production.

  • Protein production.- Ex: Insulin gene for insulin.

  • Ex: Bacterial enzyme modifies Type A or Type B blood to Type O.

Environmental Cleanup

  • Oil/hydrocarbon digestion.

  • Neutralize copper, mercury → bioinert forms.

  • Sewage treatment.

Killing Tumors

  • Engineering Salmonella to swim to tumor cells to deliver drugs → apoptosis.

Other Uses

  • Botulinum toxin in improperly canned foods.- Clostridium botulinum bacteria.

    • Even small amounts are poisonous (paralysis, respiratory failure).

    • No honey or corn syrup to infants because of this bacteria.

Emerging Diseases

  • Bacterial strains can develop drug resistance.

  • MDR (Multidrug resistance) – mutations and/or acquisition of genes conferring resistance to one or more drugs used to stop strain.

Antibiotics Widely Used; Necessary for Healthcare

  • Most antibiotics kill bacteria (-cidal) or inhibit their growth (-static).

  • Interfere with biochemical/metabolic pathways unique to bacteria.- Therefore, ideally, should not harm human cells, but side effects exist (some mild, some severe).

Overuse

  • Sometimes in humans → prescriptions written even when not necessary.

  • Livestock → antibiotics used to make animals bigger → more food.- At what cost? Resistance is building.

Need to Understand Strains

  • Better match antibiotic to the strain that is infecting a person.

  • If antibiotic is 99% effective, then 1% of target microorganism survives, then thrives with little to no competition.

Consider MRSA (Methicillin-resistant Staphylococcus Aureus)

  • Staphylococcus aureus - strain of bacteria normally found on skin & nasal passages of ~30% people (no problems).

  • ~2% carry strain resistant to: methicillin, penicillin, oxacillin, amoxicillin.

  • Some infections from S. aureus occur in the community → often skin (e.g., boil).

  • Many infections are nosocomial – occur in hospital → often far worse (infect respiratory system, urinary system, blood).

Clostridium difficile

  • Bacteria spread through improper handwashing (hospital-acquired infection - nosocomial).

  • Antibiotics.

  • Fecal transplants (providing 'good' enteric bacteria).

How Identify Bacteria?

  • Anatomy

  • Biochemistry

Anatomy of Bacteria

  • Shape1. Bacillus/Bacilli (rod)

    1. Coccus/Cocci (spherical)

    2. Spirillum/Spirila (spiral or helical)

    3. Vibrio (comma-shaped)

  • Size: 0.22 μm - 5 μm (often, about the size of mitochondria or chloroplast).

  • Grouping1. Single-cell / Separate

    1. Clustered:- Chains

      • Diplococcus

      • Streptococcus

      • Staphylococcus

  • Structures of bacterium- Plasma membrane → outward1. Plasma Membrane: Lipid bilayer
    2. Cell Wall: Contains peptidoglycan molecules → stain with certain dyes (Gram Stain)- 'Gram-positive' vs 'Gram-negative' helps determine which antibiotic

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3. Capsule: Polysaccharide layer outside cell wall; helps protect from dehydration & immune system
4. Fimbrae: Bristle-like appendages; allow adherence to surfaces
5. Flagellum: Stiff filament, rotates like propeller; Placement? (one end, both ends, even??)

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Focus on Cell Wall and Gram Staining

  • Gram-positive:-

    • Have a uniformly dense cell wall consisting primarily of peptidoglycan.

    • Gram-stain: violet dye + iodine.- Mordant.

      • Alcohol wash removes some peptidoglycan.

      • Counterstain with red dye.

    • Thick peptidoglycan wall retains violet dye.

    • Pink & Purple, typically see purple.

  • Gram-negative:-

    • Have a very thin peptidoglycan layer and an outer membrane.

    • Thin peptidoglycan layer → no violet dye, but bind red counterstain

    • Extra outer membrane makes more pathogenic, releases LPS; resists immune system & antibiotics

Inside Plasma Membrane

  • Cytoplasm: Contains water & solutes, ribosomes, granules, nucleoid region, plasmids.

  • Chromosome: Single circular strand of DNA; contains bacterial genome.

  • Plasmids: Small circular pieces of DNA.- May contain 1 or few genes.

    • Self-replicating within cell.

Pilus/Pili

  • Extension of cell surface.

  • Hair-like extension from bacterial cell surface.

  • Longer than fimbrae, shorter than flagella.

  • Involved in bacterial adherence to surfaces and to other cells.

  • Special 'sex pilus' allows for bacterial conjugation.

  • Importance of Pili: Colitis - inflammation of colon.- Normally, beneficial bacteria colonize the large intestine, preventing bad bacteria from colonizing.

    • What about infants?- Initially sterile from placenta.

      • Colonized during birth process.

      • Feeding baby can have a major influence on what bacteria colonize baby - by passing things across.- Breast milk: proteins (and antibodies), fats, carbohydrates: lactose, oligosaccharides (oligosaccharides compete binding to certain bad bacteria).

        • Skin to Skin (DNA of parents to babies)

Biochemistry to Characterize Bacteria

  • Staining- Hundreds of different dyes

    • Ex: methylene blue (pos. charged) → stains neg. charges (nucleus, cell wall).

    • Ex: Gram stain.

  • Metabolism- Ex: aerobic vs. anaerobic (O2O_2 can be toxic for some bacteria: Clostridium).

  • Absorptive Nutrition- Take directly from environment → no digestive system within cell

    • Secrete enzymes to degrade protein, fat, polysaccharides).

  • Asexual Reproduction- Binary fission → all daughter cells identical to original cell.- Reproduction can determine how harmful bacteria are when they infect (most are innocuous).

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Bacterial Action

Lactose Intolerance

  • Gradual loss of lactase enzyme - Breaking Gal-Glu glycosidic bond.- Normal aging.

    • Sickness/ damage to intestines.

    • Autosomal recessive alleles → not produce lactase.

  • Process- Undigested sugars that go to large intestine.

    • Malabsorbed lactose, fructose get fermented by the colonic microbiota.

    • Produces Hydrogen, Methane, CO₂.

  • Test for: Hydrogen, CH₄ methane, CO₂ as they grow produce this.

  • Treatment:- Lactase enzyme.

    • Lactose-free dairy.

Necrotizing Fasciitis

  • Flesh-eating Bacteria → release enzymes that digest tissue.- U.K. case of man working in garden - the man died losing limbs, bacteria consumed him

  • Rapidly progressive and often fatal infection of the subcutaneous tissue and fascia.

  • Risk factors include diabetes, alcoholism, IV drug use, and immunosuppression.

  • Imaging studies may demonstrate soft tissue gas.

  • Intense pain, erythema, tissue crepitus, and systemic toxicity.

  • May be caused by a polymicrobial infection consisting of both aerobic and anaerobic organisms or by a single organism such as Group A Streptococci.

  • Surgical emergency that requires aggressive surgical debridement and IV antibiotics.

Antibiotics - Bacteria specific

Requirements

  • Toxic to target

  • Specific for target (minimize side effects).

What is good target?

  • Biochemical/Metabolic target (usually a protein).

  • Consider:1. DNA replication proteins?

    1. RNA synthesis proteins?

    2. Translation machinery?

    3. Cell wall production?- Cell wall synthesis target:- Cycloserine
      - Vancomycin
      - Bacitracin
      - Penicillins
      - Cephalosporins
      - Monobactams
      - Carbapenems

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      • Folic acid metabolism:- Trimethoprim

        • Sulfonamides

      • Cytoplasmic membrane structure:- Polymyxins

        • Daptomycin

      • DNA gyrase:- Nalidixic acid

        • Ciprofloxacin

        • Novobiocin

      • Cytoplasmic membrane

      • DNA-directed RNA polymerase:- Rifampin

        • Streptovaricins

      • Protein synthesis (50S inhibitors):- Erythromycin (macrolides)

        • Chloramphenicol

        • Clindamycin

        • Lincomycin

      • Protein synthesis (30s inhibitors):- Tetracyclines

        • Spectinomycin

        • Streptomycin

        • Gentamicin

        • Kanamycin

        • Amikacin

      • Protein synthesis (tRNA):- Mupirocin

        • Puromycin

GI Tract Ulcers

  • Prior to the early 80s, ulcers were believed to be caused by overproduction of stomach acid, largely due to stress.

  • Prescribed bland diet and stomach acid inhibitors.

  • Early 80s: Helicobacter pylori was suspected to be the cause/trigger.- Australian doctors Barry Marshall and Robin Warren Nobel Prize 2005.

    • Studied patients with inflamed epithelial cells.

    • Theory: H. pylori stimulates overproduction of acid, kills stomach-lining cells, and causes inflammation; possible links to (rare cancer of GI mucosa lymphoid tissue).

    • Now treat with amoxicillin, tetracycline, metronidazole (combo of any 2).- Side effects! Antibiotics also kill beneficial bacteria of gut, vagina → consume probiotics (e.g., yogurt).

Problems with Antibiotic Therapy

*If someone does not take the full course of antibiotics, they can come back.

  • Allergic reactions to antibiotics (some could be fatal).

  • Killing off 'good' bacteria along with 'bad' → may allow overgrowth of certain harmful bacteria or yeast.

  • Increasing incidences of Antibiotic Resistance- Killing of susceptible bacteria → selecting for non-susceptible.

    • Bacteria can mutate → antibiotic no longer works.

    • Bacteria can transfer drug-resistance genes to other bacteria → leads to MDR (multidrug-resistance) "superbugs".

Multidrug Resistance (MDR)

What makes bacteria resistant?
Genetic change - change in bacterial DNA → change conformation of target

Mutation

  • Error in DNA replication.

Conjugation

  • Exchange of genetic material (sex pilus).

Transformation

  • Bacteria take up DNA from environment.- Ex: O157:H7 (bad E. coli) transformed with Shigella toxin gene.

Transduction

  • Virus introduces genetic material into bacteria

Viruses

Intro to virus world and scale

  • Difficult to classify: Living or Non-living?

  • Extremely small (25-250 nm).

  • Obligate parasites → metabolically active only inside living cells; no metab. on own

Structure of Virion/Virus Particle
Capsid

  • Protein coat made of many subunits.

  • a) containment and physical interaction

  • b) molecular recognition

  • c) redirects host cell activity.

Example: Adenovirus (DNA) and Influenza (RNA)

Genome

  • DNA or RNA, but not a mix of both.

  • Can be single-stranded or double-stranded.

  • Instructions for making more virions/particles → possibly causing host cell death

Envelope

  • Not all viruses have protein coat. Just Genomes.

Baltimore classification of Viruses

  • +(positive) = sense

  • - (negative) = anti-sense

    [David Baltimore, PhD - 1975 Nobel Prize Medicine]

    *7 kinds of virus genomes

  1. Double Stranded DNA

  2. Single Strand DNA

  3. Double Stranded RNA

  4. Positive Single Strand RNA

  5. Negative Single Strand RNA

  6. Positive stranded RNA with reverse transcriptase

  7. Double Stranded DNA with reverse transcriptase

Stages of Virus Infection Cycle
Recognition/Binding

  • Utilize Unique receptors

Entry

  • Viral spike protein binds host cell surface protein (lock & key).

  • Endocytosis (whole virus).

  • Membrane Fusion

  • Nucleic acid injection (protein coat remains outside)

Uncoating

  • Viral coat proteins separate (often due to cytoplasmic pH disrupting weak bonds)

Replication

  • Of viral nucleic acids and proteins.

Assembly

  • Often self-assembly.

Exit

  • Early/Mid/Late

    *a) viral enzyme ruptures cell membrane-Lytic (Pop and spread everything at once)

    *b)Exocytosis-little at a time; cell lives (Little bit at a time)

Lytic Cycle vs Lysogenic Cycle (phages or some dsDNA/retroviruses)
Lytic Cycle

  • Proceeds Stages 1-6 without stopping.

  • Done by most virulent virions/viruses.

  • Robbery: get in, get out.

Lysogenic Cycle

  • Done by particular viruses.

  • Has latent stage between uncoating and replication.

  • Viral DNA integrates into host cell DNA.

    *

    *Change in bacterial environment → stimulates viral progression into Stage 4 → and onward

Transduction

  • Movement of DNA from one bacterial cell to another via virus (phage).

  • Virus behaves as a vector → doesn't cause disease, but transmits the agent that causes disease.

  • Popping out: integrated viral DNA plus piece of host/bacterial DNA transmit to new bact. cell

RNA Virus: Production Problem

  • Sense RNA if used by ribosome can't be replicated.

  • Complementary RNA (antisense/ -RNA) cannot be used by ribosome

RNA-dependent RNA polymerase (RdRp)

  • Brought in by virus (released during uncoating).

  • Transcribes RNA sense strand from RNA template

  • Viral only protein good target for drugs.

Reverse Transcriptase (RT)

  • Used by retroviruses (e.g., HIV-1).

  • A.k.a. RNA-dependent DNA polymerase (RdDp).

  • Transcribes complementary ssDNA from ssRNA template

Host DNA-dependent RNA polymerase (RNA Pol or DdRp) makes mRNA

Retrovirus

  • Single-stranded RNA virus.

  • RT generates DNA copy.

  • DNA copy integrates into Host genome.

Retroviral (HIV) Reproductive Life Cycle
Attachment to CD4 or CXCR2
Entry
Uncoating

*Reverse transcriptase

  • Integrase (allows it to go into Host DNA).

    *i) Provirus state.

    *ii) Activation

Host transcription, Host translation
Assembly
Exit
Life-long Infection

*HIV (retrovirus)

Herpes family viruses (group I DNA viruses)

*8 herpes viruses infect humans

1) Herpes simplex virus type 1 (HSV-1; Oral Herpes)

2) Herpes simplex virus type 2 (HSV-2; Genital Herpes)

3) Varicella-zoster Virus (Chickenpox) -Reacts after symptoms pass.

4) Esptein-Barr Virus - Infectious Mononucleosis

Influenza/Flu Virus (Group V antisense RNA)

classifications by H# N#

Hemagglutinin

  • Viral surface protein.

  • Used to enter host cell

    *H1N1 → swine flu

Neuraminidase

  • Viral surface protein.

  • Used to exit from host cell

    *H5N1 → avian flu *-

  • Antigenetic Drift - little changes.

  • Antigenetic shift-rearrangement (happens every decade)

Coronaviruses

Group 4 RNA sense virus

S-Protein

route1-membrance

route2-endocytosis

ACE-2- Strokes in sleepMutation to help suvive

-D614G (Triad)

*Upper respritory so lower lung issues don’t happen+

*Omicron Family

*BA.1

*BA.2

*BA.3

Antivirals

  • Not as successful as antibiotics against bacteria.

  • Must target virus but not eukaryotic cells.

    *Targets

    Host or Virus

  • Integrase (viral)

  • Protease (viral)

  • Reverse transcriptase

  • Capsid / Spike proteins

  • Hemagglutinin

  • Neuraminidase

Protease Inhibitor

RTIs (Reverse Transcription Inhibitors)

1) AZT (Azidothymidine) - thymidine nucleotide analog

2) Acyclovir - guanosine analog - inhibits viral polymerase

HAART - Highly Active Antiretroviral Therapy

  • Prevent Viral Entry at CD4 receptors

  • Prevent Reverse Transcriptase

  • Prevent Integrase

  • Prevent Protease activity

    HAART reduces viral numbers for Chronic Disease

Viroids

  • Naked viral RNA, about 1/10th the size of normal viral RNA

  • Do not code for proteins themselves.

  • Infects plants

Prions

  • Proteins that abnormally fold then induce other proteins to abnormally fold.

  • Destroys nerve cells b/c too much bad protein

  • Break from convention that DNA or RNA is required for infection

  • 1st noticed in sheep → "scrapie"

  • Also found in cows → "mad cow disease" (Bovine Spongiform Encephalopathy)

  • In deer, elk → "chronic wasting disease"

  • In humans → Creutzfeldt-Jacob Disease

Immune System

  • Protection against pathogens - harmful organisms

    *toll likereceptors (TRLs)- recognise nonself

    *Spleen filters circulating blood

    *Multiple systems and organs

    *T cells mature in the thymus

    *B cells mature in the bone marrow

    *Transcription factor NF-kB- damage stimulus from cytokines. Heavy metals, radiation and viral antigens

    *Lymph acts as filtration and white blood cells inspect it

Two Major Types of Defense Systems

Innate/Non-specific

  • Old, mostly bacteria

  • Symptoms

    *Primary bacteria starts cells to fight cancer

Adaptive/Specific

*Evolving and precise hits viruses

Attacks and locks

*Evolving system

Innate/Non-specific Defense System

Surface barriers

  • Skin, mucous membranes

Internal defenses

  • WBCs (phagocytes, NK cells), antimicrobial proteins, inflammation, fever

Surface Barriers

*Generalized Protein/Ex Compliment/juntions

*multilayered skin=normal bacterial flora

*mucus, lysozyme, HCl (stomach) DNase, RNase

White blood cells (leukocytes):

Granuolcytes

*Basophils- release hestermine
    *Eosinophils- Kills aintidbody covered parasite(worms)
    *Neutrophils- stimulate inflammation
   Mast Cells release hestermine when cells damaged. They cells communicate and work together and developed

from a hematopieis

Monocyte-derived cells.

*Monocytes

*Macrophages.

*Dendritlic cells Phagocytosis. All Engulf microbial particles

Lymphocytes: T cells, B cells

T cells-Kill virus infected and cancer cells activate or inactivate others

B cells differentiate for Anitibodies

*Toll Proteins recognise microbes on the white blood cells.

Antibodies:

Part of Adaptive Humoral Immunity, made by B Cells

Cytokines:

Part of Systemic, signal proteins to tell cells they will alter other cells behavoir

Major histocompatibility complex

(MHC 1 or MHC2)- Tells us what codes our body can show and recognise

*T cell receptors recognise and binds Antigens from 2MHC and antigen cells.

Internal Defenses

  • Complement System: circulating liver proteins

Phagocytes

*Taxis to chase Adhere Engulf Digest Lysozyme Exocytose, season lyme

AP-Antigien Presenting cell

Natural Killer (NK) Cells

*Check is cell heathy? Induce death on virus/cancer infected cells

  • Apoptosis

Eosinophils

*Worm or parasite releases enzymes out and kills

*Helminths worms kill them

Inflammation *Spot Tender to tell you not to touch it!

Cytokines release and attack WBC to take out area.

*Anuploid or stress will occur

*Sequesters iron and sync needed to start. Bacteria is stop from getting resources by a reaction.

Adaptive/Specific Immune System

  • specific, looking for unique targets (Antigens/Epitope)- Look at anti bodies and blood system, subcelluar and Cellular

    *Two Arms Humoral and Celluar work in Adaptive

    *Memory is the reaction

B-cells (bone) called B-cells because they mature in Bone Marrow 1. Cyto Toxic 1. Celluar Recuit and Phagyocytes
T Cells- Coordinate innate attacks CD-4
Antigen

*Foreign object

*A Fragment of an invader (Peptide/protein)

  • RNA vacine from PHzer, moderna or Astraza, J&J and Novas from sinopharm

Generation of Immune System Cells

*Phagocytosis to get bacteris that are seasoned Macrophage/Dendric cells

*APC- Antigien Presenting cell eat season and break it down

*Stem adapt and cell become froms- RBC's(others)

*Bone Marrow- Lymphocyctes- Progenitor N cells

*Plasma cells

#T Cells (4main types)

1)CD8+ - Kill Cytoxic cells. *kill your self* Apoptosis

2)CD4+ - help the cells and learn of machophages. Activate the B cells.

3) suppressor T or regulatory cell block

4) Memory T React Fast- On and turn it into necessary auttoimmune disease

###Hematoporesis

Has all the steps of bone and what come from the thymus and adaptive to stop from cancer

Humoral Responsibility Anitgen Challenege

  1. Anitgen detecing

  2. TH replicate w/Cytokines

    3.Memory

    4 Somatic

    5Fallomes

E. coli : Normal gut E. coli: Prevent growth, digest foods we can't, make Vitamins K and B12. Some bacteria do cause disease. E. coli strain O157:H7:- Produces shiga toxin, damages intestinal lining, leading to bleeding sores. Causes cramping, diarrhea, then bloody diarrhea, dehydration, and fever. Young and old are more susceptible. Complications can lead to HUS (Hemolytic Uremic Syndrome).- RBC lysis leads to renal failure.
Staphylococcus Aureus: Staphylococcus aureus - strain of bacteria normally found on skin & nasal passages of ~30% people (no problems).
Clostridium difficile: Bacteria spread through improper handwashing (hospital-acquired infection - nosocomial).
Streptococci: May be caused by a polymicrobial infection consisting of both aerobic and anaerobic organisms or by a single organism such as Group A Streptococci.
Helicobacter pylori : Early 80s: Helicobacter pylori was suspected to be the cause/trigger. Australian doctors Barry Marshall and Robin Warren Nobel Prize 2005. Studied patients with inflamed epithelial cells. Theory: H. pylori stimulates overproduction of acid, kills stomach-lining cells, and causes inflammation; possible links to (rare cancer of GI mucosa lymphoid tissue). Now treat with amoxicillin, tetracycline, metronidazole (combo of any 2).- Side effects! Antibiotics also kill beneficial bacteria of gut, vagina → consume probiotics (e.g., yogurt).
Clostridium: Ex: aerobic vs. anaerobic (O2O_2 can be toxic for some bacteria: Clostridium).
Salmonella: Engineering Salmonella to swim to tumor cells to deliver drugs → apoptosis.
Clostridium botulinum: Botulinum toxin in improperly canned foods.- Clostridium botulinum bacteria. Even small amounts are poisonous (paralysis, respiratory failure). No honey or corn syrup to infants because of this bacteria.

Viruses:
Adenovirus (DNA) and Influenza (RNA): example shown in the notes describing the capsid of a virion/virus particle
Retrovirus: Single-stranded RNA virus. RT generates DNA copy. DNA copy integrates into Host genome. Example: HIV
Herpes family viruses: Life-long Infection: 8 herpes viruses infect humans: 1) Herpes simplex virus type 1 (HSV-1; Oral Herpes), 2) Herpes simplex virus type 2 (HSV-2; Genital Herpes), 3) Varicella-zoster Virus (Chickenpox) -Reacts after symptoms pass., 4) Esptein-Barr Virus - Infectious Mononucleosis
Influenza/Flu Virus (Group V antisense RNA): classifications