Exam 1

4 Cellular Microorganisms and examples

Fungi (yeasts, molds), Protists (algae, protozoa, slime molds), Bacteria ($Escherichia\,coli$), and Archaea (methanogens).

Acellular organisms

Viruses (composed of protein and nucleic acid), Viroids (composed of RNA), Virusoids (composed of RNA), and Prions (misfolded protein)

What are the 3 domains

Bacteria, Archaea, and Eukarya.

Domain Archaea

unique rRNA sequences, lack of peptidoglycan in cell walls, and unique membrane lipids; many live in extreme environments.

Svedbergs (S)

A unit used to measure how fast molecules settle down in a centrifuge, used to distinguish ribosome sizes (e.g., $70S$ vs $80S$).

Would you find sterols (cholesterol) in bacterial cytoplasmic membrane?

No, bacteria membranes have hopanoids. Archaea have isoprenes

Size of ribosomal subunits?

Prokaryotes = 70S (50+30). Eukaryotes have 80S (60+40)

T/F, archaea have peptidoglycan in their cell walls?

False

Viruses

The smallest of all microbes, require a host cell to replicate. Composed of protein and nucleic acid

Viroids and Virusoids

Infectious agents composed of RNA.

Prions

Infectious agents composed of misfolded proteins.

Characteristics of a living cell

Energy use/metabolism, respond to environmental stimuli, homeostasis, growth/development, reproduction, biological evolution

What organism can defy the dental dogma of molecular biology?

Retroviruses

Antony van Leeuwenhoek

The first person to accurately observe and describe microorganisms

Francesco Redi

Discredited spontaneous generation by demonstrating that maggots on decaying meat came from fly eggs.

John Needham

Broths in flasks: boiled then sealed = broth became contaminated

Lazzaro Spallanzani

Broth in flasks: sealed first then boiled = no growth of microorganisms

John Tyndall

Demonstrated that dust carries microorganisms. Provided evidence for the existence of exceptionally heat-resistant forms of bacteria.

Louis Pasteur

Flasks with long curved necks. Break the necks = no longer sterile. Pebrine disease of silkworms caused by protozoan.

Ferdinand Cohn

Discovered that heat-resistant bacteria could produce endospores.

Agostini Bassi

Disease of silkworms caused by fungus

M.J Berkeley

Potato blight of Ireland caused by water mold

Heinrich de Bary

Smut and rust fungi caused cereal crop diseases

Ignaz Philipp Semmelweiss

A Hungarian doctor who concluded that handwashing could prevent childbed fever

Joseph Lister

A Scottish surgeon who implemented the use of antiseptics to clean surgical instruments to kill germs.

William Stewart Halsted

An American surgeon who became one of the first to use rubber gloves during surgery to prevent the spread of microbes.

Robert Koch

Established relationship between bacillus anthracis and anthrax. Developed Koch’s postulates (teacher Jacob Henle). Credited with development of agar, Petri dish, nutrient broth, methods for isolation

Koch’s Postulates

1. Organism must be isolated from pt with disease

2. Organism cultured outside the body (in vitro)

3. Isolated organism must cause disease in healthy animal

4. Organism must be recovered

5. The antibody should be detected in the pt’s serum

Limitations of Koch’s postulates (and potential solutions)

1. Some organisms cannot be grown in culture (study these with genomic techniques)

2. Asymptomatic host (measure microbial load)

3. Using humans is unethical (use animals)

Charles Chamberland

Porcelain bacterial filters to study tobacco mosaic disease (filtering out infectious agents)

Pasteur and Roux

Weakened viruses lose their ability to cause disease. Development of vaccines for chicken cholera, anthrax, rabies

Edward Jenner

Milkmaids that had exposure to cowpox wouldn’t get smallpox

Nosocomial Infections

Hospital-acquired infections (HAI), including urinary tract infections, surgical site infections, bloodstream infections, and pneumonia.

Micronutrients

Also known as trace elements, these include Mn, Zn, Co, Mo, Ni, and Cu; they are ubiquitous in nature and serve as enzymes and cofactors.

Autotrophs

Organisms that use $CO_2$ as their sole or principal biosynthetic carbon source.

Heterotrophs

Organisms that use reduced, preformed organic molecules from other organisms as their carbon source.

Phototrophs

Use light as their energy source

Chemotrophs

Obtain energy from the oxidation of chemical compounds, whether organic or inorganic.

Lithotrophs

Use reduced inorganic substances as their electron source.

Organotrophs

Obtain electrons from organic compounds.

Adenosine 5'-triphosphate (ATP)

The primary energy currency of the cell, composed of adenine, ribose, and three phosphate groups.

Lag Phase

The initial phase of the microbial growth curve where cells are synthesizing new components and adapting to new conditions, but not yet dividing.

Exponential Phase

Also called the log phase; the stage where the rate of growth and division is constant and maximal, characterized by balanced growth.

Stationary Phase

The phase in a closed system where growth ceases and the total number of viable cells remains constant, often due to nutrient limitation or toxic waste accumulation.

Viable But Not Culturable (VBNC)

A hypothesis for the senescence/death phase stating that cells are alive but dormant and capable of growth only when conditions become favorable.

Acellular Agents

Entities including viruses (protein/nucleic acid), viroids (RNA only), virusoids (RNA only), and prions (proteins only).

Virion

A complete virus particle that consists of at least one molecule of DNA or RNA enclosed in a protein coat and cannot reproduce independently of living cells.

Nucleocapsid

The basic structure of all virions, composed of nucleic acid (DNA or RNA) and a protein coat called a capsid.

Protomers

The individual protein subunits that self-assemble to form the viral capsid.

Enveloped Viruses

Virions that possess an outer, flexible, membranous layer derived from the host's plasma or nuclear membranes.

T/F RNA viruses must carry in their own RNA reverse transcriptase on its genome

True

Peplomers

Also known as spikes, these are viral-encoded envelope proteins that project from the surface and are involved in attachment to host cells.

Viral genome can be

Single or double stranded DNA or RNA. Can be segmented or circular

Virion release

Nonenveloped - lyse the host cell

Enveloped - first incorporated into host membrane. Budding

Lysogeny

A relationship where a temperate phage integrates its genome into the host's genome (forming a prophage) without destroying the host cell.

Induction

The process where a prophage is triggered to initiate the synthesis of new phage particles and enters the lytic cycle.

Cocci

Spherical-shaped bacteria. Streptococci (chains), staphylococci (grape-like clusters)

Bacilli

Rod-shaped bacteria. Coccobacilli (very short rods)

Vibrios

Comma-shaped bacteria that resemble rods.

Spirilla

Bacteria with a rigid helical shape. Spirochetes (flexible helices)

Mycoplasma

The smallest known bacteria, measuring approximately $0.3\,\mu m$. Does not produce a cell wall; is more resistant to osmotic pressure and can survive in hypotonic environment.

How many nm in a micrometer?

1 micrometer = 1000 nm

Where does electron transport chain occur in prokaryotes?

Plasma membrane (no mitochondrial membrane)

Amphipathic lipids

Lipids possessing both polar (hydrophilic) ends and non-polar (hydrophobic) tails.

Peripheral proteins

Membrane proteins that are loosely connected to the membrane and easily removed.

Integral proteins

Amphipathic membrane proteins that are embedded within the membrane.

Hopanoids

Sterol-like molecules found in bacteria that stabilize the plasma membrane, serving as the bacterial version of cholesterol.

Peptidoglycan (murein)

Located outside the cell membrane, unique to bacterial cell walls. Thick in gram positive (stain purple). Thin in gram negative (stain pink).

Cell wall functions

Maintain shape, protect from osmolytic lysis, protect from toxic materials, contribute to pathogenicity (ability to cause disease)

Peptidoglycan structure

Alternating sugars (N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)) , alternating D and L amino acids

Peptidoglycan cross linkage

Helical shape. Cross-linked by peptides for strength (pentapeptide bridge)

What sugar will amino acids bind to in peptidoglycan structure? Where does pentapeptide bridge attach?

Amino acids bind to NAM (L-Ala, D-Glu, DAP or Lys, D-Ala, etc.). Pentapeptide bridge connects 3rd and 4th position on NAM. Consists of 5x Gly.

Teichoic acids

Negatively charged polymers found in Gram-positive cell walls that help maintain the cell envelope and may bind to host cells.

Gram negative cell walls

Thin layer of peptidoglycan, no teichoic acid, outer membrane consisting of lipids, lipoproteins, LPS (lipopolysaccharide)

Braun’s lipoproteins

Connect outer membrane to peptidoglycan

Lipopolysaccharide (LPS)

A complex molecule in the Gram-negative outer membrane consisting of lipid A, a core polysaccharide, and an O side chain (O antigen).

O side chain (O antigen)

The part of the LPS that extends out from the cell and elicits an immune response.

Periplasmic space

Space between the outer and inner membrane in Gram-negative bacteria, $20-40\%$ of cell volume. Hydrolytic enzymes, transport proteins, etc.

Porin proteins

Proteins that form channels in the Gram-negative outer membrane allowing small molecules of to pass through. Makes so outer membrane is more permeable than plasma membrane

Plasmolysis

The shrinking of a cell that occurs when it is placed in a hypertonic environment and water leaves the cell.

Lysozyme

An enzyme that breaks the bond between NAG and NAM in peptidoglycan.

How does penicillin work?

Inhibits peptidoglycan synthesis (alters FUTURE cells after reproduction)

Protoplasts

Gram-positive cells without a cell wall

Spheroplasts

Gram negative bacteria without a cell wall. Typically retaining two membranes.

Slime layer

A diffuse, unorganized layer of extracellular material that is easily removed and aids in adherence.

Capsule

An organized, amorphous gelatinous layer surrounding the bacterium that determines serological type within a species. Composed of polysaccharides which vary based on bacterial species.

Inclusions

Granules of organic or inorganic material, also known as microcompartments, stockpiled by the cell for future use.

Magnetosomes

Inclusions found in aquatic bacteria containing magnetite particles used for orientation in Earth's magnetic field.

Nucleoid

Non-membrane bound region containing the closed circular, double-stranded DNA molecule. Usually one copy of chromosome.

Supercoiling

Protects DNA in nucleoid, assisting by nucleoid associated proteins (NAP). NAPs differ from histones in eukaryotes.

Plasmids

Small, closed circular extrachromosomal DNA molecules that replicate independently and may confer selective advantages like drug resistance. Helpful but not required for core survival

Loss of a plasmid

Curing

Fimbriae

Short, thin, proteinaceous appendages that mediate attachment to surfaces

Sex pili

Appendages that are longer and thicker than fimbriae, encoded by plasmids, and required for conjugation.

Flagella

Threadlike locomotor appendages required for motility. Must be specifically stained for observation under bright field microscope

Patterns of flagella distribution

3 parts of flagella

Filament - composed of flagellin protein

Hook - links filament to basal body

Basal body - series of rings that drive flagellar motor

Endospore

A highly resistant, dormant structure containing a dehydrated core, calcium complexed with dipicolinic acid, and SASPs (protect genetic material).