MICROBES EXAM

What gases were present in primitive atmosphere?

Water vapor, methane, ammonia, hydrogen, carbon monoxide

When was the earth formed?

4.6 billions years ago

What were the conditions of earth in the beginning?

Atmosphere was reducing (methane, CO₂, ammonia, nitrogen) with no O₂. Surface was very hot for millions of years (>100 C)

When did the earth cool and what did that allow?

4.2 bya, allowed water vapor to condense and form oceans

When did life arise?

3.5 bya , microfossils and stromalites

What are macrofossils?

Stromatolite (rock pile of dead bacteria) formed through microbial activity

What is the prebiotic soup hypothesis?

Proposes that organic molecules formed through energy sources (UV, light, lightning) in oceans. Accumulation of compounds led to early life forms

What is the importance of montmorillonite clay?

It is proposed as a catalyst for prebiotic reactions facilitating polymer formations

What is the importance of deep sea vents?

They are able to provide stable ecosystems powered by chemosynthesis . Possible origin of life as they offer consistent energy and presence of necessary biomolecules

What is the RNA world hypothesis?

RNA may have been the self-replicating enitity before the advent of DNA and proteins

What is phylogenetic inference?

The evolutionary history or natural history of organisms, derived from nucleotide sequence comparisons

What are the steps to infer phylogeny?

Acquire sequences data, align sequence data, use aligned data to generate a phylogenetic tree

How do you calculate evolutionary distances?

Counting the differences between the two strands and then dividing that number by the total amount of nucleotides in the sequence

What makes a good choice of sequence for phylogenetics?

Gene is present in all organisms of interest, not laterally transferred, an appropriate level of sequence conservation/divergence, large enough to contain a record of the historical information

What is the most useful gene sequence for phylogenetic reconstruction?

Ribosomal RNA

What are the three domains of life and their properties?

Bacteria: no membrane-enclosed nucleus, peptidoglycan cell wall, 70 S ribosomes

Archaea: no membrane-enclosed nucleus, ether-linked membrane , similar RNA polymerase to eukaryotes

Eukarya: membrane-enclosed nucleus, multiple organelles, 80S ribosomes

What are chemoorganotrophs and their properties?

Organisms that use organic chemicals (like glucose, acetate, etc) as their energy source (make ATP) . Examples are humans, animals, and fungi. [Glucose + O₂ —> CO₂ + H₂O ]

What are chemolithotrophs and their properties?

Organisms that use inorganic molecules as their energy source. Most organisms that do this live in extreme environments where organic molecules are not available. Examples are deep sea bacteria and archaea

What is carbon flow?

Produces CO₂ (waste) and supports biosynthesis

What is electron flow?

Electrons move through several proteins in the electron transport chain (ETC). They create a which establishes a gradient which then powers proton motive force which is used to make ATP

What are the key points of aerobic respiration?

Uses O₂ as final electron acceptor, high ATP yield

What are they key points of anaerobic respiration?

Uses other electron acceptors (nitrates, sulfate, etc), yields less ATP

What protein does the proton motive force power and what does it make?

ATP synthase, ATP

What are the electron receptors related to chemolithotrophs and inorganic compounds?

O₂ (if aerobic), NO₃^- , SO₄^-2, S⁰

What is carbon fixation?

The process of converting atmospheric CO2 into organic compounds, primarily through photosynthesis or chemosynthesis

What is biosynthesis?

Making new cellular materials

How can bacteria be identified?

Light microscopy (looking at size/shape/arrangement of cells), motility, and stains; capsule, spore, gram

What are the different shapes of bacteria and give one example of each?

Coccus: spherical, Staphylococcus aureus

Bacillus: rod shaped, Escherichia coli, Bacillus cereus

Spiral: rigid helix (spirilla spp.), or flexible helical (spirochetes) eg treponema pallidum

Describe the gram stain

Differentiates bacteria into gram positive and gram negative based on their cell wall. Gram positive stains purple and gram negative stains pink

What are the steps to gram staining?

Heat fix samples, stain with crystal violet, fix with grams iodine, decolorize with ethanol/acetone, and counterstain with safranin

What signifies gram positive bacteria?

Thick peptidoglycan layer (20-80nm), has teichoic acids

What signifies gram negative bacteria?

More complex with thin peptidoglycan (3-8nm), presence of an outer membrane that contains lipopolysaccharides (LPS), space between outer mem and cytoplasmic membrane is periplasmic space

What is the function of peptidoglycan and what is it weakness?

It provides structural rigidity and shape, it protects against osmotic lysis, the thicker it is the more it can withstand pressure. It is compromised by lysozyme which breaks it down and antibiotics targeting the cell wall

What are the basic features of peptidoglycan?

Alternating amino sugars form a glycan chain; N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM). Peptide chains linked to the glycan chain creating a cross- linked structure

What is important about mycoplasmas?

They lack peptidoglycan resulting in variable shapes and insensitivity to antibiotics that target that

What are some of the components of a gram- negative cell wall?

Lipopolysaccharide (LPS), lipid A, core O-antigen, phospholipid, Braun’s lipoprotein, peptidoglycan, outer membrane, periplasm, cytoplasmic membrane, porin

What is lipid A and why is it important?

Hydrophobic membrane anchor of LPS, recognized by innate immune system (Toll Like Recepttor-4) . It is responsible for causing endotoxic shock —> multiple organ failure. There are 200,00 deaths in the US due to endotoxins

What are the characteristics of the cell envelope in archaea?

Single membrane composed of monolayers of tetra-ether lipids (impermeable to protons), S-layer made of glycoprotein layers can resist extreme environmental conditions

What is the function and arrangements of flagella?

Flagella confer movement and allow bacteria to swim via rotational movement powered by an ion-driven rotary. Flagella can be arranged in monotrichous, lophotrikhous, amphitrichous, or peritrichous patterns.

What is chemotaxis?

Bacteria can move towards or away from any from chemical gradients

What are fimbriae?

Thin, filamentous structures that help bacteria adhere to surfaces via adhesins at their tips. Commonly peritrichous, important for forming biofilms

What are pili?

Similar structure to fimbriae but typically less in number and longer. Important for genetic exchange (conjugation) and motility (type IV pili)

What is E. coli P type or type 1 pili?

A type of pili composed of structural subunits (Pap A) and adhesins (Pap G) that bind to host epithelial cells, significantly in UTI s

What is bacterial growth kinetics?

The study of how bacteria grow and divide, often represented in terms of growth phases and population dynamics

What are the characteristics of the Lag growth phase of bacteria?

It is the initial stage where cells are adapting to a new environment, there is not immediate increase in viable count but cellular machinery is activated.

What factors lead to Lag phase of growth?

Depletion of ATP and ribosomes in cells, injury from prior conditions, adjusting to new medium conditions

What are the characteristics of the exponential phase (log phase) of bacteria growth?

Rapid binary fission, doubling the population size with each generations (2,4,8,16..). Mean doubling time of E. coli is approx 20 minutes. Plot of population on a log scale results in straight line

What are the characteristics of the stationary phase of bacteria growth?

Growth rate equals death rate, population stabilizes

What factors lead to stationary phase of bacteria growth?

Nutrient limitation (eg no glucose or oxygen) and accumulation of toxic waste (like lactic acid)

What is the process of binary fission?

1. Cell elongation to 2x its original length

2. DNA replication and attachment to the membrane

3. Formation of the septum to divide the cells

Describe the FtsZ protein

It is critical in cell division as it polymerizes to form a ring at the cells midpoint, marking the division site. It contracts to facilitate septum formation and subsequently disassembles for daughter cell separation

Describe the MreB protein

A protein present in rod-shaped bacteria configuring cell growth longitudinally. Actin homologue that aids in peptidoglycan synthesis machinery movement, helping separate chromosomes

What are the optimal growth conditions and expand on them

Carbon source: carbs for energy, cells are 50% carbon

Nitrogen source: vital for protein synthesis (ex: ammonium chloride)

Trace elements: required in minute amounts for enzymatic reactions (eg Cu, Co, Ni)

Growth factors: eg vitamins and nucleotides present in nourished media like blood agar plates

What is viable count?

Measures the number of living cells using colony-forming units on solid media

What is optical density (turbidity)?

Measures light absorption through liquid cultures, indicating cell density based on how turbid the medium appears

What is minimum cardinal temperature (Tmin)?

Lowest temperature at which microbial growth occurs. Below is when growth ceases due to membrane gelling

What is optimum cardinal temperature (Topt)?

Temperature that promotes maximum enzymatic activity

What is maximum cardinal temperature (Tmax)?

Highest temperature at which microbial growth occurs. Above this temperature enzymes denature and cellular structures collapse

What are psychrophiles?

Microorganisms that thrive at low temperatures (<15 C)

What are mesophiles?

Microorganisms who thrive in intermediate temperatures (15 - 45 C)

What are thermophiles?

Microorganisms who prefer high temperatures (45 - 80 C)

What are hyperthermophiles?

Microorganisms who survive in extremes (>80 C) , found in hot springs and hydrothermal vents

What temperature and pressure kills known germs including viruses?

Autoclaving at 121 C and under high pressure (139 kPa)

What is D-value?

Measures the time required to reduce bacterial population by 90%. Used in food preservation to ensure safety and eliminate viable cells effectively

What are viruses and some of their main characteristics?

Infectious, obligate intracellular parasites, unable to replicate independently. They do not exhibit all characteristics of living organisms and are composed of nucleic acids (DNA or RNA) surrounded by a protein coat (caspid). They cannot make ATP and do not have ribosomes

What size classifies pandoravirus?

MASSIVE 1 micrometer , 2.5 million base pairs (dsDNA)

What sizes do viruses usually range?

20 nm to 1.5 micrometers

What is virion?

The extracellular state of a virus, consists of a nucleic acid enclosed in a capsid

What distinguishes retroviruses?

Use RNA genome and replicate with a DNA intermediate (eg HIV)

What distinguishes hepadnaviruses?

DNA genome that replicates via RNA intermediate (eg Hep B)

What are the steps of the virus replication cycle?

1. Attachment: virus binds to host cell receptors

2. Penetration: virus enters the cell endocytosis

3. Uncoating: capsid breaks down, releases viral genome

4. Synthesis: host machinery synthesizes viral nucleic acids and proteins

5. Assembly: viral components assemble into new virions

6. Release: mature virions exit the host cell, often via budding

What is the intracellular state of a virus?

The genome is released upon entry into the hostel cells, leading the virus replication. The virus manipulates the host cellular machinery for its own replication and assembly

What phases occurred during the One-Step Growth Curve ? (when E. coli is infected with bacteriophages)

Eclipse phase: separation of coat and nucleic acids

Latent period: replication and assembky

Rise period: increased detection of extracellular viruses

What is burst size?

The number of virions released from one cell, typically less than 1,000

What are some common example viruses?

Poliovirus: 5% paralysis, 95% asymptomatic

Herpes virus: causes cold sores and genital infections

Measles and Mumps viruses: paramyxovirus family, enveloped and helical

When did fungi evolve on land?

430 million years ago

What are organoheterotrophs and what is the main example?

Organisms that obtain both carbon and energy by consuming organic compounds. They break down polymers outside their cells using hydrolytic enzymes. The main example is fungi.

What are the distinctive features of fungi?

Cell walls made of chitin, eukaryotic cells; mostly haploid and predominantly aerobic

What are the phylogenetic classifications of fungi and their distinctions?

1. Microsporidia: approx 1300 species , mostly parasitic (eg. on bees)

2. Chytridiomycota (Chytrids): waterborne, flagellated spores, essential for ecological functions

3. Mucoromycota (Zygomycetes): known for food spoilage, Rhizopus nigricans

4. Ascomycota (Sac fungi): largest group of fungi with significant economic relevance, penicillium and aspergillus

5. Basidiomycota (Club fungi): includes mushrooms and related fungi, known for macroscopic fruiting bodies

What are yeasts?

Unicellular fungi that reproduce by budding

What are filamentous fungi?

Multicellular fungi comprised of hyphae, forming mycelium networks; exhibit polarized growth

What are dimorphic fungi?

Can switch between yeast-like and filamentous forms based on environmental conditions

What is hyphal growth of fungi?

Occurs as the tip where growth can be rapid. Hyphae release enzymes for nutrient absorption into their environment

What are the two hyphal structures?

Septate: divided by perforated septa allowing nutrient flow

Coenocytic: uninterrupted with multiple nuclei

What is special about Spitzenkörper and what does it contain?

A structure at the tip of the hyphae in the apical region. It contains membrane-bound vesicles filled with enzymes for cell wall biosynthesis. It also contains actin filaments that facilitate the movement of materials into the growing tip

How many bacteria live within us?

3.8 × 10^13

What is the weight of the total bacterial biomass in a person?

3 lbs

Describe the body sites where microbiota are found and their charactersitics

Skin: low diversity (<180 species), main bacteria are Staphylococcus epidermidis, Propionibacterium acnes

Nasal Cavity: harbors opportunistic pathogens like Neisseria meningitidis

Oral Cavity: rich in many species (>300), primary colonizers include Streptococcus sanguis which attach to teeth surfaces

Stomach: acidic with pH of 2, includes Helicobacter pylori, capable of causing gastric ulcers and cancers

Intestinal Tract: small intestine has lower bacterial density but colon has massive fermentation housing 10^10/11 bacteria

What is an example of how microbiota changes with age?

Bifidobacterium decreases after age 60

What is dysbiosis and what are some treatments?

Dysbiosis is an alteration in the microbiota composition that can lead to health issues. Treatments include fecal microbiota transplant (FMT) which is used to treat antibiotic resistant infections and a change in diet

What are the stages in disease process?

Entry into host, multiplication in the host, interference with host defenses, and host damage (role of endo and exotoxins

What are the properties of exotoxins?

Heat labile, soluble simple proteins, secreted extracellularly (many are enzymatic), often encoded by bacteriophages and plasmids

What are the 3 types of extoxins and describe them?

1. Enterotoxins: affects GI tract, abnormal fluid secretion, examples are: Cholera toxin, heat- labile enterotoxin, Shiga toxin

2. Cytotoxins: target general tissues, kill cells enzymatically. example is Membrane-disrupting cytotoxins which form pores in host cell membranes (ex: streptolysin O)

3. Neurotoxins: interfere with nerve impulse transmission, example is Botulinum toxin

What is the mechanism of botulinum toxin?

Composed of heavy and light chains (A-B toxin), heavy chain enters neuron by binding to glycoprotein receptors, light chain inhibits acetylcholine release causing flaccid paralysis. Floppy baby syndrome for infants exposed to spores in honey

How does cholera toxin work?

1active (A) and 5 binding (B) subunits. A enters cells and increased cAMP which causes severe fluid loss (15 L/day) . Binds to GM1 ganglioside, disrupting ion transport

What are endotoxins and their effects?

Heat-stable lipopolysaccharides (LPS) present in the outer membrane of Gram-negative bacteria. When released upon cell lysis can cause toxic shock, esp following antibiotic treatment. Vesicles containing lipid A (a toxic component causing triggering effects) can bleb off from bacteria and enter host tissues

What is the main difference between exotoxins and endotoxins?

Exotoxins vary significantly among pathogens, presenting unique symptoms. Endotoxins exhibit similar effects across diff bacteria primarily causing toxic shock responses

What are the ways a virus can be classified?

Morphologically

Helical or Icosahedral form

Naked or Membrane- bound (enveloped)

What are the 4 ways viruses are transmitted?

Inhalation: via respiratory tract

Ingestion: through GI tract (primarily for naked viruses)

Inoculation: contact w skin or mucous membranes (iatrogenic transmission eg rabies from blood transfusion)

Congenital: from mother to fetus (rubella)

What are the different laboratory diagnoses you can do with viruses and what parts of the virus do they use?

Electron miscropy (EM) —> whole virus

Immunological tests for detections —> viral antigen

PCR —> viral nucleic acid

IgM/ IgG in blood tests —> specific antibody response