Microorganisms Flashcards
What elements do eukaryotic and prokaryotic cells have in common?
- Cytoplasmic membrane
- Cytoplasm
- Ribosomes
- Genome (Chromosome + Plasmid)
What kind of nucleus, organelles, internal organization, and division method do eukaryotes have?
Membrane bound nucleus, membrane bound organelles, complex internal organization, and division through mitosis/meiosis
What are two major groups of eukaryotic microbes and their subgroups?
Protists: protozoa, algae, slime molds/water molds
Fungi: yeasts, molds, mushrooms
What is a protist? Give three examples.
A Protist is a uni/multicellular eukaryotic microorganism that does not differentiate into tissues. E.g. Protozoa, Algae, Slime Molds/Water Molds
What differentiates protozoa, algae, and slime/water molds?
Protozoa: animal-like
Algae: photosynthetic and plant-like
Slime/water mold: filamentous
What is a fungi? Name three examples.
Saprophytic (decomposer) organisms with true differentiated multicellularity that can be unicellular, filamentous, or multi-cellular. E.g. yeast, molds, mushrooms.
What differentiates yeasts, molds and mushrooms?
Yeasts: unicellular fungi
Molds: filamentous fungi
Mushrooms: multicellular fungi
What kind of nucleus, organelles, internal organization, and division method do prokaryotes have?
Non-membrane bound nucleus, non-membrane bound organelles, simple internal organization, and division through binary fission.
What are two major groups of prokaryotic microbes?
Bacteria (eubacteria) and Archaea (archaebacteria)
Compare and contrast Bacteria and Archaea based on genetics, metabolism, and pathogenicity.
Bacteria: genetically diverse, diverse metabolic style, can be pathogen/non-pathogen
Archaea: genetically and biochemically distinct from bacteria, diverse metabolic style, non-pathogen.
What is a virus? What is its size? What is unique about their metabolism?
Viruses are acellular obligate intracellular parasites. They are extremely small and they lack independent metabolism because they lack ribosomes and rRNA.
When did anaerobic life first appear?
Anaerobic life first appeared 3.8-3.9 million years ago
When did photosynthetic bacteria oxygenate the earth, and what did it cause?
2 billion years ago, photosynthetic bacteria oxygenated the earth and allowed the evolution of modern eukaryotic microorganisms.
When did the first plants and animals appear?
The first plants and animals appeared 0.5 billion years ago.
What is the difference in prokaryotic vs eukaryotic ribosomes?
Prokaryotes have 70S ribosomes and 16S small subunit rRNA.
Eukaryotes have 80S ribosomes and 18S small subunit rRNA.
What is a phylogenetic tree?
A graphic representation of evolutionary distance between organisms.
What are the three distinct domains of life in microorganisms? Compare their genetics with those of animals and fungi.
Bacteria, Archaea and Eukarya. Microorganisms of these domains are more genetically diverse than plants and animals.
How do you define phylogenetic species?
A group of strains that share certain diagnostic traits, are genetically cohesive, and have a unique recent common ancestor.
What are three elements that define if strains are of the same phylogenetic species?
- most (but not all) characteristics in common
- greater than 97% sequence similarity in the 26S rRNA gene
- high degree of genome similarity discovered through DNA-DNA hybridization
What is an example of a microbe that is viewed through dark-field microscopy?
Treponema palladium: the causative agent of syphilis.
Give 6 Types of Cell Morphology and examples.
- Coccus (round) - Streptococcus pyogenes
- Bacillus (rod) - E. coli
- Spirillum (spiral) - Spirillum volutans
- Spirochete (spiral and flexible) - Treponema pallidum
- Budding/Appendaged bacteria (appendaged) - Caulobacter crescentus
- Filamentous bacteria (stringed) - Streptomyces griseus
Which morphologies are results of selective forces?
Small cells with high SA-V ratio: result of optimization for nutrient uptake
Helical/Spiral: development of swimming motility as a result of environments near surfaces
Filamentous: development of gliding motility
What is the average size for E. coli and Staphylococcus aureus?
E. coli: 1.0 x 3.0 micrometers
Staphylococcus aureus: 1.0 micrometer diameter
What are examples of very big and very small prokaryotes?
Mycoplasma genitalium: 0.3 micrometers
Epulopiscium fishelsonii; 80 x 600 micrometers
What is the advantage of high SA:V ratio?
They support greater nutrient exchange per unit cell volume and tend to grow faster than larger cells.
What are the lower limits of cell size?
<0.15 micrometer diameter is unlikely
Why are pathogenic bacteria small?
They are missing many genes whose functions are supplied to them by the host.
What is the purpose of a cytoplasmic/plasma membrane?
It is a vital semipermeable barrier that separates cytoplasm from the environment and allows specific substances to enter and leave the cell.
What is the phospholipid bilayer?
Double layer of phospholipids that have the hydrophobic fatty acid tails pointing inwards and the hydrophilic fatty acid heads facing outwards.
What components is the cytoplasmic membrane composed of?
- Phospholipid bilayer
- Embedded proteins (integral and peripheral)
- Mg2+ and Ca2+ (stabilizes membrane by forming ionic bonds with the negative phospholipid heads)
What is the periplasmic space? How big is it?
Gel-like space in between the two phospholipid bilayers of a gram-negative bacteria that holds many proteins. It is around 15 nanometers wide.
What is a periplasmic protein?
Proteins embedded in the periplasmic space of gram-negative bacteria that allow transport into and out of the cell.
What is the difference between an integral protein and a peripheral protein?
Integral membrane: embedded in the membrane in a way where it penetrates the membrane partially or fully (transmembrane protein)
Peripheral membrane: embedded on the surface of the membrane without penetrating it.
What is the difference between Ester link and Ether link
Ether linkages (C-O-C) in Archaea join the isoprenes to the glycerol heads.
Ester linkages (C-O-CO) in Eukarya/Bacteria join the fatty acids to glycerol heads.
Whats the difference between a lipid bilayer and a lipid monolayer?
Lipid bilayer: Archaeal membrane with 2 layers of 20C glycerol diether.
Lipid monolayer: Archaeal membrane with one layer of 40C diglycerol tetraether.
What is the evolutionary advantage of a lipid monolayer over a bilayer?
Lipid monolayer membranes are extremely heat resistant and commonly found in hyperthermophillic Archaea.
What are the three major classes of transport systems in prokaryotes? How do they differ?
- Simple transport: driven by energy in proton motive force
- Group translocation: chemical modification of the transported substance, driven by phosphoenolpyruvate
- ABC transporter: periplasmic binding proteins are involved and energy comes from ATP.
What are three examples of simple transport?
- Uniporters: transport in one direction across the membrane
- Symporters: co-transporters, aka transports two molecules at once
- Antiporters: transport one molecule across the membrane in one direction, and another molecule in the other direction.
How do ABC transporters work?
Solute binding protein in the periplasm attracts specific substrates, depositing them into an integral membrane transporter. ATP hydrolyzing protein supply the energy needed to send the substrate to the other side of the membrane.
What is the difference between ABC transport systems in gram positive and gram negative bacteria?
Gram-negative: use periplasmic-binding proteins found in between two membranes.
Gram-positive: use substrate-binding lipoproteins anchored to external surface of cell membrane
What do ABC transport systems take into the cell?
Organic compounds (sugars, amino acids), inorganic nutrients (sulfate, phosphate) and trace metals.
How does group translocation work?
PEP donates a phosphate to a phosphorelay system, transferring it through a series of carrier proteins and deposits it into a sugar (glucose, fructose, mannose) as it is brought into the cell.
What are 4 functions of the cell wall of bacteria and archaea?
- Cell wall prevents expansion (lysis)
- Protects against toxic substances (large hydrophobic molecules such as detergents and antibiotics)
- Helps evade host immune system and stick to surfaces
- Partly responsible for cell shape
Difference between gram negative and gram positive cell walls?
Gram-negative cell wall: Thin peptidoglycan layer and lipo-polysaccharide outermembrane.
Gram-positive cell wall: thick peptidoglycan layer
What is peptidoglycan?
A polysaccharide that provides strength to the bacterial/archaeal cell wall.
What are the horizontal linkages in the peptidoglycan of gram negative and gram positive bacteria?
Horizontally: N-acetylglucosamine and N-acetylmuramic acid joined together through a beta 1,4 glycosidic linkage.
What are the vertical cross linkages in the peptidoglycan of gram negative and gram positive bacteria?
gram-negative: peptide bond formed between DAP and the terminal D-alanine of another glycan chain
gram positive: linkage MAY be formed through a Glycine bridge between Lysine and terminal D-alanine.
What are teichoic acids and lipoteichoic acids?
Teichoic acids: acidic substances embedded in the peptidoglycan of gram positive bacteria
Lipoteichoic acids: acidic substances covalently bound to membrane lipids and stick out of the peptidoglycan.
What prokaryotes lack cell walls and why?
Mycoplasmas: group of pathogenic bacteria with sterols in membrane that have a role in rigidity and strength
Thermolasma: species of archaea with lipoglycans in membrane used as a strengthening effect
What is the lipopolysaccharide (LPS) layer? What are the components within the LPS layer?
A layer in the outer membrane in a gram negative bacteria. It is made of Endotoxin (lipid A) which attaches to a core poly saccharide which attaches to O-polysaccharide
What are porins?
Tri-opening channels for movement of hydrophilic low-molecular weight substances in the outer membrane of a gram negative bacteria.
How does the positive and negative Cell Wall structure interact with the gram stain?
G-ve: crystal-violet iodine complex is extracted from the cell by alcohol and appear invisible
G+ve: crystal-violet iodine complex is not extracted from the cell because the cell wall dehydrates and its pores close preventing CV-I from escaping and retaining the stain.
What are the cell wall types of archaea?
- Single membraned cell wall of psudomurein instead of peptidoglycan
- S-layers
- No cell wall.
Whats the 3 differences between peptidoglycan layer and pseudomurein?
- Alternates polysacharrides N-acetylglucosamine and N-acetyltalosaminuronic acid (…G-T-G…)
- Its glycosidic bond is beta 1,3 which is immune to lysozymes, allowing archaea to be unaffected.
- It has the normal L amino acids rather than D amino acids
What are S-Layers?
The most common type of cell wall type among archaea (and some bacteria) that consist of paracrystalline structured protein/glycoproteins. Some archaea only have an S-layer without any other cell wall component, but most have other elements.
What are proteins?
polymers of amino acids that account for 50% of dry mass of most cells and are used as enzymes, defence, storage, transport, cellular communication, movement, and structural support.
what is the nucleoid?
the nucleoid is the region that contains the genome
What does the typical bacterial genome consist of?
Single circular double-stranded DNA chromosome, and may also contain one or more plasmids.
What are plasmids?
Plasmids are smaller circular, self-replicating, double stranded DNA that carry NON-ESSENTIAL genes that gives them selective advantages.
What are ribosomes? Which ribosome is in bacteria?
Molecules of protein + rRNA that translates the mRNA strand into specific amino acids which form polypeptides and proteins. Bacteria have 70S ribosomes.
What are the parts of the 70S ribosome? What type of rRNA is used?
30S subunit (small subunit): contain 16S rRNA
50S subunit (large subunit): contain 23S and 5S rRNA
What is the difference between plasma membrane proteins and cytoplasmic ribosomes?
Plasma membrane proteins: create membrane proteins as well as proteins to be exported from the cell
Cytoplasmic ribosomes: cytoplasmic proteins
What are structures found on the outside the cell’s surface?
- Capsules/Slime Layers
- Fimbriae
- Pili
What are capsules and slime layers?
Polysaccharide/protein layers with varying thickness and rigidity that assist in attachment to surfaces, protect against phagocytosis and resist desiccation.
How are fimbriae and pili similar and different?
Similar: filamentous protein structure that assist in surface attachement
Different: fimbriae form pellicles, Pili may be involved in twitching motility (IV) and conjugation.
What are cell inclusion bodies? What are 4 types
Visible aggregates in cytoplasm for storage.
- Carbon storage polymer
- Polyphosphates
- Sulfur globules
- Magnetosomes
What are the two types of Carbon storage polymers and what do they do?
Poly-beta-hydroxybutyrate (PHB): stores lipids
Glycogen granules: polymer of glucose
What are two types of inorganic inclusion bodies?
Polyphosphate granules (volutin): storage of phosphates and energy
Sulfur globules: storage of sulfur used in energy generation
What is a magnetosome?
Magnetic inclusion bodies (granules of Fe3O4 or Fe3S4) that give the cell magnetic properties which allows it to orient itself in a magnetic field and migrate along earth’s magnetic field.
What are gas vesicles?
Spindle-shaped, water impermeable structures made of protein that are filled with gas which decreases cell density and allows them to be buoyant.
What are endospores? Where do they appear?
Highly differentiated cells that are resistant to heat, harsh chemicals and radiation. They appear in the dormant stage of bacterial life cycle and are ideal for dispersal via wind, water or animal gut.
What type of bacteria produces endospores?
Only produced by some gram positives including anaerobic/aerobic gram +ve rods.
What are the protective layers of the endospore?
- Spore coat and cortex: protect against chemical, enzymes, physical damage and heat
- Two membranes: permeability barriers against chemicals
- Core: dehydrated to protect against heat, contains Ca-dipicolinic acid and small acid soluble proteins (SASP) to protect against DNA damage.
What forces can endospores resist?
- Boiling for hours
- UV radiation
- Chemical disinfectants
- Dessication
- Age
What are the stages of a lifecycle of a spore forming bacterium
Stage 1: Asymmetric cell division but identical chromosomes
Stage 2: Cell division divides cell into the mother cell and the prespore
Stage 3: Mother cell engulfs the forespore which allows the forespore to be surrounded by two membranes
Stage 4: Thick layers of peptidoglycan form between the two membranes to create the the cortex
Stage 5: Protein layers surround the core wall to create the spore coat and/or exosporium for protection from chemicals and enzymes
Stage 6: endospore matures and core is dehydrated
Stage 7: Mother cell is lysed and mature spore is released
What is a flagellum? What are the types of flagella?
Hollow protein filament for swimming motility that can be used for identification.
- Monotrichous: single flagellum
- Amphitrichous: flagella at opposite ends
- Lophotrichous: multiple flagella in a single tuft
- Peritrichous: flagella distributed around cell
What are the parts of a flagellum?
- Filament: rigid helical protein composed of flagellin
- Hook: coupling between filament and basal body
- Basal body (motor): central rod that passes through series of rings (L, P, MS, C)
What is the difference between a polar and a subpolar monotrichous flagellum?
polar: extends from the end
subpolar: extends from the rest of the body
How does a flagella move?
Mot proteins form a channel that allows H+ to move into the cytoplasm which provides the energy to turn the flagellum like a propeller
What is the proton concentration inside and outside of the bacteria?
Outside bacteria: high H+
Inside bacteria: low H+
How are flagella synthesized?
- MS ring synthesized in inner membrane
- C ring synthesized in the inner membrane
- Mot protein synthesized in inner membrane
- P ring synthesized in the peptidoglycan layer
- L ring synthesized in the outer membrane
- Early hook synthesized from the L ring
- Late hook cap synthesized at the end of the early hook
- Filament is synthesized as an extension of the hook.
What are the different swimming motions in flagellated bacteria?
Peritrichous: bundled flagella to run (CCW), tumble flagella (CW)
Polar: CCW-CW (forward and backward), CW-reorient-CW (forward, reorient, forward)
What are examples of motions in non-flagellated bacteria?
Gliding: motility mechanism via gliding-specific proteins. (helical motion)
Twitching: motility mechanism via type IV pili. (grappling hook)
What is taxis? What are the 5 types?
Directed movement in response to chemical or physical gradients.
- Chemotaxis: response to chemicals
- Phototaxis: response to light
- Aerotaxis: response to oxygen
- Osmotaxis: response to ionic strength
- Hydrotaxis: response to water
How does chemotaxis work?
Bacteria respond to temporal (not spatial) difference in chemical concentration. In the presence of high concentration, tumbling is delayed and running is lengthened.
What is the difference between prokaryote and eukaryote SA:V ratio?
Eukaryote SA: V ratio is lower since they need more sophisticated transport mechanisms, therefore it grows slower.
How are Mitochondria related to prokaryotes?
1.70S ribosomes
2. surrounded by 2 membranes
3. most closely related to genus rickettsia: phylum roteobacteria and obligate intracelllular pathogen
How are chloroplasts related to prokaryotes?
- 70S ribosomes
- surrounded by two membranes
- most closely related to cyanobacteria
What are the 5 pieces of evidence that mitochondria and chloroplasts evolved from bacteria?
- semi-autonomous: individual metabolism and division
- circular chromosomes and lack histones
- 70S ribosomes
- two membranes
- outer membrane has porins
What are the two parts of a virus?
Nucleic acid genome (DNA or RNA) and protein coat (capsid) together forming a nucleocapsid. Sometimes they may have a lipid envelope surrounding the nucleocapsid.
What are the traits of viral genomes?
- DNA or RNA: never both
- Single stranded/double stranded
- Circular/linear
- Segmented
- may be small [3.6 kb for some ssRNA viruses (3 genes)] or large (150 kbp for some dsDNA viruses (>100 genes)]
What is a capsid?
A protein coat that surrounds the genome that allows the transfer of viral genome between host cells.
What is the structure of a capsid?
Made of protomers (polypeptides) and form a capsomere.
