Exam 1 Flashcards
What did Anton Van Leeuwenhoek do?
Used microscope to see microorganisms
What did Louis Pasteur do?
Disproved spontaneous generation
Pasteurized milk
Rabies vaccine
What did Robert Koch do?
Discovers bacteria responsible for anthrax
Koch’s postulate to prove microorganism causes a specific disease
What did Carl Woese do?
Proposed three domain classification of living organisms
Shape of coccus
Round
Shape of bacillus
Rod
Shape of vibrio
Curved rod
Shape of spirillum
Sprial
What is the shape of the cell determined by?
Organization of the cell wall
What shape is pleomorphic
No regular shape
What are hyphae?
Irregularly branching filaments that are composed of chains of cells
What are mycelia?
Three dimensional networks of hyphae
What are trichomes?
Smooth unbranched chains of cells that may have a polysaccharide sheath coating
Average size of bacteria
0.5-5 micrometers
What is the large bacteria?
Spherical Theomargarita namibiensis of 700 micrometers
Cigar shaped Epulopiscium fishelsoni of 600 micrometers
Composition and function of the nucleoid
DNA, RNA, proteins
Genetic information storage and gene expression
Composition and function of the chromosome packaging proteins
Protein
Protection and compaction of genomic DNA
Composition and function of the enzymes involved in synthesis of DNA, RNA
Protein
Replication of the genome, transcription
Composition and function of the regulatory factors
Protein, RNA
Control of replication, transcription, and translation
Composition and function of the ribosomes
RNA, and protein
Translation (protein synthesis)
Composition and function of the plasmids
DNA
Variable, encode non-chromosomal genes for a variety of functions
Composition and function of the enzymes involved in breaking down substrates
Protein
Energy production, providing anabolic precursors
Composition and function of the inclusion bodies
Various polymers
Storage of carbon, phosphate, nitrogen, sulfur
Composition and function of the gas vesicles
Protein
Buoyancy
Composition and function of the magnetosomes
Protein, lipid, iron
Orienting cell during movement
Composition and function of the cytoskeletal structures
Protein
Guiding cell wall synthesis, cell division, and possibly partitioning of chromosomes during replication
What is topoisomerase?
Enzyme that helps chromosome coil upon itself to compact it
What are sulfur globules?
Composed of elemental sulfur. Thiomargarita have these as a by-product of oxidation of sulfide and can be further oxidized when sulfide is limited
What are carboxysomes?
In Cyanobacteria they contain enzymes for the conversion of inorganic carbon into organic matter
What does FtsZ do?
Protein that forms the Z-ring which is needed for cell division
What is FtsZ related to?
Tubulin (protein that serves s a main building block of eukaryal micro tubules in the cytoskeleton)
Identify the 3 proteins in the cytoskeleton of bacteria and describe their role
FtsZ- aids in cell division
MreB- forms filaments in a helical pattern on the inside of the plasma membrane for structure and shape
ParM- forms filaments that direct plasmid movement to either side of the cell during division to ensure plasmid segregation
In depth explanation of FtsZ function
- FtsZ monomers form filaments that bundle together to form the Z-ring on the inside of the plasma membrane
- the ring interacts with the plasma membrane to direct synthesis of the bacterial cell wall
- the ring contracts through controlled release of the units by GTP hydrolysis
- as this is happening the the cell envelop is faced forced inwards at the division site by reoriented cell wall synthesis
- when cell division is finished the Z-ring has disappeared
What is MreB?
A protein in bacterial cell cytoskeleton that is related to actin (a eukaryal cytoskeleton protein)
In depth explanation of MreB function
- MreB forms long helical bands inside of the plasma membrane
- universal in non-spherical bacteria, never present in cocci
- guides cell wall formation to form an elongated shape
What is ParM?
A protein in bacterial cell cytoskeleton to separate the plasmids at cell division
In depth explanation of ParM function
- forms actin-like filaments along the axis of bacteria
- moves plasmids to opposite sides of cell (copies of the same plasmid are found both cells after division)
- building blocks form on the plasmid and then extend out to slowly move apart the two plasmids to the opposite sides
What is the cell envelop composed of?
Plasma membrane, cell wall, outer membrane
What is the plasma membrane made of?
Phospholipid bilayer with a polar and non-polar portion. Polar heads interact with the water on the outside and inside of the cell
What are hopanoids?
Sterol-like molecules that stabilize the plasma membrane. Only about 10% of bacteria produce them but they are abundant in soils and sediments
More about the plasma membrane
- fluid structure
- lipids move around freely
- fluidity depends on temperature
- half of the mass is proteins embedded in the plasma membrane
Key functions of the plasma membrane proteins
- control of access of materials to the cytoplasm through differential permeability
- capture and storage of energy through photo systems, oxidative electron transport, and maintenance of chemical and electrical gradients
- environmental sensing and signal transduction
What are aquaporins?
Protein channels that facilitate the transportation of water through the plasma membrane. Not always present as water can also pass through the plasma membrane without a protein
What is a hypotonic solution and what is the outcome?
It is when the cell cytoplasm has a higher solute concentration than the external environment. Cause water to move into the cell (uniform the concentration) however if too much water is moved in the cell can explode but the cell wall helps the cell keep its structure.
What is a hypertonic solution and what is the outcome?
It is when the cell cytoplasm has a lower solute concentration than the external environment. This will cause the cell to lose water and deflate and could lead to the cell collapsing but the cell wall helps the cell keep its structure.
What are the 3 types of transport in and out of the cell and a brief description of each
- Facilitated diffusion- one kind of molecule moves across the membrane from higher to lower concentration through a protein
- Symport (co-transport) - moves molecules against concentration gradient by coupling the movement with another molecule that is moving in its respective concentration gradient. Symport facilitates movement of both molecules in the same direction
- Antiport (co-transport)- same type of transportation as symport but this facilitates the movement of both molecules in opposite directions
What are ABC Transporters?
ATP- binding cassette and consist of 4 components; membrane channel that is formed by two hydrophobic subunits, two hydrophilic subunits located on the cytoplasmic surface and contain the ATP binding domain, and an associated subunit is a high-affinity solute-binding protein that binds to substrates outside and delivers them to the membrane bound components
Energy capture in plasma membrane
- electron transport chains create proton motive force (PMF)
- can be used for respiration/photosynthesis
- can be used to derive energy for motion (flagella)
Sensory systems in plasma membrane
-embedded proteins can detect environmental changes, alter gene expression in response
Process of protein secretion through the plasma membrane
- protein that is going to be moved out of the cell is identified with a signal peptide (a short sequence of hydrophobic amino acids at the amino-terminal end of the protein)
- SecB protein binds to nascent polypeptide a it leave the ribosome to prevent folding and delivers it to SecA
- SecA associates with SecYEG (a membrane channel complex)
- using energy from the hydrolysis of ATP SecA facilitates movement through SecYEG
- once it has crossed a signal peptidase removes the signal peptide and the protein folds into its functional conformation
What is bacterial cell wall made of?
Peptidoglycan
What is the purpose of the cell wall?
Structural purpose against osmotic pressure, mechanical forces, and shearing forces. Not a permeability barrier
What is the structure of peptidoglycan?
Glycan backbone with alternating molecules of NAM and NAG which are connected by beta 1,4 glycosidic bonds. NAM acid carries a peptide chain used to crosslink peptidoglycan stands
Composition, location, and function of Lipopolysaccharide (LPS)
Lipid, polysaccharide
Outer layer of Gram-negative outer membrane; lipid portion embedded in membrane; polysaccharide exposed on surface
Stabilizes membrane; elicits an inflammatory response in the human body
Composition, location, and function of lipoteichoic acid (LTA)
Lipid, polysaccharide
Found in peptidoglycan layer of Gram-positive bacteria
Unknown; elicits an inflammatory response in the human body
Composition, location, and function of peptidoglycan
Polysaccharide backbone crosslinked with peptides
In Gram-positive bacteria, usually exposed to environment. In Gram-negative bacteria, covered by the outer membrane
Maintains shape and provides structural integrity to cell
Composition, location, and function of porins
Proteins
Embedded in Gram-negative outer membrane
Form pores that allow diffusion of nutrients and water through outer membrane
Composition, location, and function of TonB-dependent receptors
Proteins
Embedded in Gram-negative outer membrane
Catalyze high-affinity active transport of molecules across outer membrane
Composition, location, and function of flagella
Protein subunits
Extend outward from surface, except in spirochetes, where periplasmic flagella wrap around cell
Provide motility
Composition, location, and function of pili
Protein subunits
Extend outward from cell
Allow attachment; tip often binds to specific molecules. In some bacteria, pili are retractable and allow twitching motility
Composition, location, and function of capsule
Usually lose network of polysaccharides
Covers surface of cell
Protects from phagocytes; contributes to biofilm formation
Composition, location, and function of surface array (s-layer)
Protein
Covers surface of cell
May protect from bacteriophages
What is polar flagella?
Flagella only at the ends of the bacteria
What is monotrichous?
Single polar flagellum
What is lophotrichous?
More than one flagella at one or both ends of the bacteria
What is peritrichous?
Multiple flagella spread out on the surface of the bacteria
Average length of flagella
5-10 micrometers
Structure of bacterial flagella
- anchored to the cell envelop with the basal body
- basal body is a disc like structure and interfaces with the motor that drives rotation of the filament
- central rod of the basal body turns into the curved hook
- curved hook is what spins and the filament is attached to it
- flagella filament is attached to hook and this is what propels the bacterium
- flagellar motor is attached at the plasma membrane where it converts energy from the PMF for the rotation of the filament
- units of the flagella pass through a pore in the basal body and assemble at the tip
Bacterial motion with flagella
Run- all flagella point in the same direction and causes the bacteria to move forward
Tumble- flagella point in many directions and causes bacteria to tumble and orient in a different direction
What is chemotaxis?
Process of using chemical signals from the environment to direct motility. Used by bacteria with flagella so that run and tumble motions are not completely random.
What is gliding motility?
Non-flagellated bacteria, such as myxobacteria and Cyanobacteria, slide smoothly over surfaces. This movement is not well understood.
What is twitching motility?
Jerky movement that is caused by fibres on the surface called pili. The pili attach to a surface and retract to move the bacteria.
What is the main purpose of pili?
Allows bacteria to attach to surfaces and other cells.
What are sex pilus/conjugal pilus?
Connects bacterial cells in order to transfer plasmid DNA
What are fimbria?
Cell surface fibres (pili but they lack the function of conjugal pili)
What is a stalk?
A tubular extension of the entire cell envelop. Increases the surface-to-volume ratio of bacteria which is ideal in habitats with low nutrient concentrations.
What are capsules?
A thick layer of polysaccharides that surround the cell. Used by pathogens to shield themselves from host defence cells.
What is a biofilm?
A layer of microorganisms and polysaccharides
What is a surface array/S-layer?
Crystalline-like layer of protein that provides protection but requires lots of reassures to build
Taxonomy levels
Phylum Class Order Family Genus Species
Characteristics that bacteria are classified by
DNA sequence data Size/shape Gram type Colony morphology Presence of structures such as capsules or endospores Physiological/metabolic traits
Archaeal pathogens?
No known human pathogens
Habitat of Halobacterium salinarium?
3.0-5.0 M NaCl
Dead Sea, salted foods
Pyrococcus furiosus habitat?
100°C
Hydrothermal vents
Picrophilus oshimae habitat?
0.7pH
Sulfur-rich volcanic regions
Methanogenium frigidum habitat?
15°C
Ace lake, Antarctica
Size of archea?
0.5-5 micrometers
Cytoplasm of archea?
Inclusion bodies
Single circular chromosome
Tetramer histone proteins
Cytoskeleton of archaea?
Has characteristics of both bacteria and eukaryotic cytoskeleton
Plasma membrane of archaea?
Glycerol-1-phosphate
Phytanyl side chains (repeating isoprene units)
Ether linkages
Phytanyl sometimes connects and forms a biphytanyl which makes it very stable
Cell wall of archaea
Made pseudomurein
NAG and NAT
Only L amino acids
Cell surface of archaea
S-layer
Cannulae (hollow glycoprotein tubes which links cells together to form a network)
Describe the archaellum
Grows from the base rather than the tip
Anchoring structure under the plasma membrane
Solid flagellum
List the 4 major phyla of archaea
Eurarchaeota (halophiles) (methanogens)
Crenarchaeota (thermophiles)
Thaumarchaeota (key member of TACK)
Nanoarchaeota (key member of DPANN)
What are crenarchaeota known for?
Thermophiles and hyperthermophiles
Temperature of thermophiles and hyperthermophiles
60°C-80°C
80°C+
What are acidophiles
Thrive in low pH
What are barophiles
Thrive in high pressure
Adaptations for survival of archaea
Tatraether lipids/lipid monolayers
Modified proteins (more alpha helical regions, more salt bridges/ side chain interactions, more arginine/tyrosine, less cysteine/serine)
Strong chaperone protein complexes
Thermostable DNA-binding proteins
Reverse DNA gyrase enzyme to increase DNA supercooling
How do halobacterium survive denaturing of DNA and proteins?
Higher GC bonds in DNA
Highly acidic proteins that remain more stable in high salt environments
Methanogen habitats
Anaerobic
Swamps
Animal digestive tracts
What are mesophiles and psychrophiles?
Thaumarchaeota
Biogeochemical cycling of C and N in ocean
M- 15-40°C
P- less than 15°C
Example of nanoarchaeota and its buddy
Nanoarchaeum equitans and Ignicoccus (crenarchaeota)
Plasma membrane structure of bacteria, archaea, and eukarya
Phospholipid bilayer
Bilayer or monolayer (sulfo-, glyco-, isoprenoid-)
Phospholipid bilayer
Plasma membrane lipid structure of bacteria, archaea, and eukarya
Ester linkages, straight fatty acid chains
Ether linkages, branched isopreoid chains
Ester linkages, straight fatty acid chains
Plasma membrane sterols of bacteria, archaea, and eukarya
No (some have sterol like compounds)
No
Yes
Plasma membrane proteins of bacteria, archaea, and eukarya
High abundance
High abundance
Low abundance
Cell wall of eukaryotes
Fungi have chitin
Algae have cellulose
Protozoa do not have cell wall
Cellulose vs chitin
Made of repeating glucose molecules with oxygen bond between sugars
Made of repeating NAG molecules with oxygen bond between
Cytoskeleton of eukarya
3 major pieces
- microtubules (tubulin) (intracellular transport, separation of chromosomes in mitosis and meiosis, cell movement)
- microfilaments (actin) (maintains cell shape, relate division furrow, cell movement)
- intermediate filaments (various proteins) (nuclear structure, cell-cell interactions)
Requirements of early life
Metabolism
Growth
Reproduction
Biological instructions
Antonio van Leeuwenhoek was the first person to observe fruiting structures of molds using an early microscope
False, it was Hooke
What are stromatolites?
Ancient microbial fossil records
What is polyhydroxybutyrate granules?
Example of an inclusion body in a bacterial cell
What enzyme is responsible for condensing DNA
Topoisomerase
