Microbiology Final Exam (all cards)
What are the 3 metabolic classes? Within these classes, what are the prefixes
1) Energy source: from chemicals (chemo-troph)/from sunlight (photo-troph) 2) Electron source: from organic chemicals like sugars+aa's (organo-troph)/from inorganic chemicals like H2S and iron (litho-troph) 3) Carbon source: from organic chemicals like sugars+aa's (hetero-troph)/from CO2 (auto-troph)
Explain the 3 bacterial homologs of the bacterial cytoskeleton, and the 1 unique bac protein. What is each one's *general* function (cell shape, division, both)?
1) MreB ('spring'): actin homolog; cell shape 2) FtsZ ('ring'): tubulin homolog; cell shape and cell division 3) Crescentin ('fiber'): intermediate-filament homolog; cell shape MinD is unique to prokaryotes: cell division site selection. It oscillates from pole to pole and helps find the cell's middle for division
Describe the bacterial flagellum
-Massive structure assembled on the exterior of cell -Made of protein "Flagellin" (aka H-antigen): Visible filament is a polymer of single protein Flagellin -Helical shape--moves in helical motion -Rotates at very high speed to propel the cell body (200 rotations/second) -Driven by the cell's transmembrane proton current -One of two known rotational motors in biology Our immune system is very sensitive to flagellum! Flagella is found in certain bacterial cells
What are the ways of assessing evolutionary relatedness?
-Numerical Taxonomy (traits comparison: the more closely related the organisms, the more traits they will have in common). Can be innacurate and has many disadvantages. Better to look at the genome. -Phylogenetics (compare Molecular clocks: the more closely related the organisms, the more similar the sequence of some biomolecule [such as 16S rRNA]/fewer changes in the sequence) -Polyphasic approaches (some combo of the above)
How can metal ions act as cofactors? What are some examples?
1) Add extra chemistry to proteins, 2) Help proteins fold properly, 3) Stabilize protein-protein interactions Ex: Zn and Fe
What are the 5 main components of the gram negative envelope? Briefly explain what each does
1. Outer Membrane Shields peptidoglycan and plasma membrane; diffusion barrier to hydrophobic and hydrophilic compounds (though porins let small hydrophilic molecs thru) 2. Lipopolysaccharide (LPS) Unique sugar-lipid hybrid in outer leaflet of outer membrane 3. Murien Lipoprotein (a.k.a. Braun's Lipoprotein) Attaches outer membrane to peptidoglycan 4. Porins Pores present in the outer membrane that allow diffusion of small hydrophilic molecs 5. Periplasm Space between the inner and outer membranes
Describe the properties of the bacterial cytoplasm
70% water No empty space and very little "free" water Hydration shells around molecules Wide variety of proteins and metabolites
Define batch growth
A closed bacterial culture system with specific nutrient, temperature, pressure, aeration and other environmental conditions to optimise growth. nutrients are not added, nor waste products removed during incubation. cells experience log/exp/stationary/death phases. growth rate cannot be controlled
Define the bacterial nucleoid?
A region of the cell that contains the chromosomal DNA. DNA in bacteria is not compartmentalized, but DNA tends to be in this region
Talk about MreB. What is it? In what cell shape is it required for shape/growth?
Actin homolog (structural and functional) found in rod-shaped bacteria. Forms spiral cables (literal helices in the cell. The MreB helix rotates in the cell, and pg synthesis provides the E for this movement). It is required for rod shape/growth.
Define active transport, PTS transport, and siderophores. How do these occur?
Active Transport: Energy (ATP) is expended for proteins to pump solutes against a gradient. For example ABC transporters. PTS Transport: Energy is expended and substrate is changed during transport. Often used for sugar transport. Siderophores: Secreted organic molecules that bind extracellular iron are taken up by active transport. All 3 need energy to move things against a gradient
Advantages and disadvantages of using CFU plating to count cells?
Advantages: Allows you to measure the number of viable cells Disadvantages: Cumbersome Only works with culturable bacteria Assumes each colony originates from a single cell; what about cell chaining/clumping? (one cell becomes one colony. But also, a clump of cells can become one colony)
Advantages and disadvantages of using a hemocytometer to count cells?
Advantages: Do not need to grow cells Works for any sample Disadvantages: Cells must be evenly distributed Cannot distinguish which cells are alive or dead
Advantages and disadvantages of using particle counting to count cells?
Advantages: Do not need to grow cells Works for most samples Disadvantages: Cannot handle cell clumps Can't distinguish between D/L cells
What are some advantages and disadvantages of numerical taxonomy?
Advantages: Trait information is very useful and meaningful Works well if microbes are known to be closely related Disadvantages: Trait choice is arbitrary. All traits are weighted equally. Some traits are simple, some very complex. Traits may or may not be related to one another. Same traits may arise through different mechanisms.
What are some advantages and disadvantages to DNA being compartmentalized in a nucleus?
Advantages: contains/protects the DNA and concentrates and localizes all the transcription factors. Disadvantages: compartmentalization delays signaling signal response time and regulation. In bacteria, signaling is immediate. Also, transcription and translation are coupled in bacteria bc there's no compartmentalization (saves time!)
Why does E coli not exponentially grow for 2 days to take over the world?
Antibiotics in environment slows growth, competition for resources by neighboring cells, not enough nutrients for all cells to keep thriving and reproducing
Describe the archaeal cell structure. What makes it different from bacteria
Archaea typically live at colder/hotter temps than other bacteria. -Unusual cell walls: "Pseudo" pg's that are Similar in function but structurally different from bacterial pg--Uses N-acetyltalosaminuronic acid in place of N-acetylmuramic acid, Uses L-amino acids rather than D-amino acids in crosslink -have an S-layer protein shell (As in bacteria, but some archaea have ONLY an S-layer!) -Unusual lipids/cell membs: extensive branching of lipids in the cell membrane; way more branching than bac. This is beneficial because as you heat fatty acids you get more membrane fluidity. More cross-linking causes less molecular space in the membrane and thus it lowers the fluidity. This is good because too much fluidity can cause loss of shape. -Membrane monolayer reduces motion: Accounts for extreme membrane stability of hyperthermophiles
Define thermophiles. How do they survive?
Bacteria/archaea that have a high optimum growth temperature. Thermophiles have several adaptations that let them survive at high temperature: -They have thermostable proteins that fold properly at high temps (disulfide bonds stiffen proteins, preventing them from folding improperly then denaturing at high temps) -increased GC pairs increases DNA melting temp, incr supercoiling of DNA, DNA binding proteins prevent denaturing -have more saturated fatty acids in membranes (low fluidity). -extensive branching between lipids makes intermolecular contacts (strengthening membrane)
Explain size diversity in terms of microorganisms (getting bigger/smaller). hint: discuss diffusion
Bacterial cells range from 0.2um - 1mm They can be bigger or smaller depending on if that size gives them enough space to store energy and nutrients. You need DNA, ribosomes, etc within a cell. Have to fit this! This is why there's not much wiggle room to get smaller than 0.2 um. They also can't get huge because (1) diffusion would become too slow and inefficient, (2) DNA can't be copied fast enough to handle all the protein synthesis requirements of a larger cell, and (3) < surface area : volume ratio. That is, it has a lot of space where you need to take nutrients to, and lots of space where you need to take waste away from. This is done by diffusion to save energy, but if a cell is huge but the cell membrane is relatively small, it just can't keep up. It will have to have active processes, which in turn require more energy and produce more waste. In the end, it's most energy efficient to be small if you're unicellular.
What are barophiles? How do they survive? What do we still not know?
Barophiles require high pressure for survival - die at low pressures. Barophiles are also often psychrophilic (ocean floor is 2˚C) or hyperthermophiles (thermal vents). How barophiles survive crushing pressures is still a mystery. At high pressure, DNA replication fails. Unclear why.
Describe the two types of growth environments and contrast the growth phases that the cells experience
Batch culture: Closed system, No nutrients enter, No waste products leave. Poor model for the environment and many infections, where there is a continuous flux of materials and waste prods, cells experience log/exp/stationary/death phases, growth rate cannot be controlled Continuous culture: Open system, Fresh nutrients flow in, Waste products flow out. (s.s.), cells stay at exponential phase, growth rate can be controlled
Give an example of a bacterial symbiosis
Bioluminescent vibrio fisherae and the Hawaiian bobtailed squid: the bacteria grow on the light organs within the squid, and the squid provides nutrients and protection to the bacteria. The squid feeds at full moon, so when they glow they can feed on the water surface and they won't be a stark silhouette against the moonlight for predators to see them below. The squid can then turn the light off by squeezing their light organ and push the bac out
contrast the features of the Ebola and Zika viruses in terms of sense and genome (RNA and segmentation)
Both have single-stranded RNA and are nonsegmented (the genome is all on one piece of RNA or DNA). Ebola: neg-sense Zika: pos-sense
What is the difference between complex and synthetic growth medium?
COMPLEX: "rich". Contains poorly defined ingredients such as: yeast extract, beef extract, blood, etc. SYNTHETIC: "minimal" or "defined". Precisely defined ingredients, including salt, carbon, nitrogen, and energy sources in precise amounts.
Explain growth optima. What helps stabilize the cell as environment changes?
Can make a curve for a bacterium, showing the effect of some parameter/condition on the growth rate. This curve is unique for each bacterium. Looks like an upside-down parabola. Peak is the 'optima' or optimal conditions. Min and max points at the extremes are where growth arrests. Homeostasis helps stabilize the cell as the environment changes
What are the effects of low T's on cells?
Causes membranes to shatter Makes proteins inflexible and causes them to denature Slows metabolism to a crawl (metab rxns are slower)
What are psychrophiles? How do they survive
Cells that thrive at lower than normal temps. -Their metabolism is optimized for low temperature -Membrane fatty acids have extensive unsaturation (> unsat'd fatty acids in membrane = can't pack together as tightly = > fluid) -Proteins are more "flexible" so can function at lower temperatures
What are some culturing methods for un-culturable bacteria?
Co-culture: there may be a complex molecule that your bacteria requires that you can't buy. There's molecules that certain organisms need that can only be produced by other organisms Growth in natural environment: can grow in a sealed box in the natural environment
What are 2 advantages of complex medium? Of synthetic?
Complex: cheaper, often nutrient-dense Synthetic: less process variability, preferred from Regulatory perspective
What is a vibrioid shape? How does this shape happen? Describe its onset of division.
Crescent shape (curved rod). Crescentin forms a filament that runs along the concave side of the cell. Strains opposite side (convex side) of the cell, leading to increased pg formation. (>strain=>pg synth) MreB elongates (crescentin on bottom), then MreB centers at middle with FtsZ at onset of division (crescentin still on bottom)
Define the S-layer. What are some advantages of it?
Crystalline shell made of protein/glycoprotein (proteins with attached sugars). Not essential and not all bacteria have an S-layer. Often found in free-living bacteria and archaea. Advantages: Protects cells from: • Phage • Immune system • Physical damage
Define extracellular polysaccharides and name some advantages of them
EPS are Extra, non-essential layers beyond the peptidoglycan layer. (More often present in Gram-positives). Can be anchored to the pg ("capsule") or kind of just hanging out loosely above it ("slime layer"). Capsule gives colonies a rough-looking appearance and slime layer gives colonies a wet/mucoid appearance. Advantages: makes adhesive (cells stick to surfaces) and cohesive (cells stick together), Desiccation (drying) resistance, Protection from the immune system: - prevents phagocytosis - shields antigens from antibodies
Explain why the 16S rRNA gene is the most common molecular clock. How can its sequence reveal evolutionary relatedness? Who's a famous name here?
Every microorganism has a 16S, and it is comprised of conserved and variable regions. Through looking at the variable region, you can find differences in the sequence of bases allowing for determination of various species. Variable regions are good for differentiating taxa according to evolutionary descent. -Relatively constant regions (compare ancient relatives) -Highly variable regions (compare recent relatives): The more similar the 16S sequences, the more evolutionarily related Carl Woese! used 16s rrna to discover archaea are different from bacteria
What was the Great Oxygenation Event?
First mass extinction--cyanobacteria began producing O2 by photosynthesis. Before, any free oxygen they produced was chemically captured by dissolved iron or by organic matter. The GOE started when O2 produced by the cyanobacteria started escaping into the atmosphere, after other oxygen reservoirs were filled (the organic matter and dissolved iron became saturated and could no longer capture any more O2). The excess free O2 accumulated in the atmosphere. This was toxic to obligate anaerobic organisms, leading to their near-extinction
3 ways to count cells? Describe each method briefly
Hemocytometer: add cell sol'n and manually count within squares CFU's by plating: find 'sweet spot' dilution where you can count the most the easiest Particle counting: uses current to count particles
Define porins. What do they do? What's their structure? Compare membranes.
Found in GN's *outer* membrane. Passive "pores" on the GN outer membrane that let molecules move through the outer membrane. It is composed of 3 beta-barrel channels. Outer membrane is a diffusion barrier: protects from dangerous chemicals but also prevents nutrient uptake. Porins allow small molecules to diffuse into the cell. *from wiki:* Porins are water-filled pores and channels. Porins are primarily involved in passively transporting hydrophilic molecules of various sizes and charges across the membrane. Additionally, porins can regulate permeability and prevent lysis by limiting the entry of detergents into the cell. In gram-negative bacteria, the inner membrane is the major permeability barrier. The outer membrane is more permeable to hydrophilic substances, due to the presence of porins. Porins have threshold sizes of transportable molecules that depend on the type of bacteria and porin
Define periplasm
Found in GN. A membrane-enclosed compartment separate from the cytoplasm. It is the space in between the OM and IM
Define teichoic acids. What are they good for?
Found in GP. Teichoic acids are attached to the pg, and anchor the pg wall to the inner plasma membrane. They are very negatively-charged due to phosphate groups. They protect the inner membrane. Due to their highly negative charge, teichoic acids repel hydrophobic detergents from inserting in membrane.
Explain the structural domains of LPS, naming the properties and functions of the domains
Found in the outer memb of GN bac. Sugar-lipid hybrid with 3 domains: O-antigen, core, and lipid A. 1. O-antigen: Polysacc tails of highly repeating, highly variable sugars which can extend longer than the cell itself. Each bacterium has a unique O-antigen (thus each bac strain is recognized by different antibodies) 2. Core: A series of sugars that is highly conserved in all GN bacteria. Very negatively charged. Charge barrier against detergents 3. Lipid A: Anchors LPS to outer membrane Unusual phospholipid: Phospho-sugar backbone (not glycerol) with multiple (4-6) fatty acids. Immune system reacts strongly to Lipid A "endotoxin" (The toxic activity of LPS; endotoxins are considered to be a toxin kept "within" the bacterial cell and released only after destruction of the bacterial cell wall though destruction is not necessarily required. Today, the term 'endotoxin' is mostly used synonymously with LPS)
Describe the structure of the flagellar motor in GN and GP bacteria
GN: top to bottom. Flagellum, L ring, P ring, stator, (anchored ot pg, generates torque), rotor, then switch complex (changes direction of rotation) GP: not well understood
Gram positive vs gram negative bacteria?
GP: has a thick peptidoglycan 'cell wall' and an inner membrane GN: has an inner and outer membrane with a thin peptidoglycan 'cell wall' iN betweeN
Define chemostats. (also, What are the main properties of them?)
In a continuous culture, a chemostat is a bioreactor to which fresh medium is continuously added at a rate equal to the rate at which leftover culture liquid+stuff flows out. Keeps volume constant. -Continuous flow, continuous growth. -It's at steady state (nutrient conc is constant) -dilution rate (nutrient flow) can be controlled, hence growth rate can be controlled:.... -growth rate is proportional to the dilution rate (In other words, cells grow faster when nutrient flow is faster.) -Cells stay in exponential phase and never enter stationary phase -Requires limiting nutrient in the medium, which in turn also affects growth rate as well as dilution rate (there's a card on this)
How does high temperature affect cell growth rate? What happens when temp gets too high? Why?
In general, growth at higher temperature allows a faster growth rate (enzyme activity is increased) temp too high: growth rates fall because enzymes denature. Damages (denatures) protein structure and Melts (denatures) DNA to single strands. also disrupts membranes (makes more fluid)
Talk about crescentin. What is it? In what cell shape is it required for shape?
Intermediate filament homolog (structural and functional) found only in crescent-shaped bacteria. -Forms filament that runs along concave side of cell -Strains opposite side of cell, increasing rate of peptidoglycan insertion Crescentin is required for crescent shape
Define chemotaxis
It's how bacteria moves; Chemotaxis is the movement of an organism in response to a chemical stimulus. Bacteria, and other single-cell organisms, direct their movements according to certain chemical 'attractant' in their environment. Biased random walk!
Define murein lipoprotein
Membrane protein found in GN bac. Anchors the outer membrane to the pg cell wall, providing structural integrity to the outer membrane
What are vitamins?
Most common type of growth factor. They are organic molecules that most often function as cofactors. A vitamin is an organic molecule which is an essential micronutrient, that an organism needs in small quantities for the proper functioning of its metabolism.
How might the huge radiation resistance of Deinococcus radiodurans have evolved?
Most likely, this bacterium became resistant to desiccation which ended up giving them the ability to also being resistant to very unnatural levels of radiation
What are the criteria for a molecular clock?
Must... ...be found in all representatives of the group studied ...have the same function in all representatives ...be sufficiently similar between different organisms so that the sequences can be aligned ...be sufficiently different between different organisms so that the sequences each have their own "signature".
What are nutrients? Differentiate between macronutrients, micronutrients, and growth factors. Give some examples of each
Nutrients are the raw materials required for the growth and metabolism of cells. Different organisms need different combinations and amounts of nutrients. -Macronutrients: Elements required in large amounts by most cells (i.e. CHONPS) -Micronutrients: *Elements* required in trace amounts, sometimes only by certain microbes (i.e. Co, Cu, Mn). Some microbes are unculturable; we don't know what trace elements they need to grow -Growth Factors: *Organic compounds* required in small amounts by certain microbes (i.e. vitamins [most common], amino acids, peptides, nucleotides, or other small organic molecules). Most microbes can synthesize all of these compounds from simple precursors; however, some require one or more pre-formed from the environment. Such bacteria will not grow in the lab if these compounds are not supplied.
Talk about vitamin B12. What's its relationship to swiss cheese?
One of nature's most structurally complex small molecules. Explains requirement for cobalt as a trace metal (micronutrient) because B12 has a cobalt center. Functions as an organic cofactor for two (known) enzymatic reactions in humans and many additional reactions in bacteria and archaea. Can only be synthesized by certain prokaryotes, and Is produced industrially by bacteria grown under special conditions to increase yield. The bacteria that produces B12 also is in swiss cheese, and is responsible for its flavor and holes (CO2)
Define chemotroph
Organisms that get their energy source from chemicals Opposite is getting energy from photosynthesis
Define passive and facilitated diffusion. How do these occur?
PD: Molecules pass directly through membrane. FD: Molecules pass through membrane by way of proteins. Both need a gradient (moving things from [hi] to [lo])
Define peptidoglycan. What is its structure?
Peptidoglycan is a polymer consisting of sugars and amino acids that forms a mesh-like cell wall in GN and GP bacteria. It is made from alternating sugars (-glycan) and amino acids (peptido-). D- and L- amino acids are included in these chains: D- is involved in crosslinks.. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer
Describe the key characteristic of new peptidoglycan synthesis; how is it like this?
Pg synthesis is localized. Pg's synthesize and cell wall forms around it. In coccoid and rod (longitudinal). Pg synthesis machinery is localized due to the bacterial cytoskeleton.
Positive- vs negative-sense?
Pos-sense: the RNA can be immediately translated into protein by the host cell (the RNA is 'already' mRNA) Neg-sense: the RNA must be converted to the sense RNA by an RNA poly before translation. The RNA must make a reverse complement of itself in order to be read as mRNA.
Describe the prokaryotic chromosome and how it fits within the cell
Prokaryote chromosome is a covalently closed circular molecule that is 1000x the cell's length. It fits due to supercoiling and DNA binding proteins. Goes in the nucleoid (section of cell where DNA is found; not compartmentalized)
Describe onset of division for spherical and rod cell division
Spherical: FtsZ forms at center at onset of division Rod: MreB elongates, then FtsZ forms at center at onset of division
What happens when peptidoglycan is removed from rod-shaped cells? How can this be done? Why does this happen?
Removal of pg causes loss of cell shape [][] --- +lysozyme to digest pg ----> oo (this happens because surface : vol ratio decreases, increasing pressure, so it becomes thermodynamically more stable to form into a spherical shape). The increasing pressure is Turgor pressure (important force that favors breaking/inserting of new pg's). Pg synthesis happens at areas being 'pressed' by turgor pressure
Describe the role of cytoskeletal proteins in rod cell division
Rod: MreB elongates, MinD finds middle, FtsZ cuts
Explain bacterial navigation in terms of runs and tumbles, and the biased random walk.
Run: flagella spins CCW; moves cell in straight line toward attractant Tumble: flagella spins CW; stops forward motion, so cell tumbles and changes direction Biased random walk: chemotaxis. Movement toward attractant = longer runs (on avg) Movement away from attractant = shorter runs (on avg)
What is the difference between selective and differential growth medium?
SELECTIVE Favors the growth of one organism over another. Example: Including an antibiotic would favor growth of bacteria that are resistant. DIFFERENTIAL Allow different species to grow, but indicates biochemical differences between the species. (a medium can be both selective and differential! ex is MacConkey medium)
What is MacConkey medium?
Selective and differential medium Selective: Contains bile salts (detergents) and crystal violet (dye) that ONLY gram-negative bacteria can grow on because of protective outer membrane. Differential: Contains neutral red, which causes lactose fermenters to turn red. (The dye turns red at low pH, a result of acid produced during fermentation.)
How does low temperature affect cell growth rate? Why?
Temp too low: growth rates fall because the membrane fluidity and enzymatic activity decreases
What are some environmental restraints on cell growth?
Temp, pH, pressure, oxygen, salinity, moisture, light, osmotic stress
Define Homeostasis
The maintenance of stable intracellular conditions by regulatory mechanisms that compensate for changing environments
Define sacculus
The structure that describes the peptidoglycan cell wall 'envelope', which retains the strength and shape of the cell.
How is bacterial cell shape defined?
The peptidoglycan layer and cytoskeleton. The peptidoglycan 'sacculus' retains the strength of the shape of the cell, and the MreB/crescentin in the cytoplasm actually facilitates this shape
The proteins in the bacterial cytoskeleton were only recognized in the 1990s. Why might it have taken so long to discover?
The relatedness homologs is apparent at the structural (3D) level, but not their amino acid sequence. This is why bacteria were thought to lack a cytoskeleton
What happens if MreB is depleted in a rod cell?
The shape will become long and 'deflated'/very unshapely due to unchecked cell division due to pg synthesis.
What does the peptidoglycan cell wall protect against?
Thick wall offers good protection against osmotic stress Even the thin pg layer in GN provides protection from osmotic pressure
What are alkaliphiles? How do they survive?
Thrive at high pH. Cell surface barrier is key to survival in this environment (?also not sure what this means)
What are halophiles? What is an important thing they do?
Thrive at high salt concentrations. Use special pumps to replace Na+ with other (less harmful) cations such as K+
What are acidophiles? How do they survive?
Thrive at low pH. They have altered membrane lipids to decrease proton permeability into the cell. Most acidophile organisms have evolved extremely efficient mechanisms to pump protons out of the intracellular space in order to keep the cytoplasm at or near neutral pH. Therefore, intracellular proteins do not need to develop acid stability through evolution. Also poorly defined proton extrusion mechanisms (?not sure what this means)
Talk about FtsZ. What is it? In what cell shape is it required for shape/growth?
Tubulin homolog (structural and functional) found in most bacteria. It is required for coccoid shape/growth. Forms "z-ring" structure at the cell equator. During cell division, FtsZ is the first protein to move to the division site, and is essential for recruiting other proteins that produce a new cell wall between the dividing cells.
Describe the outer and inner membranes of gram-negative bacteria
Unlike the inner membrane, it has inner and outer leaflets. Top leaflet: lipopolysaccharides (LPS) --> modified phospholipids Bottom leaflet: phospholipids Inner is just phospholipids
What is desiccation? What effect does this have on a cell?
Very dry conditions. Low water concentration limits protein functions
Define flagellum
a long, tail-like structure made of protein Flagellin that helps a cell to move, as it spins in a helical motion.
Define gram stain
a method of staining used to distinguish and classify bacterial species into two large groups (gram-positive and gram-negative). 1. add methanol to stick cells to slide surface 2. add crystal violet stain (stains cells reversibly) 3. add iodine which binds the stain to GP cells 4. wash with ethanol (stain sticks on GP, washes off GN) 5. add safranin counterstain (GP stays purple, GN turns pink)
Define microbe
a microscopic organism, especially one that causes disease
Define cofactor
a substance (other than the substrate) whose presence is essential for the activity of an enzyme.
Define heterotroph
an organism deriving its nutritional requirements (C source) from complex organic substances (sugars, aa's)
Define autotroph
an organism that can produce nutritional organic compounds (such as carbohydrates, fats, and proteins) from simple inorganic substances like CO2. i.e., organisms that get their carbon source from CO2 (like plants)
Classify animals, plants, fungi, cyanobacteria, most bacteria, and algae in terms of the three metabolic classes
animals, fungi, most bacteria: chemoorganoheterotrophs (consume organic carbon compounds like sugars, fats, and proteins for energy, electrons, and carbon) plants, algae, cyanobac: photolithoautotrophs (get energy from sunlight, extract electrons from chemicals; usually water, and obtain carbon from CO2) Remaining classes are found ONLY in the microbial world
Discuss pH homeostasis
as you add acid then base to a cell sol'n, as external pH lowers then rises, the internal pH of the cell hardly changes
What does LPS do for a cell?
contributes greatly to the structural integrity of the bacteria, and protects the membrane from certain kinds of chemical attack. LPS also increases the negative charge of the cell membrane (from the negative core polysacc) and helps stabilize the overall membrane structure.
What is the affect of extreme high temperature on a cell, in general?
denatures proteins, melts DNA, desiccation of the cell, disrupts the membrane (incr fluidity which is bad b/c too much fluidity is not stable, and a cell can be at risk of rupture), metabolism speeds up
Define molecular clock
figurative term for the technique that uses the mutation rate of biomolecules to deduce the time in prehistory when 2 or more life forms diverged. Usually look @ nucleotide sequences for DNA or AA seqs for proteins
Define symbiosis
interaction between two different organisms living in close physical association, typically to the advantage of both.
Why can't humans produce all 20 amino acids?
it's energetically costly, and we can simply just get them from food, so there's no need to produce them. Through evolution, many organisms lose ability to make things
Define lipopolysaccharide
large molecules consisting of a lipid and a polysaccharide. Has an O-antigen, core polysaccharide, and lipid A. Found in the outer leaflet of the outer membrane of Gram-negative bacteria.
What does a hypertonic solution do to a cell? How can you protect it?
means [solute]out > [solute]in, causing H2O to rush out of the cell, causing it to shrivel. Can protect the cell by synthesizing and/or pumping in solutes to increase intracellular osmolarity
Define lithotroph
organisms that get their electron source from inorganic chemicals such as H2S and iron
Define organotroph
organisms that get their electron source from organic chemicals such as sugars and aa's.
Define phototroph
organisms that get their energy source from sunlight
How does a bacterial cell "know" what shape to be? How does shaping cells occur?
pretty sure its just 'cytoskeleton' Peptidoglycan synthesis determines cell shape: the pg cell wall must grow during cell growth and division. This requires controlled hydrolysis of existing peptidoglycan to insert new peptidoglycan. Executed by PG synthesis machinery (enzymes)
l- vs d- amino acids?
represents a form of chirality. l-aa's are biologically relevant to us. d- are actually toxic and will kill cells. bac synthesize d-aa's but don't really use them for proteins
Define nonsegmented
the genome is all on one piece of RNA or DNA
Explain why the limiting nutrient is important to a chemostat?
the growth rate is controlled by the availability of a single component of the medium (the limiting substrate/nutrient). It is the continuous introduction of fresh medium that feeds the limiting substrate to the culture and the dilution rate (that is, the rate of addition of fresh medium) determines the specific growth rate of the culture