General Exam II Qs Flashcards
How do we recognize reduction/oxidation?
Hs follow electrons, more Hs reduction
Less Os, reduction
More Os, oxidized
O2-
superoxide ion, very toxic bc it wants to grab more electrons from DNA and proteins
Cellular Defense against O2- (superoxide) ?
superoxide dismutase
H2O2
Hydrogen peroxide, highly toxic bc wants more electrons, steals from DNA and proteins in cell
Cellular defense against H2O2?
Catalase (enzyme) breaks it down into O2 and water
Why don’t all bacs use oxygen as an electron carrier?
They lack one or both of the two enzymes that defend against superoxide (O2-) and hydrogen peroxide (H2O2) (catalase/superoxide dismutase)
(facultative anaerobes probably have one, obligate anaerobes have neither)
Plasma membrane
(function and composition)
found on outside, outer boundary of cell, thin selectively permeable barrier that surrounds and encloses the contents and controls the movement of materials into and out of the cell (((the cell chooses that goes in, what comes out)))
Composed of: phospholipids and proteins (hopanoids rather than sterols in some bacs)
Phospholipids
(function and composition)
Major lipid component of membrane, glycerol, two fatty acids, and a phosphate group
(Phospohlipids in bacteria have an ester bond)
review slides for structure reveiw
Amphipathic structure-
(function and composition)
((hint the plasma membrane has this))
hydrophobic and hydrophilic (polar head and non polar tails)
-Forms lipid bilayer
-water can pass through, molecular oxygen can pass through, CO2 can, glycerol cannot pass through
-proton won’t make it through, it’s charged but mainly it’s always surrounded by a cage of water
Rules for freely passing through the plasma membrane? (sans protein help)
Rules for passing through:
1) Small (<180 Daltons MW)
2) Non-polar or weakly polar
3) Non-ionic
Glucose/fructose pass through bc they have a protein to help
Hopanoid
(structure and function)
(looks like cholesterol but with OHs instead)
-Sterol like lipid present in some bacteria (similar to cholesterol)
-amphipathic (polar and non-polar parts)
-Maintain membrane homeoviscosity (regardless of environmental conditions)
-Bacteria add more hopanoids to increase fluidity of membrane, -
-disrupts tight packing between phospholipids ((when cold)) ((fatty acid tails))
-Holds glycerol heads together when hot
Fatty Acid Saturations, ideals for cold/hot?
Saturated- ideal for heat, keeps from slippin and slidin
Unsaturated- good for cold, prevents stiffening and breakage (usually ~kinky~ ooo)
Fatty Acid Length ideals cold/hot
Cold- Ideally short, want to minimize van der waals
Hot- Ideally long, want to maximize van der waals
Plasma membrane: What percentage proteins and phospholipids?
Equal, ~50/50
Define Simple diffusion
(just goes on through the cell membrane) must be small, non-polar or weakly polar, and nonionic
Facilitative diffusion:
Something goes through cell membrane with the help of a protein
Diffusion
- going from high concentration to a low concentration
Active transport
-usually ATP, against the gradient, low to high
How do diffusion and active transport work in relation to equilibrium?
Diffusion works toward equilibrium
Active transport works against equilibrium
Attempt to explain the cup of MnMs example (representing the electron transport chain)
-the Mnms represent the energy, cup is the electrons
-everytime an electron is transferred from one molecule to another, they lose energy (this can be used to do work, or just generate heat)
-protons pumped to outside, proton gradient used to drive ATP synthesis
-dump empty cup into waste receptacle, O2, becomes H2O
Respiration
-Membrane and membrane proteins being used to capture energy in the form of a gradient
*ATP synthase there synthesizing ADP + Pi (inorganic phosphate) into ATP
-O2 reduced to H2O
-NADH oxidized to NAD+
ADP+Pi= ATP
(protons being ejected by protein channels in membrane)
Indirect Active Transport
transporting not ATP against the gradient, low to high
The Lake on a hill proverb? (related to gradients)
whenever you have a gradient it’s a source of potential energy, like a lake on a hill
Photosynthesis-
Use of sunlight to drive the production of glucose from CO2 and H2O
ATP synthase is there synthesizing ADP + Pi (inorganic phosphate) into ATP
H2O oxidized (I think?)
NADP+ is reduced to NADPH
What allows a cell to perceive its environment?
**proteins
Cytoplasm:
function and 4 main things it contains
liquid stuff inside the cell
1) Water (primarily)
2) Macromolecules (proteins, DNA, RNA etc)
3) Molecular building blocks and metabolites (amino acids, nucleotides, sugars etc)
4) Inorganic ions- (K+, Na+, Cl- etc) (they help the DNA not hate itself)
-consists primarily of water
(after lysing cells, gets real snot like, slimeyness from proteins, dna and rna)
Signal Transduction
process in which binding of an extracellular messenger to the cell surface receptor is translated into changes in biochemistry, cell biology, and gene transcription that make it possible for the cell to respond to the information that was received.
(signaling molecule to cell receptor)
Nucleoid:
Define and what’s its deal
No membrane around the supercoiled DNA, so not a defined nucleus
-it’s all real negative so it doesn’t like being together
-(DNA is like tiny children in back of the van)
-Charges neutralized by adding Cations in the nucleoid, which will bind to negative charges of the DNA
-(no histones in bacteria!!)
-Nucleoid is very dynamic, when needs a gene it makes it available, then recoils back up
Topoisomerases
Initiates supercoiling (hydrolyzes ATP and twists the DNA)
makes things more curly and tightly bound
Inclusion bodies:
What are they?
What are they used for?
What are they not?
-Granules of a substance, used for nutrient storage
-Non-membrane bound
ex elements stored: carbon, nitrogen, phosphorous, sulfer
NOT organelles (despite functioning quite like them)
Sulfer Globules
Inclusion bodies in thiomargarita namibiensis
(sulfer storage, S0 which gives lower energy electrons than being oxidized straight from H2S for high energy electrons, but still good!
Polyhydroxybutyrate
(PHB)
Inclusion body
PHB: for carbon storage
in globules, not membrane bound
(used also for surgical sutures fun fact)
review slides for structure
(in spirillum often I think? or at least sometimes)
Cyanophycin
Inclusion body
-produced in excess of nitrogen
(used to be called blue green algae, they aren’t they’re cyanobacteria)
-probably original photosynthesizers
-has amino acids on the structure
-long chains of arginine (pirate amino acid)
-storing nitrogen
review slide for structure
Volutin
(and stained what color on slides?)
Inclusion body
Made by wide range of bacs,
-phosphorus storage (cells use for ATP synthesis, nucleotides, phospholipids etc)
-(stained red/purple on slide)
-join together in long chains in excess of phosphorous
see slides for structure if needed. but basically just phosphoruses (phosphates) holding hands
Definition of an organelle?
A small structure in a cell that is surrounded by a membrane and has a specific function
(Think of them as sacs with specific enzymes carrying out certain functions)
Gas vesicles
shape/used by who and for what?
-used by cyanobacteria
-Gas vesicles in cytoplasm
-proteins forming the structures
-empty hexagonal vesicles bound by proteins (they’re crystals the gays wear on necklaces shape)
(no membrane, but proteins form a membrane of sorts)
(function: buoyancy, they want to be by the surface bc they’re photosynthetic bacteria)
Carboxysomes
Shape/ What do they have/do and why not organelles?
-Contains all enzymes needed for Calvin cycle, got rubisco carrying out binding of CO2 to an organic skeleton
-hexagonal
Not technically membrane bound, so an organelle? Science says no rn
Magnetosome:
what are they, do what, and why not organelle?
-Microaerophiles
-prefer to be a bit down in murky lake soil
-have chain of iron oxide crystals (magnetite Fe3O4) (gregigite Fe3S4)
-Are membrane bound, but no enzymes
Bacterial Cell Wall-
what it do/composed of?
-protects bacterial cell from changes in osmotic pressure/mechanical shear forces
-structure (gives shape)
composed of: peptidoglycan
(for reference, euk red blood cells gonna lyce just from a little pressure change, vs thousands of psi for many bacteria)
Lysozyme
what is it, what it do to bacs?
(should be called lysase or hydrolase) enzyme that breaks or cuts bacteria
-will eat cell wall, turn bacillus into a sphere (pleiomorphs would stay the same, they don’t got no cell wall)
Peptidoglycan-
structure and components
- Polysaccharide of
modified glucose
subunits (BETAGLUCOSE)
(peptide chain linked to the NAM subunit)
-heteropolymer composed of polysaccharide chains which are cross-linked through short peptides. The polysaccharide moiety (glycan) is made up of beta-1,4 glycosidically linked N-acetylglucosamine (NAG) and (NAM) N-acylmuramic acid residues.
(beta glucose is for structure)
feel free to confusedly look at the slides for this one’s structure pg 48 bac cell structure
Distinguishing characteristic of two distinct groups of bacterial cells?
Gram positive-(purple) monoderms (thicker)
Gram negative-(pink) diderms (thinner)
(not always the case though, mono=gram positive not always)
Why can diderms evade our immune systems?
Peptidoglycan (outer layer of monoderms) is immediately detected by body, diderms easily slide under radar bc they’re surrounded by phosphates
Monoderm
(what is it, layers of cell wall look like what, unique things it only has (hint de: the two acids)
-Usually gram positive (thicc cell wall)
(cytoplasm) then
-plasma membrane
-periplasm
-dummy thicc peptidoglycan
Contains:
-teichoic acid (gives strength to peptidoglycan outer layer)
-lipoteichoic acid (has fatty acids attached, anchors in the membrane through the peptidoglycan)
BOTH ACIDS only found in monoderms** (give strength to the wall)
Diderm
(what is it, layers of cell wall look like what)
-usually gram negative (thin cell wall)
(cytoplasm)
-plasma membrane
-periplasm
-peptidoglycan
-final outer membrane (phospholipids)
diderms more able to hide in our bodies, our bodies can detect peptodiglycan bc only bacs have it
-Outer membrane of diderm is phospholipids, so they generally have an advantage to living in euks
-lysozyme eats the top layer (lipopolysaccarriddes) but they’re protected by middle peptidoglycan
Describe the Flagellar composition
(all together bb!)
**see slides, but
Filament- made of proteins (flagellin) ((FliC)
(forming hollow tube)
~20,00-30,000 per flagellum (5-10 um long)
Corkscrew
Hook- FLgE 120 subunits, gives counter angle, so whole thing gets wide swath through liquid, long propeller (holds at angle to make more effective)
(basically works by spinning)
Hook and filament made up of flagellum
Basal body/motor- NOT flagella proteins
-protons flow through, causes filament to turn
Flagella
do what, who has them
Here for the moves (movement)
Mono and diderms can have flagella, more complex in diderms
Filament-
made of proteins (flagellin) ((FliC the protein))
(forming hollow tube)
~20,00-30,000 per flagellum (5-10 um long)
Corkscrew
Hook-
FLgE (protein)
-120 subunits, gives counter angle, so whole thing gets wide swath through liquid, long propeller (holds at angle to make more effective)
(basically works by spinning)
Basal body/motor-
NOT flagella proteins
-protons flow through, causes filament to turn
Monotrichous-
bacteria with only one flagellum (if bacillus, then coming off a pole)
Lophotrichous-
(cabbage patch kid) flagellum tuft on one side
Amphitricus
-flagellum tuft on both sides
Chemotaxis-
-ability to move towards good, away from harm
-If the concentration is decreasing, then bacs will random tumble and go off into other direction
Peritrichous-
all around perimeter flagella
Internal Flagella:
do what and who has them?
-Spirillum are spiral bc of the inside flagella
Turns entire cell like corkscrew, have high advantage in high viscous environments (mucus) ((often sexually transmitted diseases))
(Endo flagella)
Pilus/fimbrae-
-shorter more numerous, made of pilan protein subunits, making helix hollow tube
-usually have adhesive protein tip
-role to stick to things
-(a lot of these in dental plack)
-some bacs can use twitching motility, bacteria is walking along on stilts (pilae)
Swimming motility- (by what to do what)
Caused by flagella, allows cells (bacs) to have pool parties and swim aroond
Motility-
-tells us are the bacs swimming or not
-can tell by seeing are they all swimming in same or different directions?
Non-motile would be all bacteria going same direction, no swimming
Twitching motility-
bacteria walking along on stilts (pilae)
Capsules-
what are and what do?
-composed of polysaccharides, hides cell from host’s immune system, (bc of the sugars on the outer layer) ((some bacs have em, some don’t)
-helps to hide, hold onto water, and stick to things
Monoderms can be
pathogenic if they have a capsule
Resists desiccation (don’t dry out)
-very adhesive
- the smoother ones had a capsule, rough appearance didn’t made capsule
Conjugation-
bac really wants to share DNA, captures a homie and injects the DNA (how many antibiotic resistant genes are passed on)
Surface arrays (s-layers)
(hint: it’s a bacterial specialized external structure)
Describe the composition and structure/appearance
Composed: crystalline proteins (looks like scales)
Role: protection ( knight in shining armor, it’s the armor)
-rigid outer boundary
We think it may be protection from bacteriophages (bacteria eaters), (viruses)
What elements do all living organisms require?
(bonus for percentages of importance)
CHOPKINS CaFe bb
C+N most important (I think)
Atmosphere percentages let’s go!
(N2, O2, Ar, CO2)
78% N2
20% O2 gas
0.934% Argon
0.036% CO2
(We can’t fix our own nitrogen, we reply on the bacs to do it)
(we cant just breathe and fix these gases, most elements are unavailable to us in an inorganic form)
Biogeochemical cycling-
provide definition
-transitioning elements/chemicals between their organic and inorganic form
Our Elements of Focus: (for biogeochemical cycling)
-Nitrogen
-Carbon
-Oxygen
-Sulfer
-Phosphorus
Nitrogen metabolism/cycle:
-name each step/oxi or red:
1) N2 gas -> NH4+
2) NH4+ -> R
2) NH4+ -> NO2- & NO3-
3) NO2- & NO3- -> N2
1) N2 gas, becomes NH4+ (nitrogen fixation, reduction)
2) NH4+ bound to organic skeleton (nitrogen assimilation)
2) NO2- and NO3- (oxidation) ((from ammonium)
3) Those to N2 again (denitrification, reduction, ((losing oxygens)))
50% of the farmer fertizlier will rise to the skies
What organisms are capable of nitrogen fixation?
-ONLY prokaryotes
Nitrogen metabolism/cycle:
-Add associated molecules with each step:
1) Nitrogen fixation (reduction)
2) Nitrogen assimilation
2) (oxidation)
3) Denitrification (reduction)
1) N2 gas, becomes NH4+ (nitrogen fixation, reduction)
2) NH4+ bound to organic skeleton (nitrogen assimilation)
2) NH4+ -> NO2- and NO3- (oxidation) (nitrification) ((from ammonium)
3) Those to N2 again (denitrification, reduction, ((losing oxygens)))
Phototrophic nitrogen fixers-
how to identify/what do?
-proks who can photosynthesize (usually bacs I think??)
-usually have sun or color in the name
(ex.
Cyanobacteria
* Heliobacteria
* Rhodospirillum
* Chlorobium)
Non-phototropic nitrogen fixers-
what are the two and where to find them?
-proks who don’t photosynthesize (usually bacs I think)
-Rhizobium
-Azotobacter
Rhizobium
(nitrogen fixer, what kind and where find?)
-Mutualistic relationship with plants, like legumes
-Plant provides sugars and a house free of oxygen (root nodules are in legumes, little houses, give the rhizobium an anoxic environment)
-the bacteria provides nitrogen (plant cant get itself) for amino acids
Azotobacteria
(nitrogen fixer, what kind and where find?)
-Free living diazotrophic soil bacs next to plant roots,
-Roots get their nitrogen
-Azotobacterial get sugars secreted by plants
What term refers to a nitrogen fixer or “N2 eater”?
Diazotrophic
(two nitrogen eats)
Why do we describe nitrogen fixation as a very expensive process
We say it’s expensive bc it takes 16 ATP + 8e-
(so it’s gotta be the sun or something else providing sugars constantly in order for the proks to be doin this)
Key enzyme for nitrogen fixation? (for phototrophic and non phototrophic fixers)
**and what is it sensitive to?
Nitrogenase for both,
O2 bc it steals all the freaking electrons
3 places Nitrogen fixation can occur?
1) -Anoxic environments.
2) -Heterocysts (specialized cells)
3) -Metabolically adaptive cells
Example of anoxic environment for nitrogen fixation?
-root nodules are in legumes, little houses, give the rhizobium an anoxic environment
Heterocysts-
what are why help nitrogen fixation?
-Specialized cells (hard coating that limits exposure to oxygen)
((cyanobacteria do this))
Converts cells into heterocysts under nitrogen limiting conditions
-Degrades Photosystem II (bc photosystem II is responsible for making O2)
-once becomes heterocyst, cell gives up all reproductive potential (altruism example) becomes dedicated to fixing nitrogen
3) Metabolically adaptive cells-
what are, and how do nitrogen fixation?
(bacterial hamster on wheel)
-Azotobacters use aerobic respiration
-Highest aerobic metabolic rate of any organism when they’re in this mode (imagine bacteria hamster on wheel)
-O2 is used immediately, doesn’t linger in cell, so doesn’t come in contact with nitrogen cycle
What is the end product of nitrogen fixation?
Ammonia/ammonium
What is assimilation in the nitrogen cycle?
& what are the only inorganic nitrogen compounds that can be used?
Fixing NH4+ to organic molecules,
(ammonia and ammonium only forms of inorganic nitrogen that can be incorporated directly into biologicals molecules
-other forms of nitrogen are converted to ammonia before they can be used for assimilation
Ammonia assimilation in the nitrogen cycle pathway 1 name?
Does it require ATP?
-GS-GOGAT Pathway
(for the two enzymes involved)
GS- glutamine synthetase
GOGAT- Glutamate synthase (oxoglutarate aminotransferase)
-ATP required
GS-GOGAT (nitrogen assimilation)
which enzyme comes first?
1) Glutamine synthetase
2)Glutamate synthetase
Nitrogen assimilation pathway 2 name/enzyme involved?
Does it require ATP?
-GDH
Glutamate dehydrogenase
-Pathway doesn’t require ATP
When ammonium concentration HIGH, which pathway is used?
(For nitrogen assimilation)
-only GDH pathway used bc it is driven by equilibrium
When ammonium concentration LOW, which pathway is used?
(For nitrogen assimilation)
-must use ATP to drive the reaction (GOGAT pathway) (against equilibium sorta)
