Midterm Material (8.23 - 10.6) Flashcards
what are the most numerable microbes on earth?
viruses
what are the 4 categories of microbes?
bacteria, archaea, eukaryotes, viruses
what is the most effective means we have to study/identify most microbes?
DNA sequencing and analysis
how do we know that our mitochondria are ancient symbiotic microbes?
mitochondria have DNA and it’s codon usage is classically bacterial
what are the probable type of bacteria that chloroplasts are descendants of?
cyanobacteria
what gene do we use to identify bacteria?
the rrn gene
what is the rrn gene? why do we use it to identify bacteria?
it makes the 16s ribosomal RNA subunit, we use it bc it is an essential gene, highly conserved but also highly specific to all bacterial species
what is the general reason for performing a Gram stain?
a general way to distinguish cell types, able to see overview of morphological characteristics of bacteria
what 3 categories do Gram stains allow us to sort bacteria into?
Gram negative, Gram positive, Indeterminate
what are the characteristics of Gram negative bacteria?
- 2 membranes w cell wall in between
- maintains red coloration
what are the characteristics of Gram positive bacteria?
- 1 membrane with VERY thick cell wall
- stains purple
what are the characteristics of Gram indeterminate bacteria?
- typically do not stain or something else weird happens
what are the 3 major components of all bacteria?
- envelope, nucleoid, ribosomes
describe the inner membrane of Gram negative bacteria
- has an electrical charge and proton gradient, required for functional cell
- many proteins in here too, transport guys
what are some key component of the outer membrane in Gram negative bacteria?
- contains LPS molecules to help maintain water preventing dehydration and allowing for some general protection
- lipids cannot flip between leaflets, strict composition maintained
what type of linkages exist in bacterial vs archaeal phospholipids?
bacterial - ester linkages
archaeal - ether linkages
what are the roles of cis/trans bonds in phospholipids?
they aid in maintaining or changing fluidity of the membrane, trans bonds lead to more rigidity and cis bonds give some kinds which allow for some more fluidity
what are the benefits of ether linkages in archaeal phospholipids? how are archaeal phospholipids different?
- these ether linkages allow their phospholipids to be very stable
- branched terpenoids (more rigid/stable membrane)
- some extremophiles fuse their leaflets
- these guys live in extreme conditions so they need all the protection and optimization they are able to get their pili on
what are lipopolysaccharides (LPS)? what are their roles? where are they found?
they are lipids with huge head groups and 6 tails, they are used mainly for protection, they are found on the outer membrane
what are the 3 components of LPS molecules? which are essential? which are variable?
- core polysaccharide: essential and specific
- the O antigen: incredibly variable, literally some of the most antigenic stuff we have
- lipid A: essential
what are the 6 roles of membrane proteins?
structural support, detecting environmental signals, secretion of proteins and small molecules, transport in and out of cell, making energy probably ATM, making reducing power probably NAD+/NADH
how is the cell wall formed in Gram negative bacteria?
these are formed via somewhat complicated cross linking structures, made in strands and crosslinked
how does penicillin affect the cell wall of Gram negative bacteria?
targets cross links, targets actively growing bacteria and basically makes them explode as they rip themselves apart from unstable cell wall linkages
what is the S-layer that is formed by some bacteria? what is its function?
it is a protective protein-sugar layer, it is a bunch of teichoic acid stuff
how do materials get across the cell wall and to the inner membrane?
to get things to the inner membrane, enzymes called sortases might be necessary if the bacteria has huge S-layer
what does it mean for a bacterial chromosome to have specific domains?
domains are specifically and independently supercoiled regions of the genome with proteins that compact and relax it even more than natural interactions
what is coupled transcription/translation? why are bacteria able to do it?
trsc going right into trl because bacteria do not have a nucleus and everything is happening all together in the cytoplasm
what are the locations of the beginning/ending of bacterial chromosome replication called?
oriC and terC
why are highly transcribed genes always located in the same direction as the replication fork?
to prevent blockages when proteins are being made all at once
what are the steps of cell division?
- cell wall elongates and DNA is replicated
- cell wall and plasma membrane begin to divide
- cross-wall forms around divided DNA
- cell separates
what does it mean to say that bacterial chromosomes replicate bidirectionally?
the replication forks are going both directions and we get multiple rounds of replication going all at once as things become available
name a couple: macronutrients, cofactors, and micronutrients
macro: C, N, P, O, H, S
cofactors: Mg, Fe, K, Ca
micro: Co, Cu, Mn, Mo, Ni, Zn
types of bacteria based on - CARBON Source
heterotroph: break down organic molecules to obtain and recycle C
autotroph: fix CO2, assemble into macromolecules
types of bacteria based on - ENERGY Source
phototroph: energy from light
chemotroph: energy from redox reactions
types of bacteria based on - ELECTRON Source
lithotrophs: inorganic molecules donate electrons (Fe, S, N, etc)
organotrophs: organic molecules donate electrons
types of active transport
symporters, antiporter, ABC transporters
what is the most abundant type of transporter?
ABC transporters
ways to grow bacteria
liquid media, solid media, purify one species and grow it, and grow bacteria as communities
define the following: rich media, minimal media, differential media, selective media
rich media: undefined, designed to grow fast
minimal media: only gives essentials, grow slower
differential media: used for tests to determine what is in the population
selective media: used for tests to restrict growth and select for microbes that grow under certain conditions
what are the phases of growth for bacteria?
lag, log, stationary, death
what do bacteria form when they are allowed to grow naturally on solid surfaces?
biofilms
what are the characteristics exopolysaccharides (EPS) in biofilms? what are they used for?
EPS are thick, sugar coating, allows communication, coats entire surface, allows bacteria to not dry out, if cells die the DNA will be redistributed to those in the matrix, can be antibiotic resistant
what are the stages of sporulation?
stage I - septum forms near one pole, DNA replicates and extends into an axial filament
stage II - septum separates forespore from mother cell, DNA pumped through septum until each compartment gets a chromosome
stage III - mother cell engulfs forespore, surrounding it with a second membrane
stage IV - chromosomes of mother cell disintegrates
stage V - forespore develops a cortex layer of peptidoglycan between original forespore membrane and the membrane from the mother, coat proteins deposited on outer membrane
stage VI - dipicolinic acid is synthesized and calcium is incorporated into the spore coat
stage VII - mother cell releases spore
what are some bacteria that form spores?
B. subtilis, B. cereus, B. anthracis, C. tetari, C. botulinium, C. dificilus
what is the point of spore formation?
allows bacteria to survive, adds 2 extra cell walls, can literally survive for months as a spore, basically impervious
what are heterocysts? what are their purposes?
specific cyanobacteria cells that have different gene expression, they are able to fix nitrogen in an oxygen free environment after they modify their gene expression, basically they fix N2 and allow it to then diffuse to all the cells around it which are photosynthesizing and require oxygen for other processes
what does the filamentous growth pattern of streptomyces entail?
go look at this diagram and understand it more maybe, or also just know that streptomyces does in fact have filamentous growth patterns
what environmental factors affect bacterial growth?
pH, temperature, osmolarity, oxygen, pressure
classifications of bacteria based on: temperature, pH, osmolarity, oxygen, and pressure
temp: hyperthermophiles, thermophiles, mesophiles, psychrophiles
pH: alkaliphile, neutralophile, acidophile
osmolarity: halophile
oxygen: strict aerobe, facultative microbe, microaerophile, strict anaerobe
pressure: barophile, barotolerant
what does it mean to grow vs to survive?
growth: making more cells, active, functional
survival: no growth, sitting and just trying to survive, vibing but not growth, typically leads to adaptations presenting themselves
what are some adaptations of psychrophiles and thermophiles?
psychrophiles: proteins are more flexible, different codon usage, antifreeze proteins (prevent ice crystals)
thermophiles: enzymes stable at high temps, membranes stable at high temps, have more chaperones to aid in folding, chromosome consists of more proteins which aid in stabilization of DNA
what are some adaptations of barophiles?
not sure
how do bacteria protect against osmotic stress?
- move water into/out of cell
- make small molecule solutes
- open pressure sensitive channels to move solutes out of cell
what do we know about halophiles?
they be pink, they typically photosynthesize, they need to be near the surface of where they live to obtain that light
what does it mean to portray internal pH as a function of external pH?
most bacteria are able to regulate their internal pH so that they are able to tolerate environments of higher/lower pH because their insides are still able to function appropriately
how to alkaliphiles adapt to low proton environments?
they are able to bring in Na+ at times if there are no protons able to be present and used
what does it mean for bacteria to be: aerobic, microaerobic, or anaerobic?
determines how much oxygen they can handle
why is oxygen so toxic to anaerobes?
they may not have enzymes to deal with reactive oxygen species and this oxygen would just destroy their metabolism and insides
talk about starvation/programmed cell death in terms of MazE and MazF
brain hurty - look at diagram
basically under no stress/no starvation proteins E and Z are bound together and synthesized as normal
when starvation occurs, protein E is degraded and gone, protein F induces cleavage of mRNA and growth stasis leading to cell death, meanwhile G6PD is being chopped up into little bits by proteases
when these G6PD pieces diffuse out of the cell, they bind to protein E in other bystander cells and thus cause E and F to unbind from each other and F to induce mRNA cleavage, growth stasis, and ultimately cell death, releasing nutrients
protein F may also be referred to as a toxin and protein E is the antitoxin which stabilizes it and until it no longer can
what are some ways we control bacterial growth?
sterilization, high temp high pressure treatment, pasteurization, cold, filtration, irradiation, chemicals and disinfectants
what features are involved in the general structure of viruses?
capid, genetic material, lack of metabolic activity, may have tail to help with infection, may have enclosed membrane stolen from host cell
what are the two phases of a viral lifecycle?
lytic phase and lysogenic phase
what does it mean for a virus to undergo lysogeny?
goes under the radar
phage DNA integrates into the host genome to form prophage, this integrated phage DNA can replicate with the bacterial chromosome now, this can now hang out for a while until there is stress in which can it can then become lytic again
what are the 3 ways viruses protect their genomes?
- circularization w sticky ends
- RecA recombination (terminal redundancy)
- covalently bound proteins on ends
what are some characteristics of T4 phages?
- need 3-4 phages before lysing of cell occurs, DNA in geometric head, some other general stuff lol
how do viruses get into cells?
every virus recognizes some receptor(s) on the outside of the target cell(s)
do all viruses lyse the cells they infect?
no, may try to replicate and shed without lysing so as to bypass and not notify cellular response mechanisms
what are some characteristics of papilloma viruses?
cancer - follow this diagram through and see the weird things about it
what is a genome?
all the genomic information that makes up an organism. for any given bacteria this may include its chromosome(s), and any plasmid(s) or viruses. bacterial genomes are highly variable.
how do viruses behave as genomic information in bacteria?
they may be integrated into the bacterial chromosome and replicated along with it OR they may behave as a plasmid and replicate independently.
how do genomes make a living?
- must be compacted to fit into the cell
- replicated and passed to daughter cells
- must be transcribed into RNA
- are allowed to change over time and lead to bacterial evolution
what types of RNA may a genome be transcribed into?
mRNA (very unstable, small portion of all RNA in a cell), tRNA, rRNA, stable small RNA
vertical gene transfer
genes passed via replication to progeny - how multicellular organisms work
horizontal gene transfer
genes passed via transformation, conjugation, or transduction
a major reason that bacteria evolve at much faster rates than other life forms
transformation
- naked DNA is taken up by cells
- may take up any DNA at low levels, specific DNA at high efficiency, or take up at high efficiency but only at certain times
- must have a membrane that is permeable enough for this process
conjugation
- picking up certain plasmids
- must have an origin of replication
- transfers in the like single stranded replicated stuff and then the new cell is responsible for finishing the creation of the new plasmid
transduction
- phage method
- phages infect a cell and package host DNA into their capsids, capsids go out and infect other bacteria, new host DNA in new cell may undergo recombination events to get into the genome of the new cell
what are the different means of transformation bacteria employ?
- taking up any and all DNA at low levels
- take up only very specific DNA (typically own species DNA) but at high rates of efficiency
- take up DNA only at specific time points (under certain conditions) but with high rates of efficiency
what is an example of how base sequences in DNA are not really random?
- A/T bonds are much more flexible and may be found more readily at promoter sequences and regulatory regions (ie open faster, melt lower bc 2 H bonds)
- base stacking of Gs to promote binding of proteins that recognize them
why do a lot of regulatory proteins and RNA pols bind to the major groove of DNA?
the major groove gives better access to specific bases - the minor groove may be used for more generalized DNA binding
what types of proteins bind to the major and minor groove of DNA?
major - regulatory proteins
minor - structural proteins
why may operons be advantageous for bacteria?
- favors horizontal gene transfer (less likely to lose proteins that work together)
- allows their genomes to be smaller but more efficient in terms of protein numbers
- allows 97% of their genomes to be coding
what are some differences between eukaryotic and prokaryotic chromosomes?
- proks have operons and 97% of genomes tend to be coding
- euks do NOT have operons and 98% of genome tends to be non-coding
- euks have introns/exons > may lead to alternative splicing
what are some characteristics of nucleoid structure?
has separate, supercoiled domains, able to relaxed individual parts of the chromosome, contain histone-like anchoring proteins
how is DNA supercoiled?
- may be positive or negative
- topoisomerases put in and take our supercoils
- type II topos (gyrase) put in supercoils via double stranded breaks
what is meant by semiconservative DNA replication?
must always have 1 old and 1 new strand, replication bubble has 2 replication forks
what is meant by bidirectional replication?
replication begins at a fixed origin and progresses in opposite directions
characteristics of DNA replication
- bidirectional
- begins at origin (oriC)
- 2 replications forks progress in opposite directions
- one strand is synthesized continuously in the 5’ -> 3’ direction (leading strand)
- other strand is synthesized discontinuously in Okazaki fragments 5’ -> 3’ (lagging strand)
- ends at terminus (terC)
- 5’ - 3’ because looking for the 3’ OH
termination of DNA replication
this shit confuses me I’m not gonna lie
- replicated passed each other, replication forms linked catenane of sister chromosomes, protein passes linked chromosomes through each other forming a catenane
proteins involved in DNA replication (those involved in mural - lecture 6)
DNA pol III, probably topos, ssb proteins, helicase, ligase, sliding clamp loader, RNA primer and DNA primase
fun fact about the TATA box promoter
does NOT actually really, truly exist in nature! just a general average of Ts and As that tend to define promoters lol - easiest to bust open
where are promoter consensus sequences located?
-35 and -10, downstream of start of gene
what is codon bias?
specific species may pick one specific codon for an amino acid despite there being 2-5 that may potentially code for it
ex. a bacteria may specifically code Leu as CUU instead of any other one of Leu’s 6 possible codons
what are rare codons?
may be translated slowly if activated tRNAs are not readily made for that specific codon sequence, this may be a problem if putting a gene from another species into a new species
what happens to misfolded proteins?
the cell may briefly try to refold the protein, if this does not work the cell will simply degrade the protein
transcription
going from DNA to RNA
- honestly just draw out this diagram a few times
- -35, -10, +1, promoter, sigma, RNA polymerase, terminator, topoisomerases
composition of the ribosome
- 30S subunit (small), 1 essential RNA, 16s rrn gene
- 50S subunit (large), 2 essential RNA, 23s + 5s genes
translation
once again, maybe be able to draw this process out and what not
- shine-delgarno sequence, initiation factors, 30S subunit, 50S subunit, fMet tRNA, more charged tRNAs as you go alone, release factors, stop codon(s), in bacteria also need chaperones and proteases
how many stop codons do bacteria have?
bacteria tend to have AT LEAST 2 stop codons, if not more, really gotta get the point across
some inhibitors of transcription and translation
transcription - rifampin, rifmycin, actinomycin D
translation - streptomycin, dox, erythromycin, cycloheximide, tetracyclines
signals needed on DNA (gene) for transcription and translation
promoter (-35 and -10), +1site, start codon, open reading frame (ORF), stop codon, terminator
signals needed on mRNA for transcription and translation
+1 at very beginning, AUG will be in there, ORF will be there, stop codons will be there, NEED terminator
signals needed on protein for transcription and translation
fMet, stop codons, idk this one was kinda weird in my notes, idk if I truly understood it but good enough I suppose for now
remodeling the genome
adding DNA to the genome
- this includes horizontal gene transfers, restriction and modification, and recombination
also changing the genome by mutation and DNA repair (both involved in vertical gene transfer)
restriction and modification of genome
- restriction and modification of genes prevent cutting of restriction enzymes
- examples are EcoRI and BamHI
- this is in lecture 8 and I am confused at the moment
homologous recombination
this stuff also confuses me, need the Rec proteins, will form a Holliday Junction at some point, must make 2 dsDNA cuts, end with 2 pieces of dsDNA
outcomes of recombination
- 2 circular DNA pieces + 1 recombination event = joined together larger circular DNA
- 1 circular DNA + 1 linear DNA + 1 recombination event = linear strand which will probably be degraded bc dsDNA free ends
- 1 circular DNA + 1 linear DNA + 2 recombination events = joined together larger circular DNA
types of mutations
silent (most frequent), loss-of-function (2nd most frequent), gain-of-function
sources of mutations
- DNA replication (main, DNA pols)
- chemistry of bases
- external mutagens (UV, chemicals, reactive oxygen species (ROS))
what is the overall acceptable mutation rate in DNA replication?
approximately 10^-9 -> 10^-11 errors/bp
what factors contribute to correcting the overall mutation rate during DNA replication?
- errors of DNA pol III (10^-4 - 10^-5 errors/base/round)
- proofreading 3’ - 5’ exonuclease pol II (10^-2 errors/base/round)
- DNA repair mechanisms (10^-3 errors/base/round)
name some systems of types of DNA repair
photoreactivation, nucleotide excision, base excision, methyl mismatch, recombination, translesion bypass synthesis
photoreactivation
- uses phrB gene, fixes pyrimidine dimers, repairs via a cyclobutane ring cleavage
- needs visible light (>300nm) in order to generate energy to break the dimers
nucleotide excision repair (NER)
- uvrABCD genes, fixes helical destabilizations (ex pyrimidine dimers), repairs vis excising a patch of nucleotides
- energy required to bend DNA and accentuate dimer
- nicks the DNA to strip out the ssDNA that contains the dimer
- DNA pol I comes along to synthesize the DNA and everything sealed up by ligase
base excision
- lots of genes used, fixes various modified bases, repairs via glycosylases removing base from phosphodiester backbone
- glycosylase binds to the messed up base, endonuclease cleaves the backbone, pol I and ligase to their thang
methyl directed mismatch repair
DAM Methylase <3
- fixes transitions and transversions, repairs via nicking on non-methylated strands (new messed up ones) and then excising those nucleotides
- I am growing fond of DAM methylase, I wonder if it’s stockholme syndrome
translesional bypass DNA synthesis
- last ditch effort, just trying to all for replication before it’s too late “cell goes to hell”
- fixes gaps, part of the SOS system, somewhat error prone
where does gene regulation occur?
DNA rearrangements, making mRNA* (trsc regulation), mRNA stability, translational control, post translational control (protein stability/activity)
what is an example of DNA rearrangement gene regulation?
salmonella bacteria synthesizing 2 different flagella protein, causes different colony morphology, the DNA literally flips around to express differently
how do cells regulate gene expression by controlling transcription?
classic repressor/activator protein stuff here, I actually have questions about this slide in the note, but basically just knowing that regulatory proteins bind around promoters and what not, activator proteins and repressors may also have inducer ligands which cause them to bind or unbind
what types of systems sense the outside environment?
2-component signal transduction regulatory systems
how do 2-component regulatory systems work?
sensor on cell membrane detects signal (ex. a kinase), signal triggers (or prevents) autophosphorylation, phosphate transfers to a response regulator that binds DNA to either stimulate or repress a target gene, when the signal is done a phosphatase removes the phosphate and down-regulates the system
the lac operon
I feel like I’m just going to have to relearn everything about the lac operon, it also regulates transcription
general lac regulation in regards to LacI, the LacI repressor, LacO, inducers, and LacZYA
when the LacI repressor binds to LacO the expression of the operon is repressed, when the inducer (lactose->allolactose) binds to the LacI repressor its affinity for LacO decreases, the repressor comes off and transcription of the operon occurs
sugar hierarchy and catabolite repression - elaborate on graphs relating the usage of glucose and lactose
if glucose and lactose are present the cell will grow (OD measures) and use up all glucose first, go through a lag as metabolism switches over, and the continue growing and utilize lactose
when measuring units of B-gal, if lactose is present and glucose is gone the cells will continually produce B-gal, if glucose becomes present the expression of B-gal will stop
example of protein function inhibition
glucose - present vs glucose - absent
when glucose is present the LacY transporter is blocked and does not allow lactose into the cell
when glucose is absent the glucose transporter becomes phosphorylated and the lactose transporter allows lactose in
what is the role of CRP and cAMP in the expression of lacZYA?
they allow for maximum expression of the operon by increasing trsc initiation
what is the relationship between the lac operon regulation and cAMP
when glucose is present, cAMP is down regulated and not required, when glucose runs out and the cell needs to switch over to lactose, cAMP is upregulated and goes to help increase lac operon transcription
how does the cAMP receptor protein (CRP) work?
CRP aids in maximizing operon expression by grabbing RNA pol and physically holding it tightly onto the DNA, also aids in the DNA opening up for transcription
brief explanation of trp regulation and stuff about trp synthesis
when there is enough trp in the cell the expression rips through the leader peptide and makes the 3:4 terminator system and when there is not enough trp around the pol slows down and makes the 2:3 hairpin which induces the creation of more trp in the cell
why is ATP synthesis and the ETC always membrane bound?
must create an electrochemical gradient and use a proton motive force to generate the ATP
what compounds store energy? what is their energy used for?
ATP - used for catabolic reactions
ADP - use for one off single reactions
PEP - comes from glycolysis, used to make aromatic amino acids and substrate ATP one at a time
Acetyl Phosphate - makes ATP and lipids
what compounds store reducing power?
NAD and FAD (adenine derivatives, used for ETC) (and NADP for anabolic, biosynthetic reactions) - pick up electrons to shuttle around, NADH FADH2 NADPH are all the reduced forms
glycolysis (EMP) - start, end, does it feed other things? ATP used/made, reducing power used/made
starting with glucose, ending with pyruvate, maybe it feeds other things,,,i think G6P feeds into ED pathway, 2 (net) ATP made, 2 NADH made
a big ass pathway of rearranging P on sugars until we break it down enough to 2, 3C pyruvate
entner-doudoroff (ED) - start, end, does it feed other things? ATP used/made, reducing power used/made
start with sugar acids, end with pyruvate, parts of it feed both glycolysis and the PPP, 1 ATP (net), 1 NADH, and NADPH made
used 1 ATP to make 1 G3P, pyruvate and 2 ATP, also used to allow bacteria to expand their potential carbon sources
pentose phosphate pathway (PPP) - start, end, does it feed other things? ATP used/made, reducing power used/made
start with ribulose-5-P, end with pyruvate and used to make riboses and feed biosynthesis, 1 ATP and 2 NADPH made
makes lots of intermediates for anabolic reactions, geared towards biosynthesis of RNA and DNA
let’s talk about fermentation
alternative to glycolysis when oxygen is absent, we use this cycle if we need to and to clean stuff up but some bacteria use it bc they can and sometimes even prefer to
can make alcohol as high a percent as possible until the bacteria off themselves
what is the point of TCA cycle?
- convert pyruvate to CO2 (2 CO2 per turn)
- make reducing power (3 NADH and 1 FADH2 per turn)
- make a couple ATP (1 GTP goes to ATP per turn)
- regenerate a 4C sugar as this is a ever going cycle
what is even the point of completely oxidizing glucose?
get as many e- as possible over to the ETC so they can enter as high energy e-, used to make ATP, and then exit as a lower energy terminal electron acceptor, the electrochemical gradient allows the protons to come back in as ATP in ATPsynthase
what is glyoxylate bypass?
it begins with lipids, works in low oxygen, there is no loss of CO2 (conservation), and there is limited transfer of e- to carriers
this happens in bacteria that may be missing some enzymes from TCA and not able to get as much energy out of it as possible but rather just making enough energy and reducing power just to survive
why do some microbial pathways matter to animals?
these pathways allow bacteria to grow in a lot of places and a lot of weird ass places, they also matter for infections because we can take advantage of and inhibit certain things that happen specifically in bacteria
elaborate a little on breaking carbon ring structures
bacteria are able to break the ring structures of some weird ass molecules in order to harness the energy from these compounds, sometimes breaking these rings releases a lot of energy so the cell must also have a very efficient way to take are of this release of energy and use it then in a meaningful way
what are the aims of catabolism?
- break down carbon compounds into CO2 and make intermediate for anabolic (biosynthetic) reactions
- make ATP
- make reducing power (NADH, NADPH, FADH2)
what different metabolic systems use an electron transport system (ETS)?
organotrophy - organic electron donors (animals and most bacteria)
lithotrophy - inorganic electron donors (weird bacteria that use metals)
phototrophy - light absorbed excited electrons (photosynthetic bacteria and plants)
very broadly, what is an electron transport system?
a series of successive redox reactions in the membrane of a cell, typically coupled with a proton motive force
some information about the redox tower
- strongest e- donors undergo oxidation reactions
- strongest e- acceptors undergo reduction reactions
- the bigger the e- drop the more energy you make and the faster the reaction occurs
- smaller e- drops may be used by bacteria that grow slowly
- all these reactions are half reactions that are written from a reduction perspective
when coupling redox reactions, what is meant by a direct vs indirect coupling?
direct - reactants directly interact ie 1/2 O2 and 2H+ to make H2O
indirect - intermediate molecule carries electron(s) ie e- donor > NAD+, FAD+, NADPH+ > e- acceptor
where do ETS happen in bacteria?
in bacteria the ETCs are located across the inner (cytoplasmic) membrane
remember, bacteria do NOT have mitochondria!
what are cytochromes?
they are electron carriers involved in ETSs, typically with HEME prosthetic groups with Fe in the center
some bacteria may have different centers based on their environments and what not
give a very broad summary of ETSs
- electrons lose energy as they go along the structures
- protons are transferred across the membrane as the electrons move
- the complexes are transmembrane
what way does the ATP synthase face in bacteria and mitochondria?
- ATPase faces inward (to cytoplasm) and the charge difference drives ATP synthesis
- we accumulate H+ outside cell (periplasm)
what way does ATP synthase face in chloroplasts?
- ATPase faces outward and pH drives ATP synthesis
- we accumulate H+ in the cytoplasm
- weird ass backwards stuff here going on
what are the two ways the proton motive force (PMF) stores energy?
- separation of charge
- gradient of H+ concentration
*need a PMF that is large enough to make ATP but not one so large that it damages the membrane
what does the PMF power?
flagella, ATP formation, drug efflux pumps (antiports, symports, uniports), ETS, probably some other things
where are the Fo and F1 subunits of the ATP synthase in bacteria/mitochondria vs chloroplasts?
Fo subunit is in membrane and the top is out in bact/mito and inside in chloroplasts
F1 subunit is in the cytoplasm in bact and matrix of mito, then facing outside of chloroplasts
what is some of the general structure/rotor information about the ATP Synthase?
- the arm holds the globular domain
- torque is stored in the central stock
- hexamer doesn’t actually move, the confirmations change as the C ring rotates
- alpha subunits have a bind, make bond, and eject conformations
some general ATP Synthase information
highly conserved across many biological species, may not all be the same same but can see the similarity in certain amino acid parts of it
how is the iron oxidation ETS different from other ETS
cytochrome C, rusticyanin, and cytochrome C4 oxidize Fe2+ to Fe3+ outside the cell and then transport those electrons in to the system, Fe NEVER actually enters the cell, fun fact this system can run backwards in very specific bacteria
what photosystem(s) do cyanobacteria and plants have?
PSI and PSII - absorb light at 840nm and 870nm
what photosystem(s) do green bacteria have?
PSI - only absorb 840 nm light
what photosystem(s) do purple bacteria have?
PSII - only absorb 870 nm light
in photosynthesis, what absorbs light and carries electrons?
chromophores with either chlorophyll a or chlorophyll b
how are cells able to acquire building blocks?
- can make through biosynthesis
- can share from cell to cell
- can transport into cell (usually Na+ pumps)
what bacteria are able to fix carbon via the Calvin cycle?
cyanobacteria (they photosynthesize), purple bacteria, and lithotrophs (bacteria that fix S and Fe)
what pathways fix carbon?
- the calvin cycle (most prominent!)
- reductive (reverse) TCA cycle, reductive acetyl-CoA pathway, 3-hydroxypropionate cycle (these are all adaptation type things that mostly reducer bacteria)
some information about the Calvin cycle
the Calvin cycle condenses CO2 and H2O with intermediate R15B, this pathway is very expensive (6 ATP and 6 NADH), rubisco is responsible for splitting 6C sugars into 2, 3C sugars, idk there’s just a lot of carbons going on in this cycle between like 3, 5C guys and 6, 3C guys and then to 5, 3C guys and around we go
where does rubisco live? why does it live here?
the carboxysomes, this is in order to concentrate CO2
what types of cells do reverse TCA?
anaerobes and archaea (probably most ancient form of carbon fixation) (I’m also pretty sure this requires ATP)
what types of cells run the reductive acetyl-CoA pathway?
methanogens and anaerobic soil bacteria (clostridium)
what are some characteristics of the reductive acetyl-CoA pathway?
- no O2 present
- requires less ATP than reverse TCA
- in methanogens, only 5% of their CO2 goes to biosynthesis and the rest goes to making energy
what type of bacteria fix carbon via the 3-hydroxypropionate cycle?
green photosynthetic bacteria, pretty rare and they require bicarbonate
what are some ways bacteria allow nitrogen to come into their cells and be fixed?
- assimilatory nitrate reduction
- nitrogen fixation
- denitrification
- anammox
*comes into the cells as ammonia
what absolutely CANNOT be present in order for N2 reduction reactions to occur?
oxygen
what are some steps that bacteria take to ensure oxygen is not present when they are fixing nitrogen?
- make protective proteins
- plants make O2 scavenger molecules
- light/dark reactions are separated (N2 fixation only occurs in dark)
- specialized cells may be formed
how many ATP are required for nitrogen fixation?
16 ATP - nitrogen fixation is very expensive, you also need some kind of reducing power
how is nitrogen fixed?
the enzyme nitrogenase - it reduces nitrogen in a series of steps that happen in the enzyme’s cofactor site
how do bacteria get nitrogen?
they have root nodules which are homes for bacteria that fix nitrogen for the plant (these bacteria also have good communication and horizontal gene transfer)
what are the building blocks of anabolic reactions (biosynthesis)?
carbon, nitrogen, oxygen, hydrogen, sulfur, and trace metals
what macromolecules and cofactors are built via anabolic reactions (biosynthesis)?
amino acids, nucleotides, small molecules, and fatty acids
what are microbes used for in the food industry?
edible microbes, making food, preserving food, preventing food spoilage, industrial microbiology
what are some fun facts about mushrooms (which are technically microbes, begin as spores)?
- they are 25% protein and contain all our essential amino acids
- PA produces 63% of all white mushrooms in the US
- PA mushrooms bring in $500+ million every year
what is spirulina?
the blue food supplement, a dried cyanobacteria - rich in proteins, vitamins (B12), and minerals
what are the means by which we preserve food?
acid, alkali, high sugar content, freezing/refrigeration, drying, high temp and pressure
what do you want to know about bacteria and disease?
who are they? how many are there? where did they come from?
what are the functions of food additives?
- improve shelf or storage life
- ensure nutritional value
- maintain uniform quality and enhance quality parameters
how does clostridium botulinum cause human sufferance? how have we tamed it?
C. botulinum produces botulinum toxin which inhibits synaptic vesicle fusion in the terminal of a peripheral motor neuron, this prevents the activation of muscle cells and leads to paralysis
we have now “tamed” this toxin and use it as botox, anti aging stuff, in the future it may be used for other health benefits as well
