module 2: metabolism, genetics, and environmental microbiology Flashcards
are bacteria limited on how much they can replicate?
no, their only limit is their environment/resources
describe how bacteria grow as a species
they grow in size in their species (numbers). they do not grow as humans do in size
how do bacteria grow?
they double
describe the “surface area to volume ratio”
at a small size, the ratio is small and very efficient. cell exchanges with its world, gets gasses & nutrients, etc.
as the ratio gets bigger, the SA to V ratio gets worse and the diffusion isn’t as efficient
why cant you have huge bacteria?
there’s not enough surface area to volume exchange to efficiently get everything diffused out of/into the cell that it needs to survive
how do bacteria reproduce?
binary fission
describe the steps of binary fission
- DNA has to get replicated
- cell starts out with one circular chromosome
- a whole other circle chromosome has to get produced
- the two circles move to different ends of the cell
- SEPTUM pierces off in the middle
- pops apart into 2 separate cells
what is important about the septum?
the cell wall has to be re-established here
are bacteria clones?
yes. clones = exact replica
what doubles faster than any other bacteria?
E. coli
what is a closed growth system?
a flask or incubator. humans can also be considered a closed growth system.
describe the “standard closed system growth”
- lag phase (bacteria have a period of time where they get used to their environment)
- log phase (they grow rapidly… exponential growth)
- stationary phase (dying cells = replicating cells)
- death phase (more cells dying than are replicating)
describe mutations
when DNA is getting replicated, the cells will all be the same species but might have some small genetic differences as the population grows
describe what a “biofilm” is
a new hypothesis that some bacteria have the ability to live in a community. they are still single-celled, but live in a mass or clump
what is special about a biofilm? where are they commonly found?
they are very hard to kill. they are found in joint replacements (knee, hips, shoulder)… called a “biofilm infection”
how do biofilm infections grow?
they start as a little colony, then grow into a scaffold where they excrete protein so they can grow into a pod/film. the outside of the film take the brunt of the antibiotic
what are the 4 environmental factors of microbial growth?
oxygen, temperature, UV light, pH
describe oxygen in terms of microbial growth
oxygen is not required for all bacteria
what is aerobe
with oxygen
what is anaerobe
no oxygen
obligate aerobes…
do require oxygen
obligate anaerobes…
do NOT require oxygen. oxygen is harmful to them
facultative anaerobes…
flexible. can handle oxygen. some use it, but are fine without it as well
aerotolerant anaerobes…
don’t use/need oxygen, but are fine with it being around
microaerophiles…
use a very specific amount of oxygen. they live just under the surface of the ocean
describe temperature in terms of microbial growth
temperature ranges for bacteria can go from way below freezing to way near incineration levels. this means bacteria can live in any temperature range
describe UV light in terms of microbial growth
sunlight is the requirement for survival for some bacteria (photosynthetic). sunlight can also be the killer for others
describe pH terms of microbial growth
most bacteria like the middle range around 7. some thrive in either end.
neutrophil: prefer to grow around 7 pH
acidophiles: acid loving bacteria
describe the big picture concept of cellular respiration
taking glucose in, converting it, going through a cycle, the electrons go to the transport chain, converts it, makes ATP
what does “sequestered” mean for a cell?
means that something is taken in and locked into a biomolecule inside the cell. for example. CO2 in a photosynthesizing microbe
what is the universal input for photosynthesis, regardless of the organism being oxygenic/not
carbon dioxide
describe what it means to be an “autotroph”
the organism makes their own food
describe what it means to be a “heterotroph”
the organism obtains food from an outside source
where do “phototrophs” get their energy from?
get energy from sunlight
where do “chemotrophs” get their energy from ?
get energy from chemical compounds
what does metabolism describe?
all the chemical exchanges going on inside the cell. all the break downs, build ups, transfers, chemical reactions, and energy transfers
what are the two different metabolic pathways?
anabolic & catabolic
what does “anabolic” mean?
DNA synthesis. it means to build up, with smaller substrates adding to each other to build big polymers
what does “catabolic” mean?
Glycolysis. it means to break down, and to release energy
define: rate limiting step
prevents a process from moving forward if the substrate is not present. in the instance of glycolysis, one example of a rate limiting step is whether NAD+ is present
what is “phosphprylation”
process of bacteria making ATP. specifically, when ADP adds another phosphate, this is called phosphorylation. there are now 3 phosphates
what is “dephosphorylation”?
breaking off a phosphate, making it into ADP. this releases some energy
what are enzymes?
they lower the activation energy. can be proteins, catalyze (to make faster) reactions, and be reusable. typically named “-ase” or “-zyme”
what are exoenzymes?
they harvest their own sugars from the outside world. they break down large particles so they can diffuse into the cell
what are endoenzymes?
enzymes found within the cell
in simple terms, describe glycolysis
- glucose goes in
- becomes G3P
- becomes 2 separate pyruvate, 3 carbons in each
what is the first step of glycolysis?
a 6-carbon glucose molecule goes in
describe the “energy investment phase” of glycolysis
ATP is going in. to even get glycolysis going, we burn/use 2 ATP molecules
what would be considered the “middle” step of glycolysis?
when there are two “G3P” made… this is when the 6 carbon sugar from the first step is split in half
what is the “rate limiting step” of glycolysis?
NAD+ available to pick up an electron… this is called REDUCTION (LEO says GER)
what is the final product of glycolysis?
you end with 2 pyruvate… each contains 3 carbon
list the inputs of glycolysis:
- glucose
- 2 ATP
- NAD+
list the outputs of glycolysis:
- 2 3-carbon pyruvate
- a little ATP
- NADH
where does glycolysis occur in the cell?
cytoplasm
is oxygen required for glycolysis?
no
what occurs after glycolysis?
the 2 pyruvates are holding a lot of energy, stored in the strong covalent bonds between the carbons. to get that energy out, more metabolism has to happen.
describe the transition step between glycolysis and the citric acid cycle
glycolysis –> pyruvate –> transition step –> CAC
pyruvate goes in, NAD+ is reduced to NADH (think energy that will be used later), and the output is acetyl CoA
describe the big picture of the citric acid cycle:
the cycle turns twice, one per pyruvate. a bunch of enzymes do the work. acetyl CoA goes in, and ATP comes out, along with reduced forms of electron carriers
what does it mean for an electron carrier to be “oxidized”?
oxidized = they lost an electron
what does it mean for an electron carrier to be “reduced”?
reduced = they’re carrying an electron
list the inputs of the citric acid cycle:
- acetyl CoA
- oxidized forms of electron carriers (NAD+ and FAD)
- ADP
list the outputs of the citric acid cycle:
- reduced forms of electron carriers (3 NADH, 1 FADH2)
- a little CO2
- one ATP per cycle (so 2 in total)
where does glycolysis occur?
cytoplasm
after the citric acid cycle loads energy onto the electron carriers, where do they take it?
electron transport chain
what is the overall purpose of the electron transport chain?
to take back electrons from the electron carriers
what two things come to the ETC and start the process?
NADH and FADH2 come to the ETC and drop off their electrons
after dropping off electrons, what happens to NADH and FADH2?
they become oxidized, and turn into NAD+ and FAD
once the electrons are at the ETC, where do they go?
the electrons stimulate hydrogen protons inside the cell to be driven to the outside, across the membrane
once hydrogen goes across the membrane, what is waiting outside?
a high concentration of hydrogen protons… aka “a proton storm”
what is caused by the “proton storm” and how does it relate to ATP synthase?
the proton storm is referred to as “the proton motive force.” ATP synthase is an enzyme that is driven by the proton motive force
what drives the production of ATP?
the hydrogen flowing back through the ATP synthase. as hydrogen flows through ATP synthase, it forces phosphorylation of ADP into ATP
how does oxygen relate to the ETC?
oxygen comes into play at the end of the chain. when electrons come off the domino effect chain, they end up connecting to oxygen, and this creates water. this is also known as the “final electron acceptor”
list the inputs of the ETC:
- energy, in the form of reduced electron carriers (NADH & FADH2)
- O2 gas
list the outputs of the ETC:
- NAD+, FAD
- ATP
- small amt of water
describe the overview of fermentation:
fermentation is just glycolysis plus some weird byproduct, like lactate. the whole process follows glycolysis and involves regeneration of NAD+. fermentation is in no big rush.
list the inputs of fermentation:
pyruvate
list the possible outputs of fermentation:
- lactic acid
- alcohol
- acetone
is fermentation aerobic or anaerobic?
anaerobic
are anaerobic cellular respiration the same as fermentation?
NO. anaerobic respiration is a whole different type of cell respiration… where at the end of the ETC, oxygen is not used
describe the big picture of environmental microbiology
the study of microbes in the air, water, and soil & how elements cycle through the planet
define “biogeochemical cycling”
how elements like water move through the living & non-living world
what are the major microbial roles of biogeochemical cycling?
- decomposers
- primary producers (photosynthesizers)
what is bioremediation?
use of organisms such as microbes & bacteria to decontaminate affected areas. it helps clean up pollution naturally
give an example of how microbes play a role in the carbon cycle
prochlorococcus: cyanobacteria living in the oceans, sequesters CO2 from the atmosphere
what are genes?
sections of base pairs in DNA that contain hereditary information
describe what the “central dogma” is
gene –> DNA –> RNA –> protein
what did Griffith discover?
he found that there was some compound or material within bacterial cells that allowed them to exchange information throughout the population. he discovered TRANSFORMATION through mice experiment
describe transformation as seen in bacteria
living bacteria can take in little sections of DNA from dead cells and claim it to be their own, resulting in them exhibiting those characteristics
what is the “dangling hydroxyl” end of DNA? what else is it referred to as?
3’ end. aka OH
what is the “finished phosphate” end of DNA?
5’ end
what are the nitrogen bases of DNA?
A,T,C,G
what is the end of a nucleic strand with a free phosphate group called?
5’
during denaturation of DNA, what happens?
the inside nitrogen bases become unbonded, allowing the complementary bases to open up. it does NOT mean the sugar phosphate backbone falls apart
describe “haploid”
bacterial cells only have one copy of each chromosome
what is DNA gyrase?
the unwinder enzyme. it helps DNA open up & unwind so it can be read. also referred to as “topoisomerase”
describe NAPS
these keep the tightly bound supercoils of DNA bound down
what are plasmids & describe them in bacterial cells
plasmids are “the bling”… or accessory genes.
F plasmids, R plasmids, and Toxins are found in bacterial cells. they code for something special beyond what species they are
what’s the biggest structural difference between RNA and DNA
RNA has an OH (hydroxyl), DNA has H (hydrogen)
who is credited with discovering genetic information?
George Beadle & Edward Tatum
what is the goal of DNA Replication?
DNA making more DNA. to replicate and make an exact copy
describe the main 3 steps of DNA replication
- initiation
- elongation
- termination
describe the plasmids of bacteria
they are circle shaped and must double
what is the role of DNA helicase?
enzyme involved in breaking hydrigen bonds & the unwinding of DNA
what forms after the nitrogen bases are broken apart?
the replication fork forms
describe what “bidirectional DNA synthesis” means
once the origin opens up, new DNA will be built in both directions
what is DNA polymerase?
the enzyme used to build new nucleotides! DNA polymerase is the building enzyme of growing chains of nucleotides
describe the directions of DNA polymerase
it can only read the template strand in the 3’ to 5’ direction.
it will only build to the 3’ OH end of the growing strand
describe what “semiconservative replication” means
when new DNA is made, they contain old and new sides
describe what the leading strand is:
the side growing TOWARDS the replication fork in one continuous path
describe what the lagging strand is:
the antiparallel strand coming OUT of the replication fork. this means it has to build backward, resulting in Okazaki fragments
what are the concepts attached to gene expression?
- central dogma (gene to protein)
- transcription/translation
what is a gene?
section of DNA that codes for protein
what is the main goal of transcription?
to make mRNA
what does RNA polymerase do in transcription?
the builder of RNA
what is the product of transcription?
mRNA
once transcription occurs, where does the mRNA go?
goes to the ribosome
what happens in translation?
mRNA is read by the ribosomes, and tRNA brings amino acids, as well as matching codons. tRNA plays a pivotal role in bringing the proper amino acid to the growing polypeptide chain
what are codons?
located in the mRNA, they say which amino acid to bring
what are anticodons?
on the tRNA, they are the key-shaped structures that match the pair of each amino acid to be brought to the building chain
what are the 3 possibilities in horizontal gene transfer?
- conjugation
- transduction
- transformation
describe conjugation (horizontal gene transfer)
sister cell moving DNA from one cell to another
describe transduction (horizontal gene transfer)
involves bacateriophage. moves DNA out of bacteria
describe transformation (horizontal gene transfer)
random DNA in the environment that is engulfed by bacteria
