MCB study guide 3

difference between gram negative and gram positive cell envelopes

only mention gram negative here

Gram negative: thin layer of peptidoglycan, more complex cell envelope, porin and TonB proteins-transfers molecule sinto the periplasmic space more enzymes able to contain cytoplasm, bigger plasma membrane, varying width of periplasmic space inner membrane, periplasmic space, then outer membrane(gram positive does not have outer membrane), contain LPS 

LPS: made up of lipid A, core polysaccharide, and O antigen

Lipid A: inner region-does structure and stability, embeds with the inner leaflet lipids, ALSO acts as an endotoxin(if you kill it it will release deadly lipids into the cell

Core polysaccharide: smaller part of LPS, connects lipid A to O antigen, also responsible for attaching to diff s surfaces

O antigen-outermost and biggest region, can modify it’s sugars that way the host cell isn’t aware that the bacteria entered and escapes the immune response 

Also contributes to negative charge on cell surface, stabilize outer membrane, creates a permeability barrier, protection from host defenses 

difference between gram negative and gram positive cell envelopes

only gram posiitve here:

narrower/smaller periplasmic space,  large pores  throughout it’s matrix thicker layer of peptidoglycan, teichoic acids present ONLY in gram positive, they interact covalently with peptidoglycan and have a fatty acid tail allowing for the embedding in the plasma membrane, they’re found in peptidoglycan(in periplasma) and functions to prevent plasma membrane from floating into space , carries a negative charge and can act like a physical barrier

gram stains for gram positive vs gram negative

Gram stains for gram positive; their thick layer of peptidoglycan traps crystal violet, when adding alcohols you dehydrate the cells which shrinks the pores and seals them shut so crystal violet can’t get out 

Gram negative stains: gram negative have an outer membrane layer, some crystal violet sticks out here, alcohol pulls the crystal violet out of the outer membrane lipids-some fo the membrane lipids are stripped in the process 

Iodine stabilizes the crystal violet, safranin stains the gram negative bacteria 

Flagella and pilli – structure, mechanism of movement

counter clockwise vs clockwise and why bacteria tumble

Flagella-3 parts: filament-longest and most obvious part of flagella

Basal body: the most internal part, also an anchor to the cell envelope for filament 

Hook protein: a flexible coupler filament sits inside the hook, allows for connection to the basal body 

Mechanism of movement: 

Flagella spins like a propeller: counterclockwise is run or directed forward movement 

Clockwise is tumble

Bacteria don’t do backward movement 

Tumble only happens because smth happens in the enviro and dirupts run causing cell to stop and tumble

Flagella and pilli -specific ways that chemotaxis happens

also definition

high conc of attractant and repellent

what happens when CheY is unphosphorylated vs phosphorylated

name the steps

define chemotaxis

positive chemotaxis

high conc of attractant result

high conc of repellant

How this happens: phosphorylation state of CheY dictates running vs tumble 

When CheY is phosphorylated-tumble

When Chey is unphosphorylated-run

Steps: chemoreceptor detects a chemical signal in the environment

1. receptor transmits that signal to CHeW

2. CheW passes it to CheA

3. CheA phosphorylates CheY, then it becomes CheY-P

4. CheY-P travels to the motor switch causing a clockwise rotation/tumble

5. cheZ removes the phosphate from CheY-P resetting it back to CHeY and the run resumes

Chemotaxis: directed movement towards or away from a chemical attractant, must have flagella + chemoreceptors to do this 

Positive chemotaxis-towards a chemo attractant, negative chemotaxis-running away from a chemo repellant 

High conc of attractant-cheA activity is suppressed, cheY-P is unphosphosphorylated, continues to run 

High conc of repellant-CheY-P  is phosphorylated and a tumble occurs 

talk abt basal body rings in gram negative bacteria

talk abt FlIN and FliG

talk abt steps specifically to make flagella move

where are each off the 4 rings embedded

what is the importance of FliM and FliN

what is the C ring also apart of

what is the stator Made up of

what is the start anchored to

what does MotA and MotB form

Basal body contains 4 rings, in gram negative bacteria that’s L ring embed in outer membrane/lipopolysaccharide 

layer, P Embed in  ring-peptidoglycan layer 

MS ring, embed in plasma membrane 

C ring, embed in cytoplasmic inner plasma membrane 

L and P for anchoring basal body 

Gram negative rotor: is the MS and C ring, called the switch complex, assembled from FliM and FliN-critical for rotation and direction switching 

FliN

is apart of C ring-might interact directly with the stator-where torque is generated 

stator=made up of MotA and MotB-amchored in cell membrane surrounding rotor-together these proteins form a channel allowing protons to flow down their concentration gradient from the outside cell to inside cell, 

Movement steps

1: proton motive force creates a higher conc of protons outside the cell than inside 

2: protons flow inward through the MotA/MotB channel-releasing energy and causing a conformational change in MotA, which pushes against FliN on C ring 

3: this repeated p ushing generates toque/rotational force causing the MS ring and C ring to spin 

4: spinning rotor turns the rod/shaft that runs up through the basal body rings 

5: rod connect to hook, connecting to filament, spinning the filament and boom, movement 

Gram positive basal ring-no outer membrane, 

Directions f rotation depends on C ring switch complex/FliM/FliN/Flig-responds to chemotaxis signals to fip rotation and let cell t umbel 

capsule info

what do capsule and slime layers do together

what is capsule composed of

it is blank and blank and blank to cell surfaces

it can’t be removed easily or not

what does it help protect against and why

what does it also do

Capsule+ slime layers: aid in attachment to solid surfaces+biofilms, polysaccharides 

Capsule:composed of polysaccharides  thick and itghtly organized, adhered tightly to cell surfaces, can’t be removed easily, help protect the cell from dessication bc they have high water conc, help bacterial cells escape the host cell immune response 

slime layer

is it thiner or thicker than a capsule

talk abt the adherence(tight or loose

what thing does the slime layer do that the capsule does two

compare it’s ability protect the host cell immune response

what is is great for , can capsule do this

explain the texture

if you have a capsule, will you have a slime layer or s layer

much thinner than capsule,

doesn’t adhere as tightly,

protect the cell from dessication due to high water content, aid in attaching ,

protecting from host cell immune response, not as much,

great for gliding motility(capsule can’t do this), soft and gel like 

If you have a capsule-no slime layer or s layer, vice versa 

talk about S layers:

what does it act as

what is it’s relationship with. water-what does this protect from-multiple things

comment on it’s structure + shape

comment on it’s ability to protect the host

what does it help prevent

how does it come together

where do you ee s layer in-domain wise

acts as a physical layer,

makes water highly impenetrable, protect bact from ion and pH fluctuations, osmotic stress, enzymes, and predation,

highly structured, not soft or flexible,

ca protect host, but not as great, 

helps prevent damage,

comes togehtter via self assembly 

archaea

endospore info general

define an endospore

blank contains blank, there’s no blank here, packaged with blank

the blank wall, becomes a new blank on blank

blank, highly blank, blank cross linked with blank, there are blank blank here

blank, blank but incomplete blank blank blank, contributes to blank blank

blank blank, which is the physical barrier

blank and blank blank, 70 tightly cross linked blank, physical barrier

blank-blank layer, only in blank organisms

Endospore- a dormant metabolically inactive structured formed by bacteria when nutrients are depleted, ushe for soil dwelling orgs, allows them to survive a lot 

Core-contains DNA, no water, packed with ca-DPA

Core wall-becomes new cell wall on germination

Inner membrane-highly impermeable tightly cross liked with proteins, germination receptors here

Cortex: thick b ut incompletely cross inked peptidoglycan, contributes to heat resistance

Outer membrane-physical barrier

Out and inner coat-70 tightly cross linked proteins, physical barrier 

Exosporium-glycoprotein layer, only in some organisms

endospore sporulation

what is it triggered by

blank blank blank once blank initiates sporulation

it’s an all ornothing thing meaning that it’s blank and occurs for 10 hours

blank forms inside blank cell, the blank blank forms first, then blank, then blank, blank is pumped into the core, blank water/sporangium, then blank lyses to blank the spore

Sporulation: triggered by nutrient deprivation, amster regulator Spo0A once phosphorylatted initiates sporulation,

irreversible

spore e mother, inner membrane, cortex, coat layers. CA-DPA, displacing , mother cell, release

endospore germination

what does it mean

what is it triggered by

what is it detectd by , where are they located

what are the steps once they are triggered

the ____rehydrates, ____ is released, the ___ is degraded, the __ ___ becomes the new ____ ____, and the cell resumes ____ ___activity 

Germination: the return from dormant to active:

triggered by favorable enviro condiiton signals like the presence of nutrients: like specific amino acids or sugars.

They are detected by germination receptors located in the inner membrane.

spore, CA-DPA, cortex, inner membrane , plasma membrane, normal metabolic

reasons that spores are resistant

blank of the core by blank, prevents blank from damaging blank and blank

blank is able to bind to and coat the blank, blocking blank and blank from damaging it

altered cortex cross linking-contributes to maintaining the …

blank which include blank and blank

blank and blank coats prevent…

dehydration of the core by CA-DPA- prevents heat from damaging proteins and DNA 

SASPS-small acid soluble proteins: bind to and coat the DNA, blocking UV radiation and chemical stuff from damaging it 

dehydrated state of the spore-heat resistance 

Physical barrier layers: inner membrane, outer membrane,

inner and outer protein coats-prevent antibiotics, chemicals, and enzymes from reaching the core

archaean morphology size and shape

name three shapes you see in archaea usually and the one that isn’t present in bacteria

compare the size of eukarya to one of the other domains

more shapes

what is the micrometer range

Irregular shapes, rectangular shapes, or squared which isn’t present in bacteria, wider range of unusual morphology 

Small like bacteria, micrometer range 

Sphere, rod, irregular, flat/rectangular, triangular 

.5-5 micrometers,

archaeal cell structure

-ctyoplasm and cytoskeleton

cytoplasm does not have a ….

the ribosomes are blank just ike blank

protein composition of ribosomes is more similar to…

cytopskeleton: have both blank and blank features, further you go in the timeline, the closer you are to which domain

there are homologs of blank blank blank like actin and tubulin

A. membrane bound organelles/nucleus,

ribosomes are 70S like bacteria

eukaryotes 

B.  Cytoskeleton-have both eukaryotic and  bacterial features,

eukaryotes

have homologs of bacterial cytoskeletal proteins-like actin and tubulin

plasma membrane archaea cell structure

compare the linkages of archaea vs eukaryotes

they also have a difference in blank and blank. what two things are used here

there’s also no blank form

can lysosome and beta lactic work here

they also use blank instead of blank

what unit do they use for 20 carbon molecule, what is this 20 carbon molecule called, how is it linked to glycerol

more likely to use monolayer or bilayer, what does that mean

C.  Plasma Membrane - important features

                    Ether linkages instead of ester linkages, UNIQUE to only archaea bc other two use ester, 

Difference in organization and composition-use pseudomurein instead for polysaccharides, plasma membrane and cytoplasm option,  use diff sugars, hase 1-3 beta glycosidic bonds instead of 1-4, has diff amino acids that cross link,

no D form in achaea so lysososyme and beta lactam  won’t work against archaea, uses NAT instead of NAM 

Uses isoprene unit for 20 carbon moelculed called phytanyl linked to glycerol via 1 carbon 

More likely to use monolayer can be bilayer though , which is 2 hydrophilic head groups 

cell wall morphology

they don’t have a true __ layer

they do have blank though

they have blank blank but diff blank

some have just a blank blank as their entire cell wall, which provides physical and blank protection, some archaea lack a cell wall

D.  Cell Wall – morphology

peptidoglycan

pseudopeptidoglycan

similar function, chemistry

, some have just an S layer as their entire cell wall, provides physical and osmotic protection, some archaea lack a cell wall 

flagella

compare the way that they rotate

what directions can archaea move in , what can’t they do

what does bacteria use to spin

how does the flagella size compare to bacteria

what are they composed of

which direction do they grow

E.  Flagella – structure, mechanism of movement

just liek bacteria

forward and backwards, not spin or tmble like bacteria,

archaea hydrolyzes ATP and uses that

Diff bc they are thinner,

composed of two diff versions of flagellin protein,

grow from BASE not TIP 

cannulae, hami

what’s their def

what 3 things do they do

what is the hami definition

what are they also great for

remember that arches DNA is more eukaryal and why

hollow glycoprotein tubes that link cells together to forma  complex network,

o communication, but shared nutrients, surface structures, and 

filamentous structures coming off surface of the cell that have grappling hook configuration-helpings with attachment

Great for biofofilms , and helping archaea from not getting removed from the enviro 

A’s DNA is more eukaryal, 

bc they have histones like eukaryotes,

 Metabolism, catabolism, anabolism: what they are, how they are all interrelated

metabolis m is the sum of all chemical reactions in an organism (catabolism + anabolic)

Catabolism: the energy releasing from, breaking down 

Anabolism: the one that requires energy to build products 

Coupled by the energy released by catabolism fuels anabolism or is used for the process of anabolism 

 Metabolic pathways: what are they

they’re a sequence of ___ ___ chemical reactions

they are not determined by __, enzymes are encoded by genes

A sequence of enzymatically catalyzed chemical reactions 

Metabolic pathways are not determined by enzymes, enzymes are encoded by genes 

of embed-meyerhof, pentose phosphate, and entire duodoroff pathway talk abt embed Meyerhof pathway

it is the __ ___ pathway for blank blank to blank

functions in blank or blank of blank

it has blank phases

1st…

2nd..

occurs in cytoplasmic matrix of all major groups of microorganisms, plants, and animals

most common pathway for glucose degradation to pyruvate

functions in presence or absence of O2

two phases

breaks glucose into 2 pyruvate, generates 2 ATP and 2 NADH

pentose phosphate pathway

what does it break down

what 2 things are generated

what is it important for

what’s the last important thing here

how many ATP do you make from it

breaks down glucose 6 phosphate

generates NADPH-reducing powder

produces 5-carbon sugars-pentoses

biosynthesis of nucleotides and amino acids

genertes precursore metabolites

0 ATP

talk abt entire-duodoroff pathway

what is it used mainly by or who

what does it break down

how much ATP is generated and NADH

is it more or less efficient then embed morph pathway

used mainly by gram negative bacteria

breaks glucose into 2 pyruvate

generates only 1 ATP and 1 NADH-less efficient than EMP

also generates 1 NADPH

What are enzymes, transition state, activation energy and what is the relationship between the 3?

Enzymes-speed up the rate of a rxn by lowering the Ea to make it quicker 

Transition state; the highest energy/energy peak of reaction, most unstable point of reaction, 

Activation energy: the amt of energy it takes to hit the transition state/start a chemical reaction 

Lock and Key Model vs. Induced Fit: difference between the two

Lock and key: have to have substrate with specific confirmation to fit, it’s a rigid model, doesn’t allow for flexibility in structure or enzyme it’self 

Induced fit model: there is still specificity, only specific substrate will fit, when substrate binds to active site, the enzyme active site binds to it and changes the final confirmation of it a bit

cofactors, haloenzymes, and apoenzyme

Cofactors: non protein components that bind to enzyme to create active site that has a structure that is complimentary to substrate, organic 

Haloenzymes: apoenzyme + cofactor, the complete catalytically active form of an enzyme 

Apoenzyme: protein part only that binds to a non protein cofactor to form a haloenzyme 

 Prosthetic groups vs. coenzymes

Organic or Inorganic mol  like zinc or magnesium that are firmly attached to an enzyme, permanent components of the proteins 

coenzymes/cofactors are loosely bound to the protein, aren’t permanent, detach after the reaction

Environmental effects on enzymes (pH, temperature, substrate concentration)

Enzymes all function best at a specific pH and temp , small changes are okay, drastic changes mean enzyme denaturation

Substrate concentration: the more substrate available, the higher the rate of enzyme catalzyed reactions

Understanding of Km, Vmax and how they relate to microorganisms

what does a low km mean, what does this also mean in terms of scavenging for nutrients

what does a high km mean, what does this also mean, in what setting would this kind of organism good in

what does this determine

Km: substrate concentration required by the enzyme to operate at half of it’s maximum velocity

Vmax: the peak rate of an enzyme-catalyzed reaction when the enzyme is fully saturated with substrate

Low km: means the enzyme reaches half max velocity at a low substrate concentration bc enzyme has a high affinity for it’s substrate, meaning org is good at scavenging for nutrients when they are scarce, good for nutrient poor enviro 

High km: means that the enzyme needs a high substrate concentration to reach half max velocity bc enzyme has a low affinity for it’s substrate, works well when nutrients are abundant 

how well an org competes for limited nutrients in their enviro, low Km will outcompete others when nutrients are scarce 

Enzyme inhibition (Competitive vs. non-competitive) similarities, differences

what do competitive inhibitors look like and where do thhey bind

talk abt how it effects km and vmax

where do noncompetitive inhibitors compete/bind to

what does this use

what happens to the substrate

how does it effect tkm and max

Competitive:inhibitors compete directly at the active site for binding with the substrate, look a lot like the natural substrate, it binds to active site 

Increase km and doesn’t affect vmax 

Noncompetitive inhibitor-don’t compete at active site of the enzyme, binds at a diff site somewhere on enzyme that’s not active site, causes a conformational change that changes site of the active site, natural substrate won’t be able to fit into site 

Decreases vmax, km stays the same 

Why metabolic regulation is important and 3 major mechanisms-how they work

start with just metabolic channeling

what is the definition

how do they do it

what does it allow the cell to do

allows the cell to coordinate blank blank activities through the blank blank of reactions

also creates blank concentrations of blank and blank in blank locations

which domain uses it the most and why

which domain uses it less and why, which specific type uses it

why does blank use it not as much

Metabolic channeling-controlling where enzymes and metabolites are located within the cell,

by moving them between compartments,/physical organization of metabolism 

run similar pathways simultaneously and independently without interference,

diff metabolic activities, physical seperation

, creates diff concentrations of enzymes and metabolites, even of the same molecules, etc in diff locations

Eukaryotes , membrane bound orgs 

Prokaryotes use it less, gram neg do though, periplasmic space 

Gram positive not as much due to fewer compartments 

talk abt regulation of the synthesis of a particular enzyme/post translational regulation of enzyme activity

allosteric regulation

Regulatory molecule called an allosteric effector binds to an enzyme at a specific site called the allosteric site(NOT the active site and is non covalent and reversible)

This changes the shape of the enzyme

Change reaches ll the way to the active site 

Positive effector increases enzyme activity, while negative effector inhibits the enzyme 

This process is very specific, molecule binds to a specific molecule, diff from non competitive inhibition bc you can turn the enzyme off and ON , purposeful 

With noncompetitive inhibition, smth form the enviro is effecting the enzyme non specifically 

talk abt covalent modification of enzymes apart of talk abt regulation of the synthesis of a particular enzyme/post translational regulation of enzyme activity

Covalent modification of enzymes-

An on/off switch for enzymes, chemical group is added/removed from the enzyme turning it on/off, unlike allosteric regulation, involves covalent bonds but is still reversible 

Chemical group-ushe a phosphate is added or removed from the enzyme, changing the enzyme’s activity, another enzyme is required to add or remove the group, those enzymes themselves are regulated, creating a second level of regulation 

More osphisticated than allosteric regulation: can respond to more stimuli in varied ways, second enzyme level=regulated, allows for cascade effect, meaning a small signal can be amplified into a large response 

talk abt diff between allosteric and covalent

Allosteric has 1 level of regulation, covalent modification has 2 or more 

Allosteric does not require another enzyme, while covalent modification does 

Bond type is covalent for covalent modification, while allosteric regulation is non covalent 

Allosteric is non covalent while covalent modification is covalent, 

last one, talk ab feedback inhibition

Direct stimulation or inhibition enzyme 

When a pathway produces an end product faster than the cell can use it, causes concentration of end product built up, end product binds back to an enzyme early in the pathway(pacemaker enzyme) shutting down the whole pathway 

Pacemaker enzyme catalyzes the slowest or rate limiting  reaction, by targeting this enzyme, the end product effectively locks the entire pathway bc nothing can move forward past that slow step 

When concentration of end product drops low enough, end product will detach from the pacemaker enzyme 

allosteric regulation, posiitve and negative effectors

An effector: a small regulatory molecule that binds to the allosteric site, creating the conformational change

positive effector binds to the allosteric site, causes a conformational change and turns the enzyme on, increases enzyme activity while negative effector binds to the enzyme, inhibits the enzyme turning it off

Covalent modification-how it works

Covalent modification of enzymes-

An on/off switch for enzymes, chemical group is added/removed from the enzyme turning it on/off, unlike allosteric regulation, involves covalent bonds but is still reversible 

Chemical group-ushe a phosphate, methyl or adenyl  is added or removed from the enzyme, changing the enzyme’s activity, another enzyme is required to add or remove the group, those enzymes themselves are regulated, creating a second level of regulation 

More osphisticated than allosteric regulation: can respond to more stimuli in varied ways, second enzyme level=regulated, allows for cascade effect, meaning a small signal can be amplified into a large response 

Feedback/end-product inhibition

A form of direct inhibition that works through allosteric regulation, end product is essentially acting as a negative effector 

When a pathway produces an end product faster than the cell can use it, causes concentration of end product built up, end product binds back to an enzyme early in the pathway(pacemaker enzyme) shutting down the whole pathway 

Pacemaker enzyme catalyzes the slowest or rate limiting  reaction, by targeting this enzyme, the end product effectively locks the entire pathway bc nothing can move forward past that slow step 

When concentration of end product drops low enough, end product will detach from the pacemaker enzyme 

-Understand the importance for chemoorganohetrotrophic funneling substrates towards the same metabolic pathways

Organism that gets its energy and carbon from organic comps (like glucose, amino acids, fatty acids) 

Chemoorganoheterotrophs can eat a wide variety of organic molecules but instead of having a  unique pathway for every single substrate they break down diff substrates into a few common intermediate molecules that feed into the smal central pathways

Glycolysis and TCA cycle 

Important for efficiency-central pathways/highway instead of unique pathways

Flexibility-organism can use diff nutrients but process them all the same way once broken down 

What ways can cells use to get energy?

Substrate level phosphorylation-PO4=transferred to ADP from a high energy molecule (phosphoenol pyruvate, PEP) and take phosphate off highly ractive mediate and put it on ADP and you make ATP

Happens in cytoplasm, takes place in the presence or absence of O2,

Creates the least amount of ATP production 

-

Oxidative phosphorylation 

using a chemical substrate with an ETC to generate ATP

electrons =passed down the ETC from mols with lower redox potential to higher redox potential 

Electrons move down the chain, releasing energy. Energy is used to pump protons across the membrane creating a proton motive force, protons flow back through ATP synthase, energy is used to drive ATP synthase and make energy 

O2 in aerobic respiration accepts the electrons 

Photophosphorylation -when you use light with electron transport chain for energy, photosynthesis (the light reactions)

to generate a proton gradient across a membrane

ATP synthase 

respiration but using light instead of a chemical substrate.

what is oxidation, reduction, redox potential

Oxidation=loss of electrons 

reduction=gain of electrons 

Redox potential=the tendency of a molecule to acquire electrons-higher redox potential means higher amt of ATP made

Understand amphibolic pathways 

pathways that run in both catabolic and anabolic reactions

examples- Meyerhof pathway, pentose phosphate pathway, TCA pathways 

important because it saves genome space and don’t need a bunch of enzymes for anabolic and catabolic separately

Way for the cell to be resourceful

Difference between aerobic and anaerobic respiration, and fermentation – which pathway produces the most energy and why

Aerobic: Uses Oxygen/O2 as final electron acceptor, used primarily by eukaryotes, gives us most amt of ATP due to highest redox potential than other, electron acceptor is exogenous, outside the cell, uses ETC and oxidative phosphorylation

Anaerobic use another molecule as final electron acceptor, not O2, used primarily by prokaryotes,produces less ATP than aerobic, more than fermentation, alternative electron acceptors have a lower redox potential than oxygen

Fermentation: uses substrate phosphorylation ONLY, produces 2 ATp per glucose, regenerates NAD+ without the ETC allowing glycolysis to keep running does NOT use ETC bc there is no terminal electron acceptor available in the enviro , produces a small amt of ATP, terminal electron acceptor is endogenous(inside the cell), organic molecule inside the cell is reduced, only done by gram positive microbes

Embden-Meyerhof pathway: what is it? where does it occur in prokaryotes and eukaryotes?

-most common pathway for glucose degradation to pyruvate 

Occurs in the cytoplasmic matrix of eukaryotes + prookaryotes 

Functions in the presence of absence of O2 

Two phases 

1. 2 ATP are used to add phosphates to glucose, this primes the molecule for breakdown-net energy input

2. Glucose is split into w 3 carbon molecules, oxidation occurs generating NADH and ATP is produced by substrate level phosphorylation

energy investment phase -6 carbon phase,

6-Know start and ends products of glycolysis, where energy is invested. where energy is generated

 Overall 6 carbon glucose turns into 2 3 carbon sugars 

Starting: glucose, 2 ADP, and 2 NAD+

Energy is nvested in the 6 carbon phase 

energy=generated in 3 carbon phase+ electrons made here 

Phosphates from carbon=transferred to ADP 

-What happens to the carbon

What is the difference between substrate level phosphorylation and oxidative phosphorylation?

6 carbon is split into 2 3 carbon pyruvate molecules 

Know how many ATP and NADH is generated

2 ATP consumed to add phosphates to glucose(6th and 1st carbon)

4 ATP created, so net 2 ATP 

2 NADH created 

Phosphates are added to both ends of the 6 carbon glucose molecule, then it is split in the middle

Substrate level phospho-phosphate is directly transferred to ADP, no ETC needed, happens only in glycolysis 

Oxidative phosphorylation-uses ETC and proton motive force to make ATP, far more efficient 

What happens during transition/prep step (pyruvate dehydrogenase)

The 2 private (carbon sugars )turn into 2 acetyl coA

CO2=re;eased, 1 for each pyruvate

2 NADH are produced 

Carried out by pyruvate dehydrogenase 

TCA cycle: where it occurs in both eukaryotes and prokaryotes, how many NADH, FADH2, CO2, 

and GTP are generated.  Point of regulation (isocitrate dehydrogenase)

Eukaryotes: mitochondrial matrix 

Prokaryotes: cytoplasm 

NADH: 3

FADH2:1

CO2:2

GTP: 1

REMEMBER there’s 2 molecules each of acetyl coA so you have to multiple by 2 to get the total amt 

Regulated by allosteric regulation, 

Inhibited when energy is high-high levels of NADH and ATP shut it down by feedback inhibition

When energy is low, high levels of ADP/NAD  activate it, signaling the cell needs more energy 

This controls the rate of the entire TCA cycle 

Isocitrate dehydrogenase-checkpoint enzyme where regulation of TCA cycle happens 

Concept of redox potential and how the redox potential of a conjugate pair (either – or +) determine how electrons will flow

redox potential

negative redox potential

positive redox potential

electrons always flow form hat to what

Redox potential: the tendency of a molecule to take electrons/how much a molecule wants electrons 

Negative redox potential-has a high tendency to donate electrons, wnat sto give electrons away

Positive redox potential-molecule that has a high tendency to accept electrons, wants to keep them

Electrons alays flow form negative to positive redox potential /molecules that want to give electrons away to molecules that want to keep them high

Electrons flow from carriers(donor) with more negative reduction potentials to carriers(acceptors) with more positive Eo

General concept of how the ETC works and how movement of electrons leads to generation of PMF and in turn ATP generation

NADH and FADH2 drops off electrons, they’re passed through a series of protein complexes,

electrons flow from negative to positive redox potential

final electron acceptor accepts the electrons and makes water in humans

PMF: as electrons move through the ETC complexes, energy released is used to pump protons H+ across the membrane, creating a proton gradient(more H+ on one side), this gradient is the PMF

ATP generation: protons want to flow back down their concentration gradient, can only do so through ATP synthase, protons flowing through ATP synthase cause it to spin, spinning drives ADP+P turning into ATP

chemiosmosis

1-ETC: oxidative phosphorylation, why so much more ATP generated from ETC than glycolysis and TCA

Oxidative phosphorylation: electron transport chain uses electrons form NADH and FADH2 to pump H+ protons across the inner mitochondrial membrane, creates a proton gradient (more H+ on the outside than inside), electrons flow through protein complexes (1,2,3,4,5) from negative to positive redox potential, final electron acceptor is O2 which becomes water, proton gradient drives ATP synthase to produce ATP 

Due to the huge difference in the redox potentials between the electron donor and final electron acceptor beside

chemiosmotic process

Chemiosmotic hypothesis-states that cells produce ATP by using the ETC to pump protons across a membrane, creating an electrochemical gradient(more protons on one side than the other), protons want to flow back across the membrane down their gradient, the only way they can do this is through ATP synthase, as protons flow through ATp synthase it spins and generates ATP 

Differences in bacterial ETCs compared to eukaryote and archaea: how ATP yield compares and why

Bacterial + archaea  ETC-in the plasma membrane 

Eukaryotes: in the inner mitochondrial membrane

ATP yield: eukaryotes: 36-38

Final electron acceptor for eukaryotes is O2

Bacteria and Archaea-final electron acceptor is thus an inorganic compound 

Bacteria -variable amts of ATP 

Archaea produce variable amts 

No membrane  unlike eukaryotes-have mitochondria 

Build gradient across the plasma membrane, eukaryotes use inner mitochondrial membrane 

Not as complex as eukaryotes, fewer complexes than eukaryotes 

Shorter and branched unlike eukaryotes which are linear 

Different electron carriers than eukaryotes

Less ATP than eukaryotes

ETC not as far apart on electron tower as eukaryotes, meaning smaller redox ponteital diff, less ATP 

ATP synthase how it works to generate ATP

what are the two parts

it is blank blank

where is it located for eukaryotes and plasma membrane

protons flow down their concentration gradient by a blank blank

causing blank blank to spin

blank black spinning rotates blank blank

this moves though blank (blank and blank blank blank)

causes blank blank in blank blank

allowing ADP + blank to bind making ATP

it takes blank protons to make 1 ATP

can run it in reverse to hydrolyze ATP and pump protons out

• F0 (embedded in membrane) and F1 (cytoplasmic side)

• highly conserved

• E=mitochondrial membrane, P=plasma membrane

• A subunit channel

• C subunit to spin

• C subunit, gamma spindle

• F1, alpha and beta subunits alternating

• conformation change in beta subunit

• 3

Anaerobic respiration compared to aerobic: differences, why less ATP generated

aerobic:Final electron acceptor is O2, generates more ATP , high redox potential between NADH and O2

Anaerobic: final electron acceptor is not O2 ( could be iron, nitrate, sulfare, CO2, rather an inorganic molecule, generates less ATP due to lower difference in redox potential, less positive redox potentials than O2, meaning smaller differences 

5-Fermentation: importance, under what circumstances it occurs and how does energy generated compare to aerobic and anaerobic respiration

Main importance: to regenerate NAD+ so glycolysis can keep running 

Circumstance: occurs when environmental conditions prevent the use of an ETC 

Ushe bc of no available terminal electron acceptor 

Fermentation: Endogenous( inside the cell) terminal electron acceptor , low levels of ATP , no ETC used, only 2 ATP made from glycolysis -anaerobic process 

Aerobic and anaerobic: exogenous inorganic terminal electron acceptor, high levels of ATP , more in aerobic 

-General types of fermentation: heterolactic acid vs. homolactic acid (differences

Heterolactic acid: produces both lactic acid and ethanol. Uses the pentose phosphate pathway instead of glycolysis. Starting with a 6-carbon sugar, a decarboxylation step produces a 5-carbon sugar, which is then split into a 3-carbon and a 2-carbon molecule. The 2-carbon molecule is used to recycle electron carriers. Generates only 1 ATP — less efficient than homolactic fermentation.

End products are arctic acid, ethanol and CO2

Homolactic acid: one end product: lactic acid. The enzyme lactate dehydrogenase converts pyruvate to lactic acid, pulling electrons off NADH to recycle it back to NAD⁺. Generates 2 ATP via substrate-level phosphorylation

Uses embden meyerhof parnas pathway like alcoholic fermentation

-General types of fermentation:

vs alcoholic fermentation vs. mixed acid

Alcoholic fermentation: major end product-ethanol 

Used emden Meyerhof parnas

What turns pyruvate to acetaldehyde: decarboxylation 

Pyruvate reduction to acetaldehyde makes ethanol-via pyruvate decarboxylase recycled NADH to NAD+ 

Acetaldehyde to ethanol via alcohol dehydrogenase , generates 2 ATP

Primarily used by yeast and some bacteria 

Mixed acid fermentation: produces a mix of acids, alcohols and sometimes gasses

They have different end product pathways 

It also includes steps to recycle NADH to NAD+ 

Emden meyerhof parnas pathway 

Chemolithotrophy – why less ATP generated

pull electrons off inorganic substances (instead of organic molecules) and feed them into the ETC. 

Bypasses glycolysis and the TCA cycle entirel bc inorganic molecules can’t be broek down through glycolysis or TCA 

This is still a respiratory process because it uses the ETC.

ATP yield is lower than with organic substrates because the reduction potential difference between the inorganic electron donor and the terminal electron acceptor (oxygen) is much smaller, meaning less energy is released.

8-General knowledge of metabolism of non-glucose carbon sources

Proteins and amino acids: proteases break polypeptides into indiv amino acids, these indiv amino acids have detached amino group, leaves behind an organic acid that’s used in the TCA cycle

Lipids: lipases will separate fatty acids from glycerol, glycerol enters glycolysis,  beta oxidation pathway breaks down the fatty acid into small carbon chunks , produces 2 acetyl coA sent to the TCA cycle individually for processing 

Tightly regulated pathway to prevent cell from breaking down its own phospholipids 

 19-Phototrophy-and photophosphorylation def

Photophosphorylation- def

The ability of an org to use light as an energy source 

Includes all light driven energy process 

the process of making ATP using light energy 

atp synthesis uses blank instead of chemical substrates

it’s like blank, but powered by blank

light reactions create a blank which drives blank

pigments are organized into blank, which are embedded in the blank

each photosystem has a blank

light energy get’s passed to the blank, knocks blank out, electron travels though blank, pumps blank across membrane, drives blank

light energy

respiration, light

proton gradient, ATP synthase

photosystems, membrane

reaction center

reaction center, electron, ETC, protons, ATP synthesis

chlorophyll A

Chlorophyl B

oxygenic vs an oxygenic

A: plants and bacteria

B-platns and cyanobacteria

both pigments and absorb different wavelengths

Oxygenic: uses two photosystems, splits water to replace knocked out electron, releases O2 as a byproduct,

an oxygenic: 1 photosystem, splits H2S instead of water, no O2 produced, uses bacterial chlorophyll, common in aquatic bacteria

       20-Anabolism

what do you need to have

what does it use energy /ATP from

bringing order to a system requires..

uni tends towards blank and organizing needs blank

anabolic pathway are blank, why

anabolic reactions are coupled to

Anabolism blank NADPH while catabolism blank NADP

carbon source, inorganic molecules, and 12 precursor metabolites 

catabolic reactions to do anabolism

energy

disorder, energy

irreversible, driven to completion, so we don’t waste ATP

ATP breakdwon

uses, produces

what are precursor metabolites

what can they provide in anabolic reactions

you could also say they act as

what is the diff between an intermediate and a precursor metabolite

Intermediates generated during glycolysis and TCA

Provide carbon skeletons for anabolic reactions 

building blocks for biosynthesis 

Also generated reducing power 

If it’s used to build new molecules=precursor metabolite 

When something is only used for generating aTP/energy/NADH/FADH2

Not every intermediate is a precursor emtabolite 

Only those pulled out of pathways to be used for biosynhtesis