Topic 5 Flashcards
Nitrogenase?
enzyme that converts N2 to NH3
How is NH3 used in cells?
used by cells as a nitrogen
source for building nitrogen containing molecules
Nitrogenase is comprised of two proteins called?
dinitrogenase & dinitrogenase reductase (use Fe/Mo cofactors)
Electrons come from …
Fe/S proteins
such as flavodoxin –> transferred to
dinitrogen reductase –> to dinitrogenase –> to N2.
Gluconeogenesis?
Producing glucose (for carbon/energy storage or as a precursor for biosynthesis)
T/F: Gluconeogenesis is the reversal of glycolysis.
TRUE (same steps in reverse)
Glucose is activated by …
addition of nucleotide diphosphates such as ADP-glucose, UDP-glucose
(using ATP, UTP)
Activated glucose form is used to produce polysaccharides for: (3)
- LPS (Gram negative outer membrane)
- NAM/NAG (peptidoglycan)
- Storage molecules like glycogen/starch – later used for carbon/ energy
What is Glutamate dehydrogenase and glutamine synthase used for?
- used to build nitrogen-containing molecules (e.g. amino acids)
- efficiently incorporate NH3 even at low levels
Role of Glutamine/glutamate?
act as nitrogen donors to produce many other key nitrogen-containing molecules in the cell
Fatty acids built 2 carbons at a time using by
adding _______ to growing
chain, therefore CO2 released as biproduct
malonyl-CoA(3 carbons)
ACP?
-stands for: acyl carrier protein
-“holder” of
substrates for fatty acid synthesis
Parts of a nucleotide?
pentoses (5C sugar, ribose) & nucleobases
Explain pentose phosphate pathway?
- generates ribose-5-phosphate from glucose-6-phosphate.
- generates NADPH and carbon skeletons
T/F: Purines (A/G) built using the same way as
pyrimidines (U/T/C).
FALSE: Purines (A/G) built using one pathway,
pyrimidines (U/T/C) produced separate pathway
What are the key intermediates of purines and pyrimidines used to produce final products?
IMP for purines
Orotate for pyrimidines
What are the metabolic requirements for all life? (4)
- liquid water
- source of energy to do work
- nutrients
- source of electrons for biochemical rxns
How is energy conserved in microbes?
- storing it in high energy molecules aka ATP
Metabolism
series of biochemical reactions needed for life
Catabolism
hint: cata reminds me of cut so…
- reactions used to get energy by breaking down complex molecules
Anabolism
reactions used to synthesis cellular material (energy)
Chemotrophs
- get energy by breaking down high energy molecules to low energy
Phototrophs
use energy from the sunn!!
Autotrophs vs Heterotrophs?
autotrophs use CO2 (producers/plants)
- most are chemolithotrophs or phototrophs
heterotrophs get carbon from organic molecules
- mostly chemoorganotrophs
What does ΔG stand for??
Gibbs Free Energy!
- its the measurement of free energy change of a reaction in kJ
Positive ΔG?
-endergonic (requires energy)
- non spont
reactants have less energy than products
Negative ΔG?
- exergonic (releases energy!)
- spontaneous
- reactants have more energy than products
Three things that affect ΔG
- temperature
- concentration of substrates
- concentration of products
NOTE: Review the Gibbs Free Energy equation
K= [products]/[substrates] ΔG = ΔG0 + RT lnK
Redox Reactions (chem 20/30 recap folks!) hint: OIL RIG or LEO the lion goes GER
OIL RIG: Oxidation is Losing Electrons, Reduction is Gaining Electrons
ex. if glucose is donating electrons, it’s e- donor and it is oxidized
How does the electronegativity increase in a periodic table?
classic chem question, how niice
increases across a period and upwards in a group
so the top right corner, Fluorine is the most electronegative
Redox Pair convention
ex. Glucose and CO2 –> glucose is reduced, CO2 oxidized
convention: oxidized form/reduced form
CO2/glucose
The more negative values on top of the redox tower, the redox couples have a stronger tendency to be good ________.
electron donors! (to be oxidized)
Redox couples with more positive values at the bottom are more likely to be _______.
electron acceptors! (to be reduced)
NOTE: be able to use redox tower!!
idk how to put it into flashcards
you’re doing great, we got this guys!!
Example of an electron carrier?
NAD+/NADH
remember the convention? NAD+ is oxidizing agent, NADH is reducing agent
Proteins made by cells that act as catalysts are called _______.
enzymes!
RNA enzymes?
ribozymes
i have no idea why i love this word
Tip! How do you know if something is an enzyme?
usually ends with -ase!
ex. catalase, pyruvate kinase
what is activation energy?
- the minimum amount of energy needed to result in a reaction!
aka - bonds first need to be broken to initiate a reaction
How do enzymes play a role in activation energy?
- they can lower the activation energy of a reaction!
NOTE: they DO NOT change the equilibrium or ΔG of a reaction!!
How do enzymes lower activation energy/increase reaction rates? (5)
- concentration! (increasing concentration of substrates)
- orientation of molecules!!
- electronic distribution/conformational structure of substrates ca be altered for more reactivity
- transition state stabilization
- using coenzymes/prosthetic groups (ex. metallic elements)
Competitive inhibitors?
- fit in the same active site and prevent substrate from binding
ex. this is how drugs work!
Allosteric Inhibitors?
- binds to allosteric site which changes the shape of the catalytic site
- prevents substrate from binding
Allosteric Activators?
- binds to allosteric site which changes shape of catalytic site ==> but its a good thing in this case
promotes substrate binding and catalysis
What is feedback inhibition?
it is needed in metabolic pathways!
- the end product is a negative modulator ==> it binds to the first enzyme in the pathway and inhibits activity
==> basically, the end product shuts down the whole business of making more of itself
What are the three basic terms for ATP generation?
- Substrate level phosphorylation
- oxidative phosphorylation
- photophosphorylation
Substrate level phosphorylation
- the energy from an exergonic reaction is used to make ATP by transferring a phosphate to ADP
When energy from an electron transfer reaction generate a proton motive force to drive the ATP synthase, it is called ________
oxidative phosphorylation!
- helps generate ATP from the ATP synthase
Photophosphorylation?
energy from light drives proton motive force ==> generates ATP using ATP synthase
What sugar is mostly used by many chemoorganotrophs for energy?
glucose! other sugars can also be used though
What is the process of breaking down glucose called?
easy one, you got this!
glycolysis! (flashback to bio 20)
Why is glycolysis important?
- breaks down glucose for energy
- conserved is ALL domains of life
- doesn’t need oxygen
- can be followed by respiration or fermentation
How many NADH and pyruvate are generated per glucose molecule in glycolysis?
2 pyruvate, 2 NADH
What are the 2 other names for Kreb’s cycle?
honestly, isn’t one enough…
citric acid cycle (CAC) or tricarboxylic acid cycle (TCA)
Starting of Kreb’s cycle?
pyruvate has been broken down into acetyl-COA, which then enters the citric acid cycle
Where does the Kreb’s cycle take place in eukaryotes?
hint - the powerhouse of the cell
the mitochondria!
What are the inputs of the Kreb’s cycle? (what goes in)
Acetyl CoA 2 NAD+ NADP+ FAD Pi ADP and 2 H2O
What are the outputs of the Kreb’s cycle? (what comes out)
2 CO2, CoA 2 NADH NADPH FADH2 ATP and 2H+
How many NADH and FADH2 are produced in the Kreb’s cycle per pyruvate molecule?
2 NADH
1 FADH2
What are the inputs of glycolysis (what goes in)
glucose
2 NAD+
2 Pi
2 ADP
What are the outputs of glycolysis? (what comes out)
2 pyruvate 2 NADH 2 ATP 2 H+ 2 H2O
Review both the glycolysis/citric acid cycle!!
look over the pictures of both, we might have to label them at each stage
where is the ETC
cytoplasmic membrane
When protons are pumped out of the cell…..
proton motive force
for aerobic respiration what is the terminal electron exporter
O2
electrons in etc generated by
glycolysis/CAC
molecule primarily used for biosynthetic reactions
NADPH
2 key electron carriers in ETC
1) NADH dehydrogenase and flavoproteins
2) Iron-sulfur proteins
What does NADH dehydrogenase do
transfers 2 electrons to falvoprotein
Iron sulfur clusters are metal ____
cofactors involved in electron transfer
redox potential depends on
nature of cluster and protein
Quinones are proteins T/F
false! small molecules that move within a membrane
Quinone function
link Fe/S proteins to cytochromes
Cytochromes
proteins that contain heme prosthetic groups
Last stop before terminal acceptor
cytochromes
electrons are transferred from ____ reduction potential to ____ red potential
low to high
Final acceptor gets used up?
Yes and a external source to keep going
T/F paracoccus dentrificans electrons can enter at complex 1 or 2
yes electrons can enter at different points
paracoccus dentrificans steps of etc
1) complex 1 starts with NADH (low E) pumps 4 H+ for 2e
2) Complex 2 starts with FADH2 (high E), pumps fewer H+
3) from both complexes quinone is reduced and passes e to complex 3
From NADH to H2O how many protons pumped
10
ATP synthase mechnism
F0 (membrane) and F1 (cytosol) connected by stalk, F0 spins like turbine and protons flow through driving conformational change which powers ADP+Pi
how many H+ per 1 ATP
3.3
is ATP mechanism reversible?
yep ATP can generate PMF
how many ATP per NADH
3
what does aerobic respiration spit out
fully oxidized CO2 and H2O biproduct
Chemoorganotrophs have preferred energy sources, what does that mean
they have certain sources like glucose, if they have first they will use it, but when materials are scarce they can use other things
beta-oxidation
pathway to convert fatty acids to acetyl-CoA which can be fed into CAC and respiration
catabolite repression
if better energy source was around, use of energy for other sources will be inhibited
Glyoxalate cycle
variation of citric cycle that is used to grow on 2-C molecules (like acetate or acetyl Co-A), produces less reducing power but provides oxalate
oxalate
building blocks for synthesis of amino acids, glucose, etc
E. coli is a ____ anaerobe
facultative
facultative anerobe
live/grow with or without O2, can do aerobic, anaerobic respiration and fermentation
Under anaerobic conditions, respire using….
nitrate
nitrate is more/less efficient because
less, pumps fewer H+ than with O2
How many ATP does substrate level phosphorylation produce
2
what does glycolysis lack in terms of redox and NADH
it lacks balance, NADH is produced but there is no e acceptor to regenerate NAD+
redox balance is restores using
fermentation (or CAC/respiration)
fermentation
metabolism without the use of external e acceptor, anaerobic, substrate level phosphorylation used to generate ATP
how is redox balance achieved in fermentation
excretion of reduced fermentation products
Difference between lactic acid fermentation and aerobic respiration
LAF uses only glucose, ADP, and Pi to make 2 ATP and 2 lactate, AR uses oxygen to produce 38 ATP and CO2 and H2O
heterofermentative lactic acid fermenters
generate mix of lactose and other fermentation products, avoid lactate accumulation
ethanol fermentaion
3C pyruvate produces CO2 and EtOH, NAD+ replenished, YEAST uses it (thats why bread is fluffy)
Also used to naturally carbonate ____
BEER (dont drink kids)
common theme of fermentation
generate energy rich molecule used to hydrolyze produce ATP, donate e to reduce metabolite and excrete to obtain redox balance
lithotroph (this is so cool)
rock eater, energy from oxidizing inorganic molecules
are lithotrophs aerobic or anaerobic
they can be both
common electron donors
H2S, H2, Fe2+, NH4+
Ralstonia eutropha (officially naming this Ralph)
gram neg, lives in soil and freshwater, growths as chemolithoautotroph on H2, CO2 and O2
What does Ralph produce
2 hydrogenase enzymes that split H2 into H+ and donate e to produce ATP and NADH
Describe what the enzymes produced by Ralph do
1) the membrane bound enzyme donates e to reduce quinones in ETC generating PMF creating ATP
2) Soluble (cytoplasmic) enzyme reduces NAD+ to NADH generating reducing power
where is excess ____ stores, as an electron/energy reserve to form final oxidation products like thiosulfite and sulfate (i swear if yall dont get this one)
elemental sulfur
phototrophs
use light energy from the sun to drive electron flow generating PMF to produce ATP
ATP generated by (in phototrophs)
photophosphorylation
oxygenic
generate O2 as a biproduct of photosynthesis
anoxygenic
do not generate O2
who came first oxygenic or anoxygenic
anoxygenic
photoheterotrophs
phototrophs that get carbon from organic molecules
photosynthetic reaction center contains
bacteriocholorphyll
bacteriochlorophyll
P870 absorbs light energy, goes from weak electron donor P870 (E +0.5) to very strong electron donor P870* (E -1.0)
P870* donates e to ____
quinone
cyclic photophosphorylation
electrons cycle back to P780 to return to original state
Antenna pigments
light harvesting complexes embedded in membrane, similar to heme groups but Mg instead of Fe
why different pigments
allow different phototrophs to coexist
example of Q-type reaction center
purple bacteria
anoxygenic bacteria use what type of reaction center
FeS type
some anoxygenic bacteria ___ electrons to an external electron acceptor
cyclic electron flow
MEMORIZE FIGURE OF REACTION CENTER
hi guys, wassup jk keep going
where do electron ultimately come from in reaction center for Q-type RC
H2S e donor
why does Q-type use reverse electron flow?
E’ not low enough to reduce NAD+
reverse electron transport
use PMF (costs a lot of E) to drive e- in opposite direction in ETC and reduce NAD to NADH
PSI
photosystem 1, P700, FeS type
PSII
photosystem 2, PS680, Q-type
where are these reaction centers found
membranes
phototrophic eukaryotes contain
chloroplasta
chloroplasts came from
cyanobacteria
pathway of PS
PSII gets excited, light transfers to ETC becoming highly electropositive, accepts e- from H2O to make H+ and O2 (H2O weak e- donor)
where do e- from PSII go
quinone
where do low energy e- go
PSI
PSI does what
reduce NADP+ to NADPH
ultimate e- acceptor
CO2
what does the calvin cycle do?
CO2 converted to organic molecules, costs ATP and NADPH
for every 36C how many C get drawn off for biosynthesis
6
the enzyme that does the key carboxylation step
RuBisCO
