General Exam III Qs Flashcards
Aerobic Respiration
-general jist, who’s involved
NADH donates electrons, O2 electron carrier (they get dumped on it),
protons pumped, come back in and ATP is synthesized from ADP + Pi
**feel free to confusedly look at the slides, pg 33 geochemical cycling
Electron carrier for aerobic respiration?
O2
Electron carrier(s) for anaerobic respiration?
nitrates and nitries I think???
but then complex cNor will reduce nitrous oxide (N2O) to N2 gas
Denitrification is an _______ process
anaerobic process, (usually happens in saturated soils that go quickly anoxic)
Denitrification
(define, and who does this?)
hint: blank reduces to blank etc
reductive pathway, adds electrons to nitrates and nitrites that convert them back to N2 gas
NO3- -> NO2- -> NO -> N2O -> N2 (gas)
carried out by many proks and maybe some fungi?
Anaerobic respiration
NADH donates electrons, ATP produced through ATP synthase and proton gradient driving that energy,
complex cNor reduces N2O to N2 gas
**reductive process
**how denitrification happens
The Carbon Cycle
whos involved, two ways it goes & names
Carbon fixation (CO2 to organic form, CH2O) (performed by autotrophs)
Decomposition: organic to inorganic form-
Heterotrophs (we) do this, breathing out CO2 gas
Inorganic form of carbon?
CO2, we can’t use it
Organic form of carbon?
(what are these?)
(CH2O)n (carbohydrates)
What organisms can fix carbon?
(and examples)
Autotrophs,
algae, cyanobacs, plants
What organisms change organic carbon to inorganic carbon? (Decomposition)
heterotrophs (us) we be injesting organic carbon and then breathin out CO2
What cycle most often used to carry out carbon fixation?
The Calvin Cycle
(how celestialautotrophs convert sunlight to chemical energy (sugars)
(not celestial, **photoautotrophs LMAO christ jesus I couldn’t remember the name)
Photoautotroph:
(what it is, and examples)
energy from sunlight
ex. algae, cyanobacs, plants
Chemoautotroph:
(what are, and examples)
(they get their energy from where?)
energy from chemicals
(chemilithoautotroph) fake helpful remember name
energy usually comes from H2S, Fe2+ (reduced minerals)
usually deep sea organisms, bacs/archea (purple non sulfer bacteria an ex)
Photoheterotroph:
(what are, and examples)
energy from sun, cannot fix their own carbon,
get organic carbon from others
(prominent in the Great Salt Lake) ((red coloration due to bacterial rhodalson, use sunlight to form ATP, then eat dead material for fixed carbon)) Dead seagulls everywhere, great for these bacs
Chemoheterotroph:
(what are and examples)
you bich!!
they get energy from chemicals, get organic carbon by eating organic materials by others
(if it eats, probably this)
-animals, most bacs, protozoa
The Calvin Cycle
(
oh lordy just review the slides,
begins with Ribulose 1,5-bisphosphate
but it’s employed by photoautotrophs to turn CO2 into sugar essentially
unit II geochemical cycling pg 39
uses CO2 and water to make organic carbon source (sugars and stuff)
Calvin cycle done by who now, and originally done by who?
Calvin cycle originally developed in cyanobacteria, but then went into euks to form chloroplasts (nice!)
Who does the Calvin cycle begin with?
Ribulose 1,5-bisphosphate
(Rubisco the enzyme acts on it
Alternative method for carbon fixation that isn’t Calvin cycle?
It goes by many names;
-Tricarboxylic cycle (TCA=citric acid)
-Backwards Krebb’s cycle, so not Krebb’s cycle
-Citric acid cycle
(Krebb’s cycle is all about oxidizing, this is a reductive process)
Reductive TCA cycle:
what is, and why happens?
lordy lordy slides time bb
unit II geochemical cycling pg 43
leads to the fixation of two molecules of CO2 and the production of one molecule of acetyl-CoA
a reductive process to fix inorganic carbon to the organic form, CO2 to acetyl CoA
What organisms carry out the Reductive TCA cycle?
carried out by chemoautotrophs (bacs and arcs)
(if you cant use the sun you do this)
(pretty broad amount of organisms that use this) ((typically without light))
Pretty cool, just a backwards pathway
-Methanogenic autotrophs
-Sulfur-oxidizing autotrophs
-Sulfur-reducing autotrophs
-Anaerobic ammonium oxidation (Anammox) bacteria
-Thermoacidophiles
What is the Krebs cycle?
Uses what to do what?
Uses oxygen to make energy (ATP)
What’s the starting chemical of the the Reductive TCA Cycle? (usually or at least in the slides lol)
Oxaloacetate
Ultimately who is responsible for euks coming into existence?
Cyanobacteria bb!!
-responsible for creating the oxygen that allowed the rest of us to develop (because they developed the pathway of photosynthesis)**
The Great Story of Oxygen:
It’s long, review notes in conjunction with slides pg 48 geochemical cycling
But basically ~3.2 billion years oxygen began to accumulate in atmosphere
Around what time did O2 accumulate to 1%?
2Billion years O2 content rose to 1%
Around what time did 20% O2 accumulate in atmosphere (and what did this do?)
-1 billion years ago 20% oxygen (animals and plants (aquatic) appeared)
~1.4 billion years endosymbiotic event occurred, simple eukaryotes appear
-archea was brought into other cell, archea became the nucleus
Once O2 get’s 4 electrons it becomes;
water, H2O
How did full on cells become able to photosynthesize?
Cyanobacteria one day entered a cell, and became the chloroplasts, enabling algae and plants to exist
Where does the og electron come from?
(and allows what to happen)
The og electron comes from water, which makes the efficient metabolism possible
Sulfur metabolism
usually happens where, most common inorganic form of sulfur
usually volcanic,
SO42- most common type seen oot and aboot in the wild
SO4(2-) characteristics
-highly oxidized
-very stable
-must be extensively reduced to H2S prior to assimilation
H2S can be used to make
cysteine and other
organic sulfur
compounds
In Sulfur metabolism, what is ATP doing and why?
idk man
ATP is used in first and second steps
ATP first provides 2 phosphates
Forms AMP (a nucleic acid)
ATP provideds 2nd just a phosphate (byproduct of ADP)
Purpose of all this first part is to activate the molecule prior to reduction
What happens when a phosphate is added to a molecule?
The molecule is destabilized
((higher energy, more reactive))
-usually preps it to react with something else
What does ATP usually provide/what does that look like?
(if ATP becomes ADP+Pi just providing energy, usually provides energy or a phosphate group)
**in essence* energy or a phosphate group
ATP doesn’t just provide energy, sometimes provides a phosphate group to destabilize molecule, sometimes donates a couple phosphates
What can sulfite do that sulfate can’t really?
Sulfite less stable, able to accept additional electrons from NADPH
End product of sulfur cycle?
Ends with H2S (Hydrogen sulfide, highly reduced form of sulfur)
NADPH + H+ to NAD+ means what?
-Reduction bb
NADPH-
what it do?
Always donates electrons, represents reducing power (usually in anabolic rxns)
What’s special about a reduced molecule?
It’s full of high energy electrons (lots of energy) and real reactive
ready to do/make stuff!!
Phosphorus exists in what one form in nature?
PO4-
Phospate bb
no gas phase, interconverts from organic to inorganic form
Where the nature phosphorous at?
Soil and rocks
-dissolves into water
Phosphorus Cycle:
2 steps, what are they?
PO4- 1) Adsorption: (inorganic to organic)
soil and rocks, dissolves in water
(done by bacs, algae, plants)
PO4- 2) Decomposition:
Nucleotides, Phospholipids
(done by bacs and fungi)
Phosphorus Adsorption: (inorganic to organic)
what form inorganic, done by who
inorganic form: soil and rocks, dissolves in water
(done by bacs, algae, plants)
Phosphorus Decomposition:
(organic to inorganic)
what form organic, done by who
organic form: Nucleotides, Phospholipids
(done by bacs and fungi)
What is this Metabolism?
sum total of all the biochemical reactions occurring in the cell
Catabolism reactions-
what do, and delta G is what?
breaking down reactions of larger molecules for energy (creates disorder) (generally spontaneous)
Anabolism reactions-
what do and deltaG is what?
building up biosynthesis reactions, biosynthesis of macromolecular cell components from smaller molecular units (creates order)
(generally not spontaneous, requires input of energy)
What 3 things do living organisms obtain from the catabolism of organic molecules?
1) Energy ATP
2) Electrons
-(source of potential energy) NADH (NADH usually used in catabolic pathways)
-needed to form covalent bonds (NADPH usually used in anabolic pathways)
3) Building blocks needed for anabolic reactions
-amino acids
-nucleotides
-fatty acids
-sugars
-elements CHOPKINS CaFe
What do electrons provide for living organisms?
(2 main things)
-(source of potential energy) NADH (NADH usually used in catabolic pathways)
-needed to form covalent bonds (NADPH usually used in anabolic pathways)
What do the Laws of Thermodynamics tell us? (help us predict what?)
Used to make energy-related predictions:
1 If rxn can occur
2 which direction it will occur
3 can predict WHY a rxn occurs
First Law of Thermodynamics:
Energy is always conserved, it can be transferred from one form to another, but cannot be destroyed nor created
The energy be flowin
og source the sun
Sunlight: radiant energy
(the og energy)
where it go?
-> can be transformed to heat energy
-> Chemical energy
-> Electrical energy
(each can be transferred between each other)
What does it mean for us that all energy be transferred?
In essence: we can account for all the energy that enters and leaves our biosphere (v cool)
Second Law of Thermodynamics:
In every physical or chemical change, the universe always tends toward greater disorder or randomness (entropy)
Examples of the 2nd law of thermodynamics:
(instances ((like all)) tending towards disorder:)
-dandelion
-burning paper
-draining of battery
-evaporation of gasoline
From a concentration, to less concentrated
What does Order represent?
(hint, what is it?)
Order=Potential energy
Order is a source of potential energy bb
Where does energy travel?
“energy travels in one direction” towards disorder
(from sun to us to cold heart of space)
Free energy equation, go!
Delta G= DetlaH + (-T*DeltaS)
What does Delta G represent?
Total free energy of a system
-accounting of all energy in a system sum total of all forms of energy in a system
What does deltaH represent?
Enthalpy, or heat energy involved in system
(heat energy: energy tied up in chemical bonds)
What does T represent (gibbs free energy equation)
T= Absolute temperature (heat energy of surroundings in Kelvin)
25(C)= +273.15 K = 298 K
How to convert from Celsius to Kelvin?
25(C)= +273.15 K = 298.15 K
What does DeltaS represent?
S= entropy (measure of disorder/randomness)
((measure of physical order))
In essence, each member of the gibbs free energy equation represents what?
Delta G= total change in order in universe due to the rxn
Delta H= total change in energy order
Delta S= total change in physical order
Why do we measure with delta values?
Actual value measurements basically impossible, but we can measure the change and perform calculations with that
What is the direct effect of an increase in temperature?
(delta G stuff is the topic)
The heat content is set, but entropy is directly affected by temperature
Enzymes only ______ ___ exergonic rxns
hint: enzymes aren’t what?
speed up
Enzymes are not thermodynamic genies
So how in the hell do plants and bacs use enzymes and energy from the sun to make glucose if it’s such a high +DeltaG?
Coupled reactions bb!
ATP + H2O -> ADP + Pi
Glucose + Pi -> Glucose-6-PO4 + H2O
What does ATP donate in this coupled reaction/what does this suggest about ATP?
Pi (inorganic phosphorus) bb!
ATP can be coupled with endergonic reactions
What are the two Glycolytic pathways?
hint: Glycolysis (cut sugars)
Embden-Meyerhof-Parnas
Pathway
(EMP)
Entner-Doudoroff
Pathway
(ED) hehe
Net gain in ATP from EMP (glycolysis) pathway?
2 ATPs
(also 2 pyruvates)
((unrelated side note, put in ATP to donate phosphorus to make glucose, then cut glucose to make ATP)) mind of a mastermindd
Most common starting substrate for the EMP (glycolysis) pathway?
(and others that can also be used)
Glucose
starch, galactose, fructose, mannose, glycerol
(hexose sugars)
Main way you can distuingish between ED and EMP pathways?
ED goes down to dual ending of pyruvate and glyceraldehyde 3-phosphate (which then leads to pyruvate evenutally, same end section as EMP)
EMP goes down to glyceraldehyde 3-phosphate then has two ways (one with each isomer reacting)
both end in pyruvate
SEE slide 31, metabolism unit III
**no prompt just take a peak at the enzymes and #s used for ED pathway
notes pg 7
slides pg 32 unit III metabolism
Net gain in ATP for ED pathway? (glycolysis)
1 ATP gained, only used when energy is scarce
(also 2 pyruvates)
Why use the ED pathway?
Some cells have both
-pathway is needs NADPH, or energy stressed
-if gluconates the only sugary things available
Which glycolytic pathway(s) can use carbohydrates (gluconates?)
ED only
NADPH is usually used for
anabolic rxns, create the NADPH needed for biosynthesis (usually anabolic)
NADP+ is usually used for
catabolic rxns (catabolic)
Which is typically used for anabolic rxns (NADP+ or NADPH) ?
NADPH
Which is typically used for catabolic rxns (NADP+ or NADPH) ?
NADP+
Does cell usually use glucose or gluconates first?
-glucose first, then goes to use other class of carbohydrates called gluconates (2 here, intermediates)
(gluconate cant be broken down)
What is “The Electron Problem” in a nutshell?
NAD+ electron carrier, (pretty toxic bc it loves grabbing electrons from everyone, same as O2- ion)
But to make ATP, you need them
-It’s easy to run out of NAD+, and then everything shuts down (oh nooo no ATP!)
-Krebb’s cycle also uses a lot of NAD+
-Lot of glucose hazardous bc cellular concentrations of NAD+ drop
-NAD+ toxic, maintainined in low concentrations,
-can become depleted
-glycolysis and atp synthesis would come to a halt
(this is not a good thing)
What is the solution to the electron problem?
(and the two methods)
Need to recycle the NAPDH rapidly
a) Fermentation
b) Respiration
Fermentation:
(purpose what the process does)
sole purpose is to recycle the NAPDH
A metabolic process that uses an endogenous (created within) organic molecule as a terminal electron acceptor
(waste bin for electrons)
Electrons must always be _____________ ?
(what is the name of this thing?)
accepted by something else
Electrons must be accepted by the terminal electron acceptor
**Review NAD+ and NADH
metabolism unit III pg 38
Main difference between uses of NADPH and NADH?
(anabolic) NADPH used for anabolic reactions meant to build macromolecules from their smaller parts
(catabolic) NADH generally used in catabolic reactions meant to produce ATP
What is the meaning of an “endogenous electron acceptor” as seen used in fermentation?
The electron acceptor is created within the pathway, doesn’t appear from the outside to be used as waste receptacle
(like O2 often is)
How to spot the terminal electron acceptor?
(for fermentation, so endogenous)
The molecule that accepts all the electrons before product formation (see metabolism slide 39)
Usually it’ll have right after it NADH to NAD+, remember that that means those electrons went from NADH to the molecule “right before it”
Sole purpose of fermentation?
replenish NAD+ so that glycolysis
can continue to make ATP
Lactic Acid Fermentation-
used to do what and end product?
**bonus for terminal electron acceptor
-Doesn’t make energy, used just to recycle NADH
-lactic acid end product
terminal electron acceptor:
pyruvate
Examples of Lactic Acid Fermentation doers?
Lactobacillus sp.
Lactococcus sp.
Pediococcus sp.
Streptococcus sp.
Leuconostoc sp.
a lot of yogurt and kimchi making dudes
Ethanol Fermentation-
used to do what and end product?
**bonus for terminal electron acceptor
Benefit to bacs: recycle NADH
Benefit to us: yeast uses this pathway to rise the bread from the CO2
end product of ethanol, also gives off CO2 gas
terminal electron acceptor:
Acetaldehyde
Examples of who does ethanol fermentation?
Zymomonas mobilis
Many yeasts
Mixed Acid Fermentation
-basically get to pyruvtae which then makes lactic acid OR ethanol OR Formic acid/Succinic acid/Acetic acid
(~5 paths, one end product each, pyruvate is the tri fork)
Examples of who does mixed acid fermentation?
Enterobacteriaceae
(e.g., gold ol’ E. coli)
Where do fermenting organisms gain their ATP?
the process of Glycolysis
breaking down them sugars (usually a glucose, but can be gluconates (by ED pathway)
What is the sole purpose of fermentation to the
organism?
Recycle electron carriers, get more NAD+
Respiration
a metabolic process in which electrons generated from glycolic processing are passed through an electron transport system onto an exogenous (created outside pathway) electron acceptor (usually O2 but can be NO2- NO3-)
Main difference in electron acceptor in respiration vs fermentation?
for respiration electron acceptor is outside the pathway, not inside like fermentation
thiscard is fake news I think????
Oxidizing
1) Fully oxidize pyruvate down to CO2
2) Directly make a little more ATP
3) Provides substrates for biosynthesis
Reductive TCA cycle also creates intermediates for biosynthetic reaction happens from
How many ATP are made by aerobic respiration vs fermentation?
(who is more efficient?)
~38 ATPs made through aerobic respiration
Fermentation- ~2 ATP
(hence O2 had to accumulate in atmosphere before euks could develop, needed more efficient respiration)
Each NADH ends up resulting (at end of electron transport chain) in how many ATPs?
~2-3 ATP
review slide 48 metabolism unit III for reference
Why do electrons explain why nature works?
1) electrons emit energy with every transfer
2) electrons absorb energy form photons
3) energy level can be measured during redox reactions
Electron is dropped onto O2 because it’s energy is empty
-photosynthesis fills up electorn cup with mnms (energy)
-Electrons emit energy with every transfer
-But they (the cup) can be refilled using energy from photons and light
What is Reduction Potential, and what is the unit of measurement we use?
the tendency of a molecule to acquire electrons, measured in E (volts, V)
more negative the #, the less the molecule wants electrons
the more positive the #, the more the molecule wants electrons
Molecules with a more negative E are better ____ ?
(enjoy what?)
(talking about reduction potentials)
electron donors
(enjoy giving)
Who is the donor and who is the recipient (reduction potentials) and why?
Electrons are always transferred from the
reduced form of a more negative redox couple (donor)
to the
oxidized form of the more positive redox couple (recipient)
Molecules with a more positive E are
(like to do what?)
(reduction potentials)
better electron acceptors
(like to steal!)
The energy released in the redox reaction is proportional to the _____________________ ?
difference in reduction potentials (delta E knot) between redox couples
What is the equation to determine a reduction potential?
delta Enot=
recipient-donor
For reduction potentials, Transfers from right side to
something more positive on left side
What is the donation directionality of reduction potential (redox) reactions?
Always going to donate from reduced form (on right side) to something more positive (left side)
How to determine if a reduction potential rxn is ender/exergonic? (based on the calculated E knot value)
((recipient-donor=))
More energy released, the more exergonic the rxn
-positive reduction value, rxn is exergonic and spontaneous
-negative reduction value, rxn endergonic and non-spontaneous
(-T*deltaS) =
order
(T*deltaS) =
disorder
who accepts the electrons from the NADH?
= terminal electron acceptor
(in respiration or fermentation)
What determines the order of redox reductions? (who get’s reduced first in chain and why ie who carries the electrons first and why?)
Doing it all at once too high energy, will burn up cell, rather it is stepwise with many reductions occurring
(you eat an elephant one bite at a time)
3 things to consider when wondering if a redox rxn will occur
(looking at table of E knot values)
1) is the donor in the reduced form?
2) Is the acceptor in the oxidized form?
3) is the transfer form more negative to more positive? (if no than no)
Equation for synthesis of ATP:
ADP+Pi -> ATP + H2O
DeltaG= +30.5 kj/mol (endergonic & non spontaneous)
ATP+H2O -> ADP + Pi
Whenever you join 2 phosphates together, what will be a product?
Water (bc H and an OH group)
-same with sugars joining, two OH groups
-same with nuceic acids
Synthesis of ATP problem: what serves as the energy source to drive most endergonic reactions?
ATP
What serves to drive synthesis of ATP?
(two options)
Option 1: substrate level phosphorylation
Option 2: Oxidative phosphorylation
Option 1 (For ATP synthesis:) Substrate level phosphorylation
Definition & usual coupling partner
Enzymatically coupled reaction
Coupling partner: (usually) high-energy phosphorylated intermediate
Substrate level Phosphorylation (for ATP synthesis) can happen in which glycolytic pathways, and how many times?
ED pathway- one ATP
EMP- two ATP
Two places where happen in EMP pathway
How to tell who is a coupling partner for substrate level phosphorylation?
Look to who the reactant is before ATP is formed (two of these in EMP pathway, one in ED)
(in the context of energy of hydrolysis)
How to determine the accepting form?
compound listed in table + H2O= accepting form
accepting form= compound - one phosphate group
Phosphate can be transferred from any high energy compound to the accepting form of any ________ energy compound
(energy of hydrolysis as from table)
lower
higher energy can gift a phosphate to an accepting form of lower energy
The accepting form of any lower energy compound can accept from a ________ energy compound
(energy of hydrolysis from table)
higher
lower energy accepting form can receive a phosphate from a higher energy
**Practice calculating DeltaG of rxn from chart, using energy of hydrolysis chart
metabolism unit III slide 68
(pay special attention to when 2 reactions are taking place)
Option II (for ATP synthesis) Oxidative phosphorylation:
what is and happens where?
Occurs in inner membrane of mitochondria
-occurs in phylochord membrane in cholrophyll
-Occurs at end of electron transport chain in ATP synthase
ATP synthase- where stuff flows through
Gradient is source of potential energy,
-this is a more mechanical synthesis of ATP
Using enzyme to force them together
ATP Synthase structural components
(3 phases of turning?)
Rotoe
3 Beta orange subsunits
Middle green is shaft
3 alpha subunits (light orange)
Shaft turns 1/3
Loose phase,
Open phase
Tight phase
Name and describe the three phases of the rotation in ATP Synthase:
Loose: ADP + Pi enter
Tight: enzymes squeezes everyone together in reaction to make ATP
-3 more protons come through,
Open phase: enzyme has little affinity and floats away, ATP also leaves
Review slides metabolism unit III pg 78
What is the main purpose of the Calvin cycle?
to turn carbon dioxide from the air into sugar, the food autotrophs need to grow
(fixing carbon from inorganic form to an organic form)
What is the main purpose of the Krebs cycle?
to produce energy, stored and transported as ATP
(makes CO2)
-also produces intermediates for other biosynthetic rxns
(required to make other molecules, such as amino acids, nucleotide bases and cholesterol)
What is the main purpose of the Reductive TCA cycle?
to produce carbon compounds from carbon dioxide
(inorganic to organic form of carbon done by chemoautotrophs)
What is the main purpose of anaerobic respiration?
making ATP without the prescence of O2
Example is glycolysis
What is the main purpose of aerobic respiration?
ATP synthesis
What is the main purpose of the EMP and ED pathways?
Glycolysis to produce ATP
What is the main purpose of fermentation?
Regeneration NAD+
Recycling NADH
What is the main purpose of respiration?
Extracting ATP from biological molecules, with or without O2 (uses external from pathway electron acceptor like O2 usually)
Are catabolic rxns generally oxidative or reductive?
oxidative, usually break down of molecules is done by oxidation
Are anabolic rxns generally oxidative or reductive?
Reductive, typically building molecules is a reductive process
(when you add electrons things become more high energy and reactive so has sense)
What is the role of ATP synthase?
(and where is it found?)
Converts the kinetic energy of proton
flow to chemical energy (ATP)
found at end of electron transport chain
What molecule does fermentation begin with?
Pyruvate
What is glycolysis?
The breakdown of glucose or other sugars to release energy and produce pyruvate
Why is ATP used in the first step of the (EMP) reaction? (2 reasons)
1) By phosphorylating glucose, the molecule is made more reactive
2) By phosphorylating glucose, the molecule becomes trapped inside the cell
