biochem lecture 2 pt 1 Flashcards
(248 cards)
1
Q
are pathways interconnected or do they exist in isolation
A
interconnected, often serve as feeders
2
Q
what are feeders
A
intermediates can be siphoned off into other pathways
3
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metabolism
A
sum of all chemical transformations taking place in cell/organism
4
Q
what are 2 subdivisions of biochemical pathways
A
catabolism and anabolism
5
Q
what is catabolism
A
degradative pathways
6
Q
what is anabolism
A
biosynthesis pathways
7
Q
how do metabolic reactions occur
A
through enzyme catalyzed reactions
8
Q
what does each step in a metabolic pathway bring about
A
specific, small chemical change (removal, transfer, addition of atom/functional group, etc.)
9
Q
how are percursors converted into products
A
through series of metabolic intermediates
10
Q
metabolites
A
metabolic intermediates
11
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intermediary metabolism
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combined activities of all metabolic pathways for low molecular weight compounds
12
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are DNA/protein synthesis examples of intermediary metabolism
A
no, those are macromolecular structures
13
Q
is there intelligence behind these biochemical processes
A
no; just happened through evolution
14
Q
describe metabolism
A
highly coordinated set of activities within the cell
15
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goals of metabolism
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to obtain chemical E from environment (light organic molecules and food, etc.)
16
Q
another goal of metabolism
A
convert nutrient molecules into cellular components (precursors of macromolecules like AAs nucleotides)
17
Q
yet another goal of metabolism
A
polymerize monomeric precursors into macromolecules (proteins, nucleic acids)
18
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aaandddddd another goal of metabolism
A
synthesize & degrade biomolecules needed for specialized functions (membrane lipids, intracellular messengers, lipids)
19
Q
what would happen without chemical energy
A
cell/organism can’t perform functions needed to survive
20
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describe catabolism
A
degradative; breaks down larger molecules to smaller ones
21
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what does catabolism do/release
A
releases energy
22
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what does catabolism create
A
ATP, NADH, NADPH, FADH2
23
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what does catabolism do by breaking down stuff
A
releases energy, some E can be captured and harnessed
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Q
anabolism
A
can use electrons to build structures
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why does anabolism need electron source
building stuff, need to form covalent bonds, needs electron source
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where does this reducing power/electron source come from
NADH, FADH2, etc.
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how are electron carriers used
in catabolism as source of electron flow and ATP production; in anabolism, reducing power provides electron source to form bonds and build structures
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how are both types of metabolism (catabolic and anabolic) connected
ATP/chemical energy cycle
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basically describe catabolic pathways
start w/ E rich compounds, degrade and break them down, generate reducing power and ATP
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what can ATP be used as
E source to drive anabolic processes
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what can the reducing power be used in
formation of chemical bonds to build structures
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what can happen to the energy depleted products/byproducts of what was used in anabolic processes
can be recycled and fed back into catabolic processes
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is catabolism oxidative or reductive
oxidative
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oxidation
removal or stripping off electrons from things
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describe oxidation in a metabolic context
those electrons that are stripped off are transferred to something else
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what happens to NAD/ FAD, etc. in catabolism
become reduced
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what is redox
something is oxidized, electrons are transferred to something else, other thing is reduced
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describe catabolism
oxidative, means that electrons being stripped off from E rich compounds are gonna be transferred to other things
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what are the electrons that are stripped off being used for
to generate reducing power, ATP, proton motive force etc.
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describe anabolism
reductive; adding electrons to build chemical bonds
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is the synthesis of precursors (AAs, fatty acids) reductive or oxidative
reductive b/c you're building chemical structures
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where is this input of electrons coming from
some comes from this reducing power
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generally, sum this up
anabolism is reductive, catabolism is oxidative
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do all organisms obtain E the same way (same energy source)?
no
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what else is important to sustain life besides E
carbon
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why is carbon important
we are carbon-based life forms; chem structures are carbon based; glucose, fats, proteins/AA are carbon based structures
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organic molecule
C and H
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inorganic molecule
just C, no H (like CO2)
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what is CO2
waste product
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when is CO2 generated
at the end of catabolic processes
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Co2 fixation
CO2 can be recycled; take CO2 from air and reincorporate it into organic structure
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what does calvin cycle do
involves fixation of CO2, takes CO2 from air and fixes/incorporates it into other structure
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what can the C that's taken from CO2 in the air be used for
synthesis of carbohydrate precursors, used for glucose synthesis down the road (but needs E)
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where do autotrophs get carbon from
carbon from air (CO2)
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where do autotrophs get energy from
sunlight
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what do autotrophs make
O2, H2O
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what are autotrophs
plants
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where do heterotrophs get carbon from
food
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where do heterotrophs get energy from
degradation (of molecules)
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what do heterotrophs make
CO2, H2O
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what are heterotrophs
animals
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why do autotrophs use sun as an E source
in order to do Co2 fixation, carry out calvin cycle (synthesis of carbohydrates) need E
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where do autotrophs get the E needed for carbon fixation
ATP, but need another E source to synthesize ATP
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where do autotrophs get that other E source
sunlight
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another word for autotroph
phototroph
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what does autotroph refer to
what the carbon source is
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what does phototrophy refer to
what the E source is
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what are most autotrophs in nature
also phototrophs
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why/how are most autotrophs phototrophs
able to utilize CO2 and incorporate into organic structures; utilize E from the sun to do that
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what does photoautotroph do
combines their energy source and carbon source
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example of phototrophs
plants, photosynthetic bacteria, algae, etc.
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what are organisms that prefer utilizing organic forms of carbon
heterotrophs
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what do heterotrophs utilize as an energy source
organic structures (rather than CO2, which is inorganic)
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chemotrophy
use of specific chemical comppunds as a source of energy
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chemoheterotroph
combines chemotroph and heterotroph
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how do we (heterotrophs) derive energy
use carbon from food, derive ATP energy from degradation of carbon structures that are E rich (carbs, fats, etc.)
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what are waste products for heterotrphs
CO2, H2O, etc.
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can CO2 be recycled
yes
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who can recycle CO2 and H2O
autotrophic organisms / photoautotrophs
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what do photoautotrophs generate as a byproduct
O2 (oxygen)
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how much of atmosphere is Nitrogen
Nitrogen makes up 80% of earth's atmosphere
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what requires nitrogen
all living things
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why do living things need nitrogen
for DNA, RNA, proteins, etc.
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is nitrogen biochemically useful or no
no, it's biochemically inert
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can diff life species utilize nitrogen gas in biochemical processes
no
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so what do soil bacteria do
nitrogen fixing
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what is nitrogen fixing
reduction of atmospheric nitrogen
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describe nitrogen fixing
start off w/ N2 gas, end up producing a reduced form of nitrogen called ammonia (NH3+)
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what is ammonia
gateway compound for nitrogen
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what can ammonia be used for
fed into the rest of this nitrogen cycle
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why is ammonia a gateway compound
because reduced form of ammonia is what we need to get to in order to incorporate it into organic structures like AAs, nucleotides, etc.
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what does nitrogen fixing start off with
N2 gas
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what does nitrogen fixing end up with
ammonia
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what occurs in nitrogen fixing
converts N2 into a reduced form, ammonia (NH3+)
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can atmospheric nitrogen be incorporated into organic structures
no
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what is process of nitrogen fixation important for
assimilation of N into organic structures and living things
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what plays a huge role in this nitrogen cycle
bacteria
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what role do bacteria play besides nitrogen fixing
take ammonia, oxidize it into nitrates and nitrites
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what are these bacteria called
nitrifying bacteria
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who utilizes ammonia w/ these nitrates and nitrites
plants
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what does this process of nitrogen fixation occur in symbiosis with
specific plants
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where is this conversion occuring
N2 gas that's reduced to ammonia by nitrogen fixing bacteria occurs in structures within root systems of plants
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what is this symbiosis important for
how nitrogen gets into the rest of the food chain, b/c animals eat these plants and consume nitrogen
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how do animals get this nitrogen in their system
by consuming plants that have bacteria which do nitrogen fixing
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what happens when these animals die
release waste products that include N, converted back to ammonia, continue the cycle etc.
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what is carbon cycle
how carbon flows through biosphere
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is there a lot of carbon that cycles between photo-autotrophs and heterotrophs?
YES; tons and tons annually
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what does this carbon cycle and mass cycle of carbon need to occur
microorganisms
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three types of nonlinear metabolic pathways
converging catabolic, diverging anabolic, cyclic
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what is the main cyclical pathway (most ppl think about)
TCA cycle
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what is TCA cycle (besides a cyclical pathway)
amphibolic pathway
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what is an amphibolic pathway
has intermediates used for both catabolic and anabolic pathways
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what are intermediates in TCA cycle also used for
precursors for hella synthesis reactions (biosynthetic pathways, nucleotide synthesis pathways, etc.)AND ALSO in catabolic pathways
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what happens to these intermediates in a cyclical process
can siphon them to other pathways AND regenerate them
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in cyclical pathways what do you need to do in order to keep pace w/ consumption/level of demand
need to regenerate or produce more of that intermediate/byproduct
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what is TCA cycle very much dependent on
levels of oxaloacetate & other intermediates
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why is TCA cycle dependent on oxaloacetate
b/c its last step of TCA cycle ANDDD you need it in order to feed acetyl-coA units to keep this pathway going
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what stuff is common in cyclical pathways
feeder pathways that go into the cycle, pathways that produce these intermediates that are then siphoned off into other pathways
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catabolic converging pathways
bunch of diff energy source but all converge into a common intermediate
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example of a common intermediate that diverging energy sources converge into
acetyl coA
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describe different E sources that converge to acetyl coA
carbons that come from carbs, fat, proteins, etc.
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what is acetyl coA also known as
a common currency
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what happens to acetyl coA regardless of its source
fed into TCA cycle
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most oxidized form of carbon in nature
CO2
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in catabolic mode what happens to carbons from acetyl coA
undergo complete oxidation to CO2
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what does CO2 produced indicate
complete oxidation
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why is CO2 most oxidized
hella electronegative oxygens bonded to C, withdraw electron density from the C making it more oxidized
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what is acetyl coA
a common intermediate
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why is acetyl coA a common intermediate
because you can produce it regardless of the initial E source (carbs, fats, etc).)
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why is it a useful strategy
b/c regardless of the carbon source used to generate acetyl coA, it can be fed into this common hub (TCA cycle)
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what else can acetyl coA be used as
a precursor in biosynthesis reactions
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what is another kind of nonlinear pathway
diverging anabolic processes
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describe diverging anabolic processes
take common precursors/intermediates, diversify or split off and synthesize different things
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example of different things you can synthezie
fats, components of phospholipids, cholesterol, vitamins, bile, etc.
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what is the idea w/ converging and diverging processes
can go from converging catabolic processes to common intermediate and then diverging pathways
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what are the 3 types of metabolic pathways
converging catabolic, diverging anabolic, cyclical pathways
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what is delta G standard linked to
reaction equilibrium
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endergonic
absorbs energy, positive delta G, KEQ < 1
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KEQ less than 1 indicates
unfavorable reaction
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exergonic
releases energy, negative delta G, KEQ > 1
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positive KEQ indicates
favorable reaction
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is endergonic favorable or unfavorable
unfavorable
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is exergonic favorable or unfavorable
favorable
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energy coupling
taking something unfavorable/endergonic and coupling it to an exergonic or favorable reaction
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when do you get a release of energy w/ ATP
ATP donating phosphate group to glucose
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what can you use that energy generated from releasing p from ATP
to transfer that p to a glucose
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why is ATP a useful source of E
b/c it can participate in these rxns
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what happens when you couple an exergonic and endergonic reaection
overall reaction is endergonic
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are free energy changes additive
yes; can add up delta G values
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what is needed in order to make an endergonic process occur
need to have a more exergonic process coupled to it
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how much E is released w/ ATP when you release a phosphate group
30 kJ/mol so (-30 kJ/mol)
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what do metabolic pathways couple
endergonic and exergonic steps
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what do you put energy into
making high E intermediate compounds that can be broken down to drive rxns that produce ATP, NADH, etc.
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basically what are you doing
Couple endergonic rxns (like synthesis, etc.) to exergonic reaction like hydrolysis of ATP
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is transfer of electrons b/w compounds exergonic or endergonic
exergonic (favorable, releases E)
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oxidation
loss of electrons
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in oxidation, what is the substance that loses electrons called
reducing agent
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reduction
gain of electrons (reduction of charge)
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in reduction what is the substance that gains the electron called
oxidizing agent
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what is catabolism overall
oxidative
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why is catabolism oxidative
b/c substrates start reduced and become oxidized
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what is anabolism overall
reductive
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why is anabolism reductive
substrates start oxidized and become reduced
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what are redox reaections
transfer of electrons between compounds
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why are redox reactions so prevalent
typically some amount of Energy is released in that process
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example of releasing energy in form of heat and light
when you set wood on fire, it oxidizes carbs in cellulose and glucose; chem bonds are heated, break, and release E
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when do humans release heat energy
when we biochemically breakdown glucose in cell respiration; E can be utilized
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where does the E that is used to synthesize ATP come from
PE stored in E rich molecules
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how much E is required to make ATP
+30 kJ/mol
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what does hydrolysis of ATP lead to
release of energy
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why does making ATP take energy instead of releasing it
trying to stick negatively charged p (phosphate group) to already negative ADP molecule, requires in put of E due to repulsion
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where does the E we use to make ATP come from
tarnsfer of electrons; energy coupling --> coupling exergonic process w/ this endergonic process (ATP synthesis)
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is ATP synthesis exergonic or endergonic
endergonic
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how can we make ATP if process requires input of energy
we have a source of E (oxidizing energy rich compounds like glucose, fats, etc.)
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what is a source of E to help make ATp
oxidizing energy rich compounds like glucose, fats, etc.
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is burning wood the same way as biochemical processes?
no; wood burning is one single step and release HELLA energy in one step
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are biochemical pathways one step
no; this is biochemically useless AND dangerous
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why are there many steps in biochemical pathways
incremental release of small amounts of energy which can be used for AYP synthesis
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what happens to electrons when something is oxidized
transferred to something; that's why we call it redox
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when a compound is oxidized, what does it lead to
something else being reduced (due to those electrons being transferred)
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what gets reduced in catabolism
electron carriers like NAD and FAD
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what do NAD and FAD get reduced to in catabolism
NADH and FADH
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why are electron carriers important
can serve as currency which can be cashed in to provide E to make ATP
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example of electron transfer in mitochondria
provides energy to establish proton motive force
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what are you coupling when you establish the proton motive force
couple E derived from facilitated diffusion of protons through enzyme complex (ATP synthase) which drives production of ATP
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is ATP synthesis exergonic or endergonic
enderogonic
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what are you coupling with synthesis of ATP to make it happen
free energy available from the flow of protons through AYP synthase
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what do you do in catabolism (why is it oxidative)
take reduced substrates, strip electrons from them (when you break them down), they become oxidized
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what do you do in anabolism (why is it reductive)
you put in electrons into oxidized compounds to synthesize them, become reduced
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what are important biological electron carriers and coenzymes
NADH and NADPH
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what is oxidized form of NAD
NAD+
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what is reduced form of NAD
NADH
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what is NAD
nicotinamide adenine dinucleotide
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where is NAD derived from
niacin
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what is niacin
vitamin
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what are NADH etc.
electron carriers
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can NAD get reused
yes; cycles b/w oxidized and reduced forms and gets reused
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what is the process when NADH goes to NAD+
reduced to oxidized --> oxidation
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can electron carriers get reused/recycled
yes
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what is niacin deficiency
pellagra
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what is pellagra
rough skin
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is pellagra still there
mostly eradicated
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where do we see pellagra
in alcoholics, developing countries
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where is niacin derived from
tryptophan (amino acid)
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what is FAD
flavin adenine nucleotide
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where is flavin adenine nucleotide derived from
riboflavin
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what do FAD/FADH2 and FMN/FMNH2 act as
coenzymes in several types of enzyme-catalyzed redox reactions
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what is riboflavin
vitamin
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what does FAD serve as
electron carriers
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what can FAD and NAD become
oxidized and reduced
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how many Hs can FAD accept (as opposed to...)
one or 2 hydrogens, as opposed to NAD
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who is involved in more types of reactions
FAD (more than NAD or NADP)
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what is NADP
phosphorylated form of NAD
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what is NADPH
reduced form of NADP
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what is NADPH an important source of
reducing power, source of electrons in synthesis
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is NADH also an electron source
yes
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what is more common NADH or NADPH
NADPH in biosynthesis reactions
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what are redox reactions catalyzed by
dehydrogenases
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is there a net consumption or production of NAD+/NADH
no net consumption/production
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what do dehydrogenases do
transfer electrons from one compound to another
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what are we talking about in catabolism (in terms of transfer of e-)
transfer of e- from NAD+ to reduce it to NADH (b/c other thing gets oxidized)
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NAD+ reduced to NADH will invariable involve what
dehydrogenase
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what is cellular ratio
NAD+ >>> NADH
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what does it favor
hydride transfer to NAD+ (degradation)
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what is NAD+ being reduced to NADH+ more common in
catabolism
226
what is 1st step in NAD/NADH redox reaction
substrate undergoes oxidation --> dehydrogenation
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what occurs during dehydrogenation
loses 2 H atoms (2 protons and 2 e-s)
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what is 2nd step in NAD/NADH redox reaction
oxidized form of NAD accepts a hydride ion (1 proton and 2 e-), becomes reduced
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what is hydride ion
1 proton, 2 e-
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what does transfer of e- from reduced substrate to NAD+ to oxidized form of NAD result in
reduction of NAD to NADH, and oxidation of compound that initially carried those electrons [catabolic]
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describe reduction/anabolism for NAD/NADH step 1
NADH donates a hydride ion to oxidized substrate
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is there a net of hydrogen atoms transferred/lost from reduced compound?
yes
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describe step 2 reduction of nad/nadh
substrate becomes reduced
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what do dehydrogenases cattalyze
both reduction of NAD+ to NADH but also oxidation of NADH to NAD+
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what is more common to see in anabolic processes
oxidation; transfer of e- from reduced electron carrier to something else
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describe what happens to that something else in reduction
that something else starts off oxidized and becomes reduced, NADH is oxidized to NAD+
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real life redox reaction example
oxidation of ethanol
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describe oxidation of ethanol by NAD+
ethanol is oxidized to an aldehyde, NAD+ is reduced to NADH
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how is it redox
you're coupling oxidation reaction with a reduction reaction; or removing electrons from one compound and transferring to another
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what does ethanol start off as
reduced substrate, gets oxidized; NAD+ is oxidized,gets reduced
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where are the electrons transferred from
electrons are removed from ethanol and transferred to NAD+, generates acetaldehyde
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what is more oxidized acetaldehyde or alcohol
acetaldehyde
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describe reduction of pyruvate by NADH
pyruvate is reduced to form lactic acid/lactate, NADH is oxidized to NAD+
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what does NADH do/carry out
NADH gets oxidized to NAD+, so it must carry out a reduction
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what does NAD+ do
NAD+ gets reduced to NADH, so it must carry out an oxidation
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describe oxidation of C-C bond to C=C bond by FAD/FADH
C-C bond is oxidized to C=C, while FAD is reduced to FADH2
247
where are the electrons transferred
removed from hydrocarbon chain and transferred to FAD --> FADH2
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