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