Bioenergetics and Metabolism Flashcards
What is catabolism?
Breaking down bonds to release energy. They are generally oxidative reaction
What is anabolism?
Using energy to build molecules. Generally reductive
What’s the difference between a distinct and non-distinct pathway?
Distinct pathways share a lot of similar enzymes while non-distinct does not
Factors that control amount of enzymes?
-Transcriptions regulation (rate of mRNA synthesis)
-mRNA degradation
-translational regulation (rate of protein synthesis)
-Protein degradation
What factors that control the activity of an enzyme?
-Allostery (homo-activation/ inhibition, at a site other than the active site)
-Covalent modification (regulation of enzyme by covalent factors)
-Substrate availbility (homoallostry)
-Interaction with regulatory proteins
-Sequestration (localizing enzyme to subcellular compartments)
What is the difference between allosteric control and covalent modification?
Allosteric control involves a product in the pathway to feedback either immediately or further down the line to down regulate an enzyme while covalent modification involves an attachment of a certain group in order to activate or inactivate a certain enzyme
What are the general characteristics of second messengers?
- Low amounts in the resting state
-Regulated synthesis and destruction - Small and highly mobile
- Non-protein but act through a protein
The production of second messengers alters…
the activity of the target enzymes in the cell
In what ways can ligand binding alter the receptor function?
- Ion channels can open or close
- Enzyme activity may be turned off or on
- The ability to bind/ interact with other proteins may be altered
What hormones are GPCR’s?
Glucagon and epinephrine
Describe the process of signal transduction via GPCR’s and second messengers?
- Hormone binds to the receptor and activates the G protein
- Activated G protein exchanges GTP with GDP and alpha subunit is ready for a cellular response
- GAlpha- GTP binds adenlyly cyclase which converts ATP into cAMP
- Camp binds to the inactive protein kinase A. 2 cAMP’s bind to each regulatory unit (allosteric site) –> activating PKA
- The catalytic unit of PKA then phosphorylates a target enzyme inducing a cellular response
What are the “off switches” in signal transduction?
G Protein - Intrinsic GTPase activity converts GTP back to GDP
cAMP - is converted into AMP by enzyme phosphodiesterase with H2O
Target enzyme - is dephosphorylated with phosphatase
What is enthalpy
energy in a system
what is entropy
randomness in a system
Negative DeltaG means..
-reaction is exergonic
-energy is released
-Rxn proceeds fwd spontaneous
Positive DeltaG means
-Rxn us endergonic
-energy is absorbed
-Rxn does not occur in forward direction
What does delta G tell us
force that is required to get to equilibrium, magnitude and sense of direction
What does Delta G not tell us
the rate of reaction
What are coupled reactions?
Energy released by an exergonic reaction that can drive an endergonic reaction
Coupled reaction can only occur if….
they are linked by a common intermediate
what is direct coupling?
When an enzyme can catalyze 2 reactions
Give an example of direct coupling
Phosphorylated glucose can be forced to proceed with ATP. The enzyme hexokinase couples the reaction but excluded water
What is indirect coupling?
Two consecutive enzymes can catalyze reactions
How much energy does a phosphoanhydride bond release?
-30KJ/Mol
how much energy does does a phosphoester bond release?
-16kj/mol
ATP is a metastable compound, what does this mean?
it means that it is thermodynamically (releases a lot of energy when broken apart) stable and kinetically stable (needs a lot of activation energy)
what causes ATP to be a metastable compound?
-hydrolysis cause a relief of negative charges
-There is resonance stabilization of Pi
- Solvation effect, larger water shell is formed with ADP than ATP
-Increased entropy
How would a decrease in pH change the DeltaG of a reaction?
more positive
How would a increase in pH change the DeltaG of a reaction?
more negative
What is the true substrate for most enzymes?
MgATP
Define phosphorylation
Adding a phosphoryl group
define phosphate transfer?
transferring phosphoryl group form one molecule to another
define substrate level phosphorylation
A phosphate transfer that generates a NTP
what is a phosphagen?
a phosphoamide with higher group transfer potential than ATP
Why does the hydrolysis of phosphocreatine release so much energy?
Resonance stabilization of both the Pi and the creatine
What makes thioesters have large free energies
Release of the CoA group with water forms Acetic acid which has resonance stabilization when deprotonated
What is a acyl group
removal of one or more hydroxyl groups from an oxoacid (carboxylic acid) it contain a double bond to oxygen and an alkyl group
What are the different ways ATP can form?
- Substrate level phosphorlyation - Direct transfer of a phosphate from a high energy compond to a nucleoside diphosphate
- Oxidative phosphorylation - Phosphorylation of ADP to ATP coupled to the electron transport chain from a *substrate to molecular oxygen *
- Photophosphorylation is the phosphorylation of ADP to ATP coupled to the light dependent transfer of electron in a photosynthetic cell
- Adenylate Kinase - Reaction can synthesize ATP from 2ADP
- Subtrate such as NADH and FADH2
*
What reaction does adenylate kinase catalyze?
ADP + ADP <–> ATP + AMP
Why is the reaction done with adenylate kinase important?
-Done in muscle without oxygen to produce ATP
How can tou produce ATP from AMP
AMP from pyrophosphate cleavage of ATP can converted to ADP vid ADK
ADP can then make ATP
What enzyme does transphosphorylations?
Nucloetide diphosphate kinase
What is a transphophorylation reaction?
Between nucleotide and can occur in all cell types
NTP + NDP (dNDP) <–> NDP + NTP
What are the 3 stages of aerobic catabolism?
- Breakdown of the carbon backbone to forn NADH and FADH2 –> Acetyl CoA
- Citric acid cycle will use acetyl CoA to yeild alot of CO2 and reduced cofactors
- Oxy phor will yeild alot of ATP from NADH and FADH2
What is a reducing agent
Electron donor, becomes oxized
Aka reductant
What is a oxidizing agent
becomes reduced, recieves electrons
Oxidant
what is the formula for the oxizing states of carbon
of valence electrons on atom - (# of lone pair + assigned electrons)
How can electrons be electrons be transferred?
- Transfer of hydrogen atom
- Transfer of hydride atom
- Directly as electrons
- Thru a direct combo with oxygen
Explain what oxygenase does?
It’s an enzyme that oxidizes a substrate by transferring an O2 to it.
Explaination: because the oxygen is more electronegative once on a compound the oxygen will pull the electrons
What does oxidase do?
Oxidase catalyzes ox-red reactions to make O2 the electron acceptor
What does dehydrogenase do?
It transfers two hydrogen atoms
What does reduction potential mean?
The transfer of electrons based on a molecules affinity for it
In biological systems oxidation is synonymous with…
Dehydrogenation by dehydrogenase
What is a cosubstrate
Behaves like a substrate
What is a coenzyme
Group that is tightly bond to enzyme
How can you tell the difference between NAD+ and NADH
NADH can only be seen in the visible light range, putting under a spectrometer. Mix NAD+ with lactate which will convert to NADH and pyruvate
What can an electrochemical cell tell you?
Voltage will indicate flow of electrons
The more positive E’*…
The higher affinity for the oxidized form for e-
Electron flow spontaneously from compounds with __________ to compounds with ___________
Low reduction potentials, high reduction potentials
For electron transfer, delta E must be what?
Positive
