Ch. 10 - Introduction to Metabolism Flashcards
Metabolism
the total of all chemical reactions in the cell
catabolism
biodegradation
- breakdown of larger molecules into smaller ones -breaks covalent bonds and releases energy, so these reactions are exergonic
- catalyzed by enzymes
- most reactions are oxidations (provides reducing power to NAD and NADP when they turn into –> NADH and NADPH by receiving electrons in the form of hydrogen from oxidized compounds)
*spontaneous reactions*
anabolism
biosynthesis
- synthesis of a larger molecule from a smaller one(s)
- creates new covalent bonds and requires energy input so these reactions are endergonic
- catalyzed by enzymes
- mostly reduction reactions (giving electrons to other compounds)
*non spontaneous reactions*
Chemoorganotroph
energy source: obtains energy from oxidation of reduced organic compounds (glucose) (also called a chemoheterotroph)
**HUMANS are chemoorganotrophs**
Chemolithotroph
energy source: use inorganic compounds for aerobic or anaerobic respiration (nitrate, sulfate, CO2)
autotroph
can fixate CO2 as a carbon source
heterotroph
can only use organic molecules as a carbon source
oxidation
removal of electrons from a compound (charge will become more positive)
reduction
addition of electrons to a compound (charge will become more negative)
reducing power
ability of an organism to have enzymes that can reduce other compounds (NADH and NADPH)
-when NAD and NADP are reduced *gain electrons in the form of hydrogen* they now have reducing power because they can give that hydrogen electron to other compounds
math equation for whether a reaction is spontaneous or not
G= H-(T*S)
- if G is negative, reaction is spontaneous (exergonic)
- if G is positive, reaction is not spontaneous (endergonic)
G=amount of energy available
H=change in enthalpy (heat)
T= temp in Kelvin
S= change in entropy (amount of order)
exergonic reaction
chemical reactions with a negative G value that release free energy *exergonic reactions proceed spontaneously*
endergonic reaction
chemical reactions with a positive G value that require energy input *endergonic reactions do not proceed spontaneously*
Role of ATP in metabolism
exergonic (spontaneous) breakdown of ATP is coupled with endergonic (non-spontaneous) reactions to make metabolic reactions more favorable
Endergonic reaction alone versus Endergonic reaction coupled with ATP breakdown
Endergonic reaction alone: reverse reaction is more favorable than forward reaction
Endergonic reaction with ATP breakdown: forward reaction is more favorable than reverse reaction *the activation energy required to perform an endergonic reaction is typically larger than the energy of the exergonic reaction*
(describe picture)
ADP is being reduced through endergonic reactions (energy input via electrons) *non spontaneous and anabolism*
ATP is being oxidized through exergonic reactions that are releasing energy in the form of electrons
*spontaneous and catabolism*
Oxidation-Reduction Reactions (quick facts)
- many metabolic processes involve electron transfer
- oxidation/reduction reactions transfer energy via electrons
transfer of electrons from a donor to acceptor:
- results in energy release, can be used to form ATP
- the more electrons a molecule has, the more energy rich it is
oxidation: removing electrons or a hydrogen atom removes energy so oxidations are exergonic *occurs spontaneously*
reduction: adding electrons or a whole hydrogen atom adds energy to a molecule so reductions are endergonic *occurs non-spontaneously*
C6H12O6 -> 6CO2 + 12H2O (C is in oxidized form because it is giving its electrons to the electronegative O2. O in H2O is in most reduced from because it is obtaining electrons and H atoms)
Redox (Reduction) Potential
tendency of a compund to donate electrons (be oxidized) or to gain electrons (be reduced)
- meausred in Eo
- more negative Eo = better electron donor
- more negative Eo = better electron acceptor
reactions that have two seperate half reactions (one oxidizing one reducing) have two different reduction potentials for each half reaction
-the greater the difference of the Eo of the donor reaction (oxidizing) and Eo of acceptor (reducing) reaction, the more negative the G value
**SO = greater the difference in Eo of oxidizing and Eo of reducing reaction, the more spontaneous the reaction will be**
Redox Tower
- represents range of possible reduction potentials for redox couples in nature
- reduced substances near the top of the tower have the greatest tendency to donate electrons (have electrons to give away)
- oxidized substances in the lower part of the tower have the greatest tendency to accept electrons (oxidized substances that have an affinity for electrons)
- the farther the Eo difference from donor to acceptor, the greater the amount of energy released **greater difference in Eo, more exergonic and spontaneous the reaction is**
Electron Transport Chain
- first electron carrier in transport chain (NADH) has the mose negative Eo value which means it is an electron donor
- the potential energy stored in this oxidization of NADH for its hydrogen atom (an electron and proton) is used to form ADP by joining ADP and Pi together
- first electron carrier (NADH) is oxidized
Enzymes
- are always proteins
- catalysts
substrates = reacting molecules that enzyme breaks down
products = substances formed by reaction
-some enzymes are composed solely of one or more polypeptides, some enzymes have polypeptides AND nonprotein components
Apoenzyme
-protein component of an enzyme
Cofactor
nonprotein component of an enzyme made up of two parts:
- prosthetic group - firmly attached to enzyme
- coenzyme - loosely attached, can act as carrier/shuttle
Holoenzyme
apoenzyme + cofactor (entire enzyme)
Transition-state complex and activation energy
transition-state complex = when substrate is binded to enzyme before a product is made
Ea (activation energy) - energy required to from transition-state complex
How Enzymes lower Ea
- By increasing substrate concentrations at active site of enzyme (more substrate converted)
- orienting substrates properly with respect to each other in order to form the transition-state complex
- enzyme model is fit specifically for enzyme-substrate interaction
Environmental effects on Enzyme Activity
significantly impacted by:
- substrate concentration
- pH
- temperature
Riboenzymes
- can catalyze peptide bond formation
- can self-splice/self-replicate
Regulation of Metabolism
3 major mechanisms:
- metabolic channeling
- regulation of the synthesis of a particular enzyme (transcription and translation)
- regulation of enzyme activity (regulating direct activation or inhibition of a critical enzyme’s activity)
Metabolic Channeling
differentialization and localization of enzymes
compartmentalization of enzymes = differential distribution of enzymes and metabolites among separate cell structures or organelles
Regulation of enzyme activity
- allosteric regulation
- covalent modification
Allosteric Regulation
-most regulatory enzymes are allosteric
enzyme activity altered by small molecule called an allosteric effector:
- binds non-covalently at regulatory site
- changes shape of enzyme at catalytic site and alters activity of catalytic site **catalytic site is where substrate binds**
- positive allosteric effector- increases enzyme activity
negative allosteric effector - inhibits enzyme activity
Covalent Modification of enzymes
addition or removal of a chemical group (phosphate, methyl, etc.)
advantages:
- respond to more stimuli in varied ways
- adds second level of control to the catalyzing process
**these chages are usually reversible** (not permanent)
Phosphorylation and dephosphorylation
Phosphorylation = is the addition of a phosphate (PO43-) group to a protein or other organic molecule. (reducton of a molecule by adding energy)
**addition of energy and endergonic**
Dephosphorylation = oxidation of a molecule by a phosphate being exergonically taken away from the molecule
**loss of energy and exergonic**
ATP dephosphorylizes and becomes ADP and PO43-, but ADP and phosphate become phosphorylized and become ATP
**every reaction has an exergonic and endergonic half reaction**
Feedback Inhibition of enzymes
end-product inhibition
-inhibition of one or more critical enzymes in a pathway regulates the entire pathway (catalyzes slowest or rate-limiting reaction in the pathway)
PICTURE:
- each end product regulates its own branch of the pathway
- each end product regulates the initial pacemaker enzyme
