Quiz 2 Reading Info Flashcards
Energy transductions
conversions of one form of energy to another
Antoine Lavoisier
French chemist who recognized that animals somehow transform chemical fuels (food) into heat and that this process of respiration is essential to life
First law of thermodyanmics
Total amount of energy in the universe is constant
The form of energy may change, but energy cannot be created or destroyed
Second law of thermodyanmics
in all natural processes, the entropy of the universe increases
What type of systems are living organisms?
they are open systems
Gibbs Free Energy, G
expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure
Exergonic and endergonic reactions refer to
Change in delta G
Endothermic and exothermic reactions refer to
Change in enthalpy (H)
Exothermic reactions
delta H is negative
heat is released
surroundings feel warm
ex: gas burning
Endothermic reactions
delta H is positive
heat is consumed
feels cold, since energy is taken from the environment
Enthalpy, H
is the heat content of the reacting system. it reflects the number and kinds of chemical bonds in the reactants and products
Entropy, S
quantitative expression for the disorder in a system
Units of G and H
joules/mole or cal/mole
Units of S
joules/moleKelvin (J/molK)
How do cells become so ordered and seem to disobey the second law of thermodyanmics?
the order produced within cells as they grow and divide is more than compensated for by the disorder they create in their surroundings in the course of growth and division
isothermal systems
function at essentially constant temperature and constant pressure
cells are isothermal systems
Is heat flow a source of energy for cells?
No
Cells only use free energy to do work
Standards condition for the cell
25ºC - temperature
101.3 kPa / 1 atm - pressure
pH 7 - [H+] concentration
55.5 M - constant water concentration
Standard transformed constants
use the prime ‘ mark because they are occuring in the biochemical standard state
What is not included when solving for Keq and the mass-action ratio, Q ?
H20, H+, and/or Mg2+
Their concentrations are not included
Relationship between K’eq and ΔG’º?
ΔG’º = -RTln(K’eq)
What happens when K’eq is >1.0?
ΔG’º is negative and the reaction proceeds forward
What happens when K’eq is <1.0?
ΔG’º is positive and the reaction proceeds in reverse
What happens when K’eq is 1?
ΔG’º is zero and the reaction is at equilibrium
What does the standard free-energy change tell us?
in which direction and how far a given reaction must go to reach equilibrium in the biological standard condition
Does ΔG change?
Yes, unlike ΔG’º
It is a function of reactant and product concentrations and of the temperature of the reaction
ΔG equation
ΔG = ΔG’º +RTlnQ
Mass-action ratio
Q
ratio of product to reactant concentrations at a given point in the reaction
What happens as a spontaneous reaction proceeds to ΔG?
Since the number of products increases and Q becomes a larger decimal, ΔG approaches 0
Makes sense. As the reaction approaches equilibrium, ΔG approaches 0
ln(1) = 0
What is the criterion for spontaneity of a reaction?
The value of ΔG NOT ΔG’º
Concerned with the current conditions
What happens when you immediately remove the products of a reaction?
the ratio of product/reactants remains a small decimal, so ΔG has a large negative value
What is the natural log of a decimal?
negative. the smaller the decimal, the more negative the log is
Do ΔG’º and ΔG represent the actual amount of free energy available for use?
No! They represent the theoretical maximum amount
In reality, there is always less energy than these amounts
Does free energy change depend on the pathway?
No. All that matters is the starting and final products
Can enzymes change equilibrium constants?
No because equilibrium constants are not dependent on pathways
They can just change the rate/kinetics not thermodynamics
In energy coupling what do we do with K’eq and ΔG’º?
ΔG’º is additive
K’eq is multiplicative
What determines which reactions take place in biological systems and which do not?
1) their relevance to that particular metabolic system
2) their rates
even if useful to biological system, certain reactions may be too slow to use
5 categories of reactions for living cells
1) Reactions that make or break C-C bonds
2) International rearrangements, isomerizations, and eliminations
3) Free-radical reactions
4) Group transfers
5) Oxidation-reductions
Homolytic cleavage
each atom leaves the covalent bond carrying one unpaired electron (a radical)
Heterolytic cleavage
one atom retains both bonding electrons
this generates unstable carbanions, carbocations, and hydride ions
still, more common than homolytic cleavage
Nucleophiles
functional groups rich in and capable of donating electrons
Electrophiles
functional groups electron-deficient and seek electrons
Is the carbon atom a nucleophile or electroophile?
depends on which functional groups are attached to it! Can be both!
How are carbanion and carbocation intermediates created?
they are too unstable to be created alone, so functional groups containing electronegative species (O and N) help form them
Carbonyl groups
have a partial positive on carbon
can facilitate the formation of a carbanion on an adjoining carbon by delocalizing the carbanion’s negative charge through the carbonyl
What reactions is the carbonyl group essential to?
Aldol condensation
Claisen condensation
Decarboxlation reaction
Aldol condensation
common route to the formation of a C-C bond
carbanion attacks the carbonyl’s carbon. electron’s move through the carbonyl creating a negative charge on oxygen that changes to an alcohol
Claisen condensation
the carbanion is stabilized by the carbonyl of an adjacen thioester
similar to aldol condensation, except the thioester is the leaving group, so the carbonyl remains intact
intramolecular rearrangement
redistribution of electrons results in alterations of many different types WITHOUT a change in the overall oxidation state of the molecule
How do intramolecular rearrangements work?
different groups in a molecule may undergo oxidation-reduction with no net change in oxidation of the overall molecule;
undergo cis/trans rearrangement;
positions of double bonds may be transposed
Example of intramolecular rearrangement
fructose 6-phosphate to glucose 6-phosphate during glycolysis
Elimination reaction that does not effect overall reaction oxidation state
loss of water from an alcohol bond that results in a C=C double bond
How does acyl group transfer work?
involves the addition of a nucleophile to the carbonyl carbon of an acyl group to form a tetrahedral intermediate
How do glycosyl group transfers work?
nucleophilic substitution at C-1 of a sugar ring
this substitution could take place through SN1 or SN2 pathways
How do phosphoryl group transfers work?
they attach a good leaving group to a metabolic intermediate to “activate” the intermediate for subsequent reactions
for example, attaching a phosphoryl group to an otherwise poor LG like -OH
How many covalent bonds can phosphorous form?
5
What do the phosphorous bonds actually look like?
4 bonds with intermediate character between single and double bond character
Makes them tetrahedral
What does Pi (orthophosphate) have?
a partial positive charge on P to act like an electrophile
the oxygen groups take electron density away from the central P
Kinases
family of enzymes that catalyze phosphoryl group transfers with ATP as a donor
What is another type of group that activates molecules besides phosphoryl groups?
thioalcohols (thiols) -SH
activate carboxlyic acids by forming thioesters
What is the most highly oxidized form of carbon?
O=C=O
carbon dioxide
Dehydrogenation
common oxidation reaction where two electrons and two hydrogen ions are lost
Oxidases/oxygenases
catalyze oxidations where the carbon atom is directly covalently bonded to an O2
What generally happens in oxidation?
energy is released
Ex: campfires are oxidized by oxygen molecules in the air and release energy
How do most living cells obtain the energy needed for cellular work?
by oxidizing metabolic fuels such as carboydrates or fats
Catabolic pathways and oxidation
Catabolic pathways are oxidative reaction sequences that result in the transfer of electron from fuel molecules, eventually to oxygen
this process is highly exergonic, which provides energy to synthesize ATP, the goal of catabolism
Cofactors
facilitate reactions in the form of coenzymes and metals
bind to enzymes (either reversibly or irrevisibly) and promote a particular kind of chemistry/reactions
How does the role of ATP work from catabolism to anabolism?
Hetereotropic cells obtain free energy in a chemical form by catabolism of nutrient molecules
They use that energy to make ATP from ADP+Pi
ATP then donates some of its energy to endergonic processes, such as the synthesis of metabolic intermediates and macromolecules from smaller precursors
Why is ATP hydrolysis exergonic?
electrostatic repulsion in ATP is lowered
Pi product is stabilized by the formation of several RESONANCE structures not possible in ATP
phosphoryl-action potential ΔGp
the actual free energy of hydrolysis of ATP under intracellular conditions
for example, often times Mg is bound to ATP
What concentrations do we take into consideration when calculating ΔGp?
Have to consider the free concentrations, not the total concentrations in a cell
This means that the energy released by ATP hydrolysis is greater than the standard free energy change ΔG’º
Why is ATP used so frequently?
Besides its chemical properties, in the course of evolution, there has been a very strong selective pressure for regulatory mechanisms that hold cellular ATP concentrations far above equilbrium concentrations
important to be able to maintain high levels of ATP to drive hydrolysis of ATP forward
Other phosphorylated compounds that have large free energies of hydrolysis
1) Phosphoenolpyruvate (PEP)
2) 1,3-biphosphoglycerate
3) Phosphocreatine
Commonality between all phosphorylated compounds with large free energies of hydrolysis
several resonance forms of Pi available stabilize this product relative to the reactant
Thioesters
sulfur replaces the usual oxygen in an ester bond
the sulfur has less resonance stabilization than oxygen in ester
this makes a greater free energy change with its hydrolysis products, that are stabilized
Example of a thioester
acetyl-CoA
uses this property that its carboxylic acid product is more resonance stabilized than the original thioester
How does ATP normally provide energy?
Normally involves group transfers, not just simple hydrolysis
How does group transfer with ATP work?
A part of the ATP molecule (either Pi or PPi or AMP) is first transferred to a substrate molecule (covalently bonded)
This raises the molecules free energy content (more free energy to perform metabolic transformations)
Then, the transferred moiety transfered in the first step is displaced, released Pi PPi or AMP
When does direct ATP hydrolysis occur?
muscle contractions
High energy phosphate compounds
ΔG’º of hydrolysis is more negative than -25 kJ/mol
Low energy phosphate compounds
ΔG’º of hydrolysis is less negative than -25kJ/mol
Does energy of hydrolysis come from breaking the P–O bond?
No! Breaking one bond requires an input of energy actually
It is the overall change from products to reactants that releases energy
List phosphate compounds in terms of decreasing energy
PEP>1,3- biophopho..>PCr>ATP>glucose 6-phophate>glycerol
ATP’s intermediate position is useful
Why does ATP not dissociate in water?
Although thermodynamically unstable, it is kinetically stable
Takes a while to overcome activation energy, without an enzyme
Adenylylation
nucleophilic attack of ATP at the alpha position displaces PPi and transfers AMP as an adenlyl group
Why is adenylyation often the mechanism of breaking ATP for energy coupling?
can break the PPi to release even more extra energy by using a inorganic pyrophosphatase enzyme
How does polymerization of nuclei acids work?
Cleave the phosphate groups in the nucleoside triphosphate monomers
How does polymerization of amino acids work?
donation of adenlyl groups from ATP to activate them
Overall how does polymerization work?
couple endergonic reactions with exergonic breakdown of a nucleoside triphospate
How is energy used in transport processes across cell membranes, like Na+ and K+?
ATP interacts with the enzyme, not the substrates
the transport of Na+ and K+ is driven by cyclic phosphorylation and dephosphorylation of the transporter protein, with ATP as the phosphoryl group donor
How does muscle contration work?
direct hydrolysis of ATP
Mysosin contracts to hold ATP and then when it dissociates into ADP+Pi the muscle relaxs until another ATP molecule binds
Nucleoside diphosphate kinase
carries phosphoryl groups from ATP to other nucleotides
Adenylate kinase
during periods of intense demand for ATP, the cell lowers the ADP concentration and at the same time replenishes ATP
enzyme helps
Phosophocreatin
PCr reservior can quickly replenish ATP
creatine kinase helps in this exergonic reaction
polyP
a linear compound composed of many tens or hundreds of Pi residues, linked through phosphoanhydride bonds
Polyphosphate kinase 1 and 2 (PPK-1, PPK-2)
PPK-2 is believed to act primarily in breaking down polyP to generate GTP and ATP
PPK-1 is believed to act primarily in breaking down ATP to form polyP longer chains
polyP and bacteria
high levels of polyP correspond to greater expression of genes in adaptation to threats
in making new antimicrobial drugs, could attack the PPK enzymes to diminish the amount of polyP available
Electromotive force (emf)
the force proportional to the difference in electron affinity
the spontaneously flow of electrons to a species with a high electron affinity has the ability to do work
Glucose serves as …
a source of electrons
as glucose is enzymatically oxidized, the released electrons flow spontaneously through a series of species to O2
Examples of using electron flow to do work
flow of electron provides energy for ATP synthesis
enzymes couple electron flow to the production of a transmembrane pH difference
flagellar motion in E. coli
Reducing agent
electron donating molecule
will give up electrons to reduce another
Oxidizing agent
electron accepting molecule
will accept electrons to oxidize another
Conjugate redox pair
involve an electron acceptor and an electron donor
Examples of conjugate redox pairs
Fe3+(electron acceptor) and Fe2+(electron donor)
Cu+(electron donor) and Cu2+(electron acceptor)
NADH(electron donor) and NAD+(electron acceptor)
General trend of conjugate redox pairs
the electron acceptor is more positive
it wants an electron
Order of increasing electronegativity
H
How can you determine the oxidation of carbon?
often, if carbon has less Hydrogens, species are pulling electrons from carbon and it is being oxidized
ex: H3C-CH3 is less oxidized than H2C=CH2 (less hydrogens)
dehydrogenation
often synonymous with oxidation
as you lose hydrogens, something is oxidized
How are electrons transferred from one molecule to another? (4 ways)
1) Directly as electrons
2) As hydrogen atoms (proton+electron)
3) Hydride ion
4) Direct combination with oxygen
Reducing equivalent
term used to designate a single electron equivalent participating in an oxidation-reduction reaction
standard reduction potential
Eº
affinity of the electron acceptor of each redox pair of electrons
Relationship between Eand flow of electrons
Electrons will flow to more positive E’º
E’º has a greater ability to be reduced (gain electrons)
ΔE’º
given as E’º of the electron acceptor - E’º of the electron donor
*this occurs at typical biological standard conditions
ΔE
gives the strength of the tendency for electrons to flow to the electron acceptors
n in oxidation/reduction calculations
n is the number of electrons transferred in the reaction
How is the ΔG’º so largely negative for oxidation of glucose to CO2? Like more than ATP synthesis needs?
this occurs in a series of controlled reactions, some of which are oxidations, rather than one big reaction
Types of Coenzymes
NAD, NADP, FMN, FAD
NAD+ or NADP+
accept a hydride ion and are reduced
makes no charge on the ring nitrogen (called the quinonoid form)
Is NAD+ overall positive?
no! Just indicates the charge on the ring
actually, these molecules are overall negative
NAD versus NADP
NAD is used mostly in oxidizations because it has a high concentration of NAD+ which makes it being reduced favorable
NADP is used mostly in reductions because it has a high concentration of NADPH which makes it being oxidized favorable
When are reductions seen?
in anabolic reactions
(NADPH) is used
When are oxidations seen?
in catabolic reactions
NAD is used
Oxidoreductase
catalyzes reactions involving NADPH and NAD
Rossman fold
NAD and NADPH coenzymes, losely bind to this fold in electrons. They are able to move around
Is there a net production of coenzymes?
No! They are used catalytically
niacin
vitamin that NAD and NADPH derive their rings from
get vitamin from tryptophan
definciny leads to pellagra
Flavoproteins
enzymes that catalyze oxidation-reduction reactions using either FMN or FAD as coenzyme
Flavin nucleotides
FMN or FAD coenzymes
Why are flavin nucleotides used more than NAD and NADPH?
they have the ability to be involved in either one or two electron transfers
Does the Eº change for flavin nucleotides?
yes! Depends on if they are tightly bound to an enzyme or not
Cryptochromes
a family of flavoproteins that mediate the effects of blue light on plant development and the effects of light in circadian rthymns
eukaryotic cells
Photolyases
found in prokaryotic cells
use the energy of absorbed light to repair chemical defects in DNA
Fatty acid oxidation / B-oxidation
make a carbon that wasn’t a good electrophile into a good electrophile by creating a carbonyl group
then you can break up the hydrocarbon chains of fatty acids
Why is it surprising to see methane on mars?
methane less oxidized than CO2 and is higher in energy than CO2
What is the terminal electron acceptor?
oxygen
Where does the energy go when it moves to O2 in the electron transport chain?
energy is pumped as protons to form a concentration gradient
from this concentration gradient we can power ATP synthase
What do we do to keep high concentration of NAD+ in the electron transport chain?
dump electrons into the chain
