Samenvatting Metabolism (WBBY058-05), ISBN :9781319114657
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Course
Metabolism (WBBY05805)
Institution
Rijksuniversiteit Groningen (RuG)
Book
Biochemistry
This summary includes all the information that you need for the course Metabolism. The summary is 140 pages long, because it contains a lot of information, but also a lot of describing pictures which means that you can go fast through it. By reading and understanding this summary you don't even hav...
TEST BANK for Biochemistry 10th Edition by Jeremy Berg; Gregory Gatto Jr.; Justin Hines; John L. Tymoczko; Lubert Stryer (Complete Chapter 1-32)
Metabolisme & Biochemie werkcollege en self-test antwoorden voor H 1, 2, 7, 8, 9 en 11
Samenvatting Metabolisme en Biochemie Deeltentamen 1 & 2
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METABOLISM // LECTURE 1 // ATP and Gibbs energy
Glycolysis Fermentation // CH. 15 & 16.1
• Metabolism is a tightly integrated network of reactions
• Not all exam-relevant material will be presented in the lectures → Make
summaries of the book
➢ Basic principles
◼ ATP AND GIBBS ENERGY
➢ ATP, carrier of Gibbs energy
→ Two high-energy phosphate bonds
→ You don’t have to learn structures, unless indicated
→ It has these 3 phosphate bonds → 2 of these bonds contain a high energy → The last
phosphate is not an energy rich bond
➢ Gibbs energy is the driving force
Second Law of Thermodynamics = In all spontaneous processes Gibbs energy is dissipated
… at constant (environmental) temperature and pressure
→ The Gibbs energy is the driving force
→ Spontaneous = can’t divert its direction
→ For glucose there are transport proteins in the cell membrane so it can pass the
membrane
→ The transport goes from high concentration to low concentration → But there also go
molecules from left to right, but less frequent → It’s a chance process that it’s more likely to
go from left to right that drives the net flow from left to right → Entropy = probability
creates a net flow from left to right → Doesn’t cost energy
→ Normal sodium goes from positive side to negative side → They will energetically be
pulled from right to left → So the entropy would drive the sodium from left to right, but
the energy will drive it from right to left → We can’t decide who will win
, ➢ Gibbs energy balances energy and entropy
→ The change in Gibbs energy → 2nd law → If the change in Gibbs energy is negative (- dG),
then the process can occur in that specific direction
➢ Gibbs energy of a biochemical reaction
→ If we look at the Gibbs energy of ATP hydrolysis
→ Driving force of ATP hydrolysis:
1. Negative charges on phosphate repel each other → There is an energetic driving
force to pull these apart
2. Resonance stabilization of inorganic phosphate (Pi) → This phosphate has one
double bond which can binding to every O → See picture below → Many ways of
realizing the same molecule → Entropy effect
3. Two molecules are formed from one → Entropy effect → Positive driving force
4. ADP and Pi are stabilized by bound water molecules
→ However, it is difficult to calculate G from first principles
➢ Computing reaction Gibbs energy
1. A spontaneous reaction has a negative G.
2. G0’ is defined under standard conditions, in a water solution at pH 7.
3. Concentrations should be expressed in moll-1 (M), the partial pressure of a gas in
atmosphere (atm).
4. Check for yourself that the second equation follows naturally from the first, if you
remember that at equilibrium there is no driving force. Hence, at equilibrium G = 0.
5. If you can compute the G0’ from the equilibrium constant, you can also do the
inverse. Check for yourself that Keq = e-G0’/RT.
→ The relevant change in Gibbs energy tells the direction of the process, but it depends on a
standard delta G (delta G0) of the reaction which is the property of the reaction and is
always the same for a certain reaction → You can find it in a table
→ But it (delta G) also depends on the actual concentrations → The more products there
are, the higher the Gibbs energy change, so the more positive / less negative → This will
diminish the driving force
, ◼ What makes ATP a good carrier of Gibbs energy?
ATP hydrolysis: G0’ = 30.5 kJ mol-1
→ ATP hydrolysis has strong driving force, hence ATP is capable of driving uphill reactions.
→ There are reactions with even more negative G0’. These are required to recharge the
carrier, i.e. drive the synthesis of ATP from ADP.
→ ATP is stable in the absence of enzymes
➢ Other carriers of Gibbs-energy
creatine-P + ADP → creatine + ATP
→ Creatine-P is a short-term storage form of Gibbs energy in skeletal muscle (for the initial
5-6 sec of a sprint).
→ These are the most common carriers of Gibbs energy, which you will encounter in this
lecture series.
➢ G and G0’ are additive
→ You can add delta G values
→ The reaction in the opposite direction has the same delta G, but with a minus (-)
→ So the glucose hydrolysis can’t happen spontaneously, but can happen when it’s
coupled to the hydrolysis of ATP
→ An enzyme is a catalyst → It can overcome a barrier of Gibbs energy → It can couple
reactions → So the phosphorylation of glucose would never happen if it can’t be coupled to
the downhill reaction
➢ Enzymes couple uphill and downhill reactions
→ The production of glucose-6-P would be thermodynamically infeasible without an
enzyme to couple it to ATP hydrolysis
→ You learned in Chapter 8 that enzymes are catalysts: they speed up the reaction by
lowering its activation energy. An equally important function of enzymes, however, is to
couple thermodynamically infeasible reactions (endergonic reactions, i.e. with a positive G)
to an exergonic reaction (with a negative G). The overall process is feasible if the overall G
is negative.
◼ GLYCOLYSIS
→ When there is no Oxygen, the pyruvate can be fermented to produce ethanol or lactic
acid, but there are many more options
, ➢ Glycose is a favorite fuel for many organisms
→ We start focusing on the conversion of glucose to pyruvate
➢ Did you know that…
• Glycolytic enzymes were the first enzymes ever discovered
• 1860 Pasteur proves that fermentation requires living cells
• 1897 Eduard Buchner proves that fermentation takes place in yeast extracts
without living cells (Nobel prize 1907)
• 1909 - 1942 Identification and purification of glycolytic enzymes
→ In 1860 Pasteur showed that living yeast cells catalyze the conversion of sugars to
alcohol. This was a revolutionary insight, since until then fermentation had been studied as a
chemical process. The Buchner brothers brought about the next revolution by showing that
the cell itself was not required, but an extract of the cell was sufficient to catalyze
fermentation. Many famous scientists have contributed to the elucidation of the individual
biochemical reactions in glycolysis and the purification and characterization of the enzymes.
From chemistry, via cell biology, to biochemistry.
➢ Glycolysis in cancer research
→ Cancer cells use a lot of glucose and they use it in a very energetically favorable way →
They produce pyruvate and lactate, they don’t use oxygen
➢ Glycolysis in top sport
→ Short and intense exercise depends primarily on glycolysis. → You use the creatine
phosphate first, but after that glycolysis
→ Glycolysis can be upregulated 400-fold during a 100 m sprint.
→ Glycolysis shuts down within seconds
➢ Glycolysis
,→ Glucose is split at some point in to 2 compounds → DHAP ad GAP which both contain 3
C’s
→ You don’t get the ATP like that, but you first have to invest ATP
→ So if there is no ATP you can’t use glycolysis because ATP is needed
→ It always needs to maintain a minimal level of ATP to be rescued→ This is a challenge for
the cell
→ In the second part you get 2 ATP, but you have DHAP and GAP, so in fact you have 4
ATP yield
→ In microbes there are many variants of this pathway
➢ Glycolysis, detailed overview
→ This is an important picture (Berg, p. 452). It is too detailed to discuss on the screen, but
you will need to know all reactions by heart. This includes the names of the enzymes and
metabolites and the order of the reactions. You do not need to know the structures of the
metabolites. However, you should study the structures to be able to recognize the reaction
type.
→ You need to know the names of the reactions and which conversions catalyze → So you
need to know this pathway by hard
→ You don’t know the structures, but you have to be able to interpretate the structure,
because that can happen in the exam
➢ A limited number of reaction types
→ Enzyme names often reveal the reaction type
→ 1. Note that the reaction is classified irrespective of its direction. For instance, a ligation
reaction running in the reverse direction (i.e. splitting of a bond, yielding ATP) is still called a
ligation reaction.
2. In the enzyme names you will recognize the reaction type. E.g. enzymes that catalyze an
oxidation-reduction reaction are often called dehydrogenase, particularly if the electron
acceptor is NAD+ or FAD.
3. A special type of group transfer reaction is the transfer of a phosphate group between
ATP and another compound. The enzymes catalyzing such reactions are called kinases. You
will need to know this as kinases occur frequently in energy metabolism.
➢ Hexokinase
, → Kinase = Enzyme = A transferase that transfers phosphate from ATP to an acceptor
molecule
→ So it’s always ATP and can be a glucose kinase like hexokinase, but it can also be a protein
kinase
➢ Induced fit
→ An enzyme is a complex machine with a mechanism that allows the reaction to happen
→ In this case it’s an induced fit
→ They bind their substrate precisely in the active side of the enzyme, but not always→
Often the molecules of the substrate wonders around and when it binds tightly enough the
enzyme starts folding around it and then it’s caught and then it remains there → This is
important because we only want glucose to react with the ATP and not water for instance
→ So only when glucose is recognized the enzyme will fold around it and the ATP can bind
more tightly and then can donate its phosphate
→ The active site closes around glucose and ATP.
→ Thus, the ATP in its activated form is protected from water. Why?
→ Function of the induced-fit mechanisms: Due to the closure of the active site, H2O is
excluded. Thereby, H2O cannot react with ATP and this mechanism prevents ATP
hydrolysis without making use of the Gibbs energy. Thus, the enzyme has evolved such
that it does not catalyze the futile hydrolysis of ATP. This feature is not unique for hexokinase.
Also other kinases (phosphofructokinase, phosphoglycerate kinase, pyruvate kinase) close their
active site around the substrate before ATP can bind and transfer its phosphate.
➢ Glucose 6-phosphate isomerase
→ Isomerase – identical atomic composition of product and substrate = reaction where you
need the same elements composition, but you make another isomer → So you rearrange the
atoms in this molecule
→ First the ring opens and then the double bond moves to the second C → So there is a
redox reaction → If then the ring closes again, it closes on the 2nd C → Now you have a 5-
ring
➢ Phosphofructokinase
→ Kinase – Phosphate transfer from ATP
→ ATP is the donor of the P
→ You see symmetry
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