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110 Cards in this Set

  • Front
  • Back
What are the uses for compartmentalization within a cell?
Incompatible reactions are isolated.
Isolate harmful reactions.
Futile cycles are avoided.
Reduce time molecules float around before finding each other to react.
Release local bursts of ions quickly.
Give 3 examples of when harmful reactions are isolated.
Acidic reactions and enzymes in lysosome.
Promoters of cell death in mitochondria.
Peroxide reactions limited, free radicals contained.
Give an example of when incompatible reactions are isolated.
S-S bonds in proteins bound for the Rough Endoplasmic Reticulum (which is an oxidizing environment).
-SH bonds in proteins which are bound for the cytoplasm (which is a reducing environment).
Give and example of when futile cycles are avoided.
Fatty acid oxidation in mitochondria and fatty acid synthesis in cytoplasm (compartmentalization is useful).
Give an example of when time is reduced for molecules to find each other.
Perioxide in peroxisome more likely to find a catalase enzyme in small volume of organelle.
Give an example of when a local release of ions.
More Ca in SER. SER branches out over cytoplasm, local signal can cause release of Ca. Quicker than if released from a single, local store.
What are the three components of the cytoskeleton?
Actin, intermediate filaments and microtubules.
Which cytoskeletal structures have polarity?
Actin and microtubules.
From where do all microtubules emanate from?
The centrosome (which has gamma tubulin).
What are two motors that act on microtubules, and in which way do they travel?
Kinesin: Plus end
Dyenin: Minus end
What is the likely mechanism for an enzyme-catalyzed reaction, when thinking about cell crowding?
Protein A binds to Protein C, protein B passes through.
Why is diffusion of macromolecules very limited in the cell?
Due to cell crowding. Proteins are big molecules, meaning movement is slow. Reactions may take a long time, especially if multiple enzymes are used.
What are the 3 ways of dealing with the problems of cell crowding?
Molecular machines.
Molecular motors.
Compartmentalization.
What change can ATP binding make to a motor protein?
A conformational change.
What kind of effect can this conformational change have?
The motor has a 'leg' which moves more to the right than the left in the conformational change. This makes it more likely to bind right. Does NOT make it 100% certain it will bind to right, just more biased.
What equation can the previously discussed principle be expressed as?
ΔG(0') = RTln ([Products]/[Reactants])

or simply: ΔG(0') = -RTlnK (with a NEGATIVE)
If ΔG is greater than 0, what does this mean?
Energy has been put into the reaction (i.e. it is not spontaneous).
What is K and ΔG at equilibrium?
1 and 0, respectively.
How do metabolic reactions proceed if energy is required (there is a positive ΔG)?
ATP hydrolysis into ADP and a Phosphate ion.
How is the increase positive ΔG of a reaction balanced out by ATP hydrolysis?
ATP hydrolysis has a very negative ΔG, meaning it compensates.
Why do some glycolysis reactions have a positive ΔG, but are able to proceed in the right direction?
Since the enzyme that catalyzes the following reaction with the product initiates the reaction too quickly for the product to revert back to its substrate-state.
Why is the RTln term negative?
Since the products to reactant ratio becomes less than 1.
What effect does this have on ΔG?
Cancels out the positive ΔG, making the overall ΔG negative, and allowing the reaction to continue in the right direction.
What does this mean in terms of equilibrium?
Products are removed, meaning the equilibrium is shifted to the right, making the reaction more favourable and making ΔG more negative.
What are the two major properties of ATP that allow energy to be contained?
The energy within the bonds of the ATP molecule itself.
Concentrations of ATP being held at values much larger than equilibrium.
How are ATP molecules used efficiently, instead of spontaneously hydrolysing and creating too much energy?
The activation energy for reactions within the cell is lowered, meaning hydrolysis can be put to work.
Which protein structures are integral in the efficiency of this theory?
Molecular machines.
What analogy can be used to denote enzymes?
A jig.
What is an appropriate example of an enzyme as a molecular jig, and in which metabolic process is this found?
Phosphoglycerate kinase, in glycolysis.
What is the substrates and products of the reaction this enzyme catalyses?
Substrate: 1, 3 bisphosphateglycerate, ADP.
Product: 3 phosphoglycerate. ATP.
What are the binding sites on the PGK molecule?
2 distinct sites, one for 1,3 PGA and one for ADP.
What is the evidence for this?
High ADP concentration, varying concentration of PGA. Only concentration of PGA affects the speed of the reaction.
What mechanism does this experiment rule out?
1,3 PGA binding, depositing the Pi, unbinding, ADP binding and picking up the Pi. This would require one site, which the experiment shows is not the case.
How does phosphate transfer occur in this reaction?
In-line attack with inversion of configuration (of oxygen groups around the phosphate atom)
What kind of state does the phosphate group that underwent an inline attach undergo?
A high energy transition state.
What makes the transition state high energy?
The phosphate is on a plane, and the leaving and attacking Oxygens are perpendicular to this plane. They are negative and in close proximity, making it high energy.
What effect does the transition state have on the rate of the reaction?
Limits the rate of both the catalyzed and uncatalyzed reactions.
How do enzymes speed up the reaction in terms of the transition state?
Stabilize the phosphate group by using positively charged groups on the enzyme.
What are the positive groups on the enzyme that stabilize the phosphate group in the transition state?
Lysine 219 and Arginine 39.
Which ion's positive charges also help to stabilize the high energy transition state?
Magnesium 2+
How does PGK promote phosphate transfer to ADP?
Over transfer to water.
What is the danger involved with when it comes to 1,3 PGA?
Water may cause hydrolysis of the main molecule and the phosphate group, meaning a Pi is lost instead of being bound to ADP.
How can this danger be avoided, but what is the problem with this?
By blocking water molecules from binding to PGA, but substrates must get close enough to bind.
How is this problem overcome?
The enzyme is a hinge-like structure, with the two sides binding ADP and 3PGA. When both bind, hinge turns 32 degrees to allow phosphate transfer. Avoids hydrolysis,

Lys 219 is on C part (left) and Arg 39 is on N part (right). Also come into proper position.
Where does the majority of energy get released during an enzyme-catalyzed reaction and so is the rate limiting step?
Unbinding of the substrates.
Which reaction is faster, the dephosphorylation of 3PGA and then the reaction of 3PGA reaction that is catalyzed by GAPDH, or just the dephosphorylation of 3PGA?
Further reaction catalyzed by GAPDH (500 times faster).
Why is this?
Direct transfer of 1,3 PGA between PGK and GAPDH speeds up the reaction.
Is there thought to be a high or low concentration of Enzyme vs Substrate in the cell?
High.
What hypothesis does this support?
All substrates bound, allow for much enzyme-enzyme interaction to facilitate reactions. Many glycolytic enzymes are in complexes and minimal transfer occurs.
What is the structure of kinesin?
Two monomers wound around each other, which 'feet' at the bottom, which step along microtubules.
How many types of subunit form actin?
1
What is a motor protein that works on actin?
Myosin.
What are the two types of myosin, and where are the found?
2: Found in muscle.
5: Found in cells, not only in muscle.
How does kinesin move along a microtubule?
Conformational changes resulting from ATP hydrolysis.
What is the original state of kinesin heads, in terms of nucleotide binding, and what effect does this have on the motion?
Both heads bound to ADP, causes random movement.
At what point does ADP unbind?
When a kinesin head binds to the microtubule.
What can then bind to the kinesin head?
ATP
What does this cause?
The second kinesin head's neck to change conformation, causing the kinesin head to flop in front and bind to the microtubule.
What happens when the second kinesin binds?
ADP unbinds, ATP is hydrolyzed in the first head. New ATP binds to second head.
What happens when the second ATP binds?
The first kinesin head is flopped forward. This process continues to produce stepping.
How frequently are myosin and kinesin heads bound to their cytoskeletal component?
Myosin: Briefly at the power stroke.
Kinesin: One head is usually bound all the time.
Which way does the myosin head move towards on actin?
The negative end.
What is the molecular machine present in the mitochondria inner membrane that allows ATP formation to occur?
FoF1 ATP Synthase.
What are the subunits present in Fo, and how many are there?
One A subunit, one B subunit and 10-15 C subunits.
What are the subunits present in F1, and how many are there?
3 Alpha subunits, 2 beta subunits, 1 gamma subunit (extends up into Fo), one delta subunit and one epsilon subunit.
What is the structure of subunit a in F0?
Two half channels, one on the left and one on the right. They aren't connected.
Which two subunits in Fo face each other, and what type of environment do they make?
C and A, form a hydrophilic environment.
What happens when a hydrogen ion enters through the channel present in the A subunit?
It binds to aspartic acid (Asp 61) on the C subunit, making it neutral and hydrophobic. The environment changes to hydrophobic.
What change does the hydrophobic environment cause?
The rotor moves into the plasma membrane, which is also hydrophobic.
What does the shift of the rotor cause for another C subunit?
It shifts into the region of the A subunit with the second half channel, and the H ion unbinds. It then can enter the matrix.
What subunit is used to connect the Fo and F1 subunits?
The gamma subunit.
When the F1 subunit isn't connected to Fo, what is its function?
ATP hydrolysis,
How does the rotating movement of the Fo subunit affect the action of the F1 subunit?
The bulge in the gamma subunit causes conformational changes in each αβ complex (of which there are 3).
What are the 3 types of state an αβ complex can be in in relation to Gamma subunit orientation?
Open, loose and tight.
When the gamma bulge is on an αβ complex, what state is the complex in?
Open.
What are the following states, in order?
Loose and tight.
What happens in the open state?
ADP and Pi enter the active site. ATP from previous cycle exits.
What happens in the loose state?
ADP and Pi are held in place.
What happens in the tight state?
ADP and Pi are forced together to form ATP.
In what conditions could the ATP synthase machine run in reverse?
If [H+] was high in the matrix than in the intermembranous space.
What direction would the gamma head turn, and what would happen to ATP?
Counterclockwise and ATP would be hydrolyzed.
What would be needed for this, in terms of ATP concentration?
A high ATP concentration.
How does a potassium channel keep larger ions from entering the cell?
Steric hindrance does not allow for a large ion to pass through the channel.
How does a potassium channel keep smaller ions from entering the cell?
The carbonyl groups around the end of the K channel need to compensate for the H2O molecules which hydrated and stabilized the ion previously. The carbonyl groups are spaced specifically to bind to an ion the size of K, and Na is too small, meaning they can't bind and the absent H2O can't be compensated for. So Na stays bound to H2O, making it too big to pass through.
What are the types of pumps, in terms of paired molecule transport?
Symporters (2 in same direction) and antiporters (2 in opposite directions).
What is a major example of the Major Facilitator Superfamily?
Maltose Symporter in Yeast (aka) permease.
What is the function of Maltose Symporter, and how does it achieve this?
Accumulates maltose against its concentration gradient by symporting with high concentration of H+ ions.
What is the action of FCCP?
Makes the hydrogen concentration on either side of the membrane equal.
What type of molecule is FCCP, and how does it alternate between scores?
FCCP is a weak acid. In protonated form, it is hydrophobic and can diffuse through the membrane. In ionised form, is hydrophilic can't move through membrane.
How does this regulate proton concentration?
Protonated form inside: Less acidic. Dissociates to produce more H+, until equilbrium is reached.

Ionized form outside: Takes up protons until equilbirium is reached.

If these is deficit on inside, protonated form can just diffuse through membrane.
What effect does FCCP have on maltose transport?
It stops it by stopping symport-action.
In what conditions is the lac operon activated?
Absence of glucose and presence of lactose.
What does the gene LacY code for?
A channel which allows lactose to enter the cell.
What does the gene LacZ code for?
β-Galactosidase, which catalyzes the hydrolysis of lactose to glucose and galactose.
What type of pump is a Lactose Permease?
Symporter.
What are the two molecules that bind to the lactose permease protein?
Hydrogen and lactose.
When the two molecules have bound, what happens to the lactose permease and the bound molecules?
It everts to the inside of the cell, and the molecules unbind.
After the molecules have unbound, what happens?
Eversion occurs again.
What is the structure of the lactose permease protein?
12 helices which are split into 2 six helix domains.
What is the mechanism that allows for lactose permease function?
When a hydrogen is unbound to a Glutamate group, the glutamate is hydrophobic and so favours arginine, which is on the other side of the protein and is also hydrophobic.

When hydrogen binds, the glutamate is hydrophilic, meaning it's repelled by the arginine, and the protein everts.
How many Glutamates are present in lactose permease, and in which section are they (there are 3 sections)?
Two, both in the right section, one facing out and one facing in.
What does the outer glutamate do?
Lactose binding and proton transport.
What does the inner glutamate do?
Proton translocation. Does not bind a sugar.
What does the arginine do?
Lactose binding but not proton transfer.
What is the first step of lactose permease action?
H+ enters and binds to outward glutamic acid, making it neutral and hydrophobic. The residue is buried into a hydrophobic pit.
What is the second step of lactose permease action?
Sugar enters. The buried glutamate is forced out of the pit and interacts with the sugar. This is a hydrophilic environment, and H+ unbinds and binds to histidine. Arginine and Glutamate form a salt bridge.
What is the third step of lactose permease action?
The inward facing E is now facing the hydrophobic pocket, meaning it must get protonated.
What is the fourth step of lactose permease action?
The sugar detaches from the lactose permease. This causes the unward conformation to become unstable. The H+ unbinds from inward E, making it a hydrophilic residue facing a hydrophobic pocket.
What is the fifth step of lactose permease action?
Outward conformation is adopted due to unfavourable E.
What would happen if H+ concentration were equal on the 2 sides of the membrane?
The lactose permease would randomly flip between the two sides.