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Cellular Chemistry > CC1 - How do cells do chemistry? > Flashcards

CC1 - How do cells do chemistry? Flashcards

1
Q

How do enzymes speed up reaction?

A
  1. Stabilizing the transition state
  2. Orientation
  3. Covalent catalysis
  4. Cofactors
  5. Acid-base catalysis
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2
Q

What is the Burgi-Dunitz angle?

A

The perfect angle of attack of a nucleophile at a carbonyl center.

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3
Q

Define kcat.

A

(Catalytic turnover) The rate of product formation when the enzyme is saturated with substrate and therefore reflects the enzyme’s maximum rate.

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4
Q

What is a first order reaction?

A

Has a rate proportional to the concentration of one of the reactants. e.g., radioactive decay.

rate = k[A]

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5
Q

What is a second order reaction?

A

Has a rate proportional to the concentration of two reactants (or the square of a single reactant):

rate = k[A][B]

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6
Q

What is the specificity constant?

A

A measure of how efficiently an enzyme converts substrates into products:

kcat/Km

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7
Q

How can enzymes have rates quicker than the rate of diffusion?

A
  1. Electrostatic steering
  2. Reducing dimensionality of search
  3. Quantum tunnelling
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8
Q

How do enzymes compare to non-biological catalysts?

A

Enzymes:
- faster
- more diverse
- more specific

Non-bio:
- more stable
- cheaper

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9
Q

State the Michaelis-Menten equation.

A

v = Vmax.S
———–
Km + S

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10
Q

Describe a Lineweaver-Burke plot.

A

1 = Km . 1 + 1
– —– — —
v Vmax [S] Vmax

Plot: 1/v vs 1/[S]

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11
Q

Describe an Eadie-Hofstee plot.

A

v = Vmax - v
– ——– ——
[S] Km Km

Plot: v/[S] vs v

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12
Q

Describe a Hanes plot.

A

[S] = Km + [S]
—- —— —–
v Vmax Vmax

Plot: [S]/v vs [S]

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13
Q

Define kcat/Km.

A

kCAT/Km is a second-order rate constant that describes how efficiently an enzyme converts substrate into product

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14
Q

What is a Cleland diagram?

A

A notation for showing when substrates bind to an enzyme and products leave. This is especially useful for multi-substrate enzymes.

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15
Q

What are the 3 types of two-substrate reactions?

A
  1. Ordered - binding of two substrates in a specific order.
  2. Random - binding of two substrates in a random order.
  3. Ping-pong - one substrate binds, modifying the enzyme, before being released. This allows a second substrate to bind the modified enzyme, leading to the formation of a second product and restoration of the original enzyme.
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16
Q

What is the ternary complex constant?

A

Kab, describes the binding affinity and specificity of an enzyme for two substrates simultaneously.

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17
Q

State the ternary complex equations for ordered, random, and ping-pong mechanisms.

A

Ordered: Kab = Kd.Km, where Kd is from the first substrate to bind, and Km is from the second substrate to bind.

Random: Kab = K’a.Kb = K’b.Ka

Ping-pong: Kab = 0 i.e., there’s no ternary complex

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18
Q

How can you distinguish between ternary complexes and ping-pong mechanisms?

A

A LW-B plot of the two-substrate equation.
- If the slope is dependent on [B], it must be ternary.
- Ping-pong mechanisms don’t form ternary complexes, so the slopes will be independent of [B].

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19
Q

How can you distinguish between ordered and random binding mechanisms?

A

Product inhibition patterns.
- Random binding can have competitive inhibition by either product.
- Ordered binding can only have competitive inhibition by the first substrate and last product.

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20
Q

List methods to study enzymes and what they shows us.

A

Rapid mixing and analysis: pre-steady state kinetics and intermediates.
^^ with different ligands: structure
SDM: function of individual residues
Binding analysis: Kd for ligands
Isotopes: test rate-limiting steps
Single molecule studies: heterogeneity, small movements, rare events.
Inhibitors: identify key residues and therapeutics
Computationally: QM/MM

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21
Q

What is burst kinetics?

A

A type of pre-steady state kinetics where the reaction is initiated by the rapid addition of substrate, forming an enzyme-substrate complex (ES). During the burst phase, a large amount of product is formed in a short period of time, which is referred to as the “burst”. This is followed by a slower steady-state phase, where the rate of product formation is slower and more steady.

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22
Q

What is caged ATP and why is it useful?

A

A modified form of ATP that has a photolabile protecting group attached and is removed by light. The use of ‘caged’ ATP allows for precise control over the timing and location of ATP release, which is particularly useful for studying fast biological processes that require rapid ATP hydrolysis, such as muscle contraction and neuronal signaling.

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23
Q

What is QM/MM?

A

Quantum Mechanics/Molecular Mechanics

The quantum mechanics region is typically used to model the most chemically active parts of the system, such as the active site of an enzyme or a reaction center in a protein. The molecular mechanics region is used to model the less reactive regions, such as the solvent or protein matrix.

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24
Q

What are metal ions used for in vitro?

A
  1. Mechanical e.g., bone, tooth, shell
  2. Signaling e.g., calcium influxes
  3. Gas coordination
  4. Cofactors in catalysis
25
Q

How does abundance differ from bioavailability?

A

Abundance: the amount of something
Bioavailability: the ability to metabolize something

26
Q

What is the chelate effect?

A

The chelate effect is a phenomenon observed in coordination chemistry, which describes the enhanced stability of a metal ion complex that is formed when a ligand binds to the metal ion at multiple sites.

In chelation, a ligand contains two or more donor groups, which can simultaneously bind to a metal ion to form a chelate complex. The chelate complex is typically more stable than a comparable complex with a non-chelating ligand that binds at the same number of sites. This is because the chelating ligand can exert a greater control over the geometry and electronic properties of the metal ion, resulting in a more stable complex.

27
Q

What is the Irving-Williams series?

A

The Irving-Williams series, also known as the stability series, is a series of metal ions arranged in order of their relative stability in aqueous solutions.

28
Q

Why are magnesium ions substituted in XRC?

A

They’re harder to detect due to their lower electron density, and so are substituted for manganese ions.

29
Q

What is PIXE?

A

Particle-Induced X-ray Emission - identifies material composition.

When a high-energy proton strikes an atom in the sample, it can knock out one or more electrons from the inner shells of the atom. This creates an electron vacancy, which is filled by an electron from an outer shell, and results in the emission of X-rays with characteristic energies. By measuring the energies of the emitted X-rays, the elemental composition of the sample can be determined.

30
Q

What is extended x-ray absorption fine structure (EXAFS)?

A

Extended X-ray Absorption Fine Structure (EXAFS) is a spectroscopic technique used to determine the local atomic structure around a particular element in a material. It is based on the analysis of the absorption of X-rays by the material as a function of energy.

31
Q

What is quench flow rapid reaction?

A

Quench flow rapid reaction uses stopped-flow techniques but the reaction is stopped by quenching the mixture with a solution that stops the chemical reaction. Only 1 time point obtained per experiment.

32
Q

What is the difference between a transition state and an intermediate?

A

While both transition states and intermediates play critical roles in chemical reactions, a transition state is a high-energy, fleeting species that represents the highest point on the reaction pathway, whereas an intermediate is a relatively stable species that exists between the reactants and products, and is formed as a step in the reaction pathway.

33
Q

What are the two classes of enzyme inhibitors? Give examples of each.

A

Reversible e.g., competitive, non-competitive, un-competitive, including TS analogues.

Irreversible e.g., active site labeling, affinity labels, mechanism-directed inhibitors.

34
Q

What are residue-specific irreversible inhibitors?

A

Residue-specific irreversible inhibitors are a type of enzyme inhibitor that covalently modifies the active site of an enzyme, rendering it inactive. These inhibitors are designed to target a specific amino acid residue in the active site of the enzyme, thereby selectively inhibiting its activity.

35
Q

What are the advantages and disadvantages of photoaffinity labels?

A

Pros:
- not reactive until in the correct location
- irreversible, so easy isolation

Cons:
- UV light can damage proteins or the cell
- UV can’t penetrate in living organisms

36
Q

What are mechanism-directed inactivators? Give an example of one and its therapeutic use.

A

(Suicide inhibitors) Class of enzyme inhibitors that selectively target and irreversibly inactivate a specific enzyme or class of enzymes by covalently modifying the enzyme’s active site or an adjacent binding site.
e.g., deprenyl is a monoamine oxidase inhibitor that controls symptoms and slows progression of Parkinson’s disease.

37
Q

Describe QuikChange SDM.

A
  1. Use PCR with mutagenic primers to create the mutant DNA.
  2. Digest the parently methylated and hemimethylated strand.
  3. Transform mutated molecules into competent cells for nick repair.
38
Q

What is artificial amino acid mutagenesis?

A

A tool for protein engineering that allows for incorporation of artificial amino acids to enhance protein properties and functions.

39
Q

What are the pharmacokinetic properties?

A

Absorption
Distribution
Metabolism
Excretion

40
Q

What is Lipinski’s rule of 5?

A

No more than 5 H-bond donors
No more than 10 H-bond acceptors
Molecular weight <500 Da
LogP < 5

41
Q

What is a transition metal?

A

An element whose atom or ion has an incomplete d sub-level.

42
Q

Describe cytochrome P450.

A

A family of enzymes found in most organisms. Cytochrome P450 enzymes are named for the characteristic absorbance peak of their heme iron center at 450 nm in the reduced state.

The primary function of CYP450 enzymes is to catalyze the oxidation of organic compounds using molecular oxygen, resulting in the formation of a hydroxylated metabolite. This oxidation reaction involves the transfer of electrons from NADPH to the cytochrome P450 enzyme, which activates the heme iron center and facilitates the transfer of an oxygen molecule to the substrate.

43
Q

How is crystal field theory related to d-orbitals?

A

It describes how degeneracy of electron d-orbitals is broken by surrounding charge of coordinating ligands. The crystal field splitting energy depends on the orientation and strength of the ligands, giving either a high or low energy state.

44
Q

What is the role of ferritin and transferrin?

A

Ferritin: iron storage
Transferrin: transports iron in the blood

45
Q

What is the Fenton reaction?

A

A chemical reaction that can occur in cells, converting hydrogen peroxide into ROS in the presence of free iron ions.
This can occur when antibiotic treatments destabilize FeS centers of iron storage molecules.

46
Q

What is ferroptosis?

A

Ferroptosis is a type of programmed cell death that is characterized by the iron-dependent accumulation of lipid peroxides, which can lead to the destruction of cellular membranes and ultimately cell death.

47
Q

Why is seeding oceans with iron thought to be a good idea?

A

Iron is a limiting nutrient for phytoplankton growth, which are photosynthetic organisms that form the base of the oceanic food chain and are responsible for a significant portion of global carbon fixation. By adding iron to iron-deficient regions of the ocean, it is thought that phytoplankton growth could be stimulated, resulting in increased carbon dioxide uptake through photosynthesis. As the phytoplankton die and sink to the ocean floor, they could sequester the carbon they absorbed from the atmosphere for thousands of years, effectively removing it from the atmosphere.

48
Q

Why is animal feed not ideal?

A

The seeds contain phytic acid - an anti-nutrient that impairs absorption of calcium, iron, and zinc.

49
Q

Why is zinc a useful ion in biological system?

A

High charge density
Strong Lewis acid (electron acceptor)
Not redox active (binds to DNA proteins so this is preferred)
Strong binding to N and S ligands
Rapid ligand exchange

It has important roles in protein folding, assembly and catalysis.

50
Q

What are zinc reporters?

A

Zinc reporters are genetically encoded biosensors that detect changes in the concentration of zinc ions (Zn2+) in living cells. Zinc reporters typically consist of a protein domain that specifically binds to zinc ions, such as the zinc finger motif, fused to a reporter protein that produces a signal in response to zinc binding.

51
Q

What is eutrophication and what causes it?

A

The presence of high phytic acid levels in animal feed requires supplementation of inorganic phosphate in stock diet. Excretion of inorganic phosphate then leads to eutrophication due to bodies of water becoming overly enriched with nutrients. This causes excessive algae growth that results in an imbalance of the ecosystem and potential to harm aquatic life.

52
Q

What are the challenges posed by phytase addition into feedstock, and how can these be overcome?

A

The feed is steamed to kill off Salmonella, but this inactivates a lot of the phytase added and it’s too expensive to add after steaming. Engineering approaches are therefore being used to stabilize the enzyme during heat treatment.

53
Q

How can proteins tune metal ion behaviour?

A
  • Formation of coordination complexes with protein residues to change reactivity and stability of the metal.
  • Electrostatic interactions with charged residues.
  • Controlling the shape and orientation of ligands around the metal ion.
54
Q

How are catalytic antibodies generated?

A

Catalytic antibodies are generated through a process called immunization, in which animals are immunized with a small molecule or hapten that is chemically linked to a larger carrier protein. The animal’s immune system produces antibodies that can recognize and bind to the hapten, and through a process of affinity maturation, a subset of these antibodies can develop catalytic activity.

55
Q

What is a bait and switch immunization?

A

Bait and switch immunization is a technique used in immunology to generate antibodies that can recognize specific targets with high affinity and specificity.
First, the bait molecule is chemically linked to the target molecule, creating a “bait-target” complex. The immune system of the animal is then exposed to the bait-target complex, leading to the production of antibodies that recognize the complex.
In the second step, the bait molecule is removed, leaving only the target molecule as the immunogen. The antibodies produced in response to the bait-target complex are now specific for the target molecule, and can be isolated and purified for use in a variety of applications, such as diagnostic assays, therapeutic agents, and research tools.

56
Q

What is reactive immunisation?

A

In this technique, a reactive chemical species is chemically modified to make it immunogenic, and then used as the immunogen to generate antibodies in an animal, such as a mouse or rabbit.

57
Q

What is in vitro compartmentalization?

A

The IVC method involves creating small droplets or vesicles, typically a few micrometers in size, which can be used as separate reaction chambers to perform biochemical reactions, including transcription, translation, and enzymatic reactions.
This allows for the screening of large libraries of molecules, such as enzymes or antibodies, in a high-throughput manner, as well as the study of single molecules at the single-cell level.

58
Q

What is phage-assisted continuous evolution (PACE)?

A

Phage-assisted continuous evolution (PACE) is a technique that uses bacteriophages to rapidly evolve biomolecules, such as enzymes or antibodies, for desired functions or properties.

59
Q

What are the pros and cons of de novo design?

A

Pros:
- start with no existing enzyme or substrate analogues
- applicable to challenging enzymes e.g., membrane-bound
- no experimental limit
- publicly available software

Cons:
- needs a lot of computer time
- still needs wet lab optimization
- harder is there’s substantial conformational changes

Cellular Chemistry (7 decks)

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