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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

glutathione reductase

A

reduces glutathione once it has been oxidized (uses NADH)

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2
Q

prolyl isomerase

A

isomerises proline into cis form when it is made in trans

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3
Q

6 classes of enzymes

A
  1. hydrolases
  2. lyases
  3. ligases
  4. oxidoreductases
  5. isomerases
  6. transferases
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4
Q

Intramolecular forces

A

Covalent Bonds holding structures together

  • much stronger than electrostatic interactions
  • still move due to vibrational energy
  • can still move in the following ways:
    • rotational
    • stretching (symmetrical or asymmetrical)
    • rocking
    • scissoring

Newman projections relating the relative energies of different rotational positions of atoms

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5
Q

Intermolecular forces

A

Weak and short-range electrostatic interactions

  • hydrogen bonding
  • dipoles (induced (dipole-dipole, ion), permanent
  • ionic
  • hydrophobic exclusion

Inversely related to the thermal energy within a system

Force can be calculated using Coulomb’s law

  • proportional to the two charges
  • inversely proportional to the radius squared and to the dielectric constant

Though they are individually weak, they have cumulative effects that can end up being very strong.

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6
Q

Permittivity

A

relates to the polarizability of a medium. The extent to which the medium attenuates the force between two charges or dampens coulombic interactions

Common dielectric constants to be aware of
Vacuum - 1
Water - 80
Benzene - 4
Protein interior - 4
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7
Q

Factors that affect dielectric constant

A

polarizability of the medium and pressure

more molecules/unit volume increases the dielectric constant

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8
Q

van der waals

A
  • act at the point of contact

- attractive forces that result due to induced dipoles caused by repulsion of outer electron clouds

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9
Q

van der waals radius

A

data shows that the repulsion between 2 molecules actually starts before the calculated radius based on the outer electron orbitals. This is the van der waals radius. If enough pressure is exerted on two molecules to overcome the van der waals radius, a chemical reaction occurs.
- started as a “smudge factor” when dealing with the gas laws after they started messing with super high temperatures and saw that their calculations were off. They assumed when writing the gas laws that the molecules did not interact at all.

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10
Q

london-jones thought experiment

A

has to do with the van der waals radius. There is a point where the energy is negative on the graph, which is where they are most attracted to one another. This happens just before you hit the van der waals radius.

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11
Q

first law of thermodynamics

A

conservation of energy

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12
Q

second law of thermodynamics

A

the total entropy of the universe (both the system and its surroundings) must increase in every spontaneous process.

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13
Q

third law of thermodynamics

A

the entropy of a perfect crystalline structure is 0

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14
Q

different types of dipole interactions

A

dipole-dipole
dipole-induced dipole
ion-dipole
- this interaction is what causes the shells of hydration to form around an ion in solution.
- the first shell of hydration is the strongest because the distance between it and the ion is shortest.
- areas of hydration are also found around protein surfaces. They may extend into solution depending on how strong the charge at that point is.

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15
Q

what is required for hydrogen bonding

A

donor - hydrogen bound to electronegative atom

acceptor - lone pair electrons

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16
Q

structure of water

A
  • water is sp3 hybridized
  • has a dipole which goes towards the electronegative oxygen atom
  • tetrahedral structure
  • strongest bond occurs between a dimer of water molecules
  • look at actual numbers and determine whether or not you get them correct
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17
Q

flicker clusters

A

a water molecule can actually form 4 hydrogen bonds, which is behind its special properties. Flicker clusters are areas of increased structure of water molecules within a disordered bulk solution. They are short-lived

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18
Q

ice structures

A
  • hexagonal structures with vacuum in the middle that form when the energy of the hydrogen bonds surpasses the thermal energy of the system
  • there is ambient thermal energy in every system that makes the ice structure constantly melt and reform
  • starts melting on the outside because the hydrogen bonding is less stable along the edges.
  • increasing thermal energy increases the amount of time that molecules spend outside of ideal collinear hydrogen bond formations and causing them to melt.
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19
Q

effect of adding salt and small inert molecule to ice

A

salt melts ice by disrupting the space between the hydrogen bound water molecules due to their large size
small inert molecules stabilize ice structure by filling vacuum (void)

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20
Q

numbers associated with H2O molecules

A

R = 2.976 A, alpha is about 6 degrees, beta is about 57 degrees (tetrahedral angle divided by 2). Dimer dipole moment is 2.6 D.

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21
Q

measurements of water with 4 hydrogen bonds

A

R = 2.82 A, angle between all is 109.47 degrees

22
Q

thymidylate synthase

A

enzyme that converts dUMP into dTMP (thymine precursor)

  • example of induced fit/TS binding
  • medications are used as TS analogs to prevent DNA replication in cancerous cells
23
Q

relationship between Km and binding

A

lower Km correlates with higher affinity because Km is a dissociation constant

24
Q

dihydrofolate reductase

A

the enzyme that converts dihydrofolate into tetrahydrofolate, which is a methyl group shuttle used in the synthesis of dTMP.

  • methotrexate is a T.S. analog for the enzyme, which stops its progress entirely (binds 1000 times for tightly than its actual substrate.
  • aminopterin is a substrate analog, which means that it competes, but it must be added in much larger quantities to make a difference than mexotrexate does.
25
Q

acetoacetate decarboxylase

A

the enzyme that converts acetic acid to acetone using a schiff base intermediate from a lysine side chain in the active site. This poses an engineering problem in that the lysine, which is typically protonated at physiological pH must be deprotonated in order to act as a nucleophile.

26
Q

Human Pancreatic Ribonuclease

A
  • enzyme that breaks down phosphodiester bonds in RNA.
  • Uses general acid/base catalysis with 2 histidines acting as opposite players in the reaction. One histidine acts as a general base to abstract the 2’ hydrogen, making the oxygen a better nucleophile. The oxygen then attacks the phosphate group. The histidine on the opposite side of the active site acts as a general acid and donates its hydrogen, helping to break the bond between the 5’ oxygen and the phosphate.
  • uses water to perform the opposite functions (with the seconds histidine abstracting a hydrogen from water and then the remaining hydroxyl group nucleophilically attacking) to return the enzyme active site to its original state
  • this action would show a bell curve because there are two species acting with opposite ionization.
27
Q

Lysozyme

A
  • example of both induced fit and covalent intermediate catalysis
  • cleaves glycosidic bonds in peptidoglycans of bacterial cell walls between D and E sugars. The first three sugars fit into the active site as well, and then the 4th sugar changes conformation to be an induced fit.
  • the original model for the mechanism of action turned out to be incorrect, which was proven in a variety of ways. One of the clearest ways is that the lactone transition state analog fit the finally proposed mechanism due to its half chair conformation and the carbocation analog did not fit as well.
  • due to induced fit, the enzyme still sped the rate of reaction even without the reactive side chains in the active site.
  • as it turns out, the glutamate donates a hydrogen to break the glycosidic bond and the aspartate nucleophilically attacks the anomeric carbon to create the covalent intermediate. With the help of water in the active site, glutamate removes a proton, leaving a nucleophilic hydroxyl, which attacks the anomeric carbon and returns aspartic acid to its original state.
28
Q

Hemoglobin structure

A

tetramer made of 4 subunits found in RBCs/erythrocytes.
Each subunit is made of globular protein regions comprised of alpha helices.
- heme unit is an iron (2+) bound to 4 nitrogens of porphyrin ring
- iron is also covalently linked to the proximal histidine, which is connected to the F helix of the subunit.
- when oxygen is not bound, a water molecule is weakly bound

29
Q

HbS

A

Glu6Val mutation in beta chains that results in the association of multiple beta subunits. This association creates a chain of hemoglobin that can give RBCs a sickled shape and may cause cell lysis or block block vessels.

30
Q

Hb Philly

A

Tyr35Phe in one of the chains that results in reduced cooperativity

31
Q

Hb Hiroshima

A

His146Pro mutation in beta chain that reduces cooperatively due to loss of Bohr effect

32
Q

Hb Iwate

A 
His87Y mutation (distal histidine) in alpha chains that leads to increased oxidized heme and pseudo cyanosis 
- presumably because the distal histidine sterically prevents oxygen from binding straight on
33
Q

Hb Saskatoon

A

His63Y (distal histidine) mutation in beta chain that leads to oxidized heme and pseudocyanosis

34
Q

Hemoglobin subunit alpha helices

A

A, B, C, E, F, G, H
- D was lost at some point during evolution.
alpha subunit has 141 residues, beta subunit has 146 residues

35
Q

how much does Hb increase blood oxygen capacity

A

87-fold

36
Q

what function does NO play

A

vasodilator

37
Q

what other functions does hemoglobin sometimes play?

A

iron metabolism and antioxidant

38
Q

myoglobin

A

oxygen storage in muscle tissue

39
Q

methemoglobin reductase

A

enzyme that can reduce iron that is spontaneously oxidized (preventing it from binding oxygen)

40
Q

cooperative binding (sequential allosteric cooperatively)

A

approximately 1 A shift in conformation from the deoxyribose to the oxy state. The change in conformation of one subunit prompts the change in conformation of those subunits with which it is touching. This type of cooperativity yields a sigmoidal curve when graphed, while the non-cooperative activity of myoglobin (only one subunit) displays a rectangular hyperbola

41
Q

competition with carbon monoxide

A

CO binds the game group with much greater affinity than oxygen, which also means that it is released MUCH more slowly. When it binds iron, it changes the conformation of the hemoglobin to the R state, but does so much less reversibly than does oxygen. This prevent the hemoglobin from transitioning back to T state and reduces the amount of oxygen being offloaded into the tissues.

42
Q

why does a hyperbaric chamber improve outcomes for those with CO poisoning over just giving 100% oxygen NC?

A

the high pressures of pure oxygen in a hyperbaric chamber allow more to be dissolved in the blood, which makes possible oxygen delivery to the tissues without the need for hemoglobin.

43
Q

why does CO bind more tightly than O2?

A

the carbon is capable of not only the sigma bond which also occurs between oxygen and iron, but is also capable of pi orbital “back bonding” which involves a favorable shift in electron density

44
Q

oxygen dissociation curves

A

percent saturation = pO2/(Kd + pO2) for myoglobin

for hemoglobin, because it is cooperative the equation involves all terms raised to the nth power.

45
Q

p50

A

point at which 50% of hemoglobin is saturated with oxygen.

- lower p50 correlates with higher oxygen affinity (similar to the Km in enzyme kinetics)

46
Q

positive allosteric effectors

A
  • activators

- bind preferentially to the relaxed state

47
Q

negative allosteric effects

A
  • inhibitors

- bind preferentially to inactive state

48
Q

Bohr Effect

A

oxygen affinity is inversely related to the hydrogen ion concentration and CO2.
- pH sensor of hemoglobin protein areas that detect changes in pH and change conformation of the hemoglobin. (His and Asp)

49
Q

how do carbonic anhydrase inhibitors work to decrease altitude sickness?

A
  • altitude sickness is caused when there is not enough partial pressure of oxygen to
50
Q

bisphosphoglycerate mutase

A

rearranges phosphate group from 1,3-bisphosphoglycerate to 2,3-bisphosphoglycerate, a negative allosteric effector of hemoglobin.
(the next step in the normal process would be from 1,3-bisphosphoglycerate to just 3-phosphoglycerate.
- from 2,3-bisphosphoglycerate, the reaction can continue through the activity of 2,3-bisphosphoglycerate phosphatase, which removes the 2 carbon phosphate group

51
Q

glucose-6-phosphate dehydrogenase

A

enzyme that uses glucose-6-phosphate (part of glycolytic cycle) into NADPH for multiple uses, including methemoglobin reductase reducing the spontaneously oxidized iron in heme and the reduction of glutathione by glutathione reductase (used in antioxidant processes (can turn H2O2 into 2 H20s!)

Biochemistry (6 decks)

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