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BIOL 115 Flashcards

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1
Q

What is human serum albumin?

A

It is the major protein present in blood plasma (40g/L) (total protein content of blood is 70 g/L)

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2
Q

What is the structure of serum albumin?

A

Mr of 66500 and pI of 5.67

Entirely alpha-helical in content

a single polypeptide chain with 585 amino acids and 17 intra-chain disulfide bonds

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3
Q

What is unusual about the animo acid sequence of albumin?

A

it has an unusually high percentage of Cys (amino acid responsible for disulfide bonds)

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4
Q

What is alumins role in drug transport?

A

A number of hormones and drugs compete for a spot to bind on albumen which is important as small molecules not transported on proteins may be excreted in urine.

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5
Q

What is albumins role in lipid transport?

A

Albumin contains multiple binding sites for long-chain fatty acids or small heterocyclic or aromatic carboxylic acids (as inside the molecule is hydrophobic)

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6
Q

What is evans blue?

A

A molecule with high affinity for serum albumin which is easily detected via emission sectroscopy.

It was also used to determine how much blood was in a person by seeing how diluted it became when a known ammount was added.

It is however a carcinogen and no longer used.

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7
Q

What is the EF hand?

A

It is a protein motif made of 29 residues and binds to calcium.
It has a helix-loop-helix configuration

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8
Q

What is calmodulin?

A

It is a calcium modulated protein made up of 4 EF hands which after binding to calcium is able to bind to and activated kinases.

When calcium is bound it opens hydrophobic patches allowing it to bind to signalling molecules

It has a vaguely dumbell shape with 2 EF hands on each side

It is very well conserved among vertebrates with minimal changes in the genetic code over a long time.

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9
Q

What enzymes does calmodulin target?

A

Phosphorylase kinase, myosin light chain kinase and Ca2+ ATP-ase are some examples

It targets enzymes with a mixture of basic and hydrophobic amino acids (which can adopt an aplha helix)

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10
Q

What happens to a red blood cell when dissolved in urea?

A

It dissolves into two Alpha-Beta dimers

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11
Q

What is the difference between the binding curves for Haemoglobin and Myoglobin?

A

Myoglobin has a curve wich gets higher % saturation at a lower partial pressure

Haemoglobin has a sigmoidal shape which allows for it to be more cooperative (has a lower affinity for oxygen allowing for easier oxygen delivery)

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12
Q

How do haemoglobin and myoglobin interact?

A

Haemoglobin does a good job of getting oxygen around the capillaries but myoglobin is more responsible for facilitating diffusion of oxygen to areas of demand.

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13
Q

What are the regulators of haemoglobin and what do they do?

A

Regulators are H+, CO2 and 2,3-BPG and in significant quantities makes haemoglobin bind less tightly so they are able to release oxygen effectively.

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14
Q

What is the Bohr effect?

A

The chage of the oxygenn dissociation curve in response increased acidity due to oxygen debt

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15
Q

How would a loack of BPG affect oxygen binding?

A

It would unload very little oxygen in capillaries.

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16
Q

How does temperature effect haemoglovin affinity?

A

Higher affinity at lower temps.

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17
Q

How does the binding of an oxygen to haemoglobin affect the distance between iron atoms in beta chains?

A

The distance decreases (3.99 to 3.34nm)

This also pulls His F8 along with it which in turn pulls along more of the haemoglobin molecule resulting in a change in shape of the molecule

This makes it so that 2,3 BPG can no longer bind as there is not enough space in the central space.

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18
Q

What is responsible for stabilising the T state in haemoglobin?

A

8 electrostatic bonds involving C-terminal amino acids of each subunit (especially penultimate Tyr)

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19
Q

How does the movement of iron in haemoglobin result in the molecule changing shape?

A

As it drags His F8 the EF and FG corner follow resulting in the breaking of the 8 electrostatic bonds and the one alpha-beta subunit rotates 15 degrees

This change in shape is what results in the R state where 2,3-BPG can’t bond

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20
Q

What is retinol and why is it important?

A

One of the active forms of Vitamin A and is used as:

An anti-oxidant
A steroid hormone
A component of night vision

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21
Q

What is the history of enzymes?

A

Yeast + sugar = alcohol (louis pasteur)

Term “enzyme” - wilhelm kuhne

Fermentation in cell-free extracts from yeast therefore biological catalyst (buchner brothers)

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22
Q

What are the functions and uses of biological catalyst?

A

Regulate flow of molecules through metabolic paths
Built cell structures
Break down pathogens (e.g tears)

Used industrially in washing, cheese curdling, stonewashed jean manufacture and fondant centres to prevent crystalisation

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23
Q

How do enzymes speed up protein folding?

A

Prolyl isomerase is responsible for speeing up the swap between cis and trans amino acids to be thermodynamically favourable allowing for it to fold more quickly

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24
Q

What is a katal and what is a International activity unit?

A

A katal is the unit for the amount of an enzyme that converts 1 mol of substrate per second in standard conditions.

IAU (U) is the amount of enzyme that catalyses 1 micromole of substrate per minute under standard assay conditions

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25
Whats the difference between exo/endothermic and exo/endogonic?
thermic - internal energy changes gonic - free energy changes
26
What is Km?
Km is michaelis constant and is where the substrate conc corresponds to half of Vmax (used to determine how effectively a substrate binds to an enzyme) Unit is nmol L^-1
27
Describe induced fit
The enzyme binds to the active site and this triggers a change in the structure of the enzme to the transition state of the substrate reducing the activation energy required.
28
Why are there substrate binding sites next to the catalytic site of the enzyme?
This reduces randomness (entropy) as only one binding point needs to be hit for the enzyme to fit into the catalytic site whereas otherwise it would have to be perfectly orientated for the reaction to happen. This drastically inreases rate of reaction
29
How does induced fit improve specificity?
The open confomation allows substrate binding and the closed conformation reconstitutes catalytic site therefore enzymes only active when the intended substrate is bound.
30
What are cofactors?
They are inorganic molecules that bind near or in an active site to activate an enzyme by extending the range of chemical reactions that can take place. They also assist in substate binding, stabilization and orientation.
31
What are coenzymes?
non-protein organic molecules that bind to a catalytic site to extedn the range of reactions that can take place.
32
Why is enzyme kinetics useful?
It provides a way to describe how enzymes work under different conditions.
33
What is Vmax?
The maximum rate of reaction at a specific enzyme concentration. (Measured in nmolmin^-1) INCLUDE IN COURSEWORK Vmax is only an estimate as you have to extrapolate to infinity to find its value.
34
What are the assumptions and limitations of the michaelis-menten equation?
Assumes no reverse catalysis product inhibition that can affect the reaction.
35
How does the michaelis-menten equation show represent the curve ad low and high concentrations?
Changing the substrate conc at low concentrations will increase Velocity (rate of reaction) more as the numerator changes drastically whereas the denominator changes less Vice versa is also true for high concentrations explaining the curve
36
How can Km be useful?
Enzyme inhibitors require a lower Km than the substrate its trying to inhibit to function properly and the Km can measure this. It also allows the study of isoenzymes to determine which is more efficient at breaking down the same substrate.
37
What is Kcat (turnover number) and why is it useful?
Kcat is a standardised measure of Km which represents the number of substrate molecules broken down per molecule of enzyme per second. This allows the comparison of different enzymes that break down different substrates.
38
What are the mathematical methods to accurately determine Vmax?
Reciprocal plots (lineweaver-burk or Eadie-hoftsee plots)
39
What is an example of irreversible inhibition?
Aspirin (acetylsalicylic acid) Blocks prostaglandin synthesis (by blocking cyclooxygenase) and therefore blocks inflammatory response. or 5-fluorouracil (5-FU) which is a chemo drug that blocks DNA synthesis It inhibits thymidylate synthase which is vital in pyramidine production.
40
What are the pharmacological uses and side effects of aspirin
Normal doses - pain killer/anti-inflammatory Low doe - thrombosis prevention (inhibits COX1 in blood platelets preventing aggregation) Side effects - stomach ulcers due to it preventing acid secretion (COX1)
41
How does irreversible inhibition work with kinetics?
It is difficult to use michaelis menton kintetics to describe it as the active enzyme conc changes which goes against michealis. The Km stays the same but the Vmax decreases.
42
What is competitive inhibition and what does it rely on?
The inhibitor competes directly with the substrate and relies on having a lower Km or higher concentration to compete with the enzyme.
43
What is an example of a competitive inhibitor?
Methotrexate which inhibits Dihydrofilate reductase and stops the production of pyramidine production stopping cell replication.
44
How do competitive inhibitors affect kinetics?
The inhibitor increases the Km in a michealis-menten graph and the Vmax remains the same resulting in a shallower curve. In a lineweaver-burk plot Km increases with the inhibtor because more inhibitor = lower affinity for substrate. The lines cross over at the X axis.
45
46
How do non-competitive inhibtors affect kinetics?
Short answer: Vmax increases, Km doesn't change (essentially less active enzmes) In lineweaver-burk they cross over at Y axis.
47
What are mixed non-competitive inhibitors?
Binds allosterically away from active site and unlike regular non-competitive it does affect how the enzyme binds to the substrate. (increases Km and decreases Vmax)
48
How do mixed non-competitive inhibitors affect kinetics?
Vmax decreases, Km increases Lineweaver-burk crosses above Y axis but before X axis
49
What are uncompetitive inhibitors and how do they work?
The inhibitor only binds to the enzyme substrate complex and not to the enzyme on its own. When it binds it locks the substrate in place.
50
How do uncompetitive enzymes affect kinetics?
Vmax decreases and Km decreases.
51
How do you measure Km for a substrate in a reaction with two substrates.
You need to keep the concentration of one of the substrates in excess and vary the other to find Km with lineweaver-burk. Then repeat with the other substrate.
52
What are the two types of sequential displacement reactions?
A sequential displacement reaction is one where a ternary complex (a complex of three distinct molecules) forms It can be ordered or random Crossing over lineweaver-burk plot (same as mixed non-competitive)
53
53
How can we find the active site of an enzyme?
We can use irreversible inhibitors to identify the catalystic residues which is usually the most reactive and tends to be the active site.
54
What is the chymotrypsin catalytic triad?
The triad of Ser195, His57 and Asp102 which is responsible for the fast breakdown of proteins in digestion. His57 polarises OH group os Ser195 Ser195 becomes a reactive alkoxide ion (nucleophile) Asp102 positions His57 and counters the positive charge If Ser or His is mutated the activity of the enzyme reduces 1million times and 20,000 for Aso
55
What is the peptide hydrolysis path by chymotrypsin?
1) Sustrate binding, proton abstratcion 2. Unstable tetrahedral transition state 3. Acyl enzyme intermediate, release of first peptide 4. Abstraction of proton from water by His57 5. Second tetrahedral transition state 6. Regeneration of active site, release of second peptide
56
What is feedback inhibition?
Where the final product of a reaction pathway behaves as an inhibitor for a previous step enzyme.
57
What is allosteric regulation?
The binding of a molecule at another destinct site on an enzyme to the active site that can postively or negativley affect enzyme activity.
58
What are isoenzymes and give an example?
Different versions of the same enyme with different catalytic properties allowing for the same reaction to have different affects on metabolism in different tissues or to take place under different conditions. An example is lactate dehydrogenase which is an enzyme made up of 4 subunits but any of the subunits can swap between 2 different types for different functional purposes in different tissues.
59
Where does protein phosphorylation take place?
It occurs on -OH groups of Ser, Thr and Tyr
60
What enzymes phosphorylate proteins and which dephosphorylate?
Protein kinases are reponsible for phosphorylation Protien phosphatase removes them
61
What effects does phosphorylation have?
Can induce regulation of enzymes by promoting the binding of other regulatory proteins. Can change the shape and charge of existing enzymes possibly blocking active sites activating and deactivating them.
62
How does thrombin change fibrinogen to fibrin?
It removes fibrinopeptides allowing them to recognise each other and bind together forming a clot
63

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