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4BBY1013 > Protein Structure and Enzymes > Flashcards

Protein Structure and Enzymes Flashcards

L5 L6 L11 L12

1
Q

How can you distinguish between L and D Isomers of amino acids?

A

By imagining in the 3D plane that youre holding the hydrogen of the α carbon, the groups should be able to be read clockwise to spell CO-R-N (carboxylic acid, residual group and nitrogen).

The L isomer will spell CO-R-N whereas the D isomer will no.

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2
Q

Is there rotation at the amide plane for dipeptides?

Why?

A

There is no rotation at the amide plane for dipeptides.

This is because the electrons from the C=O of the amide bond will slightly dissociate to for a partial double bond, which allows for no rotation.

https://upload.wikimedia.org/wikipedia/commons/0/08/Amide_Bond_Resonance.jpg

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3
Q

What is the length and enthalpy of a hydrogen bond?

A

Length of 0.28 nm

ΔH is 3kcal

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4
Q

Why are α-helices right handed?

A

The amino acids are L isomers which is why the α-helices are right handed.

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5
Q

Describe the collagen fibres.

A

Left handed helices wound up in a right handed super-helix.

Made of proline (X), hydroxy-proline (Y) and glycine amino acids. Composition is -(Gly)-(mainly X)-(mainly Y)-(Gly)- and so on.

Makes up 30% of all proteins in the body.

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6
Q

How is the polypeptide chain configured in the ribosome?

Trans or cis?

A

Trans configuration as opposed to the cis which means residual groups are on opposite sides for adjacent amino acids.

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7
Q

Where are the phi and psi bonds?

A

Psi (ψ) is on the carboxyl teminus side of the α carbon.

Phi (φ) is on the amine terminus side of the α carbon.

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8
Q

How many amino acids are there per α helix rotation?

A

3.6 amino acids per rotation.

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9
Q

What is a way to differentiate between parallel and anti-parallel β-pleated sheets?

A

The easiest way to differentiate if its not already obvious, the hydrogen bonds for anti-parallel in perpendicular and for the parallel, the hydrogen bond is not perpendicular.

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10
Q

What is the difference between type 1 and type 2 β-turns?

A

For type 1, C=O is above N-H bond.

For type 2, N-H is above C-O bond.

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11
Q

What is the Ramachandran plots purpose?

A

The Ramachandran plot provides a way to view the distribution of angles in a protein structure. It also provides an overview of excluded regions that show which rotations of the polypeptide are not allowed due to collisions between atoms.

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12
Q

What is the Rossman Fold?

A

http://wiki.cathdb.info/wiki-beta/lib/exe/fetch.php?w=900&media=glossary:rossmann_fold.gif

Its a super secondary structure.

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13
Q

What is the Beta-Sandwich?

A

https://upload.wikimedia.org/wikipedia/commons/7/70/Protein_TNC_PDB_1ten.png

Its a super secondary structure.

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14
Q

What is the Beta-Barrel?

A

https://upload.wikimedia.org/wikipedia/commons/f/fb/Sucrose_porin_1a0s.png

Its a super secondary structure.

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15
Q

What is special about the membrane protein’s structure?

A

Tertiary structure is not normal.
The trans-membrane region is hydrophobic and the outside is hydrophilic in comparison to to how normally, the tertiary structure has hydrophobic region in the middle and the hydrophilic region encapsulating the hydrophobic region.

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16
Q

What is d/2?

A

Van der Waals radius of atoms

17
Q

Definition of enzymes.

A

‘Biological catalysts which speed up rate of metabolic process without affecting final equilibrium between reactants and products.’

18
Q

What defines substrate specificity?

A

The shape of the active site on the enzyme.

19
Q

What do oxidoreductases do?

A

Adds O2 or removes 2H in order to reduce or oxidise substrates

20
Q

What do transferases do?

A

Transfers functional groups of substrates

21
Q

What do hydrolases do?

A

Splits substrate by adding H2O

22
Q

What do lyases do?

A

Adds groups to C=C bonds of substrates

23
Q

What do isomerases do?

A

Isomerisation reactions of substrates

24
Q

What do ligases do?

A

Forms C-C bonds or C-N with ATP cleavage

25
Q

Why are enzymes sensitive to environmental changes?

A

Structure of the enzymes is stabalised by many weak bonds which are easily broken if temperature is too high. Change in structure affects active site.

Additionally pH changes will affect the amino acids which are charged, changing the shape of the the enzyme, affecting the active site.

26
Q

What are isoenzymes?

A

Enzymes which catalyse the same reaction but what different structures.

27
Q

What are the metal ions in certain enzymes called?

A

Cofactors

28
Q

What shape is the reaction rate of enzymes?

A

Hyperbolic shape

29
Q

Why is the initial rate of reactions used to measure the rate of reaction for enzyme catalysis?

A

At low substrate concentration, the rate of reaction is directly proportional to substrate concentration. At high substrate concentration, rate of reaction is independent of substrate concentration because the product gets in the way on substrate binding to active site. (partial product inhibition)

30
Q

Steps of chymotrypsin catalysis.

A

1) Polypeptide substrate binds (noncovalently) with side chains of hydrophobic pocket
2) H+ of Ser is transferred to His in enzyme
3) H+ is transferred to polypeptide, where its cleaved into two. N-terminal polypeptide is free and the C-terminal polypeptide is bound to Ser via acyl linkage
4) Water molecule binds to enzyme and transfers its proton to His and its -OH to the remaining substrate fragment
5) Remaining substrate fragment is released by the acyl bond being cleaved. The proton is transferred from His to Ser, reverting enzyme to its initial state.

31
Q

What is the Michaelis-Menton reaction model?

A

https://depts.washington.edu/wmatkins/kinetics/mm1.gif

Measures the relationship between reaction velocity and substrate concentration

32
Q

What is the Lineweaver-Burk plot?

A

http://static.flickr.com/27/100094824_3ee9624d34.jpg

Measures the relationship between the inverse of reaction velocity and the inverse of substrate concentration.

33
Q

What is the Michaelis-Menton equation?

A

http://3.bp.blogspot.com/-s-Ov4poMFeA/VAw7KRtwKYI/AAAAAAAATzc/8lRu-jm6wQQ/s1600/Michaelis%2B-Menten%2Bequation.png

34
Q

What is the Lineweaver-Burk equation?

A

https://www.letstalkacademy.com/ckeditor/plugins/imageuploader/uploads/57844a67.jpg

35
Q

What three asumptions are made for the Michaelis-Menton reaction model?

A

Enzyme concentration is very small in comparison to amount of substrate.
Enzyme-substrate complex concentration does not change over time.
Product concentration is negligible at low substrate concentration (so initial velocity can be used)

36
Q

What are the enzyme inhibitors and what do they do?

A

Competitive inhibitors, which block the active site.

Non-competitive inhibitors which interfere in some way with the catalytic mechanism, does not bind to active site.

37
Q

What is chymotrypsin’s active site?

A

There is Ser (195), His (57) and Asp (102)

The number refers to the amino acids number in the chain.

4BBY1013 (6 decks)

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