Proteins and enzymes, Section 1, AAs (Dr. Taylorson) Flashcards Preview

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Flashcards in Proteins and enzymes, Section 1, AAs (Dr. Taylorson) Deck (27)
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1
Q

What are the four major roles of proteins ?

A

Binding, catalysis, switching, structural.

Always a binding event at some point.

2
Q

Is the amide bond formed by hydration or condensation ?

A

Condensation. Hydrolysis breaks this bond.

3
Q

What are the two general AA forms ?

Which one is found in nature ?

A

The nonionic and the zwitterion for.

In nature, AAs always exist in the ionic form (zwitterion at physiological pH).

4
Q

What are the pKas (roughly) of the amino and carboxyl group ?

A

pKa (COO-/COOH) = 2.2

pKa (NH2/NH3+) = 9.4

5
Q

Which AAs have aliphatic (non polar and hydrophobic and non aromatic) R groups ?

A

Gly, Ala, Val, Leu, Iso.

6
Q

Which AAs has 4 possible stereoisomers ?

A

Isoleucine and threonine: because the alpha and beta carbons are asymmetric, the molecules have 2 chiral centers.

7
Q

Which is the most flexible AA ?

A

Glycine.

8
Q

Which AAs have negatively charged R groups at pH = 7 ?

A

Asp and glu (pKa of R group = 4.5)

These exist as the conjugate bases.

9
Q

Which AAs have positively charged R groups at pH = 7 ?

A
Lys and Arg (pKa of R group = 12.5)
Histidine sometimes (pKa of R group = 7.58)
These exist as the conjugate acids.
10
Q

Which AA can act as either an acid or a base ?

Why is this important ?

A

Histidine, because its side chain has a pKa around 7.
Thus, histidine is very important in acid/base catalysis (important role in many enzymes).
It also forms complexes with zinc ions in proteins, which is important for both structure and mechanism.

11
Q

Which AAs has a blocked thiol group ?

A

Methionine, whioch contain a non polar methyl thioether, which is very hydrophobic. This AA therefore cannot from disulfide bonds.

12
Q

Which AA can form a disulfide bond ?

A

Cysteine: although it’s side chain is quite hydrophobic, it is polarisable and can become a deprotonated thiolate ion and form disulfide bridges.

13
Q

What is cystine ?

Why are disulfide bonds important ?

A

2 cysteines likes by a disulfide bond.

These are important because they are the only covalent bonds stabilizing 2ary and 3ary structure of proteins.

14
Q

Which amino acids are hydrophilic ?

A

Serine, threonine, glutamine, glutamate, asparagine, histidine and tyrosine, arginine, aspartate.

15
Q

Which amino acids are hydrophobic ?

A

Alanine, isoleucine, leucine, phenylalanine, valine, proline, glycine.

16
Q

Which AAs have polar (but not charged) side chains ?

A

Serine, threonine, cysteine, asparagine, glutamine, and tyrosine.

17
Q

Which AAs are aromatic and why is this important ?

A

Phe, Tyr and Trp are aromatic and can absorb UC light at 280nm. Proteins have an optical density at 280nm because of these side chains.
Tyr is hydrophilic because it has an hydroxyl group.

18
Q

Why is proline a unique AA ?

A

Proline has an alkyl chain rather than a H atom as the second substituent on nitrogen. It cannot form a hydrogen bond with a carboxyl further down the chain and is thus called a helix breaker.
For amide bonds involving proline, the cis form (2 alpha carbons closer) is not dramatically thermodynamically disadvantaged.
In proteins, about 10% of amide bonds involving proline are cis.

19
Q

Where are hydrophobic AAs found in proteins ?

A

Usually sequestered away from the solvent towards the center of the proteins molecules. This provides one of the major driving forces for protein folding.

20
Q

Where are hydrophilic residues found ?

A

Usually outside of the proteins since they tend to interact with the solvent more easily via hydrogen bonding.

21
Q

What are the two possible configuration of the peptide bond ?
Which is favored ?

A

Cis and trans. The trans form is favored (to avoid steric hinderances), except where proline is involved.

22
Q

How are the atoms involved in the peptide bond arranged in space ?
What determines the shape of a polypeptide ?

A

They lie in a plane, because the peptide bound has partial double bond character.
The Phi torsion angle between C-N and the Psi torsion angle between C-C.

23
Q

How can the polypepide assume a repeated structure ?

A

If all Phi and Psi angles are the same.

24
Q

How are alpha helices and beta sheets formed ?

A

With certain combination of Phi and Psi angles.

25
Q

What do these angles show about the peptide bond ?

A

It exhibits flexibility.

26
Q

What is the Ramachandran plot ?

A

The physical size of atoms and groups limited the possible Phi and Psi tosrion angles that the polypeptide can adopt without causing protruding R group to bump into each other. The Ramachandran plot, originally developed in 1963 by G. N. Ramachandran, is a way to visualize energetically allowed regions for backbone dihedral angles ψ (Psi) against φ (Phi) of amino acid residues in protein structure.

27
Q

Which of the L-isomer or the D-isomer of AAs predominates in nature ?

A

The L-isomer.