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Protein Chemistry > Amino acids and peptide bond > Flashcards

Amino acids and peptide bond Flashcards

1
Q

What is the isoelectric point?

A

The pH where a protein or amino acid is uncharged. This is also the least stable pH for a protein

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2
Q

What is the bond length of the C-N bond?

A

The peptide bond is 1,32 Å

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3
Q

What issue can many cysteines in a protein cause?

A

Two cysteines can form disulfide bridges, and if there are multiple cysteines they can cause misfolding.

There can also be problems during purification and characterisation.

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4
Q

Amino acid: C

Name, tre letter code and general category

A

Cysteine
Cys

Polar, uncharged sidechain

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5
Q

Amino acid: G

Name, tre letter code and general category

A

Glycine
Gly

Polar uncharged sidechain

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6
Q

Where are glycine generally found?

A

In turns and regions of conformational flexibility

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7
Q

What is the difference between cysteine and cystine?

A

Cysteine: Reduced - has SH groups
Cystine: Oxidized - has S-groups

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8
Q

What is Ellman’s regent used for?

A

It is used for determining the amount of free thiols in proteins. The regent forms a bond with thiol and releases a thiolate ion which can de detected using absorbance at 412 nm.

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9
Q

Amino acid: W

Name, tre letter code and general category

A

Tryptophan
Trp

Nonpolar aromatic sidechain

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10
Q

Which three amino acids absorbs light and where is the light generally measured?

A

W, Y and F at 280 nm

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11
Q

What measures the total accessible surface area and what does a low value indicate?

A

ASA, measures how accessible the residues are from the outside.
The lower value the more burried the residue is in the core of the protein.

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12
Q

Amino acid: K

Name, tre letter code and general category

A

Lysine
Lys

Positively charged sidechain - pka ca 10.5

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13
Q

Amino acid: A

Name, tre letter code and general category

A

Alanine
Ala

Nonpolar, uncharged sidechain

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14
Q

Amino acid: V

Name, tre letter code and general category

A

Valine
Val

Nonpolar uncharged

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15
Q

Amino acid: L

Name, tre letter code and general category

A

Leucine
Leu

Nonpolar uncharged

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16
Q

Amino acid: M

Name, tre letter code and general category

A

Methionine
Met

Nonpolar uncharged

17
Q

Amino acid: I

Name, tre letter code and general category

A

Isoleucine
Ile

Nonpolar uncharged

18
Q

Amino acid: P

Name, tre letter code and general category

A

Proline
Pro

Nonpolar uncharged

19
Q

Where are nonpolar uncharged residues generally found?

A

In the interior of proteins

20
Q

Amino acid: Y

Name, tre letter code and general category

A

Tyrosine
Tyr

Polar aromatic residue

21
Q

Amino acid: F

Name, tre letter code and general category

A

Phenylalanine
Phe

Nonpolar aromatic sidechain

22
Q

Where are the nonpolar aromatic residues found?

A

In the interior of proteins

23
Q

Where are polar aromatic residues found?

A

On the surface or in the interior of the protein

24
Q

Amino acid: S

Name, tre letter code and general category

A

Serine
Ser

Polar, uncharged

25
Q

Amino acid: T

Name, tre letter code and general category

A

Threonine
Thr

Polar uncharged

26
Q

Amino acid: N

Name, tre letter code and general category

A

Asparagine
Asn

Polar uncharged

27
Q

Amino acid: Q

Name, tre letter code and general category

A

Glutamine
Gln

Polar uncharged

28
Q

Where are polar uncharged residues generally found?

A

On the exterior of proteins

29
Q

Amino acid: R

Name, tre letter code and general category

A

Arginine
Arg

Positively charged
pKa ca 12

30
Q

Amino acid: H

Name, tre letter code and general category

A

Histidine
His

Positively charged
pKa ca 6

31
Q

Amino acid: D

Name, tre letter code and general category

A

Aspartate
Asp

Negatively charged
pKa ca 4

32
Q

Amino acid: E

Name, tre letter code and general category

A

Glutamate
Glu

Negatively charged
pKa ca 4,5

33
Q

Where are charged residues generally found?

A

Exterior of proteins, but can be found in the interior if combined with a oppositely charged aa to form saltbridge

Protein Chemistry (10 decks)

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