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Protein informatics > Primary Structure > Flashcards

Primary Structure Flashcards

1
Q

Who organised protein structure into 4 levels and when?

A
  • Linderstrom-Land
  • 1951
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2
Q

What is the primary structure?

A
  • The amino acid sequence - the set of primary chemical bonds
  • sequence of amino acids joined together by peptide bonds
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3
Q

What are almost all proteins composed of?

A

20 alpha amino acids

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4
Q

What is the difference between the canonical set of amino acids and non-canonical amino acids?

A
  • The canonical set of amino acids refers to the 20 amino acids commonly found in proteins.
  • non-canonical amino acids refer to amino acids that are not among the 20 common ones.
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5
Q

How are non-canonical amino acids produced in proteins?

A

Produced by post-translational chemical modification of the canonical amino acids in proteins.

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6
Q

What are peptide bonds?

A

Covalent chemical bonds formed between the amino group of one amino acid and the carboxyl group of another amino acid.

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7
Q

What is the significance of the primary structure of a protein?

A

Determines the overall 3D shape of the protein, which affects its function.

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8
Q

What is the essential structure of every alpha-amino acid?

A

An amine group (NH2) and a carboxyl group (COOH) attached to the same carbon (the alpha carbon).

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9
Q

What is chirality in amino acids?

A

Refers to the fact that they are enantiomorphs, i.e., mirror images exist.

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10
Q

Which form of amino acids is found in naturally forming proteins?

A

L(S) form

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11
Q

Can some enzymes produce D(R) amino acid?

A

yes

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12
Q

What is an enantiomer?

A

A molecule that is a mirror image of another molecule and cannot be superimposed onto it.

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13
Q

What is the difference between L and D amino acids?

A
  • L and D amino acids are mirror images of each other and differ in their spatial arrangement around the alpha carbon.
  • In naturally occurring proteins, only the L form is used.
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14
Q

What is the significance of chirality in amino acids?

A

It affects the 3D structure of proteins, and hence their function.

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15
Q

What is the primary difference between amino acids in terms of their structure?

A

Each amino acid differs only in the identity of the substituent or R sidechain.

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16
Q

If the R sidechain is a hydrogen atom

A

Amino acid is glycine

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17
Q

If the R sidechain is a methyl group

A

Amino acid is alanine

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18
Q

NH2 COOH

Y

H

A

Glycine

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19
Q

NH2 COOH

Y

CH3

A

Alanine

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20
Q

What determines the 3D structure of a protein?

A

The physicochemical properties of the sidechains in amino acids.

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21
Q

How do the sidechains in amino acids affect protein structure?

A

They interact with each other and the environment to determine the folding and stability of 3D structure.

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22
Q

What is the significance of the R sidechain in amino acids?

A

Determines the unique physiochemical properties of each amino acid - determines its role in protein structure and function.

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23
Q

What are some common R-group modifications?

A
  • Phosphorylation
  • Glycosylation (both N-linked and O-linked)
  • Hydroxylation
  • Carboxylation
  • Disulfide bond formation.
24
Q

What is phosphorylation?

A

The addition of a phosphate group to a protein or peptide.

25
Q

What residues are typically phosphorylated?

Common sites of attachment

A

Residues with hydroxyl groups, such as Serine, Threonine, and Tyrosine

26
Q

What are N-linked and O-linked glycosylation?

A

Types of post-translational modifications in which a sugar molecule is attached to an amino acid residue.

R-NH-sugar & R-O-sugar

27
Q

Where does N-linked glycosylation occur?

A

On the nitrogen atom of the side chain of asparagine (Asn) residues

28
Q

Where does O-linked glycosylation occur?

A

On the oxygen atom of the side chain of Serine, Threonine, and modified amino acid residues.

Ser, Thr

29
Q

What is hydroxylation?

A

The addition of a hydroxyl (-OH) group to an amino acid residue.

OH added to R group

30
Q

Where does Hydroxylation occur?

A

On Proline and Lysine residues.

Pro, Lys

31
Q

What is carboxylation?

A

The addition of a carboxyl group (-COOH) to an amino acid residue.

32
Q

Where does Carboxylation occur?

A

Glutamate (Glu) residues.

33
Q

What are disulfide bonds?

A

Covalent bonds between two cysteine residues

34
Q

How are disulfide bonds formed in proteins?

A

By the oxidation of the thiol (-SH) groups

R-SH + R-SH -> R-S-S-R

35
Q

What is the significance of charge in amino acid classification?

A

Determines the formation of salt bridges or ion pairs between amino acids.

36
Q

How does polarity affect amino acid classification?

A

Determines the formation of hydrogen bonds between amino acids.

37
Q

What is the significance of hydrophobicity in amino acid classification?

A

Stabilize the protein core through interactions with other hydrophobic amino acids.

38
Q

How does aromaticity play a role in amino acid classification?

A

Aromatic amino acids can interact with amide or amino acid groups in proteins.

39
Q

Phi (φ)

A

The angle around N-Ca

40
Q

Psi (ψ)

A

Angle around Ca-C’

41
Q

What is a Ramachandran plot?

A

A way to visualize backbone dihedral angles Phi (φ) against Psi (ψ) of amino acid residues.

42
Q

Who developed the Ramachandran plots?

A

G. N. Ramachandran in 1963

43
Q

What do the white regions in a Ramachandran plot indicate?

A

Conformations where atoms in the polypeptide come closer than the sum of their van der Waals radii.
These regions are sterically disallowed for all amino acids except glycine.

Glycine lacks a side chain

44
Q

What do the red regions in a Ramachandran plot indicate?

A

Conformations where there are no steric clashes,
i.e. these are the allowed regions namely the α- helical and β-sheet conformations.

45
Q

What do the yellow regions in a Ramachandran plot indicate?

A
  • The allowed regions if slightly shorter van der Waals radii are used in the calculation,
    i.e. the atoms are allowed to come a little closer together.
  • This brings out an additional region which corresponds to the left-handed α-helix.
46
Q

What type of residues can occasionally adopt the left-handed helix conformation in proteins?

A

Glycine, and sometimes asparagine or aspartate with stabilizing hydrogen bonds.

47
Q

Why do disallowed regions in Ramachandran plots generally occur?

A

steric hindrance between the side chain C methylene group and main chain atoms.

48
Q

Why is glycine able to adopt phi and psi angles in all four quadrants of the Ramachandran plot?

A

Glycine has no side chain
- can adopt any phi and psi angles without steric hindrance.

49
Q

In which regions of a protein do glycine residues frequently occur?

A

In regions of proteins where any other residue would be sterically hindered.

50
Q

What are some chemical forces that help shape protein structure and function?

A
  1. Hydrogen bonds
  2. Hydrophobic interactions
  3. Chemical bonds (ionic and covalent)
  4. Disulphide bridges
  5. Van der Waals forces
51
Q

What is a hydrogen bond?

A
  • The attractive interaction of a hydrogen (H) atom with an electronegative atom from another molecule or chemical group. (nitrogen, oxygen or fluorine)

intermolecularly or intramolecularly

52
Q

How is the Ramachandran plot used in 3D structure prediction validation?

A

Used to show the empirical distribution of data points (amino acids) observed in a single structure (or a dataset of several structures)

53
Q

What is an ionic bond?

A

A chemical bond formed through an electrostatic attraction between two oppositely charged ions

54
Q

What is a covalent bond?

A

A form of chemical bonding that is characterised by the sharing of pairs of electrons between atoms

55
Q

What is a disluphide bond

A

A covalent bond derived by the coupling of two thiol (SH) groups

56
Q

What are Van der Waals forces?

A
  • The sum of attractive or repulsive forces between molecules or between parts of the same molecule
  • Relatively weak compared to normal chemical bonds
57
Q

What are hydrophobic interactions?

A
  • Specific to molecules in aqueous environments and involve the association of non-polar (hydrophobic) segments in an aqueous environment.
  • Two or more hydrophobic groups in aqueous solution will tend to coalesce, thereby causing less disruption to the hydrogen-bonded structure of water.

Protein informatics (7 decks)

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