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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
What residues are typically phosphorylated? | Common sites of attachment
Residues with hydroxyl groups, such as Serine, Threonine, and Tyrosine
26
What are N-linked and O-linked glycosylation?
Types of post-translational modifications in which a sugar molecule is attached to an amino acid residue. | R-NH-sugar & R-O-sugar
27
Where does N-linked glycosylation occur?
On the nitrogen atom of the side chain of asparagine (Asn) residues
28
Where does O-linked glycosylation occur?
On the oxygen atom of the side chain of Serine, Threonine, and modified amino acid residues. | Ser, Thr
29
What is hydroxylation?
The addition of a hydroxyl (-OH) group to an amino acid residue. | OH added to R group
30
Where does Hydroxylation occur?
On Proline and Lysine residues. | Pro, Lys
31
What is carboxylation?
The addition of a carboxyl group (-COOH) to an amino acid residue.
32
Where does Carboxylation occur?
Glutamate (Glu) residues.
33
What are disulfide bonds?
Covalent bonds between two cysteine residues
34
How are disulfide bonds formed in proteins?
By the oxidation of the thiol (-SH) groups | R-SH + R-SH -> R-S-S-R
35
What is the significance of charge in amino acid classification?
Determines the formation of salt bridges or ion pairs between amino acids.
36
How does polarity affect amino acid classification?
Determines the formation of hydrogen bonds between amino acids.
37
What is the significance of hydrophobicity in amino acid classification?
Stabilize the protein core through interactions with other hydrophobic amino acids.
38
How does aromaticity play a role in amino acid classification?
Aromatic amino acids can interact with amide or amino acid groups in proteins.
39
Phi (φ)
The angle around N-Ca
40
Psi (ψ)
Angle around Ca-C'
41
What is a Ramachandran plot?
A way to visualize backbone dihedral angles Phi (φ) against Psi (ψ) of amino acid residues.
42
Who developed the Ramachandran plots?
G. N. Ramachandran in 1963
43
What do the white regions in a Ramachandran plot indicate?
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
What do the red regions in a Ramachandran plot indicate?
Conformations where there are no steric clashes, i.e. these are the **allowed regions** namely the α- helical and β-sheet conformations.
45
What do the yellow regions in a Ramachandran plot indicate?
* 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
What type of residues can occasionally adopt the left-handed helix conformation in proteins?
Glycine, and sometimes asparagine or aspartate with stabilizing hydrogen bonds.
47
Why do disallowed regions in Ramachandran plots generally occur?
steric hindrance between the side chain **C methylene group** and **main chain atoms.**
48
Why is glycine able to adopt phi and psi angles in all four quadrants of the Ramachandran plot?
Glycine has no side chain - can adopt any phi and psi angles without steric hindrance.
49
In which regions of a protein do glycine residues frequently occur?
In regions of proteins where any other residue would be sterically hindered.
50
What are some chemical forces that help shape protein structure and function?
1. Hydrogen bonds 2. Hydrophobic interactions 3. Chemical bonds (ionic and covalent) 4. Disulphide bridges 5. Van der Waals forces
51
What is a hydrogen bond?
* 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
How is the Ramachandran plot used in 3D structure prediction validation?
Used to show the **empirical distribution** of data points (amino acids) observed in a single structure (or a dataset of several structures)
53
What is an ionic bond?
A chemical bond formed through an **electrostatic attraction** between two **oppositely charged** ions
54
What is a covalent bond?
A form of chemical bonding that is characterised by the **sharing of pairs** of electrons between atoms
55
What is a disluphide bond
A **covalent bond** derived by the coupling of two **thiol (SH)** groups
56
What are Van der Waals forces?
* The **sum of attractive or repulsive forces** between molecules or between parts of the same molecule * Relatively weak compared to normal chemical bonds
57
What are hydrophobic interactions?
* 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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