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Bioinformatics > L7-9: Protein Structure, Function and Modelling > Flashcards

L7-9: Protein Structure, Function and Modelling Flashcards

1
Q

What type of amino acids are found on the inside of proteins?

A

Aliphatic/non-polar/hydrophobic.

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2
Q

Example of structural protein

A

collagen

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3
Q

Example of storage protein

A

ovalbumin

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4
Q

Overall structure is a sufficient determinant for which typs of proteins?

A

Structural proteins

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5
Q

Which amino acids strongly absorb UV light and can aid in detection of proteins?

A

Tyrosine and tryptophan

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6
Q

Hydrophilic amino acids are often found in which part of the cell?

A

On the cell surface

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7
Q

Which amino acid can form disulphide bridges?

A

Cysteine

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8
Q

Degrees of freedom in the rotation of the peptide bonds depends upon:

A

The R group (side chain) and the environment around the amino acid

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9
Q

Four levels of protein structure

A

Primary, secondary, tertiary, quarternary

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10
Q

Primary structure of a protein

A

Order of the amino acids in the polypeptide chain

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11
Q

Secondary structure of a protein

A

Refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone

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12
Q

True or false:

Secondary structure of a protein does not involve R group interactions

A

True

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13
Q

Most common secondary structures

A

Alpha helices and beta-pleated sheets

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14
Q

Tertiary structure

A

Overall 3D structure of a polypeptide

Primarily due to interactions between the R groups of the amino acids.

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15
Q

A misfolded protein can be refolded properly using which chemical?

A

Urea

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16
Q

True or false:

Interior of a cell often contains charged amino acids

A

False. Interior of protein - uncharged amino acids or neutral charged regions

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17
Q

Which algorithm can be used to determine hydrophobicity?

A

Kyte-Doolittle

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18
Q

Which algorithm can be used to determine hydrophilicity/antigenicity?

A

Hopp-Woods

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19
Q

In motif language, [ ] mean

A

Either (one) amino acid within the brackets

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20
Q

In motif language, { } mean

A

Any amino acid except the ones in the curly brackets

21
Q

In motif language, X means

A

Any amino acid

22
Q

Which algorithm tool is used for detecting classically secreted proteins?

A

SignalP

23
Q

Which algorithm tool is used for detecting non-classically secreted proteins?

A

SecretomeP

24
Q

ICAM-1

A

90kD cell surface glycoprotein on antigen presenting cells

Central role in cell adhesion and in cell-cell contact-dependent immune mechanisms

25
Q

Counter receptor to ICAM-1

A

LFA-1

26
Q

Which amino acids are often found on the surface of cells?

A

Proline and glycine

27
Q

Proteins in an aqueous environment generally adopt which shape?

A

Globular

28
Q

An alpha helix is a _____-handed coil

A

right

29
Q

Alpha helices are stabilised by hydrogen bonds between _________

A

amine and carboxyl groups of nearby amino acids

30
Q

Peptide bond

A

O=C–NH

31
Q

The angle of the peptide bond is typically ____ or ______

A

0 or 180

32
Q

Amino acid with the most degrees of freedom around its phi and psi angles

A

Glycine

33
Q

Amino acid with the least degrees of freedom around its phi and psi angles

A

Proline

34
Q

Ramachandran (phi/psi) plots display _____

A

allowed and disallowed conformations of a polypeptide chain

35
Q

True or false:

In an alpha helix, the side chains of amino acids project inwards.

A

False. Side chains project outwards in an alpha helix.

36
Q

True or false:

Alpha helices are more thermally stable than beta pleated sheets.

A

True

37
Q

Determining protein 3D structures using x-ray crystallography - step by step

A
  1. Grow high quality protein
  2. Collect x-ray diffraction
  3. Calculate electron density maps, build and refine crystal structure
  4. Display and interpret protein’s 3D structure
38
Q

Characteristics of a protein domain

A

Spatially separated unit of protein structure
Folded independently from the rest of the structure
Often mediating a specific function

39
Q

Protein folds

A

Secondary structures in the same arrangement - major structural similarity

40
Q

Protein superfamilies

A

Similar 3D structures but often with low sequence identity between members (probably common evolutionary origin)

41
Q

Protein families

A

Conserved 3D structures with moderate to high sequence identities (>30%) - clear evolutionary relationships

42
Q

Why are new folds and superfamilies not being discovered?

A
  1. There are predicted to be a limited number of folds that are dynamically stable
  2. There will be a finite number of superfamilies
  3. We have identified the structure of all the “easy” ones
43
Q

True or false:
Homology protein modelling is unique in that it doesn’t require the sequence of interest to share significant similarity with a protein of known structure.

A

False. Homology protein modelling requires the sequence of interest to share significant similarity (normally >30% but the higher the better) with a protein of known structure.

44
Q

Homology protein modelling - step by step

A
  1. Identify a homologue of known structure (template)
  2. Produce a high quality alignment of your sequence (target) with that of the protein template of known structure.
  3. Generate model from template and run the modelling algorithm. Consequences of the changes to between overall structure of side chains is evaluated.
    Models are optimised and scored against an energy and geometry based function that includes template-derived parameters (e.g. distance matrix).
  4. Evaluate and improve the model:
    - Look for unacceptable steric clashes or geometries (do a Ramachandran plot)
    - Make sure any insertions are in appropriate positions (e.g. loops)
    - Ensure that there are no obvious problems (e.g. buried polar residues)
    - Adjust alignments and repeat model building if needed
45
Q

Methods for predicting secondary structures

A

Chou-Fasman

Garnier-Osguthorpe-Robson

46
Q

Which analysis method is used to identify transmembrane regions?

A

Kyte-Doolittle, Hopp-Woods

47
Q

Which analysis method is used to identify antigenic regions?

A

Hopp-Wood, Jameson-Wolf

48
Q

The peptide torsion or dihedral angles phi (F) and psi (Y) determine the conformation of the _________.

A

polypeptide backbone (main chain)

49
Q

Name and angle of peptide bonds

A

Omega - typically 0 or 180 degrees.

Bioinformatics (4 decks)

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