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Biomolecules > Proteins > Flashcards

Proteins Flashcards

1
Q

Most proteins contain between _ and _ amino acids linked together via peptide bonds

A

50 and 200

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2
Q

What is the average molecular weight of an amino acid?

A

110

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3
Q

What is the average molecular weight of a protein (range)?

A

about 5,000 to 200,000

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4
Q

Peptide bonds form between _

A

The amino group of one amino acid and the carboxyl gorup of another

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5
Q

Oligopeptides are composed of up to

A

about 25 amino acid residues

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6
Q

What is the convention (lhs, rhs) in representation of polypeptide chains?

A

Free amino group to the left hand side

Free carboxyl group to the right hand side

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7
Q

Which configurartion is more common in polypeptide chains, trans or cis?

A

Trans. Hydrogen on amino grou opposite side of oxygen on carbonyl

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8
Q

What is the consequence of the presence of resonance structures in peptide bonds?

A

Conformational rigidity about that bond

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9
Q

What restricts the confromational range of torsion angles?

A

Steric hindrance

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10
Q

Which symbol represents the torsion angle of C-N bonds in polypeptides?

A

Phi

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11
Q

Which symbol represents the torsion angle of C-C bonds in polypeptides?

A

Psi

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12
Q

By convention, psi and phi are _ in a fully extended planar conformation

A

180 degrees

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13
Q

Psi an phi increase with

A

clockwise rotation

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14
Q

What kind of diagram shows the possible torsion angles?

A

Ramachandran plot

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15
Q

What structure contains informartion about crosslinks between amino acid residues like cysteine (disulfide bridges)

A

Primary structure

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16
Q

Crosslinks, such as disulfide bridges, are common in _, but rare in _

A

Common in extracellular prteins

Rare in intercellular proteins

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17
Q

Give an example of a protein with crosslinks between side chains of lysine residues

A

Collagen

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18
Q

Which structure represents the regular folding of regions of polypeptide chains?

A

Secondary

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19
Q

There are _ amino acids per turn of an alpha helix

A

3.6

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20
Q

A turn of an alpha helix covers a distance of _

A

0.54nm

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21
Q

In an alpha helix conformation, side chains are positioned _

A

On the outside of the helix

22
Q

In an alpha helix arrangement, hydrogen bonding occurs between _

A

the carbonyl oxygen of each amino acid and the hydrogen on the amino group of the fourth amino away

23
Q

In an alpha helix, the hydrogen bonds run _

A

parallel to the axis

24
Q

Why is proline rarely found in alpha helical arrangements?

A

It cannot form the proper hydrogen bonding patterns due to its structure

25
Q

The protein myoglobin has how many alpha helical structures along its polypeptide chain?

A

8

26
Q

What function does proline have in alpha helices?

A

It changes the direction and terminates the helix

27
Q

What quality of polypeptide chains forces the planarity/rigidity of the beta pleated sheet arrangement?

A

The rigidity of the peptide bond (due to resonance structure)

28
Q

In beta pleated sheets, polypeptide chains are fully extended with a distance of _ between alpha carbon atoms

A

0.35nm

29
Q

If enough polypeptide chains are involved, beta pleated sheets can close up to form _

A

A beta barrel

30
Q

Describe the structure of silk fibroin

A

It has many stacks of antiparallel beta pleated sheets

31
Q

What process can reverse the direction of chains and allow the connection of ends of antiparallel regions?

A

beta turns

32
Q

Hydrogen bonds occur between _ in folded over beta pleated sheets

A

carbonyl group with the amino group of the 4th amino acid away

33
Q

Which structure refers to the 3D spatial arrangement of proteins?

A

Tertiary

34
Q

Give 4 interactions which stabilise the tertiary structure of proteins

A

Disulfide bonds between cysteine residues

Hydrogen bonds

Van der waals forces

salt bridges between oppositely charged side chains

35
Q

Where are cysteine disulfide bonds usually formed?

A

In the oxidizing environment of the endoplasmic reticulum

36
Q

In water soluble globular proteins, what is the ffect of hydrophobic forces on the structure?

A

Non polar regions are buried away from aqueous exterior

37
Q

In beta pleated sheets, how are side chains positioned?

A

They protrude above and below the plane

38
Q

In large proteins, chains may fold over and form distinc regions known as _

A

Domains

39
Q

Domains are generally connected by _

A

Relatively unfolded sections

40
Q

Give two examples of proteins with domains

A

Immunoglobulin(found in antibodies)

Zinc finger domain (DNA binding)

41
Q

What does the quaternary structure refer to?

A

The spatial arrangement of polypeptide subunits and the interactions between them

42
Q

What structure can be predicted from primary sequence of amino acids? What structure cannot?

A

Presence of alpha helices and beta pleated sheets can be predicted
Tertiary 3D native conformation cannot, special techniques must be used

43
Q

Give 3 techniques used in determining the 3D structure of proteins

A

NMR spectroscopy
Cryoelectron microscopy
X-ray crystallography

44
Q

What observation in x ray crystallography can be mathematically analysed in order to determine the 3D structure of proteins?

A

Diffraction patterns produced by the scattering of x-rays by a crystallized protein structure (aligned and rigid array of molecules)

45
Q

What effect is measured in the use of NMR in determining protein structure?

A

The effect of radio frequencies on atomic spin. There is more perturbation in regions where atoms are closer together. Distance can be inferred

46
Q

For what kind of protein is cryoelectron microscopy the mosr useful technique in determining structure?

A

Multi subunit proteins

47
Q

For what kind of protein is NMR the most useful technique in determining structure?

A

Small proteins

48
Q

Why is there no need for an external template in protein folding?

A

Proteins fold spontaneously, through ordered pathways which are encoded in the primary structure

49
Q

What is the main driving force in protein folding?

A

Hydrophobic forces

50
Q

Why can protein folding occur much faster in vivo than in vitro?

A

The presence of accesory proteins speeds up the process

51
Q

What kind of mutations are unlikely to affect protein folding?

A

Alterations to surface residues - folding is driven mainly by internal residues

Biomolecules (12 decks)

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