Proteins

Question 1

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

Answer 1

50 and 200

Question 2

What is the average molecular weight of an amino acid?

Answer 2

110

Question 3

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

Answer 3

about 5,000 to 200,000

Question 4

Peptide bonds form between _

Answer 4

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

Question 5

Oligopeptides are composed of up to

Answer 5

about 25 amino acid residues

Question 6

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

Answer 6

Free amino group to the left hand side

Free carboxyl group to the right hand side

Question 7

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

Answer 7

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

Question 8

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

Answer 8

Conformational rigidity about that bond

Question 9

What restricts the confromational range of torsion angles?

Answer 9

Steric hindrance

Question 10

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

Answer 10

Phi

Question 11

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

Answer 11

Psi

Question 12

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

Answer 12

180 degrees

Question 13

Psi an phi increase with

Answer 13

clockwise rotation

Question 14

What kind of diagram shows the possible torsion angles?

Answer 14

Ramachandran plot

Question 15

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

Answer 15

Primary structure

Question 16

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

Answer 16

Common in extracellular prteins

Rare in intercellular proteins

Question 17

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

Answer 17

Collagen

Question 18

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

Answer 18

Secondary

Question 19

There are _ amino acids per turn of an alpha helix

Answer 19

3.6

Question 20

A turn of an alpha helix covers a distance of _

Answer 20

0.54nm

Question 21

In an alpha helix conformation, side chains are positioned _

Answer 21

On the outside of the helix

Question 22

In an alpha helix arrangement, hydrogen bonding occurs between _

Answer 22

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

Question 23

In an alpha helix, the hydrogen bonds run _

Answer 23

parallel to the axis

Question 24

Why is proline rarely found in alpha helical arrangements?

Answer 24

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

Question 25

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

Answer 25

8

Question 26

What function does proline have in alpha helices?

Answer 26

It changes the direction and terminates the helix

Question 27

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

Answer 27

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

Question 28

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

Answer 28

0.35nm

Question 29

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

Answer 29

A beta barrel

Question 30

Describe the structure of silk fibroin

Answer 30

It has many stacks of antiparallel beta pleated sheets

Question 31

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

Answer 31

beta turns

Question 32

Hydrogen bonds occur between _ in folded over beta pleated sheets

Answer 32

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

Question 33

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

Answer 33

Tertiary

Question 34

Give 4 interactions which stabilise the tertiary structure of proteins

Answer 34

Disulfide bonds between cysteine residues Hydrogen bonds Van der waals forces salt bridges between oppositely charged side chains

Question 35

Where are cysteine disulfide bonds usually formed?

Answer 35

In the oxidizing environment of the endoplasmic reticulum

Question 36

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

Answer 36

Non polar regions are buried away from aqueous exterior

Question 37

In beta pleated sheets, how are side chains positioned?

Answer 37

They protrude above and below the plane

Question 38

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

Answer 38

Domains

Question 39

Domains are generally connected by _

Answer 39

Relatively unfolded sections

Question 40

Give two examples of proteins with domains

Answer 40

Immunoglobulin(found in antibodies) | Zinc finger domain (DNA binding)

Question 41

What does the quaternary structure refer to?

Answer 41

The spatial arrangement of polypeptide subunits and the interactions between them

Question 42

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

Answer 42

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

Question 43

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

Answer 43

NMR spectroscopy Cryoelectron microscopy X-ray crystallography

Question 44

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

Answer 44

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

Question 45

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

Answer 45

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

Question 46

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

Answer 46

Multi subunit proteins

Question 47

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

Answer 47

Small proteins

Question 48

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

Answer 48

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

Question 49

What is the main driving force in protein folding?

Answer 49

Hydrophobic forces

Question 50

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

Answer 50

The presence of accesory proteins speeds up the process

Question 51

What kind of mutations are unlikely to affect protein folding?

Answer 51

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