CW3: 3D Structure of proteins

Question 1

How many amino acids are there in proteins?

Answer 1

20

Question 2

Which isomer of aminio acids is found in proteins? What is the exception?

Answer 2

The L-isomer form

Glycine is achiral so doesn’t have optial isomers

Question 3

Which is the N-terminal and which is the C-terminal end of this protien?

Answer 3

N⁺H₃ is the N-terminus

COO^– is the C-terminus

Question 4

Why do amino acids alternate their orientation when joining, so that the side chains are on different sides of the backbone?

Answer 4

Side chains tend to be bulky so they alternate sides to save space

Question 5

What is the repeating pattern of the atoms in an amino acid chain backbone?

Answer 5

CNC CNC CNC CNC

Question 6

Define ‘primary structure’.

Which bonds form in this structure?

Answer 6

The sequence of amino acids in proteins.

Covalent bonds

Question 7

Define ‘secondary structure’.

Which bonds form in this structure?

Answer 7

Structural motifs in proteins, e.g. alpha-helix and beta-sheet.

Hydrogen bonds (between NH and CO groups in backbone)

Question 8

Define ‘tertiary structure’.

Which bonds form in this structure?

Answer 8

The folding up of polypeptide chains. It is the highest level for many proteins.

Various: covalent, ionic, hydrogen, van der Waals, hydrophobic

Question 9

Define ‘quaternary structure’.

Which bonds form in this structure?

Answer 9

Association of protein subunits into larger assemblies. Consists of two or more subunits.

Various

Question 10

Which end of the protein is synthesised first?

Which end is drawn on the left of the sequnce (by convention)?

Answer 10

For both: the amino (N-terminal) end

Question 11

Why is the organisation of an alpha-helix very efficient?

Answer 11

The CO group of one residue is hydrogen-bonded to the NH group of the residue four amino acids away. The bonds can form neatly and the chain is close.

Question 12

Why don’t you find glycine and proline in alpha-helices?

Answer 12

Glycine is too small and flexible and proline is too large and not flexible enough

Question 13

How many amino acids are found per turn in an alpha-helix?

Answer 13

3.6

Question 14

What is the rise per turn in an alpha-helix?

Answer 14

5.4Å

Question 15

Are alpha-helices left- or right-handed helices?

Answer 15

Right-handed

Question 16

Compare the following characteristics of DNA and protein:

• Units
• Direction formed
• Structure

Answer 16

Question 17

What are the two main forms of beta sheets?

BONUS: name the third

Answer 17

Parallel and anti-parallel

BONUS: mixed sheet

Question 18

Is this a parallel or anti-parallel beta sheet?

Answer 18

Parallel

Question 19

Is this a parallel or anti-parallel beta sheet?

Answer 19

Anti-parallel

Question 20

Is this a parallel or anti-parallel beta sheet?

Answer 20

Anti-parallel

Question 21

Is this a parallel or anti-parallel beta sheet?

Answer 21

Parallel

Question 22

Which amino acids are not present in beta sheets? Why?

Answer 22

Methionine, valine and isoleucine

Because they are hydrophobic

Question 23

In which type of beta sheet arrangement (parallel/anti-parallel) is hydrogen bonding more efficient?

Answer 23

Anti-parallel

Question 24

What is a beta turn? What are the two types?

Answer 24

A secondary structure formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain.

Types I and II

Question 25

Which amino acid is always in the third position in a type II beta turn?

Answer 25

Glycine

Question 26

What is another name for repeated motifs? Give two examples.

Answer 26

Supersecondary structure Beta-alpha-beta loop; alpha/beta barrel

Question 27

Describe the formation of a disulfide bond.

Answer 27

Two cysteines that are close to each other are oxidised to remove protons, resulting in the two sulfides bonding

Question 28

What is the name for proteins with two, three, and four subunits? Give examples of each.

Answer 28

* 2 = dimers, e.g. Cro represser (homodimer), alpha-tubulin/beta-tubulin (heterodimer) * 3 = trimer, e.g. collagen (homotrimer) * 4 = tetramer, e.g. DNA gyrase (A₂B₂), haemoglobin (α₂β₂)

Question 29

Define the terms 'homodimer' and 'heterodimer'.

Answer 29

Homodimer = a protein with two subunits of the same sort of chain Heterodimer = a protein with two subunits of different protiens that work together as a functional pair

Question 30

Define 'native', 'denatured', and 'renatured'.

Answer 30

Native = the properly folded form of a protein Denatured = the improperly folded form of a protein Renatured = returning to correct folding

Question 31

What can cause denaturation of a protein?

Answer 31

* Extremes of pH * Heat (increased heat = increased thermal energy = unfolding) * Chaotrophic agents, e.g. urea, guanidine hydrochloride, β-mercaptoethanol (a.k.a. 2-mercaptoethanol)

Question 32

Why can urea and guanidine hydrochloride cause denaturation of a protein?

Answer 32

They affect the ability of proteins to form hydrogen bonds by reducing the disulfide bonds between amino acids

Question 33

Why is β-mercaptoethanol a chaotrophic agent?

Answer 33

It can give away one of its proton leading to the reduction of a protein

Question 34

How can proteins be renatured?

Answer 34

**Spontaneously** if the protein has enough information in the primary sequence to refold Using **chaperone proteins**

Question 35

Which acid can be used to dentature proteins and how does it work?

Answer 35

Performic acid Cysteine residues are converted to cysteic acid residues, causing irreversible denaturation of the enzyme

Question 36

Why does adding and then removing β-mercaptoethanol and urea result in approximately 1% activity? What are the two options and which one is correct?

Answer 36

Option A: every molecule of ribonuclease has activity **Option B: 99% have no activity, 1% do**

Question 37

Why is the protein VMSTA not the same as ATSMV?

Answer 37

The orientation of the amino acids is reversed to the C- and N-terminal ends would be incorrect

Question 38

What holds alpha helices in place?

Answer 38

Hydrogen bonds between the NH and CO groups in the backbone

Question 39

What are the differences between an alpha helix and a beta sheet?

Answer 39

Question 40

Which amino acids form disulfide bonds?

Answer 40

Cysteine

Question 41

If somebody tells you a protein has a quaternary structure, what can you immediately say about it?

Answer 41

It is formed of multiple subunits

Question 42

Why have experiments been carried out on ribonucleases?

Answer 42

Ribonucelases are enzymes that catalyse the hydrolysis of RNA. They can be fully denatured and renatrured *in vitro* (i.e. without a chaperone). The eight cysteine residues form four disulphide bonds.

Question 43

How can extremophiles be useful?

Answer 43

They are adapted to extremes of heat so can be used in PCR