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BS1030: Biochemistry > CW3: 3D Structure of proteins > Flashcards

CW3: 3D Structure of proteins Flashcards

1
Q

How many amino acids are there in proteins?

A

20

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2
Q

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

A

The L-isomer form

Glycine is achiral so doesn’t have optial isomers

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3
Q

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

A

N+H3 is the N-terminus

COO– is the C-terminus

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4
Q

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

A

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

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5
Q

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

A

CNC CNC CNC CNC

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6
Q

Define ‘primary structure’.

Which bonds form in this structure?

A

The sequence of amino acids in proteins.

Covalent bonds

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7
Q

Define ‘secondary structure’.

Which bonds form in this structure?

A

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

Hydrogen bonds (between NH and CO groups in backbone)

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8
Q

Define ‘tertiary structure’.

Which bonds form in this structure?

A

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

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

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9
Q

Define ‘quaternary structure’.

Which bonds form in this structure?

A

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

Various

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10
Q

Which end of the protein is synthesised first?

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

A

For both: the amino (N-terminal) end

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11
Q

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

A

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.

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12
Q

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

A

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

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13
Q

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

A

3.6

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14
Q

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

A

5.4Å

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15
Q

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

A

Right-handed

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16
Q

Compare the following characteristics of DNA and protein:

  • Units
  • Direction formed
  • Structure
A
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17
Q

What are the two main forms of beta sheets?

BONUS: name the third

A

Parallel and anti-parallel

BONUS: mixed sheet

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18
Q

Is this a parallel or anti-parallel beta sheet?

A

Parallel

19
Q

Is this a parallel or anti-parallel beta sheet?

A

Anti-parallel

20
Q

Is this a parallel or anti-parallel beta sheet?

A

Anti-parallel

21
Q

Is this a parallel or anti-parallel beta sheet?

A

Parallel

22
Q

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

A

Methionine, valine and isoleucine

Because they are hydrophobic

23
Q

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

A

Anti-parallel

24
Q

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

A

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

25
Q

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

A

Glycine

26
Q

What is another name for repeated motifs?

Give two examples.

A

Supersecondary structure

Beta-alpha-beta loop; alpha/beta barrel

27
Q

Describe the formation of a disulfide bond.

A

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

28
Q

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

A
  • 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)
29
Q

Define the terms ‘homodimer’ and ‘heterodimer’.

A

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

30
Q

Define ‘native’, ‘denatured’, and ‘renatured’.

A

Native = the properly folded form of a protein

Denatured = the improperly folded form of a protein

Renatured = returning to correct folding

31
Q

What can cause denaturation of a protein?

A
  • Extremes of pH
  • Heat (increased heat = increased thermal energy = unfolding)
  • Chaotrophic agents, e.g. urea, guanidine hydrochloride, β-mercaptoethanol (a.k.a. 2-mercaptoethanol)
32
Q

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

A

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

33
Q

Why is β-mercaptoethanol a chaotrophic agent?

A

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

34
Q

How can proteins be renatured?

A

Spontaneously if the protein has enough information in the primary sequence to refold

Using chaperone proteins

35
Q

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

A

Performic acid

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

36
Q

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?

A

Option A: every molecule of ribonuclease has activity

Option B: 99% have no activity, 1% do

37
Q

Why is the protein VMSTA not the same as ATSMV?

A

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

38
Q

What holds alpha helices in place?

A

Hydrogen bonds between the NH and CO groups in the backbone

39
Q

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

A
40
Q

Which amino acids form disulfide bonds?

A

Cysteine

41
Q

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

A

It is formed of multiple subunits

42
Q

Why have experiments been carried out on ribonucleases?

A

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.

43
Q

How can extremophiles be useful?

A

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

BS1030: Biochemistry (21 decks)

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