Sesh 5: Protein Structure and Function

Question 1

What determines the amino acid sequence of a protein?

Answer 1

The nucleotide sequence of the gene encoding that protein.

Question 2

What does the folding of the protein depend on?

Answer 2

The physical and chemical properties of its amino acid residues.

Question 3

What 4 things are bonded to the central alpha carbon of an amino acid?

Answer 3

1. Amino group
2. Carboxyl group
3. Hydrogen atom
4. R group/ side chain- distinguishes amino acids

Question 4

What is the ionisation state of an amino acid?

Answer 4

The state the amino acid is in when it is in solution…e.g. NH2 gains and COOH loses protons to form a zwitterion (the deprotonated form).

Question 5

Why are amino acids classified by the chemical properties of their R groups?

Answer 5

As when joined by peptide bonds, they lose their amino and carboxyl group, so are only amino acid residues with their R group left- this group determines the protein’s structure.

Question 6

Define an amino acid residue.

Answer 6

What remains of an amino acid after it has been joined by a peptide bond to form a protein.

Question 7

Name 2 possible PHYSICAL properties of amino acids R chains.

Answer 7

Aliphatic or aromatic (carbon rings).

Question 8

What is the pKR?

Answer 8

The log of the acid dissociation constant for amino acid R chains. At this pH, there will be equal amounts of the protonated and deprotonated forms.

Question 9

Amino acids with high pKR values have ___________ charged R groups.
Amino acids with low pKR values have _____________ charged R groups.

Answer 9

1. Positively

2. Negatively

Question 10

If the solution pH is less than the pKR value, the R group will be ____________.
If the solution pH is greater than the pKR value, the R group will be _____________.

Answer 10

1. Protonated

2. Deprotonated

Question 11

Define the primary structure of a protein.

Answer 11

The linear amino acid sequence of the polypeptide chain. ‘Beads on a string’ model.

Question 12

What is the secondary structure of a protein?

Answer 12

The local spatial arrangement/folding of the polypeptide backbone, forming conformations e.g. Alpha helices, beta pleats

Question 13

Define the tertiary structure of a protein.

Answer 13

The spatial arrangement of amino acids far apart in the protein sequence to give the overall 3-D configuration of the protein.

Question 14

What can you infer about a protein if it has a quaternary structure?

Answer 14

It has multiple subunits which associate to form the protein. Not necessarily all protein subunits e.g. Ribosome made of protein and RNA.

Question 15

Peptide bond formation is a _____________ reaction as it involves the _____ of water.

Answer 15

1. Condensation

2. Loss

Question 16

Why does a protein have polarity?

Answer 16

Because the amino acid at 1 end will have a free amino group- the amino/N terminus- and 1 at the other end will have a free carboxyl group- carboxyl/C terminus.

Question 17

Name 3 properties of peptide bonds that are important for protein structure.

Answer 17

1. They are planar
2. They are rigid- form resonance structures, so unable to rotate
3. Exhibit a trans conformation to avoid steric clashes

Question 18

What are the bonds on either side of the peptide bond called, and what property makes them different to a peptide bond?

Answer 18

1. Psi bond (C-C)
2. Phi bond (C-N)

Unlike the peptide bond, these are free to rotate to give different bond angles….but are still slightly restricted due to steric clashes.

Question 19

What is the isoelectric point (pI) of a protein?

Answer 19

The pH at which there is no overall net charge on the protein. (Individual amino acids will still be charged, but their charges balance at pI)…

Question 20

An acidic protein has many _________ charged amino acids, and a basic protein has many ___________ charged amino acids.

Answer 20

1. Negatively

2. Positively

Question 21

The angles of the ___ and ___ bonds determine the conformation of the peptide ________, thus determining how the protein _____.

Answer 21

1. Phi
2. Psi
3. Backbone
4. Folds

Question 22

Describe an alpha helix.

Answer 22

A compact ribbon-like right-handed helix.

Question 23

Define the ‘pitch’ and the ‘rise’ determined by the protein’s secondary structure.

Answer 23

• Pitch= 1 complete turn of the helix

- Rise= distance between each amino acid

Question 24

What holds the alpha helix of a protein together?

Answer 24

H bonds between the backbone structure (carbonyl oxygens and amide hydrogens).

Question 25

Describe the characteristic H bonding in an alpha helix.

Answer 25

H bonds form in the peptide backbone between a carbonyl oxygen and an amide hydrogen 4 amino acids away.

Question 26

How can primary sequence affect alpha helix stability?

Answer 26

Some amino acids are more likely to form alpha helices than others.... - Small hydrophobic residues are strong helix formers e.g. Ala, Leu - Pro & Gly= helix breakers due to R group bonding

Question 27

Is a beta strand more or less compact than an alpha helix/?

Answer 27

Less. More of an extended conformation. Rise= larger (0.35nm vs 0.15 nm)

Question 28

Describe an anti-parallel beta-sheet.

Answer 28

Adjacent beta strands run in opposite directions, stabilised by many inter-strand H bonds between carbonyl oxygens and amide hydrogens.

Question 29

Why is a parallel beta sheet slightly weaker than an anti-parallel beta sheet?

Answer 29

Beta strands are running in the same direction, meaning the H bonds are at slightly different angles.

Question 30

Describe the structure and function of fibrous proteins.

Answer 30

- Simple structure with multiple repeating secondary structures, to form long strands or sheets. -Stable, so have roles in support, shape and protection. E.g. Collagen- triple helical arrangement of collagen chains with Gly-X-Y repeating seq.

Question 31

Describe the structure and function of globular proteins.

Answer 31

- Made up of several different types of secondary structures, to give a compact shape, and give rise to a variety of tertiary structures. - Roles in catalysis and regulation E.g. Carbonic anhydrase

Question 32

What are motifs?

Answer 32

Folding patterns containing 1/more secondary structure elements. Commonly found in globular proteins. E.g. Beta-barrel, beta-alpha-beta loop

Question 33

Define a protein domain.

Answer 33

A part of a polypeptide chain that folds up independently into a distinct shape to fulfill a specific functional role.

Question 34

How does the polypeptide chain of water soluble proteins fold so that they are stable?

Answer 34

Fold so that hydrophobic chains are buried on the inside, and hydrophilic charged residues are on the surface, to interact with water.

Question 35

Describe the general distribution of amino acids in membrane proteins.

Answer 35

Usually show 'inside out' distribution. Hydrophobic residues on surface to interact with hydrophobic fatty acid chains in the membrane, and hydrophilic residues buried on the inside e.g. To form a water filled pore.

Question 36

What is a protein?

Answer 36

A polypeptide= a macromolecule composed of amino acids covalently joined to give the protein sequence, which can then fold to form the protein structure. Have a role in virtually all biochemical processes.

Question 37

What are disulphide bonds?

Answer 37

Found in tertiary and quaternary structure of a protein. Relatively strong covalent bonds between cysteine residues. Most proteins with them are secreted e.g. Ribonuclease.

Question 38

What are electrostatic interactions formed between?

Answer 38

Oppositely charged groups on amino acids.

Question 39

What is a hydrogen bond?

Answer 39

A bond between an electronegative atom and a H bound to another electronegative atom.

Question 40

What is the hydrophobic effect/ hydrophobic interactions?

Answer 40

Interactions between hydrophobic amino acid side chains that come together to exclude/ displace water.

Question 41

What type of interactions are Van der Walls forces, and when are they important?

Answer 41

Dipole-dipole interactions that occur due to uneven charge distribution in covalent bonds. Important for when large molecule come together.

Question 42

What is a native conformation of a protein?

Answer 42

It is in its normally folded state and is functional.

Question 43

Briefly describe amyloid fibres and how they are formed.

Answer 43

Misfolded, insoluble forms of a normally soluble protein, that can aggregate and cause amyloidoses. Have a highly ordered structure- mainly beta sheets. Core beta sheet forms first. Then get H bonds between aromatic amino acids to stabilise inter-chain assembly.