MCGB - Protein Structure And Function

Question 1

What is a polypeptide?

Answer 1

Macromolecules made up of amino acids (which are joint covalently).

Question 2

What encodes the amino acid sequence of a protein?

Answer 2

The nucleotide sequence of a gene

Question 3

What is the general structure of an amino acid?

Answer 3

Easier to draw this out - central carbon with a H, COOH, R and NH2 group all bonded to it

Question 4

What does the base ionise to form?

Answer 4

NH2 and H+ form NH3+ (this is reversible)

Question 5

What does the acid ionise to form?

Answer 5

COOH forms COO- and H+

Question 6

Why are amino acids classified according to the chemical properties of the R groups?

Answer 6

All that is left of the amino acids once they have formed bonds is the side chains, so properties must be due to side chains.

Question 7

What is an amino acid residue?

Answer 7

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

Question 8

What is a pK value?

Answer 8

The logarithmic value of the dissociation constant, Ka, of a hydrogen atom present in a molecule.

Question 9

If the pH of an amino acid solution is lower than the pK value then what will happen to the R group?

Answer 9

It will be protonated

Question 10

If the pH of an amino acid solution is higher than the pK value then what will happen to the R group?

Answer 10

It will be deprotonated

Question 11

Give some examples of positively charged R groups.

Answer 11

Lysine, arginine, histidine

Question 12

Give some examples of negatively charged R groups.

Answer 12

Glutamate, aspartate

Question 13

What is physiological pH?

Answer 13

7.4

Question 14

What is the primary structure of a protein?

Answer 14

The linear amino acid sequence of the polypeptide chain

Question 15

What is the secondary structure of a protein?

Answer 15

Local spatial arrangement of polypeptide backbone - eg helices

Question 16

What is the tertiary structure of a protein?

Answer 16

Overall 3D configuration eg folding

Question 17

What is the quaternary structure of a protein?

Answer 17

Association between different polypeptides to form a multi-subunit protein

Question 18

What name is given to the bond where two amino acids are linked, accompanied by the loss of a molecule of water?

Answer 18

Peptide bond (condensation reaction)

Question 19

True or false - peptide bonds are planar?

Answer 19

False

Question 20

Why do peptide bonds always exhibit a trans configuration?

Answer 20

Otherwise “steric clashes” would occur - where atoms get too close and start to repel each other.

Question 21

What are the folding of the polypeptide chain and the physical characteristics of the protein both determined by?

Answer 21

The amino acid sequence of the protein

Question 22

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

Answer 22

The pH at which there is no overall net charge.

Question 23

If pH is lower than pI, what will happen to the protein?

Answer 23

Protein is protonated

Question 24

If pH is higher than pI what will happen to the protein?

Answer 24

It will be deprotonated

Question 25

True or false - peptides can vary hugely in size?

Answer 25

True - Titin, the largest in humans, has an Mr of almost 3 million

Question 26

What sort of bond holds the primary structure of a protein together?

Answer 26

Covalent

Question 27

Give one similarity between an alpha helix and a DNA helix.

Answer 27

They are both right handed helices.

Question 28

What stabilises the structure of the alpha helix that forms the secondary structure of a protein?

Answer 28

H-bonds between N-H and C=O

Question 29

Which two amino acids DON’T form alpha helices?

Answer 29

Proline (no rotation around bond) and glycine (R-group supports other conformations)

Question 30

What is the other possible conformation for a secondary structure of a protein (other than alpha helix)?

Answer 30

Beta sheet (can be parallel or antiparallel)

Question 31

What is the difference between globular and fibrous proteins?

Answer 31

Fibrous - long strands/sheets, single type of repeating secondary structure, for support/shape/protection
Globular - compact shape, several types of secondary structure, for catalysis/regulation

Question 32

What are “motifs” and “domains” an example of in terms of proteins?

Answer 32

Tertiary structures of globular proteins

Question 33

True or false - polypeptide chains fold so that hydrophobic side chains are buried and polar, and charged chains are on the surface?

Answer 33

True

Question 34

Give some examples of proteins with quaternary structures.

Answer 34

Haemoglobin, ribosomes (and any more you can think of).

Question 35

Which forces maintain the primary structure of a protein?

Answer 35

Covalent

Question 36

Which forces maintain the secondary structure of a protein?

Answer 36

H-bonds

Question 37

Which forces maintain the quaternary structure of a protein?

Answer 37

Covalent, ionic, H-bonds, van der Waals, hydrophobic

Question 38

How strong are covalent bonds?

Answer 38

Very strong (214 kJ/mol)

Question 39

Which is stronger - electrostatic interactions or hydrogen bonds?

Answer 39

They are about equal

Question 40

Which is the weakest force involved in maintaining protein structure?

Answer 40

Van der Waals forces

Question 41

What is the term used to describe disruption of protein structure?

Answer 41

Denaturation

Question 42

Give some examples of things that can denature proteins.

Answer 42

Heat (increased vibrational energy), pH (alters ionisation states of amino acids and changes ionic/H-bonds), detergents/organic solvents (disrupts hydrophobic interactions)

Question 43

True or false - protein binding is driven by the need to find the least stable conformation?

Answer 43

False - driven by desire to find MOST stable conformation.

Question 44

What are amyloid fibres?

Answer 44

Misfolded, insoluble form of a normally soluble protein.