Proteins

Question 1

Describe the structure of an amino acid.

Answer 1

Each amino acid consists of one central carbon atom bonded to a hydrogen atom (up), a carboxyl group (COOH) (right), an amino group (NH4) (left), a specific side chain (designated R) (down).

Question 2

Describe the characteristics of the side chain (R group)

Answer 2

• Variable
• Vary in sizes
• Determines the property of the amino acid

Question 3

Describe the properties of amino acids.

Answer 3

• Neutral and non polar
• Neutral and polar
• Acidic and polar
• Basic and polar

Question 4

How do we catagorise R groups?

Answer 4

R group does not carry a charge - neutral
R group contain S, O, N - polar
R group donate H+ - acidic
R group accept H+ - basic

Question 5

Describe the physical properties of amino acids.

Answer 5

• Colourless, crystalline solids
• Soluble in water
• Insoluble in organic solvents

Question 6

Describe the chemical properties of amino acids.

Answer 6

• Dissolve in water to form ions - amino group accepts H+, carboxyl group donates H+
• Amphoteric in nature - amino acid solutions can act as buffers (solutions that resist small changes in pH)

Question 7

How do amino acids link together?

Answer 7

Via the formation of peptide bonds.

Question 8

What is a peptide bond?

Answer 8

Covalent bonds formed by condensation reactions where a water molecule is removed between 2 amino acids.
OH of carboxyl group + H of amino group = O=C-NH

Question 9

State the levels of organisation in proteins.

Answer 9

• Primary
• Secondary
• Teritary
• Quaternary

Question 10

Explain the primary structure of proteins.

Answer 10

It is the type, number and sequence of the amino acids linked by peptide bonds.

Question 11

Describe the secondary structure of proteins.

Answer 11

• Localised folds and coils
• Intrachain hydrogen bond formation at regular intervals along the polypeptide backbone between O of carbonxyl group in a peptide bond and H attached to nitrogen of another peptide bond
• α-helix & β-pleated sheet

R groups are not involved in H bond formation.

Question 12

Describe the structure of an α-helix.

Answer 12

• The O of carbonyl group of residue n forms intrachain H bond with H of amino group of residue n+4 in the polypeptide backbone.
• Right-handed coil with H bonds aligned parallel to axis and side chains (R groups) projected outwards.
• 3.6 amino acid residues per complete turn of helix.

R groups are not involved in H bond formation.

Question 13

Describe the structure of a β-pleated sheet.

Answer 13

• 2 or more adjacent regions held by multiple intrachain hydrogen bonds at regular intervals
• Intrachain H bond formed via O of carboxyl group of one amino acid and H attached to N of amine group of another amino acid
• Parallel, antiparallel: same direction, opposite direction
• R groups project above and below β-pleated sheet
• β-pleated sheet favours amino acids with hydrophobic R groups.

Question 14

Describe the tertiary structure of a protein.

Answer 14

Polypeptide folds extensively upon itself to form a precise, compact globular shape involving interactions between R groups of amino acids that are far away from one another.
* Types of interactions: disulfide bond, H bond, ionic interaction, hydrophobic interactions.

Question 15

Describe the quaternary structure of a protein.

Answer 15

Associations of two or more polypeptide chains held together by hydrophobic interactions, H bonds and ionic interactions to form a precise structure between polypeptide units.

Question 16

Relate structure to function of haemoglobin.

Answer 16

• Primary structure
  type, number and sequence of primary structure -> gives rise to specific 3D conformational shape
• 2 Teritary structure
• Allosteric protein
• Heme group consists of porphyrin ring and iron ion
• Stability of protein
  contains non covalent bonds (ionic bonds, hydrophobic interactions, hydrogen bonds) -> sensitive to changes in temperature and pH

Question 17

Relate structure to function of collagen.

Answer 17

• Secondary structure being most important.
• Amino acid sequence and length not very specific
• Stability and solubility
• High tensile strength

Question 18

Relate the structure to function of G-Protein Coupled Receptor.

Answer 18

• Secondary structure
• Specific binding sites

Question 19

What is the smallest amino acid?

Answer 19

Glycine.