2.2 Applications and skills

2.2.4 Function and denaturation of proteins

  • The structure and three-dimensional shape of a protein determines its function.
  • Denaturation permanently changes the shape and of proteins and makes them non-functional.

Application: Named examples showing range of protein functions

Protein

Structure

Function

Further information

Rubisco (rubulose biphosphate carboxylase)

Globular (6 sub-units) with active sites that bind to carbon dioxide

Fixes carbon dioxide from the atmosphere, providing carbon (for synthesis of glucose) during photosynthesis

Most abundant protein on earth

Found in leaves and photosynthetic algae

See 8.1.3 (HL)

Insulin

Globular, with plasma membrane protein binding sites

Hormone that regulates glucose absorption into cells (reduces blood glucose levels)

Secreted by beta cells of the pancreas

Deficient in diabetics

See 6.1.6

Immuno-

globulins

Globular; large Y-shaped proteins

Antibodies that tag foreign bodies, called antigens, for destruction by other parts of the immune system

Produced by white blood cells, in response to a specific antigen

See 6.1.3 and 11.1.1 (HL)

Rhodopsin

Globular; protein complex made of a photopigment, opsin, and a co-factor, retinal

Light receptor that allows for monochromatic (black/white) vision in low light conditions

In the retina of the eye

Light hitting the retina causes a conformational change in rhodopsin, which eventually leads to a nerve impulse to the brain

See 12.1.3

Collagen

Fibrous (3 chains); bundles of long, parallel polypeptide chains or arranged in mesh patterns

Strengthens connective tissue, surrounds blood vessels, prevents cracks in teeth and bones

Many different forms found in cornea, skin, bones, etc.

Most abundant protein in the human body

Spider silk

Fibrous; range of structures

Immensely strong and elastic proteins used for webs, prey capture and drop lines

Some spiders infuse their silk with pheromones in order to leave a trail for potential mates

Application: Denaturation of proteins by heat or change in pH

  • Adding heat increases molecular movement. As molecules within a protein vibrate, hydrogen bonds and other intermolecular forces are broken and rearranged.

Figure 2.2.4a – Irreversible denaturation in egg white albumenFigure 2.2.4a – Irreversible denaturation in egg white albumen

  • Most proteins maintain their structure through a narrow range of pH.
  • Salt bridges are intermolecular forces that occur between the COO- group of one peptide and the NH3+ group on another.
  • H+ ions can break salt bridges, leading to a conformational change in the protein.

[Insert Fig 2.2.4b pH on protein structure]

Figure 2.2.4b – Denaturation results from a variation in pH

Nature of Science: Trends, patterns and discrepancies

  • Pattern: The majority of organisms use the same genetic code during translation to produce the standard 20 amino acids.
  • Trend: There is wide variation in the sequencing of amino acids in proteins of different species, but there are similarities in amino acid sequences in the proteins of related groups of organisms.
  • Discrepancy: Some organisms are capable of producing ‘non-standard’ amino acids by post-translational modification. An example is lanthionine, which is a modified version of alanine. It is produced by some microbes.
  • Discrepancy: In most organisms, UAG is the ‘stop codon’. However, in methanogenic archaea, UAG corresponds to an amino acid called pyrrolysine. This is a standard amino acid produced by translation.

Figure 2.2.4cFigure 2.2.4c – Heller test
Egg white albumen forms a precipitate in the middle layer when exposed to a strong acid or base.

Concept help

pH is a logarithmic scale that indicates H+ concentration. Lower pH means higher concentration of H+, and vice versa.

Try it!

Determine the optimum temperature and pH of egg white albumen using simple experiments, such as the Heller test, shown in Figure 2.2.4c.

Figure 2.2.4d – Cottage cheeseFigure 2.2.4d – Cottage cheese
Curds of casein protein are formed in milk after exposure to citric acid during the production of cottage cheese.

Course links

  • Learn how variations in pH and temperature affect the activity of enzymes in 2.1.5.
  • Similarities in amino acid sequences can be used to determine evolutionary relationships. See 5.1.4.
  • Heat interrupts the secondary structure of proteins, while pH affects the tertiary structure. HL students will learn about protein organisation in 7.1.3.