2.4 - Proteins

• Ribosomes:

  • The molecules within cells that facilitate the formation of peptide bonds and hence where polypeptides are synthesized
• Each amino acid has unique properties:

  • Polar or Non-polar
  • Differently charged
  • Some contain sulphur
  • Properties of the amino acids determine how a polypeptide folds up into a protein
• Hydroxyproline:

  • An example of an amino acid created not by the genetic code, but modification, after polypeptide formation, of proline (by the enzyme prolyl hydroxylase).
  • This modification of proline increases the stability of the collagen triple helix.
• Infinite polypeptide possibilities:

  • Could be any length
  • 20 amino acids
  • Amino acids can be in any order or combination
• DNA to RNA to Polypeptide
• Central dogma of genetics:

  • Genes are codes for making polypeptides
  • DNA is stored in nucleus, yet the polypeptide is produced in the cytoplasm (by ribosomes)
  • mRNA is a message from the nucleus to the ribosomes - instructions for how to put the polypeptide together
  • The genetic code is the sequence of bases on mRNA - tells the ribosome which amino acids to use
• Fibrous proteins:

  • Long and narrow
  • Structural
  • Insoluble in water
  • Repetitive amino acid sequence
  • Less sensitive to changes in pH, heat
  • Examples: Collagen, keratin, myosin
• Globular proteins:

  • Round
  • Functional
  • Soluble in water
  • Irregular amino acid sequence
  • More sensitive to changes in pH, heat
  • Examples: Haemoglobin, insulin, immunoglobin
• Rubisco:

  • Ribulose bisphosphate carboxylase
  • Enzyme - catalyses the reaction that fixes carbon dioxide from the atmosphere
  • Provides the source of carbon from which all carbon compounds, required by living organisms, are produced.
  • Found in high concentrations in leaves and algal cells
• Insulin:

  • A hormone – signals many cells (e.g. liver cells) to absorb glucose and help reduce the glucose concentration of the blood.
  • Affected cells have receptor (proteins) on their surface to which insulin can (reversibly) bind to.
  • Secreted by B cells in the pancreas and transported by the blood.
• Immunoglobins:

  • Also known as antibodies.
  • Two antigen (a molecule on the pathogen which provokes an immune response) binding sites - one on each ‘arm’
  • Binding sites vary greatly between immunoglobulins (hypervariable) to enable them to respond a huge range of pathogens.
  • Other parts of the immunoglobulin molecule cause a response, e.g. acting as a marker to phagocytes (which engulf the pathogen)
• Rhodopsin:

  • A pigment that absorbs light
  • Membrane protein of rod cells of the retina (light sensitive region at the back of the eye)
  • Rhodopsin consists of the opsin polypeptide surrounding a retinal prosthetic group
  • Retinal molecule absorbs a single photon of light -> changes shape -> change to the opsin -> the rod cell sends a nerve impulse to the brain
  • Even very low light intensities can be detected.
• Collagen:

  • A number of different forms
  • All are rope-like proteins made of three polypeptides wound together.
  • About a quarter of all protein in the human body is collagen
  • Forms a mesh of fibres in skin and in blood vessel walls that resists tearing.
  • Gives strength to tendons, ligaments, skin and blood vessel walls.
  • Forms part of teeth and bones, helps to prevent cracks and fractures to bones and teeth
• Spider silk:

  • Different types of silk with different functions
  • Dragline silk is stronger than steel and tougher than Kevlar
  • When first made it contains regions where the polypeptide forms parallel arrays (bottom)
  • Some regions seem like a disordered tangle (middle)
  • When the stretched the polypeptide gradually extends, making the silk extensible and very resistant to breaking.
• Genome: all of the genes of a cell, a tissue or an organism
• • The genome determines what proteins an organism can possibly produce.
  • A genome is unique to most individuals (identical twins and clones share a genome)
• Proteome: all of the proteins produced by a cell, a tissue or an organism.
• • Being a function of both the genome and the environment to which the organism is exposed the proteome is both variable (over time) and unique to every individual (including identical twins and clones).
  • It reveals what is happening in an organism at a particular time
• Environmental factors:

  • The environment influences what proteins an organism needs to produce and in what quantity.
  • Example factors would be nutrition, temperature, activity levels and anything else that affects a cell’s activities.
• Proteome is bigger than genome because:

  • Not all genes produce polypeptides
  • Multiple polypeptides and prosthetic groups can interact
  • Amino acids can be modified (e.g. Collagen)
  • A polypeptide can fold into different levels of structure (e.g. insulin)
• Denaturation:

  • The three-dimensional conformation of proteins is stabilized by bonds or interactions between R groups of amino acids within the molecule.
  • Most of these bonds and interactions are relatively weak and they can be disrupted or broken.
  • This results in a change to the conformation of the protein, which is called denaturation.
• • A denatured protein does not normally return to its former structure – the denaturation is permanent.
  • Soluble proteins often become insoluble and form a precipitate
• Heat can cause denaturation:

  • Vibrations within the molecule breaks intermolecular bonds or interactions.
• Extremes of pH can cause denaturation:

  • Charges on R groups are changed, breaking ionic bonds within the protein or causing new ionic bonds to form.
• • Thermophiles are organisms (often archaea or eubacteria) that live in relatively hot conditions (45 to 122 C).
  • In order that they can survive their proteins are stable at the higher than normal temperatures they experience.