Proteins

Structure of a Protein

• Primary Structure

  • The unique sequence of amino acids that make up a polypeptide chain

    • Linear sequence of amino acids

    • Peptide bonds linking amino acids

• Secondary Structure

  • The way in which the primary structure of a polypeptide chain folds

    • Alpha helix and beta pleated sheets

    • Hydrogen bonds between amino acids

• Tertiary Structure

  • The final 3D structure of a protein, entailing the shape of a secondary structure

    • 3D folding of the polypeptide chain

    • Interactions between R groups (hydrophobic, hydrophilic, disulfide bonds, ionic bonds)

  • 2 types of 3D structures:

    • Globular

      • ball-like structures

      • hydrophobic parts are towards the center and hydrophilic parts are towards the edges - making them water soluble

      • have metabolic roles for example: enzymes

    • Fibrous

      • long fibers that consist of repeated sequences of amino acids that are insoluble in water

      • structural roles for example: collagen in bone and cartilage and keratin in fingernails and hair

• Quaternary Structure

  • The structure formed when two or more polypeptide chains join together, sometimes with an inorganic component, to form a protein

    • Interaction between multiple polypeptide chains

    • Formation of functional protein complex

Haemoglobin

• water soluble globular protein

  • not really water soluble, but suspended in water to form a colloid

  • hydrophobic R-groups face inwards away from the water and hydrophilic R-groups face outwards towards the water

• Structure: two alpha polypeptide chains and two beta polypeptide chains

• Function: carry oxygen around in the blood

• presence of a haem group what contains an iron ion that binds to the oxygen

Collagen

• fibrous protein

• Structure: three coils polypeptide chains wound around each other with hydrogen bonds between them

  • form Covalent Cross Links with each other (by forming further chains with other collagen molecules - further increasing its strength)

  • collagen molecules wrap around each other to form Collagen Fibrils that then form Collagen Fibers

• Function:

  • form the structure of bones

  • makes up cartilage and connective tissue

  • prevents blood that is being pumped at high pressure from bursting the walls of arteries

  • is the main component of tendons - which connect skeletal muscles to bones

Comparison between haemoglobin and collagen

• Basic shape:

  • Haemoglobin is globular

  • Collagen is fibrous

• Solubility:

  • Haemoglobin is soluble

  • Collagen is insoluble

• Amino acid constituents:

  • Haemoglobin contains a wide range of amino acids

  • Collagen has 35% of its primary structure made up of glycine

• Prosthetic group:

  • Haemoglobin contains a haem prosthetic group

  • Collagen does not contain a prosthetic group

• Tertiary structure:

  • much of the haemoglobin molecule is wound into alpha helices

  • much of the collagen molecule is made up of left handed helix structures

Protein Synthesis

The Genetic Code

• Each gene codes for 1 specific protein or polypeptide

• Each gene has a specific sequence of bases arranged in triplet codons: 3 bases, 1 codon codes for 1 amino acid

  • Triplet Codons

    • 64 possible triplet codons

      • Not all the triplet codons code for an amino acid → there are stop codons and ATG codes for methionine as well as acts as a start codon

      • The genetic code is a degenerate code

        • More than 1 codon codes for an amino acid

        • Advantage: if there was a change in 1 base during DNA replication (a mutation) there is a chance that the same amino acid would still be coded for

        • so the sequence of amino acids remain unchanged and the same protein would still be coded for

      • The genetic code is non-overlapping

        • Advantages: lots of amino acids could be coded for by short stretched of DNA

        • Disadvantages: a single change in a base during DNA replication would affect more than one triplet codon so would be more likely to code for a different amino acid sequence which would then code for a different protein

      • The genetic code is universal

        • The triplet codons code for the same amino acids in all living organism

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