Protein Lessons

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Amino acids and the primary structure

20 kinds of amino acids used in protein synthesis

Amino acids are also precursors to other useful molecules

Always the L-stereoisomer (except Glycine)

Classed according to R-group

Non-polar

Polar (acidic, basic, uncharged)

Amino acids join together via peptide bonds to form polypeptide chains

Peptide bond formation is a condensation reaction (leaves a “residue”)

The linear sequence of the protein is “read” N–C terminal

This is also termed the primary structure

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Translation of amino acids

Proteins are polymers of amino acids, with the sequence decoded from an RNA template

Protein synthesis is called translation because it goes from the language of nucleotides to the language of amino acids

The ribosome brings together multiple components to assemble the polypeptide chain

Ribosomes translate according to a (nearly) universal genetic code

Translation can be divided into three stages: initiation, elongation and termination

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Polypeptide chains and how they fold

Most residues cluster in regions of secondary structure (α helix, β strands, turns)

These are thermodynamically stable structures and polypeptides will spontaneously adopt these secondary structures very rapidly

The overall conformation of a polypeptide then depends on the arrangement of secondary structure motifs relative to each other

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Tertiary structure and the forces that stabilise proteins

Tertiary structure is the folding of polypeptides where the R-groups interact (usually far apart in the primary structure)

Non-covalent forces/bonds

Hydrophobic interactions

Hydrogen bonds

van der Waal interactions

Electrostatic bonds (ionic)

Covalent links

Disulphide bonds

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Protein Interactions and Quaternary structure

Systems Biology v Reductionism (including location and time)

Proteins form networks and form larger complexes

Interactions can be Transient or Stable

Proteins interact using the same forces/attractions/bonds as observed in tertiary structures

Examples of interactions:

Conformational changes to allow interaction

Some proteins act as “scaffold” for others to bind onto

Proteins can compete for binding sites

Proteins can have prosthetic groups

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Post-translation modification

Explain the importance of the primary amino acid sequence in forming a functional protein

Explain and provide examples of the different types of protein post-translational modifications

Modification of amino acids

Modifications during protein folding

Protein modifications for transport

Protein modifications required to activate proteins