Proteins

• Proteins are polymers (and macromolecules) made of monomers called?amino acids
• The?sequence, type?and?number?of the amino acids within a protein determines its shape and therefore its function
• Proteins?are extremely important in cells?because they form all of the following:
  • Enzymes
  • Cell membrane proteins (eg. carrier)
  • Hormones
  • Immunoproteins (eg. immunoglobulins)
  • Transport?proteins (eg. haemoglobin)
  • Structural?proteins (eg. keratin, collagen)
  • Contractile?proteins (eg. myosin)
• Because all genes code for proteins,?all of the reactions necessary for life?are dependent on the function of proteins

Amino acids

• Amino acids are the?monomers?of polypeptides
• There are?20 amino acids?found in polypeptides common to all living organisms
• The general structure of all amino acids is a central carbon atom bonded to:
  • An?amine?group -NH2
  • A?carboxylic acid?group -COOH
  • A?hydrogen?atom
  • An?R?group (which is how each amino acid differs and why amino acid properties differ e.g. whether they are acidic or basic or whether they are polar or non-polar)
  • The?R?group can be as simple as another hydrogen atom (glycine), right through to complex aromatic ring structures? (eg. phenylalanine)

The generalised structure of an amino acid

Peptide bond

• In order to form a?peptide bond?a hydroxyl group (-OH) is lost from the carboxylic group (-COOH) of one amino acid and a hydrogen atom is lost from the amine group (-NH2) of another amino acid
• The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid
• This is a?condensation?reaction so water is released
• Dipeptides?are formed by the condensation of?two?amino acids
• Polypeptides?are formed by the condensation of?many?(3 or more) amino acids
• A protein may have only one polypeptide chain or it may have multiple chains interacting with each other
• During?hydrolysis?reactions, the addition of water?breaks the peptide bonds?resulting in polypeptides being broken down into amino acids

Amino acids are bonded together by covalent peptide bonds to form a dipeptide in a condensation reaction

• The same 20 amino acids make up most of the proteins found on Earth
• Around 500 amino acids have been found in nature, but only?20 are commonly found in proteins
• Eleven?of these can be naturally synthesised within cells by humans
• The other nine amino acids are?essential?(have to be in the human diet)
• You don't need to remember the names of the amino acids, but it's useful to see their names, which are usually?abbreviated to three letters
  • Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His*, Ile*, Leu*, Lys*, Met*, Phe*, Pro, Ser, Thr*, Trp*, Tyr, Val*
  • *? indicates the essential amino acids
• Because the R groups vary so much between the 20 amino acids, there is a?lot of chemical diversity?between the amino acids

An amino acid sequence of a short polypeptide. The three-letter abbreviations indicate the specific amino acid (there are 20 commonly found in cells of living organisms).

NOS: Looking for patterns, trends and discrepancies; most (but not all) organisms build proteins from the same amino acids.

• All life?except for a few species use these 20 amino acids
• The reason why only 20 amino acids are used has been the subject of a lot of differing hypotheses
  • That only these 20 were available at the origins of life, so have remained ever since,?OR
  • That these 20 amino acids are diverse enough to give the wide range of functions that proteins possess,?OR
  • Because of the theory that all organisms share a common ancestor, the link between the genetic code and amino acid sequence is fixed and is not easily altered, even by mutations
• The almost?infinite number of amino acid combinations?make polypeptides suitable to determine?all the characteristics of life
• Only a few primitive, single-celled organisms use other amino acids
• One unusual amino acid includes the trace element?selenium?and is found in many polypeptides, though at?very low frequencies
  • A discrepancy is that in some organisms, the stop codon UAG codes for this unusual amino acid containing selenium
• All life goes by the?Central Dogma?that?all genes code for proteins?and the actions of proteins determine all of an organism's characteristics

• 20 amino acids can give an almost infinite number of polypeptides
• Polypeptides are assembled at a ribosome by condensing?individual amino acids?onto a growing chain,?one by one
• This allows a?choice of 20 amino acids?each time one is added
• The?mRNA codon?determines which amino acid is added
• For a polypeptide chain of 50 amino acids in length (considered a very?short protein), there would be?2050?possible combinations of amino acids
  • This gives 1.13 x 1065?combinations
  • Standard form?is preferable for showing such a large number, but writing it out in full shows its size, which is
  • 113,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 combinations!
• Given that the average length of a protein is?300 amino acids, the number of possible combinations is so large, we can consider it to be?infinite

• The amino acid sequence of polypeptides is coded for by genes
• Despite the huge number of amino acid sequences that could be produced, only a?small fraction?of these are produced in nature
• Nevertheless,?many thousands of different polypeptide sequences?are synthesised
• The code for the sequence in which amino acids are joined together is the?genetic code, held in a sequence of DNA bases in the?genome
• The?expression?of a gene always results in the production of a polypeptide
• Three consecutive DNA bases?are required to code for?each amino acid?in a polypeptide

The central dogma of gene expression. All genes code for proteins; proteins carry out the genes’ instructions.