2.4 Proteins

2.4 Proteins

Proteins are polymers made from the sub-units amino acids, joined together to make polypeptides chains. The name ‘polypeptide’ comes from the individual bonds between amino acids, which are called ‘peptide bonds’. One protein may be made from more than one polypeptide chain linked together.

 Haemoglobin molecule – made from 4 polypeptide chains.

image credit biotutotorial.com

image credit tutotorialpoint.com

 

A peptide bond

Peptide bonds are formed by condensation (the elimination of water), and broken by hydrolysis (the addition of water).

peptide bond

image credit boundless.com

 

Amino acids – the mystery and wonder

http://www.nasa.gov/topics/solarsystem/features/left_hand_aminoacids.html read this fascinating article

  • Amino acids have been found on asteroids, sampled in outer space according to NASA scientists.

Q) What could be the possible explanation for this phenomenum? 

  • Its possible for any amino acid to appear in two forms, a left-handed and a right-handed version. For some reason, all of the amino acids on Earth are left-handed.

Q) Is this evidence for the common ancestry of all life on Earth? If aliens life-forms exist, could their proteins be based on right-handed amino acids?

image credit: NASA

image credit: NASA

 

  • Scientists can make amino acids!

 

  • ‘In 1952, US scientist Stanley Miller  conducted one of the most famous experiments in all of science. They repeatedly sent electric sparks through flasks filled with the gases thought to resemble Earth’s early atmosphere, including water vapor, hydrogen, methane, and ammonia. After 1 week of zapping the mixture, they found organic compounds including amino acids in the mixture.

read more:

http://www.sciencemag.org/news/2011/03/long-neglected-experiment-gives-new-clues-origin-life

image credit: science mag.org

image credit: science mag.org

Q) Is this the same as creating life in a laboratory? How is it different?

Essential and non-essential amino acids

There are twenty amino acids, from which all of all of the proteins on the Earth are formed. Ten are essential, meaning we have to have them in our diet. Ten are non-essential, meaning we can synthesise them in our body from essential ones. The process of changing an essential amino acid into a non-essential amino acid is called transamination

This explains why vegetarians have to eat certain foods, like nuts, to get the essential amino acids that their metabolism requires.

 

image credit ptinterest.com

image credit ptinterest.com

 

Essential and non-essential amino acids

image credit compoun.chem.com

image credit compoun.chem.com

 

 

Proteome

Because all of us have differences in our sequence of DNA (with the possible exception of identical twins), every individual has a unique combination of proteins.

All the proteins produced by a cell, tissue or an organism is called the proteome.

by contrast, all the genes of a cell, tissue or an organism is called the genome.

 

Q). How would you study a proteome? Using gel electrophoresis, in the same way that you would analyse a genome.

Watch this khan academy video for a good introduction to the technique of gel electrophoresis. Take some personal notes on the process of gel electrophoresis.

Suggestions:

Q) What is gel electrophoresis

Q) How does it work?

Q) What is it for?

remember the story of the discovery of cyclins (cell division) by Tim Hunt? He was looking at the proteome of sea urchin eggs when he made his big discovery.

Denaturation: Why can proteins be ‘cooked?’

Raw salmon vs. Cookes salmon – both tasty, but what’s the difference?

image credit: sansaire.com

image credit: sansaire.com

Proteins have a complex, three dimensional structure which is stabilised by bonds between the R groups of amino acids within the molecule. Most of these bonds are easily broken by heat, or extremes of pH. These results in a breakdown of this three-dimensional structure, or change in the ‘conformation’.

We call this change in conformation ‘denaturation’. Denaturation is permanent, a protein will not return to its proper shape if allowed to cool down! If it can be restored to its original structure, which is rare – this is called ‘renaturation’.

image credit: memegenerator.net

image credit: memegenerator.net

how to flirt with a biochemist! – use at own risk.

Cooking an egg.

Albumen is the main protein found in egg white. The structure is globular (like a ball or globe), and like other proteins with this general shape, it is soluble in water and hence can be mixed with milk and used for baking recipes.

Once cooked, the globular structure breaks down, and a new structure forms which is much less dense. What is interesting is that new bonds called sulphur bridges form, linking all the albumen molecules into a continuous sheet. Sulphur bridges occur between amino acids that contain sulphur eg. methionine and cysteine. The SH refers to Sulphur hydryl groups, which are oxidised to make the S-S sulphur bridges in the process of denaturation.

image credit thinglink.com

image credit thinglink.com

 

Revision summary and links to next topics: Enzymes, transcription and translation

 

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