Proteins, structure, function, applications

Proteins presentation for IB, AP students

1. B1-2 PROTEINS

2. Chemical d i versity in the R-groups of amino acids

3. http://commons.wikimedia.org/wiki/File:Amino_Acids.svg “ OMG I HAVE TO LEARN THE NAMES OF ALL 20 !?!?” “Relax , no you don’t , you just need an awareness of the concepts as outlined.” 2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

4. Enantiomers of amino acids cells use only the L forms to synthesize proteins, D- and L-enantiomers

5. Non-esse nti al amino acids are ma d e fr o m other a mino a cids . Hu m a n s ca n o nl y synthes i ze10 of [h e 20 s ta nda rd amino a c i ds. T yros i ne an d cys t e i ne. f or exa mpl e, are synt h es i zed fr om t he essen tia l am i n o acids p h eny lal a nin e a n d m ethi oni ne, r espective l y. The live r h as enzymes su ch as tra n samin a ses and is r esponsib l e for no n- essentia l am ino ac i d synt h esis thro u g h a p rocess ca ll ed transamination.

6. Conversion of an essential amino acid into non essential amino acid ( structure not expected ) phenylalanine is converted into tyrosine by the enzyme phenylalanine hydroxylase ,

7. 2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes. Hydroxyproline is an example of an amino acid created not by the genetic code, but modification, after polypeptide formation, of proline (by the enzyme prolyl hydroxylase). http://chempolymerproject.wikispaces.com/file/view/collagen_%28alpha_chain%29.jpg/34235269/collagen_%28alpha_chain%29.jpg This modification of proline to hydroxyproline increases the stability of the collagen triple helix. Collagen is a a structural protein used to provide tensile strength in tendons, ligaments, skin and blood vessel walls. prolyl hydroxylase

8. Essential Amino acids

9. 2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together. Proteins may consist of a single polypeptide or multiple polypeptides that fold together.

10. If a polypeptide contains just 7 amino acids there can be 20 7 = 1,280,000,000 possible polypeptides generated. Given that polypeptides can contain up to 30,000 amino acids (e.g. Titin) the different possible combinations of polypeptides are effectively infinite. 2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

11. It is possible to eat a protein rich diet and still be deficient in an essential amino acid. Animal based foods like fish , meat, milk,eggs have a balance of amino acids . wheat has low lysine content and peas and beans are low in methionine both are essential amino acids ..

12. The level a protein conforms to is determined by it’s amino acid sequence. (Polypeptide) The order / sequence of the amino acids of which the protein is composed Formed by covalent peptide bonds between adjacent amino acids Controls all subsequent levels of structure The chains of amino acids fold or turn upon themselves Held together by hydrogen bonds between (non-adjacent) amine (N-H) and carboxylic (C-O) groups H-bonds provide a level of structural stability Fibrous proteins The polypeptide folds and coils to form a complex 3D shape Caused by interactions between R groups (H-bonds, disulphide bridges, ionic bonds and hydrophilic / hydrophobic interactions) Tertiary structure may be important for the function (e.g. specificity of active site in enzymes) Globular proteins The interaction between multiple polypeptides or prosthetic groups A prosthetic group is an inorganic compound involved in a protein (e.g. the heme group in haemoglobin) Fibrous and Globular proteins n.b. although you don’t need to be able to outline the different levels of structure for knowing of them helps to understand the difference between globular and fibrous proteins. This is though required knowledge for AHL (7.3.U7 to 7.3.U10)  The four levels of protein structure.

13. Primary structure of proteins The order / sequence of the amino acids of which the protein is composed Formed by covalent peptide bonds between adjacent amino acids Controls all subsequent levels of structure

14. Secondary  structure of proteins The most common types of secondary  structures are the  α helix  and the  β pleated sheet . Both  structures  are held in shape by hydrogen  bonds , which form between the carboxyl O of one amino acid and the amino H of another.

15. Super-secondary structure Super-secondary s truc tu r e describes the different pa tt erns that a-helices or beta -shee t s common l y adopt in proteins. For exa m ple , four alpha-helices often form a coiled-coil arrangemen t known as a four-helix bundle P a ir s of adjacen t helices are often addi ti ona ll y stabilized by sal t bridges (ionic bonding) b etween charged amino ac id s .

16. T wo beta - sheets m ay stack on top of each o ther in a 'beta sandwich ' such as in the immunoglobulin fold

17. Tertiary structure of a protein The tertiary structure of a protein consists of the way a polypeptide is formed of a complex molecular shape. This is caused by R-group interactions such as  ionic  and  hydrogen bonds , disulphide bridges, and hydrophobic & hydrophilic interactions.

18. Amino acid Cysteine

19. disulphide bridges between cysteine( amino acid)

20. Effect of polar and non-polar amino acids on tertiary structure of proteins

21. Chaperones are a functionally related group of proteins assisting protein folding in the cell under physiological and stress conditions . They share the ability to recognize and bind nonnative proteins thus preventing unspecific aggregation.

22. Quaternary structure of a protein The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure. The subunits are held together by  hydrogen bonds  and  van der Waals  forces between nonpolar side chains.

23. Non conjugated quaternary structure Eg Insulin has two polypeptides linked by sidulphide bonds eg 2 Collagen consists of 3 polypeptides wound together to form a rope like structure with high tensile strength.

24. Conjugated Proteins Have one or more non-polypeptide subunits in addition to their polypeptides. Eg Haemoglobin molecule consists of 4 polypeptide chains each associated with a heme group .The inclusion of non-polypeptide subunits increases the chemical and functional diversity of proteins. The haem group binds oxygen , allowing oxygen transport. Eg many enzymes have a non-polypeptide component that contributes to the catalytic activity of their active site.

25. Cryo- electron microscopy A protein sample is applied to a sample grid and is plunged into liquid ethane to flash freeze it . The protein molecules are trapped in a thin layer of ice and images can then be obtained using a beam of electrons . Software has been developed for processing the images to increase the resolution. Cryo EM also enables function to be investigated .The freezing technique allows conformation change to be revealed as a protein carries out its task.

26. In globular proteins the hydrophobic R groups are folded into the core of the molecule, away from the surrounding water molecules, this makes them soluble. In fibrous proteins the hydrophobic R groups are exposed and therefore the molecule is insoluble. Proteins are commonly described as either being fibrous ( Insoluble )or globular (Soluble )in nature. Fibrous proteins have structural roles whereas globular proteins are functional (active in a cell’s metabolism). 2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.

27. Relationship of form and function in globular and fibrous proteins FIBROUS PROTEIN - COLLAGEN Collagen consists of 3 polypeptides wound together in a triple helix. Primary structure of the polypeptide consists of repeating sequence of 3 amino acids P-G-X. P-is proline or hydroxy proline which prevents formation of α helix, since winding of the 3 polypeptides would be impossible if there were α helix. G- Glycine - since the R group of every 3rd amino acid faces inwards towards the centre of the triple helix , glycine is the only amino acid with an R group as a single H small enough to fit. X-The R group of this amino acid faces outward and is variable producing variations of collagen present in skin,tendons,ligaments,cartilage , etc. .

28. GLOBULAR PROTEINS Have a round shape formed by folding up of [ polypeptides,stabilised by bonds between the R groups of amino acids .that have been brought together by folding. Eg Active site of enzymes .

29. Denaturation Denaturation : a str uc t u ral change i n a p ro te i n that resu lts in a l oss (usua ll y permanent) of its biologica l p roperties De n at ur a t io n occ ur s w h en t he i o n i c interac ti ons, hydrogen b o n ds and oth er wea k in t ermo l ecula r fo r ces w i thi n til e g l o bu l ar prote in , fo r med be t wee n di fferen t a m ino a c i d r es i d u es, break, c h ang i ng t h e s hape of the protei n , i n clud i ng the a c tiv e s i t e i n enz y m e s ,