Polypeptide and protein structure **structure of amino acids is very important and you must identify them Slide 1) single amino acid >more than one > polypeptide There is levels of structures of protein Protein can exist in many conformations (sometimes there is slightly differences between them and sometimes there is major differences ) At least one of these conformations is biologically active> need it to be active in human body(may be more than one conformation> active ) This two shapes (in the slide) >are they difference or the same? There is some differences between them >make big differences at the function e.g. hemoglobin > the conformation of it change to accommodate function >near lungs >it has slight open conformation so it can take oxygen >near tissues > it has slight close conformation so it can lose oxygen and prevent it to take another oxygen near tissues So we need the conformation for the function Slide 2) primary structure : amino acids binds to each other >sequence of amino acids polypeptide chain If you change the number of amino acids > you change the primary structure > you change the sequence of amino acids > you change the function >you change the whole protein *secondary structure : when amino acids come beside each other > each amino acid contain 2 parts > one is the backbone ; the second is the side chain. Backbone (alpha carbon ; carboxyl group ; amino group ) Side chain ( R group ) *the backbone can bind to each other by hydrogen bonds *the side chains can bind to each other also
>if there is side chain interactions and backbone interactions >we called it tertiary structure >secondary structure happen in most segments of polypeptide >tertiary structure is 3-D shape to all atoms in this polypeptide chain *main interaction in secondary structure is hydrogen bonds ; but the tertiary structure can involve anything *protein synthesis : transcription then translation >the sequence of amino acids (codons) >the chain stop at the stop codon > now we have polypeptide chain *it can fold around itself to give protein or more than one chain make the final protein *some proteins are consisting of one polypeptide chain and others are consisting with more than one *if there is more than one polypeptide chain in the protein >this means that the protein have quaternary structure ; but not all protein e.g. myoglobin (store oxygen inside muscles) >consist of single polypeptide ;but hemoglobin consist of 4 polypeptide chains so it has quaternary structure Slide 3) zigzag > like Z letter in English Why primary structure has zigzag structure? When amino acids bonds to each other > there is free rotation around the alpha carbon Alpha carbon bind to carboxyl and amino group > these two bonds has free rotation up or down in 180 degree > because the R group is bulky in general > it represent repulsive forces between themselves > so it fold (تلف) in free rotation > one R group up and the other down > the change > zigzag *It is important to know the primary sequence of protein? Because the final protein is determined by bonds between amino acids Also to know the abnormal
*Sickeled cell anemia > genetic disease We have sequence chain of hemoglobin( 4 peptide chains ) Single amino acid substitution in beta chain > this change glutamic acid (GAG) to valine (GTG) Any protein or enzyme in this life which make reactions > it must have active site e.g. hemoglobin has something called pocket and also each protein > this similar to active site in enzyme if there is any reaction it will happen inside this pocket glutamic acid in this chain is located in this pocket ( so what happen?) if hemoglobin protein come near to another hemoglobin molecule > it may bind to the pocket in the another hemoglobin > if the glutamic acid (negatively charged) exist it make repulsion with the another hemoglobin molecule so it prevent it to enter the pocket > so it make each hemoglobin by it self and the active site is free for oxygen binding but in the sickeled cell anemia > the glutamic acid change to valine(non-polar) so it will not make repulsion > so the hemoglobins will aggregate togother and they lost the active site of oxygen *Electrophoresis : acommon method for separating molecule in an electric field *The proteins especially globular proteins (inside hydrophobic and outside hydrophilic)because its hydrophilic outside so it follow the electric >so when we put it in abuffer solution (jell with spaces) > the protein will move according to the final charge on it. *If we make this method to hemoglobin (look the slide) > normal hemoglobin move to alonger distance than sickeled cell anemia (large aggregated hemoglobin is hard to move) Slide 4) the amino acid sequence is important to nutrition and research also *Vegeterians (they eat only plant proteins) *What is the difference(if your source is plant proteins or animal proteins)? Threre is some essential amino acids in plant proteins ; most animal proteins contain all essential amino acids so this source of protein is enough for you ; if you take from plants (the plants differ in the containing of essential amino acid and sometimes its deficient of one amino acids)
*complete protein by definition is the protein that have all essential amino acids and in abig percent >so its sufficient for the body Most plant proteins are not complete so they must take complementary proteins to complete the set of essential amino acids >because of that ; the people differ in the sources of food they eat *protein effeciency ratio : every protein have ascale from zero to one (how much this protein have essential amino acids to the total number of essential amino acids) So the proteins which have high rate > we called it high quality proteins (most in animals) its scale reach one. There is no protein have azero in scale because every protein have amino acids *soya protein is ahigh quality protein ( plant protein) Slide 5) protein like spaghetti > every spaghetti rod is similar to polypeptide chain ; interactions between spaghetti occurs random without order and follows gravity *in protein this doesn t occur >you have specific pattern for every protein from the sequence of amino acids and from the interactions between them (hydrogen ; ionic ; hydrophopic ; covalent bonds ) e.g. insulin has 6 cystein make disulfide bond between each other > so if you see globular protein and the cystein inside you expect it to make disulfide bond slide 6) the folding of protein start from the secondary structure (so there is folding in tertiary and quaternary structures also) يعني مش مرتبين بأي شكل *in ptimary structure ; there isn't any degree of ordered معين *the amino acid is two parts either backbone or side chain *In secondary structure >there is hydrogen bonding in the backbone ;but if there is bonds with the backbone and side chain so we are talking about tertiary structures
*secondary structure like spaghetti rod >there is regions near to each other and other regions far from each other >the regions near to each other try to make bonds in the backbone either of the same segment of this polypeptide chain or different segments but close to each other and this is the secondary structure *if far regions make bonds with each other (e.g. amino acid 300 bonds with amino acid 200 ) so now we talk about tertiary structure and happen between side chain and backbone *the secondary structure exist because there is free rotation around the alpha carbon *its features: periodic means that this feature repeat every regular interval *most of tertiary structure is secondary structure organizations *most of secondary structure proteins is tough and its function is structural in body like keratin ; collagen *the bonds in secondary structure is hydrogen bonds >hydrogen bonds is weak (so how the secondary structure stabilize?) >the intensive amount of hydrogen bonds in each structure stabilize it Slide 7) alpha helix has properties repeat every regular interval and its right handed شكلو نفس الزنبرك* *what factors affect the stability of alpha helix? 1-specific amino acid (e.g.proline >kinks>so the alpha helix stop >beta sheates may start or another بالعادة الزنبرك حتى يقوم بدوره الوظيفي الزم يكون على مستوى واحد ما بتالقي helix) alpha زنبرك بلف بعيد عن هاد المستوى 2-electrostatic repulsion (if there is positively charged amino acids around each other >they repulse and change the alpha helix) (or if there is positive and negative so there is too much attractive which also change the features of alpha helix ) 3-steric repulsion :if there is bulky chain amino acid like tryptophan *when the R group distribute in ahelical shape (if you look from top view >you see only circle)all the R groups are outside the helix..why?because its bulky and to give chance to the amino acid to rotate
Slide 8) repeat every regular interval There is sequence of amino acids >this chain loop and there is another sequence of amino acids >so they make bonds between each other (parallel) >if the two sequences opposite in direction to each other they called (antiparallel) *R groups come above and below the sheets to prevent the repulsion Slide 9) loop (its definition is not clear in biochemistry) but in general when we finish of secondary structure >we must have segment connecting this structure with another structure > this segment if it long we call it loop ; if it short (4 to 5 amino acids ) we call it turn ( beta bends ) >they are sharp (the first amino acid bind to the fourth amino acid ) and this stabilize it *amotif : either alpha helix or beta sheets ( or both ) If you find motif in more than one protein > each protein will have adifferent function *domain is similar to motif > exist in more than one protein > super secondary structure ; repetitive > but the proteins have the same functions e.g. leucine zipper (2 alpha helices bonds to each other > نفس المقص <شكلهم and they bind to DNA ) they called it (DNA binding domain >means that it goes to bind to DNA) *functions of domains >when you discover anew protein and you don t know its function > you search in its domains >according to it you know the function of the protein المهم األسماء في هذا الساليد )مش مهم الخصائص( (10 Slide you must know that its secondary structures *beta-alpha-beta : 2 beta sheets parallel to each other and connected to alpha helix >this is loop (the long link between alpha and beta) but the turn (is the short link between alpha and beta)