Raghad Abu Jebbeh. Amani Nofal. Mamoon Ahram

Transcription

1 Raghad Abu Jebbeh Amani Nofal Mamoon Ahram

2 This sheet includes part of lec.13 + lec.14. Amino acid peptide protein Terminology: 1- Residue: a subunit that is a part of a large molecule. 2- Dipeptide: two amino acids that are linked by peptide bond. 3- Oligopeptide (the same as peptide): a short sequence of amino acids linked together. 4- Polypeptide: a long sequence of amino acids that are linked together, and it has no defined structure. 5- Protein: a polypeptide chain(s) which has a structure and function. **The size of the proteins: We can calculate the molecular weight of each amino acid, or simply we can take the average molecular weight for all amino acids which is about 110 Dalton, then multiply it by the number of amino acids in the protein to know the molecular weight of a protein. Example: suppose you have a protein which is composed of 100 amino acids, what is the molecular weight (size) for the protein? 100*110=11000 Dalton (11 K Dalton) Peptide bonds: (Or amide bonds in organic chemistry) 1- Between 2 amino acids: 2- Formed by a condensation reaction(produces H2O) 1 P a g e

3 Features of peptide bonds: (because of resonance structure) Has a zigzag structure Double bond feature: Caused by the change of double bond in C=O location so it becomes present in C=N (This happens because of resonance). Consequences of this feature: 1- The peptide bond becomes rigid (un-rotatable) 2- Becomes planar (flat) 3- Becomes charged *Negative charge on oxygen *Positive change on nitrogen The peptide bonds can t be rotated (rigid), but the bonds within the same amino acid can be rotated causing the protein to be more flexible and has different structures. Rich in Hydrogen bonding: *Hydrogen bonds are formed between Amino acids since the oxygen in the carbonyl group is H acceptor and it s and the carbon is. * While the amino group is H donor and it s on nitrogen, and on hydrogen. 2 P a g e

4 Proline amino acid can t form H bonds because it s cyclic so the nitrogen is no longer a H bond donor and it s called tertiary nitrogen if it makes a peptide bond, however, it can form H bonds with H2O as a residue because it still has the H bond acceptor. The backbone of peptides is formed by: Amide N α-c carbonyl C R groups are branches oriented outside. R groups are in the Trans orientation. 90% of R groups orientation in amino acids is Trans (why??) *Because steric hindrance between the functional groups attached to C atoms will be greater in the cis configuration *It s More energetically favorable in the Trans orientation Exception: In Proline, both Cis and Trans conformations have about equivalent repulsion energies. So 50% of the orientation is Cis and 50% is Trans. 3 P a g e

5 Directionality in peptides: 1-Peptides start with an amino group (Nterminus) and ends with a carboxyl group(cterminus), so the peptide has polarity which means two oppositely charged ends. 2-If you want to add a new amino acid it s added to the C-terminus. Functional peptides: (The following have exceptions whether in components or structure...) Carnosine α carbon of Alanine 1- A dipeptide of -alanine and histidine. 2- The exception is that the amino group of alanine is linked to carbon instead of α. 3- The carboxyl group of alanine can still form H bonds with the amino group of histidine. Amino Carbon group of of Alanine Alanine 4- It is highly concentrated in muscle and brain tissues 5- Functions: A) Protection of cells from ROS (radical oxygen species) and peroxides. B) Contraction of muscle. 4 P a g e

6 Glutathione 1- A Tripeptide of ( -glutamate, L-cysteine, glycine). 2- The peptide bond is between the amino group of cysteine and the carbon of carboxyl group of the R-chain of glutamate this carboxyl group is connected to carbon of glutamate. Amide bond between -glutamate and cysteine Carbon of glutamate 3- Function: Carboxyl group of R-chain Anti-oxidant that removes oxidizing agents from the body such as reactive oxygen species. Examples of reactive oxygen species: A- H 2 O 2 B- Free radicals such as superoxide. Free radicals miss an electron, so they are not stable, they can take electrons from any component inside the cell (DNA, protein, F.A.). Diseases occur if the electrons are taken from: A- DNA(damaging it causing mutations) B- Fatty acids (most of F.A are in the cell s membrane, if they are damaged, the membrane is damaged, so the cell dies). How it works: The amino acid Cysteine is the functional amino acid of Glutathione; because it has a Thiol group, this Thiol group gets reduced by sacrificing its electron to the free radical so 2 Glutathiones get linked by a disulfide bond. Functional amino acid: If this amino acid is changed, the peptide isn t functional anymore. 5 P a g e

7 Some enzymes make Glutathione active again by converting it to the reduced form. Enzymes Vitamins are also anti-oxidants (e.g.: vitamin E and C), vitamin E is found in the cell membrane to protect the membrane s F.A. Enkephalins: 1- Pentapeptides (5 amino acids). 2-2 types of proteins that differ in the last Amino acid: Met-enkephalin: Tyr-Gly-Gly-Phe-Met Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu 3- The functional amino acids are tyrosine and phenylalanine (Tyr, Phe). **Note: if Tyr or Phe are replaced by another amino acid, enkephalins will lose their function. 4- Function:Relieve and reduce pain. Morphine: A pain reducer used in hospitals, it s similar to Enkephalins so it binds to Enkephalin s receptors and relieves pain. *note: There are similarities between the three-dimensional structures of opiates, such as morphine, and enkephalins. 6 P a g e

8 The important group of pain relieving Oxytocin and vasopressin: 1- Hormones 2- Composed of 9 amino acids. 3- They are cyclic and the cycle is formed by disulfide bond between amino acids of the same peptide.(between cysteine) 4- Their difference is: -Oxytocin has Isoleucine and leucine (Ile, Leu). -Vasopressin has Phenylalanine and Arginine (Phe, Arg). 5- The C-terminus is modified by an amino group added to it. 6- Functions: -Oxytocin regulates contraction of uterine muscle at labor -Vasopressin is important for: A- Renal function and maintaining salt concentration in blood B-Regulates contraction of smooth muscle C-Increases water retention D-Increases blood pressure *note: look at slide n.16 Gramicidin S and tyrocidine A: 1- Cyclic decapeptides(10 amino acids) 2- Both contain the amino acid ornithine (Orn), which does not occur in proteins(not one of the 20 amino acids that build up proteins). 7 P a g e

9 3- Peptides are made of L-amino acids and D-amino acids. 4- Function: Bacterial antibiotics (produced by the bacterium Bacillus brevis). Aspartame 1- Dipeptide (aspartic acid and phenylalanine). 2- Carboxyl end is modified by methyl group. 3- Function:Sweetener )200 times sweeter than sugar) *note: If a D-amino acid is substituted for either amino acid or for both of them, the resulting derivative is better than sweet. 4- Clinical case: Phenylketonuria (PKU) *PKU is a hereditary inborn error of metabolism * Phenylalanine in the body should be converted into tyrosine by the enzyme phenylalanine hydroxylase. If the enzyme is defected, phenylalanine converts into phenylpyruvic acid, the accumulation of this acid is dangerous because it can reach the CNS causing brain damage The cure: Infants should be examined, if they have PKU, then parents should modify the infant s diet by reducing the amount of phenylalanine in food. Aspartame can t be used by people who suffer from PKU; because it contains phenylalanine, but they can use alatame instead; because it contains alanine rather than phenylalanine. 8 P a g e

10 Protein structure Theoretically, peptides can form infinity number of different structures, but realistically just 1 or 2 structures. The structure that the protein takes is the most energetically favorable structure. Native conformation: the 3D structure of properly folded and functional protein. Structure of protein levels: Primary Secondary Tertiary Quaternary Least complex Most complex 1- Primary structure: the sequence of amino acid residues in order. 2- Secondary structure: Localized organization of parts of polypeptide chain. 3- Tertiary structure: Structure of protein in 3D. 4- Quaternary structure: Related to proteins that are formed by more than one polypeptide, polypeptides are linked together covalently or non-covalently.in other words, it describes the number and relative positions of the subunits in a multimeric protein. *note: Multimeric protein: a protein made of multiple polypeptides 9 P a g e

11 Primary Structure: (The order in which the amino acids are covalently linked together) 1- The amino acid sequence starts with N-terminus and ends with C-terminus ALWAYS. 2- The primary structure is important because it determines the secondary,tertiary, quaternary 3- If one amino acid is changed, the whole protein will change probably.(can give rise to a malfunctioning protein) Clinical case: Sickle cell anemia A- Named like that because the cell looks like a sickle. B- It is caused by a change of one amino acids in the 6th position of globin (Glu to Val). C- Glutamic acid is polar while the Valine isn t, so Valine escapes from the hydrophilic region and hides in the protein s core changing its shape. D- Each Red blood cell has millions of hemoglobin molecules. E- Clusters of damaged haemoglobin molecules causes the change of the RBC to the sickle shape. F- Red blood cells will aggregate forming blood clot in vessels and tissues. Secondary structure: Four major secondary structures: 1- Alpha helix 2- Beta-pleated sheet 3- Turns 4- Loops 10 P a g e

12 1- Alpha helix: Helical rods -Per full turn there are 3.6 amino acids. Pitch -Pitch: the linear distance between corresponding points on successive turns) Approximately 5.4 Å 1 Å = 10^-10m Full turn (3.6 Amino acids) -Stable because of the formation of hydrogen bonds within the Secondary structure (between the oxygen of carbonyl group and the nitrogen of the Amino group, R groups are not involved in these hydrogen bonds) -Amino acids that don t present in alpha helix: 1- Glycine: too small 2- Proline: Too rigid and can t form hydrogen bonds, however it can present at the end of alpha-helix. 3- Amino acids that have the same charge of R-groups don t present above each other: repulsion 4- Amino acids with branches at the β-carbon atom (Valine, Threonine, and Isoleucine): These branches need space, and repulsion occurs if they exist in the alpha helix. other. -Amphipathic α helices: R groups are polar on one side and non-polar on the 1- Present in membrane proteins that work as ion channels so there s no Repulsion between the R- groups and ions. 2- Non-polar R-groups are exposed to the F.A and polar R-groups are exposed to the inner face of the cell. 11 P a g e

13 2-β pleated sheet -Formed by more than one β strand(each β strand looks like zigzag) -Can be parallel or non-parallel: Parallel: β strands are in the same direction. Anti-parallel: β strands are in opposite direction. Notice the difference in H bonds between parallel and anti-parallel. - Β sheets can form between many strands, typically 4 or 5 or more, that depends on the protein. -β sheets can be purely anti-parallel, purely parallel, or mixed - Valine, Threonine and Isoleucine tend to be present in β-sheets -Proline normally doesn t exist at β pleated sheet: Rigid, doesn t form hydrogen bonds. Links of videos: 1) 2) 3) 12 P a g e