Lec 1 level 3-de (chemistry of amino acids)


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Lec 1 level 3-de (chemistry of amino acids)

  1. 1. Biochemistry 1for Dental Students BCH 261
  2. 2. Biochemistry BCH 261 This course Prepared by Dr.Eman Saqr Course Directors ***********Associate Prof. Dr. Ehab(Male)Assistant Prof.Dr. Eman Saqr (Female)2
  3. 3. Course ObjectivesTo give the dental student the basic knowledge of biochemistry which is related to dentistry and medicine.3
  4. 4. The study of biochemistry is essentialto understand:Basic functions of the body.How the food that we eat is digested, absorbed, and used to make ingredients of the body?How does the body derive energy for normal day to day work?How are the various metabolic processes interrelated?What is the function of genes?The study of biochemistry is necessary to give the scientific basis for disease and is useful for intelligent treatment of patients. 4
  5. 5. Lectures schedule-Male/Female Reading Quizzes Week Date/Saturday Subject assignment 26/1/2013 1 Registration Introduction of Text book of biochemistry and Biochemistry for explain the course Dental Students 2th 2 2/2/2013 syllabus edition Amino acids Chapter 2 pp. 7-12 9/2/2013 A Chemistry of Chapter 2 pp. 12-18 3 Proteins Protein metabolism Chapter 12 pp. 107-109 Quiz 1 in the time of 4 16/2/2013 practical session - urea cycle Chapter 12 pp. 110-111 - Introduction to Chapter 3 pp. 19-22 23/2/2013 5 enzyme Enzymes and coenzyme Chapter 3 pp. 23-29 Quiz 2 in the time of 6 2/3/2013 practical session Chemistry and Chapter 4 pp. 31-41 9/3/2013 7 digestion of5 carbohydrates
  6. 6. Carbohydrate metabolism I 10 30/3/2013 [Glycolysis, citric acid Chapter 5 pp. 42-50 cycle and Chapter 14 pp. 128-132 gluconeogenesis] Carbohydrate metabolism II 11 6/4/2013 [Glycogen metabolism Chapter 5 pp. 50-53 and pentose shunt] Chapter 7 pp. 61-62 13/4/2013 Chemistry of lipids Chapter 9 pp. 76-82 Quiz 3 in the time of 12 practical session 20/4/2013 Lipid metabolism. Chapter 10 pp. 83-95 13 DNA: Structure and Chapter 24 pp. 209-214 Quiz 4 in the time of 14 27/4/2013 replication practical session Genetic code and Chapter 25 pp. 215-221 15 6/5/2013 Protein biosynthesis 16 13/5/2013 Practical Exam 20/5/2013 Oral Exam 17 27/5/2013 18 1/6/2013 Final Exam 19 5/6/20136 Summer Vacation
  7. 7. Recommended Books, References & Teaching Materials•Textbook of biochemistry for dental students by DMVasudevan, Sreekumari S and KannanVaidyanathan, 2nd Edition 2011.•Biochemistry by P.C. Champe, R.A. Harvey and D.R.Ferrier 3rd Edition 2005 Lippincott’s Illustrated Reviews•Handbook of biochemistry (For allied and nursingstudents) by Shivananda Nayak B 1st Edition 2007. 7
  8. 8. Teaching Methodology:• Lecture. 1hours•Practical Sessions. 2 hoursAssessment Tools for each semester: 20% - Mid-Exam 40% - Final Exam 20% - Assignments 20% - PracticalAssignments are:• 5 marks for each of Research project, Oral, and Quizzes.• 5 marks for attendance, attitude and participation during lecture session. 8
  9. 9. Research Project• Each one can choose one type of enzyme as a subject of the project.• Five students from each group will discuss their project weekly starting from the third week according to their presence in the attendance sheet.• The only excuse is by recommended medical certificate. 9
  10. 10. Time Table for Female Group One Group Two Sunday SundayTheoretical 11-12 8-9 Class 17 Class 11 Sunday SundayPractical 12-2 9-11Office Hours Saturday 10-1210
  11. 11. Time Table for Male Group One Group Two Sunday SundayTheoretical 7-8 4-5 Class 15 Class 15 Sunday SundayPractical 8-10 5-7Office Hours Saturday 5-711
  12. 12. Biomolecules The human body is composed of 6 elements, oxygen, carbon, hydrogen, nitrogen, calcium and phosphorus. Human body is composed of about 60% water, 15% proteins, 15% lipids, 2% carbohydrates and 8% minerals. Biomolecules are covalently linked to each other to form macromolecules of the cell, eg. Glucose to glycogen and amino acids to proteins. Major complex biomolecules are proteins, polysaccharides, lipids and nucleic acids. The macromolecules associate with each other to form supramolecular systems, e.g. ribosomes, lipoproteins. 12
  13. 13. ProteinDefinition:• Proteins are group of organic compounds composed of carbons, hydrogen, oxygen and nitrogen (sulphur and phosphorus may also present).• They are the most important of all biologic substances .• They are polymers of L-amino acids linked together by peptide bonds.13
  14. 14. Amino acidsDefinition:• They are the building blocks of proteins.• They are organic compounds, which contain two functional groups, amino group (-NH2) and carboxyl group (-COOH).• The amino group is usually attached to the α- carbon atom (next to the -COOH group).• Amino acids present in proteins are of the α-L-type i.e. the amino (H2N-) group is present on the left side of the vertical formula.14
  15. 15. 15
  16. 16. Classifications of amino acids• Classification according to structure• Classification according to side chain• Classification according to metabolic fate• Classification according to nutritional requirement •16
  17. 17. Classification according to structure1- Aliphatic aminoacids:a. Mono amino mono carboxylic acids• Simple amino acids (Glycine Gly, Alanine Ala)• Branched chain a.a. (Valine Val, Leucine Leu, Isoleucine Ile)• Hydroxy a.a. (Serine Ser, Threonine Thr)• Sulphur containing a.a. (Cysteine Cys, Methionine Met)• Having amide group (Asparagine Asn, Glutamine Gln)b. Mono amino dicarboxylic acids Aspartic acid Asp, Glutamic acid Gluc. Dibasic mono carboxylic acids Lysine Lys, Arginine Arg 17
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  19. 19. 2- Aromatic amino acids:• Phenylalanine Phe, Tyrosine Tyr3- Heterocyclic amino acids:• Tryptophan Trp, Histidine His4- Imino acid• Proline Pro 19
  20. 20. 5- Derived amino acid• Derived amino acids found in protein. Some amino acids modified after protein synthesis such as hydroxy proline and hydroxy lysine which are important component of collagen. Gamma crboxylation of glutamic acid residues of proteins is important for clotting process.• Derived amino acids not seen in protein. Some derived amino acids are seen free in cells as ornithine. Others produced during the metabolism of amino acids as citrulline and homocysteine. All of these amino acids called Non-protein amino acids. 20
  21. 21. Classification according to side chain1- Amino acids having nonpolar side chain:• These groups are hydrophobic and lipophilic.• These include, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine and Tryptophan.2- Amino acids having uncharged or nonionic polar side chain:• These groups are hydrophilic in nature.• These include, Glycine, Serine, Threonine, Cysteine, Tyrosine, Glutamine and Asparagine.3- Amino acids having charged or ionic polar side chain:• These groups are hydrophilic in nature.• Acidic amino acids: They have a negative charge on the R group include, Aspartic acid and Glutamic acid (Tyrosine is midly acidic).• Basic amino acids: They have a positive charge on the R group include, Lysine, Arginine and Histidine. 21
  22. 22. Classification according to metabolic1- Purely Ketogenic: fate• Leucine is purely ketogenic because it will enter into the metabolic pathway of ketogenesis.2- Ketogenic and Glucogenic:• Lysine, Isoleucine, Phenylalanine, Tyrosine and Tryptophan are partially ketogenic and partially glucogenic.• During metabolism, part of the carbon skeleton of these amino acids will enter the fatty acid metabolic pathway and the other part into glucose pathway.3- Purely Glucogenic:• All the remaining 14 amino acids are purely glucogenic as they enter only into the glucogenic pathway. 22
  23. 23. Classification according to nutritional requirement1- Essential or indispensable:• These groups are essential for growth.• Their carbon skeleton of these amino acids cannot be synthesized by human being.• These include, Isoleucine, Leucine, Threonine, Lysine, Methionine, Phenylalanine, Tryptophan and Valine.23
  24. 24. 2- Partially essential or semi-essential:• Growing children require them in food, but they are not essential for the adult individual.• These include, Histidine and Arginine.2- Nonessential or dispensable:• The remaining 10 amino acids are nonessential.• They also required for normal protein synthesis.• Their carbon skeleton can be synthesized by metabolic pathways. 24
  25. 25. Properties of amino acids: I. Physical properties1- .Amphoteric properties:• _ In solution, amino acids behave as acids and alkalis due to the presence of acidic group (-COOH) and basic group (-NH2). On complete ionization of neutral amino acids it acts as dipolar ions (Zwitterions or hybrid), they carry both negative and positive charges, which are equal. This explains the amphoteric• property of amino acid, i.e. they can react with acids and bases.• At isoelectric point, the amino acid carry no net charge; all the groups are ionized but the charges will cancel each other. Therefore, at iso-electric points, there is no mobility in an electrical field. Also solubility and buffering capacity will be minimum. 25
  26. 26. 2- Optical activity ;• _ All amino acids except glycine are optically active. Each optically active amino acid contains one asymmetric α-C atom attached to four different groups.• They occur in D and L forms.• The naturally occurring amino acids in proteins are of the L-α amino acid form.• D-amino acids are found in some antibiotics and bacteria. 26
  27. 27. 27
  28. 28. II. Chemical properties1- Reactions due to carboxyl group:A. Decarboxylation• The amino acids will undergo alpha decarboxylation to form the corresponding amine.• Ex. Histidine ---------- Histamine +CO2 Tyrosine ---------- Tyramine +CO2 Tryptophan------- Tryptamine +CO2 Glutamic acid --- Gamma aminobutyric acid +CO2 28
  29. 29. Decarboxylation reactionCOOHICH - NH2 ------------→ CH – NH2 + CO2I IR RAmino acid Corresponding amine29
  30. 30. B. Amide formation:• The –COOH group of dicarboxylic acids (other than alpha carboxyl) can combine with ammonia to form the corresponding amide.• Ex. Aspartic acid + NH3 ------- Asparagine Glutamic acid + NH3 ------- Glutamine• These amides are components of protein structure.• The amide group of glutamine serves as the source of nitrogen for nucleic acid synthesis. 30
  31. 31. Amide formation31
  32. 32. 2- Reactions due to amino groupA.Transamination• The alpha amino group of amino acid can be transferred to alpha keto acid to form the corresponding new amino acid and alpha keto acid.• This is an important reaction in the body for the inter conversion of amino acids and for synthesis of nonessential amino acids. 32
  33. 33. Transamination reaction33
  34. 34. B. Oxidative deamination• The alpha amino group is removed from the amino acid to form the corresponding keto acid and ammonia.• In the body, Glutamic acid is the most common amino acid to undergo oxidative deamination. 34
  35. 35. Oxidative deamination35
  36. 36. Reaction due to amino group Transamination and oxidative deamination36
  37. 37. 3- Reactions due to side chains:A. Ester formation by OH group• The hydroxyl amino acids can form esters with phosphoric acid.• In this manner the Serine and Threonine residues of proteins are involved in the formation of phosphoproteins.• Similarly these hydroxyl groups can form O- glycosidic bonds with carbohydrate residues to form glycoproteins. 37
  38. 38. B. Reaction of the amide group The amide groups of Glutamine and Asparagine can form N-glycosidic bonds with carbohydrate residues to form glycoproteins.C. Reactions of SH group• Cysteine has a sulfhydryl (SH) group and it can form a disulphide (S-S) bond with another Cysteine residue.• The two Cysteine residues can connect to polypeptide chains by the formation of inter-chain disulfide bonds or link.• The dimer formed by two Cysteine residues is called Dicysteine or cystine. 38
  39. 39. Reactions of SH group39
  40. 40. 4- Special functions of amino acids:• Gamma aminobutyric acid (GABA), a derivative of glutamic acid) and dopamine (derived from tyrosine) are neuro-transmitters.• Histamine (synthesized from histidine) is the mediator of allergic reactions.• Thyroxine (from tyrosine) is an important thyroid hormone. 40
  41. 41. 5- Peptide bond:• Alpha carboxyl group of one amino acid reacts with alpha amino group of another amino acid to form a peptide bond or CO-NH bridge. Proteins are made by polymerization of amino acids through peptide bonds.• Two amino acids combined to form dipeptide. Three amino acids form tripeptide. Four will make a tetrapeptide. 41
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  45. 45. • A few amino acids together will make an oligopeptide. Combination of 10 to 50 amino acids is called a polypeptide.• Big polypeptide chains containing more than 50 amino acids are called proteins.• Acid hydrolysis (hydrochloric acid at higher temperature) of peptides bonds will break the proteins into amino acids. But hydrochloric acid at body temperature will not break the peptide bonds.• Thus in the stomach, HCL alone will not be able to digest proteins; it needs enzymes. 45