Biomolecules Amino Acids & Protein Chemistry

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1 Biochemistry Department Date: 17/9/ 2017 Biomolecules Amino Acids & Protein Chemistry Prof.Dr./ FAYDA Elazazy Professor of Biochemistry and Molecular Biology

2 Intended Learning Outcomes ILOs By the end of this lecture student should be able to Enumerate essential elements in the human body Name the 4 major macromolecules in living cells

3 Main elements of life

4 Many Important Biomolecules are Polymers made up of monomer subunits Chemical bonds

5 Polymers Monomers Carbohydrates Monosaccharide Lipids Hydrocarbon chains Proteins Amino acids Nucleic acids Nucleotides

6 Glucose How polymers formed? CH 2 OH CH 2 OH CH 2 OH CH 2 OH H C OH C H OH C H O H C OH H H C C OH O OH H H C H OH C H O H C OH H H C C OH O OH H H C H OH C H O H C OH H H C C OH O OH H H C H OH C H O H C OH H C OH In this example, 3 CONDENSATION reactions have produced 3 water molecules to produce the polymer. A HYDROLYSIS reaction (addition of water) reverses the reaction and splits the polymer releasing 4 monomer molecules. Both reactions require ENZYMES

7 Carbohydrates monomer glucose polymer cellulose supramolecular structure cell wall

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9 Lipids lipids monomer fatty acid polymer phospholipid supramolecular structure membrane

10 Nucleic Acids monomer nucleotide polymer DNA supramolecular structure chromatin

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12 Proteins monomer amino acids polymer protein supramoleculr structure Enzyme complex

13 Intended Learning Outcomes (ILOs) By the end of this lecture, the student will be able to: 1. Define protein 2. Illustrate functions of proteins 3. Describe the chemical structure of amino acids. 4. Explain amino acids classification.

14 Proteins are amino-acid polymers Amino acids linked together by peptide bonds

15 AA AA AA AA AA AA AA AA AA Amino Acids are the Building Blocks of Proteins Building unit AA Topic 12-1SANAA EISSA

16 In addition to carbon, hydrogen, and oxygen, they are essentially nitrogenous compounds They also contain sulfur

17 Proteins are synthesized from amino acids according to genetic code(central Dogma)

18 T A C A T C G A T C G DNA A U G U A G C U A G C RNA Transcription

19 T A C A T C G A T C G DNA Ribosome messenger A U G U A G C U A G C mrna U A 1 C A U 2 C trna transfer Met Ile Translation

20 T A C A T C G A T C G DNA A U G U A G C U A G C mrna A U 2 C G A 3 U trna Met Ile Asp

21 T A C A T C G A T C G DNA A U G U A G C U A G C mrna Met Ile Asp Protein

22 Functions of Proteins

23 Structural function Membranes Intercellular e.g., collagen & elastin Cell membrane & cell organelles

24 Contractile function Actin & Myosin

25 Catalytic function All bodily functions are mediated by chemical reactions Chemical reactions are catalyzed by enzymes Enzymes are proteins

26 Transport function Respiratory gases hemoglobin Lipids lipoproteins Metals transferrin, ceruloplasmin Hormones hormone-binding proteins

27 Regulatory function Hormones Receptors

28 Protective function Antibodies

29 Proteins Antibody Muscle Hormones virus Hemoglobin Enzymes

30 Other functions Rhodopsin for night vision Histones for chromosomes

31 Amino Acids NH2 C C C C C COOH R ( side chain) amino acids AA is composed of: 1-Carboxyl gp. 2-Amino gp. 3- Side chain (R). 20 natural amino acids different in R (20 R)

32 More than 300 amino acids occur naturally, but 20 of them are especially important. These 20 amino acids are the building blocks of proteins. Each of 20 amino acids has a specific genetic codon on DNA.

33 Structure of Amino acids

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35 L-Form Amino Acid Structure Carboxylic group COO - Amino group + H N 3 H R group H = Glycine CH 3 = Alanine

36 Naturally occurring amino acids in mammalian Naturally occurring amino acids in mammalian are L form D-amino acids are present in bacterial cell walls and in some antibiotic drugs.

37 Classification of Amino Acids Chemical Based on the structure of the side chain (R group) According to polarity Polarity of the side chain Nutritional Based on whether amino acid can be synthesized or not in the body Metabolic Based on the fate of amino acids in the body

38 R-Group No ring With ring Aliphatic Cyclic: all ring H & C Heterocyclic: ring contains N +H+C

39 Aliphatic aminoacids Gly [G] Glycine is the simplest amino acid three-letter abbreviation for describing aminoacid sequence of a polypeptide. Ala [A] one-letter abbreviation for very long polypeptides.

40 Aliphatic with branched chain Val [V] Leu [L] Ile [I]

41 Aliphatic with hydroxyl group Ser [S] Thr [T]

42 Aliphatic, sulfur containing Thiol group Cys [C] Met [M]

43 Acidic (dicarboxylic) aminoacids Ionized at plasma ph=7.4 Asp [D] Glu [E]

44 Amides of dicarboxylic aminoacids Asn [N] Gln [Q]

45 Basic aminoacids -amino heterocyclic Imidazole group Guanido group + H protonated at plasma ph=7.4 pk a =12.5 Lys [K] Arg [R] His [H]

46 Aromatic amino-acids Heterocyclic? Indole group Phe [F] Tyr [Y] Trp [W]

47 Cyclic imino-acid Heterocyclic Pyrrole ring Pro [P]

48 + H

49 Amino Acid Type Amino Acid Abbreviations R contains basic gp Arginine Arg R (NH3+) Lysine Lys K Histidine (H.cycl) His H R contains acidic gp (COO-) Or their derivatives Aspartic Asp D Glutamic Glu E Asparagine Asn N Glutamine Gln Q R contains OH gp Tyrosine (Ar.cycl) Tyr Y Serine Ser S Threonine Thr T

50 Amino Acid Type Amino Acid Abbreviations R contains S Cysteine (SH) Cys C Methionine (S atom) Met M No functional gp (Aliphatic) Glycine Gly G Alanine Ala A Valine Val V Leucine Leu L Isoleucine Ile I R is cyclic Phenylalanine Phe F Tryptophan (H.cycl) Trp W Tyrosine (cycl) Tyr Y Imino acid Proline (H.cycl) Pro P

51 Classification according to polarity R-Group Polar Hydrophilic Able to react with water Can form Hydrogen bond with water Non-Polar Hydrophobic Unable to react with water Can not form hydrogen bond with water

52 Classification according to polarity Polar Non polar Occur on the surface of the proteins Buried in the interior of cytosolic proteins Present in direct contact with water Away from water Share in hydrophobic interactions

53 Aliphatic amino-acids * Polar Non-Polar

54 Aliphatic with branched chain * * *

55 Aliphatic with hydroxyl group Polar

56 Aliphatic, sulfur containing Polar *

57 Acidic (dicarboxylic) aminoacids -ve

58 Amides of dicarboxylic aminoacids Polar

59 Basic aminoacids Polar positively charged + ve -amino heterocyclic Imidazole group Guanido group + H protonated at plasma ph=7.4 pk a =12.5 Lys [K] Arg [R] His [H]

60 Aromatic aminoacids Recall that phenol has limited solubility in water *Some authors consider tyrosine Less hydrophobic slightly polar *

61 Cyclic iminoacid *

62 Diamino Monocarboxylic Basic Positive: Arg Lys His Cyst Cysteine Arginine Lysine Negative: Aspar Amine Histidine Dicarboxylic Monoamine Acidic Polar uncharged Monoamino Monocarboxylic Aspargine Glutamine Polar charged Aspartic Glu Glutamic GLYCINE Hydroxy: Tyr Ser Threo Serine Threonine

63 Sulfur containing AAs: Non Polar Methionine (S): Non polar Aromatic AAs: Non Polar Phenylalanine (benzen ring) Tryptophan (indole ring)(heterocyclic) R -Branched Valine, leucine, isoleucine (bulky) Heterocyclic AAs: Non Polar Proline ( imino acid- Pyrrole ring) Topic 12-1

64 Heterocyclic AAs: Histidine-imidazole Tryptophane-Indole Proline-pyrrole Cyclic AAs: NH3+ Phenylalanine Tyrosine C HN C C C-COOH R C C C C C benzene C COO- C Imino acid Topic 12-1

65 Biological(nutritional) classification Indispensible(essential) Dispensable(non essential) Semi essential Not synthesized inside the body Can be synthesized inside the body Arginine and Histidine in children only Essential in the diet Not Essential in the diet The rate of synthesis can not satisfy the excessive needs of growing children

66 Essential Amino Acids 10 amino acids not synthesized by the body Phe, val, thr, trp, ile, met, his, arg, leu, lys P V T T I M H A L L (PVT TIM HALL) Must obtain from the diet All in diary products 1 or more missing in grains and vegetables Arg., his. are semiessential as required > synthesized. Topic 12-1

67 * *

68 Essential Amino Acids Proteins of high biological value: contains 10 essential AA e.g. animal proteins Proteins of low biological value: vegetable proteins lack one or more of essential AA Combinations of low biological value: Corn الذره ( no lysine-rich methionine ) + legums الفاصوليا as beans البقوليات ( no methionine rich lysine) Topic 12-1 = high biological value

69 Protein of high biological value

70 Essential Amino Acids The 3 Basic or positively charged: (Lysine, Arginine, and Histidine). The 3 Branched: (Valine, Leucine and Isoleucine). 2 Aromatic: Phenylalanine and Tryptophan The 2 large OH containing and S containing (Threonine and Methionine).

71 Which of the following determines the aminoacids in a human protein? A- Aminoacids of diet proteins. B- Aminoacids in the blood. C- The size of the protein. D- Nucleotide sequence of DNA. E- Enzymes that synthesize the protein.

72 An aromatic aminoacyl residue with a polar group is a)glutamine. b)cysteine. c)serine. d)tyrosine.

73 An aminoacyl residue with a charged group is a) Glutamine. b) Arginine. c) Cysteine. d) Serine. e) leucine

74 Topic 12-1