Principles of Biochemistry

Transcription

1 Principles of Biochemistry Fourth Edition Donald Voet Judith G. Voet Charlotte W. Pratt Chapter 4 Amino Acids: The Building Blocks of proteins (Page 76-90)

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3 Chapter Contents 1- Amino acids Structure: 2- Stereochemistry 3 - Amino Acid Derivatives

4 Introduction In 1839, the Swedish chemist Jacob Berzelius coined the term Protein (Greek: Proteios, Primary) for this class of compounds. Modern studies of proteins and amino acids owe a great deal to nineteenth and early twentieth century experiments.

5 1- Amino Acid Structure: Introduction All proteins are composed of 20 standard amino acids. The common amino acids are known as α amino acids because they have a primary amino group (- NH 2 ) as a substituent of the α carbon atom, the carbon next to the carboxylic acid group (- COOH; Fig. 4-1).

6 1- Amino Acid Structure: Introduction The 20 standard amino acids differ in the structures of their side chains (R groups). Figure 4-1: General structure of an amino acid. The R group different the 20 standard amino acids.

7 1- Amino Acid Structure One Amino Acid Cα is at the heart of the amino acid Cα, C, N, and O are called backbone atoms R can be any of the 20 side chains

8 1- Amino Acid Structure

9 1- Amino Acid Structure

10 1- Amino Acid Structure

11 1- Amino Acid Structure

12 1- Amino Acid Structure The 20 Amino Acids Found in Proteins

13 1- Amino Acid Structure The 20 amino acids The 20 Amino Acids Found in Proteins The side chains, R, determine the differences in the structural and chemical properties of the 20 natural amino acids. The 20 amino acids can, for example, be classified as follows: Hydrophobic Aliphatic Ala, Leu, Ile, Val Aromatic Phe, Tyr, Trp, (His) Hydrophilic Polar Asn, Gln Alcoholic Ser, Thr, (Tyr) Charged Arg, Lys, Asp, Glu, (His) Inbetween Sulfur-containing Met, Cys Special Gly (no R), Pro (cyclic) Several amino acids belong in more than one category.

14 1- Amino Acid Structure Amino Acids: Aliphatic

15 1- Amino Acid Structure Amino Acid: Proline (The only secondary (2 ) amino acid or ( imino acid.)

16 1- Amino Acid Structure Amino Acids: Aromatic

17 1- Amino Acid Structure Amino Acids: Alcohols

18 1- Amino Acid Structure Amino Acids: Sulfur

19 1- Amino Acid Structure: C - Amino Acid side chains are Nonpolar, Polar, or Charged Figure 4-6: Disulfide bonded cysteine residues.

20 1- Amino Acid Structure Classification Based on Chemical Constitution Small amino acids: Glycine, Alanine Branched amino acids: Valine, Leucine, Isoleucine Hydroxy amino acids (-OH group): Serine, Threonine Sulfur amino acids: Cysteine, Methionine Aromatic amino acids (Heterocyclic ring): Phenylalanine, Tyrosine, Tryptophan Acidic amino acids and their derivatives: Aspartate, Asparagine, Glutamate, Glutamine Basic amino acids: Lysine, Arginine, Histidine Imino acid: Proline

21 1- Amino Acid Structure: A - Amino Acids are Dipolar Ions The amino and carboxylic acid groups of amino acids readily ionize. At Physiological ph (~ 7.4), the amino groups are protonated and the carboxylic acid groups are in their conjugate base (Carboxylate, unptotonated) form (Fig. 4-2) Molecules such as amino acids, which bear charged groups of opposite polarity, are known as Dipolar Ions or Zwitterions. Amino acids, like other ionic compounds, are more soluble in polar solvents than in nonpolar solvents.

22 1- Amino Acid Structure: A - Amino Acids are Dipolar Ions Figure 4-2: A dipolar amino acid. At physiological ph, the amino acid group is protonated and the carboxylic acid group is unprotonated.

23 1- Amino Acid Structure: A - Amino Acids are Dipolar Ions Nonionic and Zwitterion Forms of Amino Acids Zwitterion = in German for hybrid ion The zwitterion predominates at neutral ph Weak acid Weak base

24 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids Amino acids can be polymerized to form chains (a Condensation Reaction); bond formation with the elimination of a water molecule (Fig. 4-3). Condensation and Hydrolysis reaction

25 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids The resulting CO -NH linkage, an amide linkage, as known as a Peptide Bond.

26 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids Formation of a Peptide

27 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids Polymers composed of two, three, a few (3 10), and many amino acids units are known respectively, as Dipeptides, Tripeptides, Oligopeptides, and Poly- peptides. After they are incorporated into a peptide, the individual amino acids (the monomeric units) are referred to as amino acid residues.

28 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids Polypeptides are linear polymers rather than branched chains; that is, each amino acid residue participates in two peptide bonds and is linked to its neighbors in a head-to-tail fashion. The residue with a free amino group (by convention, the leftmost residue, as shown in Fig. 4-3) is called the Amino Terminus or N - Terminus. The residue with a free carboxylate group (at the right) is called the Carboxyl Terminus or C- Terminus. Proteins are molecules that contain one or more polypeptide chains.

29 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids

30 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids Variation in the length and the amino acid sequence of polypeptides are major contributors to the diversity in the shapes and biological function of proteins.

31 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids Examples of Oligopeptides

32 1- Amino Acid Structure: B - Peptide Bonds link Amino Acids

33 Amino Acid are Abbreviated The 20 amino acids A Ala Alanine C Cys Cysteine D Asp Aspartic acid (Aspartate) E Glu Glutamic acid (Glutamate) F Phe Phenylalanine G Gly Glycine H His Histidine I Ile Isoleucine K Lys Lysine L Leu Leucine M Met Methionine N Asn Asparagine P Pro Proline Q Gln Glutamine R Arg Arginine S Ser Serine T Thr Threonine V Val Valine W Trp Tryptophan Y Tyr Tyrosine

34 1- Amino Acid Structure: E - Amino Acid Names are Abbreviated Amino acid residues in polypeptides are named by dropping the suffix, usually ine, in the name of the amino acid and replacing it by yl. Polypeptide chains are described by starting at the N terminus and proceeding to the C - terminus.

35 1- Amino Acid Structure: E - Amino Acid Names are Abbreviated Examples for names of Oligopeptides (tetrapeptide) Alanyltyrosylaspartylglycine; AYDG

36 1- Amino Acid Structure: E - Amino Acid Names are Abbreviated The various atoms of the amino acid side chains are often named in sequence with the Greek alphabet, starting at the carbon atom adjacent to the peptide carbonyl group.

37 1- Amino Acid Structure: E - Amino Acid Names are Abbreviated Lysine (Lys): have an ε amino group Glutamic acid (Glu): have a γ carboxyl group Figure 4-8: Greek nomenclature for amino acids.

38 Stereochemistry 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 38

39 Background Chirality Handedness : Right-hand glove does not fit the left hand. An object is chiral if its mirror image is different from the original object. 10/22/2017 Dr. Amjid Iqbal PhD (University of

40 Achiral Mirror images that can be superposed are achiral (not chiral). 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 40

41 How about molecules? Chemical substances can be handed Handed substances are said to be chiral Molecules, that are chiral are nonsuperimposable on their mirror image 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 41

42 Molecular Chirality: Enantiomers Enantiomers: non-superimposable mirror image isomers. Enantiomers are related to each other much like a right hand is related to a left hand Enantiomers have identical physical properties, i.e., bp, mp, etc. Chirality (from the Greek word for hand). Enantiomers are said to be chiral. 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK)

43 Stereoisomers Enantiomers: Compounds that are nonsuperimposable mirror images. Any molecule that is chiral must have an enantiomer. 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK)

44 Chiral Carbon Atom Tetrahedral carbon atom that is bonded to four different groups is chiral, also called asymmetric carbon atom and such molecule is called asymmetric. Its mirror image will be a different compound (enantiomer). 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK)

45 The Chirality Center - A molecule containing a carbon with four different groups results in a chiral molecule, and the carbon is referred to as a chiral, or asymmetric, or stereogenic center. 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK)

46 Amino Acids The α-carbon of amino acid is attached to four different groups is a chiral or asymmetric. Glycine is the exception. Amino acids exist in two forms, D and L, that are mirror images of each other. All amino acids found in proteins are of the L- configuration. 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 46

47 Optical activity when a substance rotates the plane of plane polarized light. Optically active molecules are asymmetric, that they are not superimposable on their mirror image. All amino acids except glycine are optically active Plane polarized light light that has been passed through a nicol prism or other polarizing medium so that all of the vibrations are in the same plane. non-polarized polarized 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 47

48 Polarimeter Figure 4-9: Diagram of Polarimeter (measure optical rotation). L= Levorotatory: rotates polarized light to the left D = Dextrorotatory: rotates polarized light to the right

49 dextrorotatory when the plane of polarized light is rotated in a clockwise direction (right) when viewed through a polarimeter. (+) or (d) do not confuse with D levorotatory when the plane of polarized light is rotated in a counter-clockwise direction (left )when viewed through a polarimeter. (-) or (l) do not confuse with L The angle of rotation of plane polarized light by an optically active substance is proportional to the number of atoms in the path of the light. 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 49

50 The Fischer Convention describes the Configuration of Asymmetric Centers. Fischer Convention: was used to describe different forms of chiral molecules. In this system, the configuration of the groups around an asymmetric center is compared to the of glyceraldehyde, a molecule with one asymmetric center. In 1891, Emil Fischer proposed that the special isomers or stereoisomers of glyceraldehyde be designated D - Glyceraldehyde and L -Glyceraldehyde (Fig. 4 11).

51 Fischer Convention Describe the Configuration of Asymmetric Centers. Configuration the arrangement in space of the four different groups about a chiral center. How do we show configurations? wedge formulas Fischer Convention cross structures use only for chiral centers! F Br H Cl Cl Br F 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) H 51

52 Fischer Convention It is used to describe different forms of Chiral molecules horizontal line is coming out of the plane of the page (toward you) substituent carbon vertical line is going back behind the plane of the paper (away from you) (R)-lactic acid H 3 C CO 2 H OH H H CO 2 H CH 3 OH H CO 2 H CH 3 OH (S)-lactic acid H 3 C CO 2 H H OH HO CO 2 H CH 3 H HO CO 2 H CH 3 H 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 52

53 Figure 4-11: The Fischer Convention.

54 The configuration of groups around any chiral center can be related to that of glyceraldehyde by chemically converting the groups to those glyceraldehyde. For α amino acids, the amino, carboxyl, R and H groups around the C α atom correspond to the hydroxyl, aldehyde, CH 2 OH, and H groups, respectively, of glyceraldehyde. Therefore, L- Glyceraldehyde and L- α - amino acids are said to have the same relative configuration.

55 L-glyceraldehyde and L-α- amino acids have the same relative configuration.

56 All amino acids derived from proteins have the L stereochemical configuration; that is, they all have the same relative configuration around their C α atoms. The Fischer system has some shortcoming, particularly for molecules with multiple asymmetric centers. Each asymmetric center can have two possible configuration, so a molecule with (n) chiral centers has 2 n different possible Stereoisomers.

57 Life is Based on Chiral Molecules: Ordinary chemical synthesis of a chiral molecule, produce a racemic mixture. Racemic mixture: is a molecule which containing equal amount of each enantiomer and optically active molecules. 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 57

58 Biosynthetic process almost invariably produce pure stereoisomers (only one isomer). Protein made of L - amino acid residues that react with a particular L - amino acid does not readily react with the D form of that amino acid. An otherwise identical synthetic protein made of D - amino acid residues, however, readily react only with the corresponding D - amino acid.

59 D-amino acid residues are components of bacterial polypeptides, these polypeptides are important part of bacterial cell walls Because of D-amino acids, bacterial cell wall is protected from peptidase (an enzyme made up of L-amino acids) produce by other organisms to digest bacterial Most peptides containing D-amino acids are not synthesized by standard transcription and translation 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 59

60 Pharmaceutical Industry Many drug are chemically synthesized as racemic mixture, although only one enantiomer has biological active (such as Ibuprofen, Thalidomide). Ibuprofen: is anti-inflammatory agent, only one enantiomer of which is physiologically active Thalidomide: is a mild sedative whose inactive enantiomer causes severe birth defects.

61 Figure 4-12: Ibuprofen. Only the enantiomer shown the antiinflammatory action. The chiral carbon is red

62 Figure 4-13: Thalidomide. the mild sedative whose inactive enantiomer cause severe birth defects. The chiral carbon is red

63 Quick Review Chiral carbons (Tetrahydrocarbon atoms): have four different groups attached. Asymmetric centers or chiral centers: is the central atoms. Enantiomers: Molecules that are nonsuperimposable mirror images. RS: Nomenclature is not used for amino acids. LD: Nomenclature used for amino acids. Stereoisomers: Compounds that have the same molecular formula but differ in the arrangement of atoms in space.

64 Quick Review A racemic mixture containing equal amount of the two enantiomers is Optically active molecules. The peptidases: enzymes that hydrolyze peptide bonds.

65 Quick Review Conclusion: 1 - α - carbon (C α ) atom is a chiral center. 2 - All amino acids in proteins are L - amino acids, except for Glycine, which is achiral. 3 - Two stereoisomers are called Enantiomers. 4 - The solid wedge-shaped bonds project out of the plane of paper, the dashed bonds behind it. 5 - The horizontal bonds project out of the plane of paper, the vertical bonds behind.

66 Amino Acid Derivatives 20 amino acids are not only amino acids that occur in biological systems. Nonstandard amino acid are also biologically important 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 66

67 Protein Side Chains May be Modified In almost all cases, there is modification of amino acid residue after the polypeptide chain synthesized. These modification include simple reactions on side chain: hydroxylation, methylation, acetylation, carboxylation, phosphorylation Large groups like lipids and carbohydrates attach to amino acid residue of certain proteins 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 67

68 Some Amino Acids are Biologically Active: The 20 standard amino acids undergo a bewildering number of chemical transformation. Moreover, many amino acids are synthesized not to be residues of polypeptides but to function independently.

69 chemical messengers for communication between cells (neurotransmitters) such as γ-aminobutyric Acid (GABA) and Dopamine Histamine: is a potent local mediator of allergic reactions Thyroxine: is an iodine containing thyroid hormone that stimulates vertebrate metabolism.

70 Glutathione (GSH) Glutathione is tripeptide and play role in cellular metabolism Glutathione is Glu-Cys-Gly peptide. It helps to inactivate oxidative compounds, that could damage cellular structures. GSH undergo oxidation and form glutathione disulfide (GSSG) 2GSH + X oxidized GSSG + X reduced 10/22/2017 Dr. Amjid Iqbal PhD (University of Cambridge,UK) 70