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PROTEIN Kuliah ke-4 BIOKIMIA FAKULTAS PETERNAKAN UNIVERSITAS BRAWIJAYA Prof. Dr.sc.agr. Ir. Suyadi, MS. Elements: C, H, O, N, (S, P)

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Presentation on theme: "PROTEIN Kuliah ke-4 BIOKIMIA FAKULTAS PETERNAKAN UNIVERSITAS BRAWIJAYA Prof. Dr.sc.agr. Ir. Suyadi, MS. Elements: C, H, O, N, (S, P)"— Presentation transcript:

1 PROTEIN Kuliah ke-4 BIOKIMIA FAKULTAS PETERNAKAN UNIVERSITAS BRAWIJAYA Prof. Dr.sc.agr. Ir. Suyadi, MS. Elements: C, H, O, N, (S, P)

2 INTRODUCTION: PROTEIN Elements: C, H, O, N, and sometimes S. Function: Enzymes, structural proteins, storage proteins, transport proteins, hormones, proteins for movement, protection, and toxins.

3 Introduction The subunits of a protein are amino acids or to be precise amino acid residues. An amino acid consists of: – a central carbon atom (the alpha Carbon C alpha ) and an amino group (NH 2 ), – a hydrogen atom (H), – a carboxy group (COOH) and – a side chain (R) which are bound to the C alpha.

4 Gugus amino dan karboksil

5 Gugus asam amino

6

7 Figure : Peptide bond linking two amino acids

8 Jenis Protein: Primer, sekunder, tertier, Quarter

9 General Structure Proteins are made from several amino acids, bonded together. It is the arrangement of the amino acid that forms the primary structure of proteins. The basic amino acid form has a carboxyl group on one end, a methyl group that only has one hydrogen in the middle, and a amino group on the other end. Attached to the methyl group is a R group.

10 General Structure Proteins are made from several amino acids, bonded together. It is the arrangement of the amino acid that forms the primary structure of proteins. The basic amino acid form has a carboxyl group on one end, a methyl group that only has one hydrogen in the middle, and a amino group on the other end. Attached to the methyl group is a R group.

11 Macam asam amino

12 General Structure There are 20+ amino acids, each differing only in the composition of the R groups. An R group could be a sulfydrl, another methyl, a string a methyls, rings of carbons, and several other organic groups. Proteins can be either acidic or basic, hydrophilic or hydrophobic. The following table shows 20 amino acids that common in proteins.

13 Proteins play key roles in a living system Three examples of protein functions – Catalysis: Almost all chemical reactions in a living cell are catalyzed by protein enzymes. – Transport: Some proteins transports various substances, such as oxygen, ions, and so on. – Information transfer: For example, hormones. Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones Haemoglobin carries oxygen Insulin controls the amount of sugar in the blood

14 Amino acid: Basic unit of protein COO - NH 3 + C R H An amino acid Different side chains, R, determin the properties of 20 amino acids. Amino groupCarboxylic acid group

15 20 Amino acids Glycine (G) Glutamic acid (E) Asparatic acid (D) Methionine (M) Threonine (T) Serine (S) Glutamine (Q) Asparagine (N) Tryptophan (W) Phenylalanine (F) Cysteine (C) Proline (P) Leucine (L) Isoleucine (I) Valine (V) Alanine (A) Histidine (H) Lysine (K) Tyrosine (Y) Arginine (R) White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

16 Proteins are linear polymers of amino acids R1R1 NH 3 + C CO H R2R2 NH C CO H R3R3 NH CCO H R2R2 NH 3 + C COO ー H + R1R1 NH 3 + C COO ー H + H2OH2O H2OH2O Peptide bond The amino acid sequence is called as primary structure AA F N G G S T S D K A carboxylic acid condenses with an amino group with the release of a water

17 Amino acid sequence is encoded by DNA base sequence in a gene ・CGCGAATTCGCG・・CGCGAATTCGCG・ ・GCGCTTAAGCGC・・GCGCTTAAGCGC・ DNA molecule = DNA base sequence

18 Amino acid sequence is encoded by DNA base sequence in a gene Second letter TCAG First letter T TTT Phe TCT Ser TAT Tyr TGT Cys T Third letter TTCTCCTACTGCC TTA Leu TCATAA Stop TGA Stop A TTGTCGTAGTGG Trp G C CTT Leu CCT Pro CAT His CGT Arg T CTCCCCCACCGCC CTACCACAA Gln CGAA CTGCCGCAGCGGG A ATT Ile ACT Thr AAT Asn AGT Ser T ATCACCAACAGCC ATAACAAAA Lys AGA Arg A ATG Met ACGAAGAGGG G GTT Val GCT Ala GAT Asp GGT Gly T GTCGCCGACGGCC GTAGCAGAA Glu GGAA GTGGCGGAGGGGG

19 Gene is protein’s blueprint, genome is life’s blueprint Gene Genome DNA Protein Gene Protein

20 Gene is protein’s blueprint, genome is life’s blueprint Genome Gene Protein Glycolysis network

21 3 billion base pair => 6 G letters & 1 letter => 1 byte The whole genome can be recorded in just 10 CD-ROMs! In 2003, Human genome sequence was deciphered! Genome is the complete set of genes of a living thing. In 2003, the human genome sequencing was completed. The human genome contains about 3 billion base pairs. The number of genes is estimated to be between 20,000 to 25,000. The difference between the genome of human and that of chimpanzee is only 1.23%!

22 Each Protein has a unique structure Amino acid sequence NLKTEWPELVGKSVEE AKKVILQDKPEAQIIVL PVGTIVTMEYRIDRVR LFVDKLDNIAEVPRVG Folding!

23 Basic structural units of proteins: Secondary structure α-helix β-sheet Secondary structures, α-helix and β- sheet, have regular hydrogen-bonding patterns.

24 Three-dimensional structure of proteins Tertiary structure Quaternary structure

25 Hierarchical nature of protein structure Primary structure (Amino acid sequence) ↓ Secondary structure ( α -helix, β -sheet ) ↓ Tertiary structure ( Three-dimensional structure formed by assembly of secondary structures ) ↓ Quaternary structure ( Structure formed by more than one polypeptide chains )

26 Close relationship between protein structure and its function enzyme A B A Binding to A Digestion of A! enzyme Matching the shape to A Hormone receptor Antibody Example of enzyme reaction enzyme substrates

27 Protein structure prediction has remained elusive over half a century “Can we predict a protein structure from its amino acid sequence?” Now, impossible!

28 Protein Classification Proteins can be described as having several layers of structure. At the lowest level, the primary structure of proteins are nothing more that the amino acids which compose the protein, and how those proteins are bonded to each other. The bonds between proteins are called peptide bonds, and they can have either single bonds, double bonds, triple bonds, or more holding the amino acids into a protein molecule. At the next level, the secondary structure of proteins, proteins show a definite geometric pattern. One pattern that the protein can take is a helical structure, similar to a spiral staircase. Hair has such a secondary structure. When examined closely, you can see the turns in the proteins of hair molecules. A second geometric pattern is the pleated sheet, where several polypeptide chains go in several different directions. I think of a sheet of paper, or a length of fabric. When viewed closely, silk fibronin, the silk protein, forms such a shape. Skin, although made of more than just proteins, provides another example of a protein with a sheet structure. The following figure shows the pleated sheet secondary structure of silk.

29 Contoh struktur protein Skin fibroin

30 Next, we find a tertiary structure to proteins. Here, we find the three-dimensional structure of the globular proteins, where disulfide bridges puts kinks and bends in the secondary structure. Again thinking about hair, some people have straight hair, some have wavy hair, and some have curly hair. The links and bends in the secondary structure causes the curls in hair. Curly hair has more kinks and bends that wavy hair, and straight hair has very few, if any bends

31 Contoh struktur protein Psoriasin

32 At the last, we see the quaternary structure of proteins. This the the form taken by complex proteins formed from two or more smaller, polypeptide chains. The polypeptide chains form pieces of a jigsaw puzzle, that when put together form a single protein. Hemoglobin provides a good example, being made from four polypeptide chains.

33 Contoh struktur protein Hemoglobin

34 PENJELASAN STRUKTUR DAN FUNGSI PROTEIN

35 Protein Function in Cell 1.Enzymes Catalyze biological reactions 2.Structural role Cell wall Cell membrane Cytoplasm

36 Protein Structure

37

38 Model Molecule: Hemoglobin

39 Hemoglobin: Background Protein in red blood cells

40 Hemoglobin: Background Protein in red blood cells Composed of four subunits, each containing a heme group: a ring- like structure with a central iron atom that binds oxygen Red blood cell

41 Heme Groups in Hemoglobin

42 Hemoglobin: Background Protein in red blood cells Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen Picks up oxygen in lungs, releases it in peripheral tissues (e.g. muscles)

43 Hemoglobin – Quaternary Structure Two alpha subunits and two beta subunits (141 AA per alpha, 146 AA per beta)

44 Hemoglobin – Tertiary Structure One beta subunit (8 alpha helices)

45 Hemoglobin – Secondary Structure alpha helix

46 Structure Stabilizing Interactions Noncovalent – Van der Waals forces (transient, weak electrical attraction of one atom for another) – Hydrophobic (clustering of nonpolar groups) – Hydrogen bonding

47 Hydrogen Bonding Involves three atoms: – Donor electronegative atom (D) (Nitrogen or Oxygen in proteins) – Hydrogen bound to donor (H) – Acceptor electronegative atom (A) in close proximity D – HA

48 D-H Interaction Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge Proximity of the Acceptor A causes further charge separation D – HA δ-δ+δ-

49 D-H Interaction Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge Proximity of the Acceptor A causes further charge separation Result: –Closer approach of A to H –Higher interaction energy than a simple van der Waals interaction D – HA δ-δ+δ-

50 Hydrogen Bonding And Secondary Structure alpha-helix beta-sheet

51 Structure Stabilizing Interactions Noncovalent –Van der Waals forces (transient, weak electrical attraction of one atom for another) –Hydrophobic (clustering of nonpolar groups) –Hydrogen bonding Covalent –Disulfide bonds

52 Disulfide Bonds Side chain of cysteine contains highly reactive thiol group Two thiol groups form a disulfide bond

53 Disulfide Bridge

54 Disulfide Bonds Side chain of cysteine contains highly reactive thiol group Two thiol groups form a disulfide bond Contribute to the stability of the folded state by linking distant parts of the polypeptide chain

55 Disulfide Bridge – Linking Distant Amino Acids

56 Hemoglobin – Primary Structure NH 2 -Val-His-Leu-Thr-Pro-Glu-Glu- Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp- Gly-Lys-Val-Asn-Val-Asp-Glu-Val- Gly-Gly-Glu-….. beta subunit amino acid sequence

57 Protein Structure - Primary Protein: chain of amino acids joined by peptide bonds

58 Protein Structure - Primary Protein: chain of amino acids joined by peptide bonds Amino Acid – Central carbon (C α ) attached to: Hydrogen (H) Amino group (-NH 2 ) Carboxyl group (-COOH) Side chain (R)

59 General Amino Acid Structure CαCα H R COOHH2NH2N

60 General Amino Acid Structure At pH 7.0 CαCα H R COO-+H 3 N

61 General Amino Acid Structure

62 Amino Acids Chiral

63 Chirality: Glyceraldehyde L-glyderaldehydeD-glyderaldehyde

64 Amino Acids Chiral 20 naturally occuring; distinguishing side chain

65 20 Naturally-occurring Amino Acids

66 Amino Acids Chiral 20 naturally occuring; distinguishing side chain Classification: Non-polar (hydrophobic) Charged polar Uncharged polar

67 Alanine: Nonpolar

68 Serine: Uncharged Polar

69 Aspartic Acid Charged Polar

70 Glycine Nonpolar (special case)

71 Peptide Bond Joins amino acids

72 Peptide Bond Formation

73 Peptide Chain

74 Peptide Bond Joins amino acids 40% double bond character –Caused by resonance

75

76 Peptide bond Joins amino acids 40% double bond character –Caused by resonance –Results in shorter bond length

77 Peptide Bond Lengths

78 Peptide bond Joins amino acids 40% double bond character –Caused by resonance –Results in shorter bond length –Double bond disallows rotation

79 Protein Conformation Framework Bond rotation determines protein folding, 3D structure

80 Bond Rotation Determines Protein Folding

81 Protein Conformation Framework Bond rotation determines protein folding, 3D structure Torsion angle (dihedral angle) τ –Measures orientation of four linked atoms in a molecule: A, B, C, D

82

83 Protein Conformation Framework Bond rotation determines protein folding, 3D structure Torsion angle (dihedral angle) τ –Measures orientation of four linked atoms in a molecule: A, B, C, D –τ ABCD defined as the angle between the normal to the plane of atoms A-B-C and normal to the plane of atoms B-C-D

84 Ethane Rotation A C B D A B C D

85 Protein Conformation Framework Bond rotation determines protein folding, 3D structure Torsion angle (dihedral angle) τ –Measures orientation of four linked atoms in a molecule: A, B, C, D –τ ABCD defined as the angle between the normal to the plane of atoms A-B-C and normal to the plane of atoms B-C-D –Three repeating torsion angles along protein backbone: ω, φ, ψ

86 Backbone Torsion Angles

87 Dihedral angle ω : rotation about the peptide bond, namely C α 1 -{C-N}- C α 2

88 Backbone Torsion Angles

89 Dihedral angle ω : rotation about the peptide bond, namely C α 1 -{C-N}- C α 2 Dihedral angle φ : rotation about the bond between N and C α

90 Backbone Torsion Angles

91 Dihedral angle ω : rotation about the peptide bond, namely C α 1 -{C-N}- C α 2 Dihedral angle φ : rotation about the bond between N and C α Dihedral angle ψ : rotation about the bond between C α and the carbonyl carbon

92 Backbone Torsion Angles

93 ω angle tends to be planar (0º - cis, or 180 º - trans) due to delocalization of carbonyl π electrons and nitrogen lone pair

94

95 Backbone Torsion Angles ω angle tends to be planar (0º - cis, or 180 º - trans) due to delocalization of carbonyl pi electrons and nitrogen lone pair φ and ψ are flexible, therefore rotation occurs here

96 Backbone Torsion Angles

97 ω angle tends to be planar (0º - cis, or 180 º - trans) due to delocalization of carbonyl pi electrons and nitrogen lone pair φ and ψ are flexible, therefore rotation occurs here However, φ and ψ of a given amino acid residue are limited due to steric hindrance

98 Steric Hindrance Interference to rotation caused by spatial arrangement of atoms within molecule Atoms cannot overlap Atom size defined by van der Waals radii Electron clouds repel each other

99 Backbone Torsion Angles ω angle tends to be planar (0º - cis, or 180 º - trans) due to delocalization of carbonyl pi electrons and nitrogen lone pair φ and ψ are flexible, therefore rotation occurs here However, φ and ψ of a given amino acid residue are limited due to steric hindrance Only 10% of the {φ, ψ} combinations are generally observed for proteins First noticed by G.N. Ramachandran

100 Sequence Similarity Sequence similarity implies structural, functional, and evolutionary commonality

101 Homologous Proteins: Enterotoxin and Cholera toxin EnterotoxinCholera toxin 80% homology

102 Sequence Similarity Sequence similarity implies structural, functional, and evolutionary commonality Low sequence similarity implies little structural similarity

103 Nonhomologous Proteins: Cytochrome and Barstar CytochromeBarstar Less than 20% homology

104 Sequence Similarity Sequence similarity implies structural, functional, and evolutionary commonality Low sequence similarity implies little structural similarity Small mutations generally well-tolerated by native structure – with exceptions!

105 Sequence Similarity Exception Sickle-cell anemia resulting from one residue change in hemoglobin protein Replace highly polar (hydrophilic) glutamate with nonpolar (hydrophobic) valine

106 Sickle-cell mutation in hemoglobin sequence

107 Normal Trait Hemoglobin molecules exist as single, isolated units in RBC, whether oxygen bound or not Cells maintain basic disc shape, whether transporting oxygen or not

108 Sickle-cell Trait Oxy-hemoglobin is isolated, but de- oxyhemoglobin sticks together in polymers, distorting RBC Some cells take on “sickle” shape

109 Sickle-cell

110 RBC Distortion Hydrophobic valine replaces hydrophilic glutamate Causes hemoglobin molecules to repel water and be attracted to one another Leads to the formation of long hemoglobin filaments

111 Hemoglobin Polymerization Normal Mutant

112 RBC Distortion Hydrophobic valine replaces hydrophilic glutamate Causes hemoglobin molecules to repel water and be attracted to one another Leads to the formation of long hemoglobin filaments Filaments distort the shape of red blood cells (analogy: icicle in a water balloon) Rigid structure of sickle cells blocks capillaries and prevents red blood cells from delivering oxygen

113 Capillary Blockage

114 Sickle-cell Trait Oxy-hemoglobin is isolated, but de- oxyhemoglobin sticks together in polymers, distorting RBC Some cells take on “sickle” shape When hemoglobin again binds oxygen, again becomes isolated Cyclic alteration damages hemoglobin and ultimately RBC itself

115 Protein: The Machinery of Life “Life is the mode of existence of proteins, and this mode of existence essentially consists in the constant self- renewal of the chemical constituents of these substances.” Friedrich Engles, 1878 NH 2 -Val-His-Leu-Thr-Pro-Glu-Glu- Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp- Gly-Lys-Val-Asn-Val-Asp-Glu-Val- Gly-Gly-Glu-…..

116 TUGAS 1.Menyusun Paper secara berkelompok tentang: PROTEIN – STRUKTUR DAN FUNGSI 2.Membuat materi presentasi ppt sebagai bahan diskusi kelompok minggu berikutnya 3.Paper dikumpulkan ke dosen paling lambat 2 mgg dari sekarang dalam bentuk soft copy (file) ke

117

118

119 The subunits of a protein are amino acids or to be precise amino acid residues. An amino acid consists of: a central carbon atom (the alpha Carbon C alpha ) and an amino group (NH 2 ), a hydrogen atom (H), a carboxy group (COOH) and a side chain (R) which are bound to the C alpha.


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