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PROTEIN Elements: C, H, O, N, (S, P) Kuliah ke-4 BIOKIMIA FAKULTAS PETERNAKAN UNIVERSITAS BRAWIJAYA Prof. Dr.sc.agr. Ir. Suyadi, MS. 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. 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 Calpha) and an amino group (NH2), – a hydrogen atom (H), – a carboxy group (COOH) and – a side chain (R) which are bound to the Calpha. Gugus amino dan karboksil Gugus asam amino Figure : Peptide bond linking two amino acids Jenis Protein: Primer, sekunder, tertier, Quarter 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. 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. Macam asam amino 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. Proteins play key roles in a living system • Three examples of protein functions Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones – 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. Haemoglobin carries oxygen – Information transfer: For example, hormones. Insulin controls the amount of sugar in the blood Amino acid: Basic unit of protein R NH3 + C Amino group H Different side chains, R, determin the COO properties of 20 Carboxylic acid group amino acids. An amino acid 20 Amino acids Glycine (G) Alanine (A) Valine (V) Isoleucine (I) Leucine (L) Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine (N) Glutamine (Q) Serine (S) Threonine (T) Tyrosine (Y) Cysteine (C) Lysine (K) Arginine (R) Histidine (H) Asparatic acid (D) Glutamic acid (E) White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic Proteins are linear polymers of amino acids R1 NH3+ C R2 COOー + NH3+ H H H 2O A R2 R3 C CO NH C CO NH C H Peptide bond H Peptide bond H F G N S T D K G S A + A carboxylic acid condenses with an amino group with the release of a water H 2O R1 NH3+ COOー C CO The amino acid sequence is called as primary structure Amino acid sequence is encoded by DNA base sequence in a gene DNA molecule = ・ G C G C T T A A G C G C ・ ・ DNA base C G sequence C G A A T T C G C G ・ Amino acid sequence is encoded by DNA base sequence in a gene T T A G Phe Leu Leu Ile Met Val TCT TCC TCA TCG CCT CCC CCA CCG ACT ACC ACA ACG GCT GCC GCA GCG Ser Pro Thr Ala TAT TAC TAA TAG CAT CAC CAA CAG AAT AAC AAA AAG GAT GAC GAA GAG G Tyr Stop His Gln Asn Lys Asp Glu TGT TGC TGA TGG CGT CGC CGA CGG AGT AGC AGA AGG GGT GGC GGA GGG Cys Stop Trp Arg Ser Arg Gly T C A G T C A G T C A G T C A G Third letter First letter C TTT TTC TTA TTG CTT CTC CTA CTG ATT ATC ATA ATG GTT GTC GTA GTG C Second letter A Gene is protein’s blueprint, genome is life’s blueprint DNA Genome Gene Protein Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Gene is protein’s blueprint, genome is life’s blueprint Glycolysis network Genome Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein Protein 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%! 3 billion base pair => 6 G letters & 1 letter => 1 byte The whole genome can be recorded in just 10 CD-ROMs! Each Protein has a unique structure Amino acid sequence NLKTEWPELVGKSVEE AKKVILQDKPEAQIIVL PVGTIVTMEYRIDRVR LFVDKLDNIAEVPRVG Folding! Basic structural units of proteins: Secondary structure α-helix β-sheet Secondary structures, α-helix and βsheet, have regular hydrogen-bonding patterns. Three-dimensional structure of proteins Tertiary structure Quaternary structure 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) Close relationship between protein structure and its function Example of enzyme reaction substrates enzyme A enzyme B Matching the shape to A enzyme A Binding to A Digestion of A! Hormone receptor Antibody Protein structure prediction has remained elusive over half a century “Can we predict a protein structure from its amino acid sequence?” Now, impossible! 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. Contoh struktur protein • Skin fibroin • 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 Contoh struktur protein • Psoriasin • 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. Contoh struktur protein • Hemoglobin PENJELASAN STRUKTUR DAN FUNGSI PROTEIN Protein Function in Cell 1. Enzymes • Catalyze biological reactions 2. Structural role • • • Cell wall Cell membrane Cytoplasm Protein Structure Protein Structure Model Molecule: Hemoglobin Hemoglobin: Background • Protein in red blood cells Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ringlike structure with a central iron atom that binds oxygen Red blood cell Heme Groups in Hemoglobin 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) Hemoglobin – Quaternary Structure Two alpha subunits and two beta subunits (141 AA per alpha, 146 AA per beta) Hemoglobin – Tertiary Structure One beta subunit (8 alpha helices) Hemoglobin – Secondary Structure alpha helix Structure Stabilizing Interactions • Noncovalent – Van der Waals forces (transient, weak electrical attraction of one atom for another) – Hydrophobic (clustering of nonpolar groups) – Hydrogen bonding 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–H A 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 δ- δ+ δ- D–H A 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 δ- • Result: δ+ D–H δ- A – Closer approach of A to H – Higher interaction energy than a simple van der Waals interaction Hydrogen Bonding And Secondary Structure alpha-helix beta-sheet 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 Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond Disulfide Bridge 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 Disulfide Bridge – Linking Distant Amino Acids Hemoglobin – Primary Structure -Val-His-Leu-Thr-Pro-Glu-GluLys-Ser-Ala-Val-Thr-Ala-Leu-TrpGly-Lys-Val-Asn-Val-Asp-Glu-ValGly-Gly-Glu-….. NH2 beta subunit amino acid sequence Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds • Amino Acid – Central carbon (Cα) attached to: • • • • Hydrogen (H) Amino group (-NH2) Carboxyl group (-COOH) Side chain (R) General Amino Acid Structure H H 2N α C R COOH General Amino Acid Structure At pH 7.0 H +H3N α C R COO- General Amino Acid Structure Amino Acids • Chiral Chirality: Glyceraldehyde D-glyderaldehyde L-glyderaldehyde Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain 20 Naturally-occurring Amino Acids Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain • Classification: • Non-polar (hydrophobic) • Charged polar • Uncharged polar Alanine: Nonpolar Serine: Uncharged Polar Aspartic Acid Charged Polar Glycine Nonpolar (special case) Peptide Bond • Joins amino acids Peptide Bond Formation Peptide Chain Peptide Bond • Joins amino acids • 40% double bond character – Caused by resonance Peptide bond • Joins amino acids • 40% double bond character – Caused by resonance – Results in shorter bond length Peptide Bond Lengths Peptide bond • Joins amino acids • 40% double bond character – Caused by resonance – Results in shorter bond length – Double bond disallows rotation Protein Conformation Framework • Bond rotation determines protein folding, 3D structure Bond Rotation Determines Protein Folding 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 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 – τABCD 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 Ethane Rotation A D B C A D B C 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 – τABCD 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 Backbone Torsion Angles Backbone Torsion Angles • Dihedral angle ω : rotation about the peptide bond, namely Cα1-{C-N}- Cα2 Backbone Torsion Angles Backbone Torsion Angles • Dihedral angle ω : rotation about the peptide bond, namely Cα1-{C-N}- Cα2 • Dihedral angle φ : rotation about the bond between N and Cα Backbone Torsion Angles Backbone Torsion Angles • Dihedral angle ω : rotation about the peptide bond, namely Cα1-{C-N}- Cα2 • Dihedral angle φ : rotation about the bond between N and Cα • Dihedral angle ψ : rotation about the bond between Cα and the carbonyl carbon Backbone Torsion Angles Backbone Torsion Angles • ω angle tends to be planar (0º - cis, or 180 º - trans) due to delocalization of carbonyl π electrons and nitrogen lone pair 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 Backbone Torsion Angles 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 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 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 Sequence Similarity • Sequence similarity implies structural, functional, and evolutionary commonality Homologous Proteins: Enterotoxin and Cholera toxin Enterotoxin Cholera toxin 80% homology Sequence Similarity • Sequence similarity implies structural, functional, and evolutionary commonality • Low sequence similarity implies little structural similarity Nonhomologous Proteins: Cytochrome and Barstar Cytochrome Barstar Less than 20% homology 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! Sequence Similarity Exception • Sickle-cell anemia resulting from one residue change in hemoglobin protein • Replace highly polar (hydrophilic) glutamate with nonpolar (hydrophobic) valine Sickle-cell mutation in hemoglobin sequence 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 Sickle-cell Trait • Oxy-hemoglobin is isolated, but deoxyhemoglobin sticks together in polymers, distorting RBC • Some cells take on “sickle” shape Sickle-cell 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 Hemoglobin Polymerization Normal Mutant 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 Capillary Blockage Sickle-cell Trait • Oxy-hemoglobin is isolated, but deoxyhemoglobin 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 Protein: The Machinery of Life NH2-Val-His-Leu-Thr-Pro-Glu-GluLys-Ser-Ala-Val-Thr-Ala-Leu-TrpGly-Lys-Val-Asn-Val-Asp-Glu-ValGly-Gly-Glu-….. “Life is the mode of existence of proteins, and this mode of existence essentially consists in the constant selfrenewal of the chemical constituents of these substances.” Friedrich Engles, 1878 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 email : [email protected] • 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 Calpha) and an amino group (NH2), • a hydrogen atom (H), • a carboxy group (COOH) and • a side chain (R) which are bound to the Calpha.