Good Morning Class!
Content Lecture 1 - Basic knowledge for Biochemistry - Cell: Structure and Function - Water Lecture 2 - Amino acid Peptide and Polypeptide Lecture 3 - Protein Structure and Function Lecture 4 - Metabolism of Protein and Amino acid - Protein structure determination (If time allow)
What do you really see here?
What are actually there? Composition? Membrane protein? Structural protein? Antibody? Transcription factor? Muscle? Chemicalreaction? Enzyme? Hormone? Receptor? Collagen? Metabolism? Ammonia & Urea?
What do you know about Protein and Amino acid? What are amino acids, peptide, polypeptide, protein? Where / How are they from / formed? What are major roles of them? What are their function? What force/bond make them? What are the differences, properties? What happen when them go wrong? When? Why? Help me!! How?
Amino acids and proteins Amino acids Amino acids are molecules containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, serve as the building blocks of proteins. Proteins (3D polypeptide) Proteins are biochemical compounds consisting of one or more polypeptides, which are short polymers of amino acid monomers linked by peptide bonds, typically folded into a globular or fibrous form, facilitating a biological function. Amino acid 1 Polypeptides Protein (Triose phosphate isomerase) 2 3
How many amino acids are there? n 20 amino acids are commonly found in human, called Proteinogenic or Standard amino acid 9 Essential amino acids 11 Nonessential amino acids What are they? Why?
What should you know about amino acid? Catabolism? Chemical bonds? Polarity? MW? n Structures? Electric charges? Optical isomer? Elements? Chiral center? Solubility? Ionization? Essential? Ketogenic or Glucogenic? Acidity? Melting temperature? Name & symbol? Functional groups? How many of them? Zwitterions? Biosynthesis?
Tetrahedral Isomerism Stereoisomers / Optical isomers / Enantiomers R R - Two optical isomer D (Right hand) and L (Left hand) amino acid (Except Glycine, R = H) - All proteinogenic amino acids are L-form. - Some D-amino acids can be found in some sea animla such as cone snail) or at cell wall of bacteria
Essential amino acids: Amino acids that animal cannot synthesize. Non-essential amino acids: Amino acids that animal can synthesize. Selenocysteine 21 st amino acid Pyrrolysine 22 nd amino acid Essential Nonessential Histidine Alanine Isolucine Arginine* Leucine Asparagine* Lysine Aspartate Methionine Cysteine Phenylalanine Glutamate Threonine Glutamine* Tryptophan Glycine* Valine Proline* Serine* Tyrosine* * Conditionally Essential Essential amino acids differ in animals.
Proteinogenic amino acid is -amino acid. O HO C CH 2 CH 2 β NH 2 CH O C OH Enzymes NH 2 CH 2 CH 2 β CH 2 O C OH Glutamic acid ( -amino acid) Proteinogenic amino acid GABA ( -amino butyric acid) Non Proteinogenic amino acid (neurotransmitter)
Properties and specific properties of amino acids depend on R-group Physical properties) - Optical * Light absorption R * Light polarization) NH2 - Structure: Stereo isoform + COOH + R NH2 + COOH + Chemical properties - Buffering because of Zwitter ion behabior NH2 + - Chemical reaction * Disulfide bond formation R * Interaction with Ninhydrin s regent NH2 * Interaction with FDNB (dinitrophynylated amino acid) * Interaction of SH with Hg 2+ of mercaptides R with Ag 2+ of ellman]s reagent Biological properties - Energy storage carbon + R - Intermediate in Nitrogen cycle - Intermediate in biological process NH2 + R NH2 R COOH + + COOH Because some amino acids have aromatic side chain. Because most amino acids have asymmetric carbon. Because sp3 of C is tetrahedral. NH2 R
http://en.wikipedia.org/wiki/amino_acid Wiki!
pka http://academics.keene.edu/rblatchly/chem220/hand/npaa/aawpka.htm ph in human body 7.3-7.4
Amino acid at physiological condition (ph 7.4 salt 150 mm) H 2 N : R C H C O OH : : + H 3 N R C H C O - O Non ionized structure Zwitterion Commonly found in human body..? Protonated gain H + Deprotonated lost H +
Zwitterionic form of amino acids
Resonance at the carboxyl group
Buffering ability of Glycine What happen at pka? Henderson Hasselbalch equation ph = pka + log [A - ] [HA] ph > pka : HA --> A - (Deprotonation) ph < pka : A - --> HA (Protonation) ph = pka : HA = A -
UV absorption of amino acids
UV absorption of aromatic amino acids
Fluorescent Characteristics of the Aromatic amino Acids
Roles of amino acids and its derivative Properties of amino acids depend on R (side chain) Function of standard amino acid - Building block of protein - Energy source (if necessary) - Precursor for Fatty acids synthesis (when excess) Non protein function of amino acids Derivative of amino acids
Non protein function of amino acids Tryptophan is a precursor of the neurotransmitter serotonin. Tyrosine (and its precursor phenylalanine) are precursors of the catecholamine neurotransmitters dopamine, epinephrine and norepinephrine. Glycine is a precursor of porphyrins such as heme. Arginine is a precursor of nitric oxide. Ornithine and S-adenosylmethionine are precursors of polyamines. Aspartate, glycine, and glutamine are precursors of nucleotides. Phenylalanine is a precursor of various phenylpropanoids, which are important in plant metabolism.
Derivative of amino acids β -aminobutyric acid (GABA) Neurotransmitter γ-aminobutyric acid is the chief inhibitory neurotransmitter in the mammalian central nervous system. It plays a role in regulating neuronal excitability throughout the nervous system. Brain development Beyond the nervous system including but not restrict to the intestine, stomach, pancreas, Fallopian tube, uterus, ovary, testis, kidney, urinary bladder, lung, and liver.
Derivative of amino acids Desmosine
Derivative of amino acids Thyroxine -alanine Homoserine Ornithine Homocysteine Statine
Derivative of amino acids Epinephrine Penicillamine Carnitine 5-hydroxylysine -Aminoadipic acid -carboxyglutamic acid
Derivative of amino acids 4-hydroxyproline Dopamine Sarcosine Citrulline Pyrrolysine Histamine
Derivative of amino acids 1-Aminocyclopropane-1-carboxylic acid Lanthionine: antibiotic Alamethicin: antibiotic
Derivative of amino acids Nisin: antibiotic
Derivative of amino acids Alamethicin
Interesting information about amino acid Post-translation modification - Glucoxylation: Aspartic acid, Serine, Threnine - Carboxylation: Glutamic acid - Hydroxylation: Lysine, Proline - Sulfonation: Tyrosine - Methylation: Lysine - Phosphorylation: Serine, Threonine or Tyrosine residues (mostly in eukaryotes) Aspartic acid, Hstidine residues (mostly in prokaryotes). Proline: protogenic amino acid that side chain form ring with amino group interfere Helix structure (Helix preaker), often form unstructured region of protein involving in protein interaction
Peptide bonds, Peptide and Polypeptide Peptide bonds =? Peptide =? Polypeptide =?
Peptide bond formation C-terminus N-terminus
Peptide bond formation Hydrolysis (Break bond) N-terminus Condensation (bond formation) C-terminus
Physical properties of peptide
Resonance of peptide bond Behave like double ebon Majority isomer is Trans
Peptide and Polypeptide residue
Rotatable angle in peptideφ (phi) and Ψ(psi) Φ Ψ Φ Ψ Φ Ψ Φ phi Ψ psi Dihedral angles
Rotatable angle in peptideφ (phi) and Ψ(psi) Φ Ψ Φ Ψ Φ Ψ Φ Ψ Φ phi Ψ psi Dihedral angles
Ramachandran Plot Φ andψ angle effect conformation of peptide
Naming: Peptide Dipeptide Tripeptide R 1 O R O N 2 H CH C N CH C OH H Oligopeptide (> 3, < 50 residues) R 1 O N 2 H CH C N CH C N CH H H R 2 2 O R 3 O C OH N-terminus =? NH 2 -terminus Amino-terminus C-terminus =? COOH-terminus Carboxly-terminus N H R 1 CH O C N H R O R CH C N CH H O C N H R 2 3 4 CH O Hexapeptide 6 residues R O R 5 6 C N CH C N CH H H O C
3 Types of peptide 1. Digestied protein - Milk - Peptone - Tryptone 2. Ribosomal peptide - Peptide hormone: Insulin, Glucagon, growth hormone, leptin, gastrin, prolactin, etc. - Prohormones
3.Non-Ribosomal Peptide Glutathion (tripeptide) -L-Glutamyl-L-cysteinylglycine (Antioxidation) Gramicidin S (antibiotic) is produced by Bacillus brevis, is a cyclodecapeptide. cyclo(-val-orn-leu-d-phe-pro-) 2
3.Non-Ribosomal Peptide (cont.) Bacitracin A S (antibiotic), is produced by Bacillus subtilis, is a mixture of related cyclic polypeptides produced by organisms of the licheniformis group of Bacillus subtilis var Tracy, isolation of which was first reported in 1945. These peptides disrupt both gram positive and gram negative bacteria, by interfering cell wall and phospholipid synthesis.
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