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Transcript
Molecules of Life Shekhar C. Mande Basic course, CDFD: Molecules of Life, 23-Aug-2007 Ecosystem Rain forest, desert, fresh water lake, digestive tract of animal for bacteria Includes all living organisms and non living matter such as air, water and minerals Community All species in an ecosystem Only includes living things from bacteria, to fungi, to plant to animal Population All individuals of a single species Includes only individuals from a specific species such as a plant, an animal, a bacterial colony Organism One single individual Serves as a representative of the species and describes overall form and function of an organism Organ A specialized structural system of an organism The brain or the thymus of an animal Tissue A specialized substructure of an organ The nervous tissue and epithelial tissue are both part of the brain Cell A single cell A neuron, a skin cell, a root cell, bacteria, yeast, paramecium Molecule A single large or small molecule such as a protein, DNA, sugar or fatty acid Molecules are the smallest part of biological systems; they can be studied for their chemical, physical properties, but are of particular interest for their usefulness in biological systems. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Composition of Cells • C, H, N, O, S & P make up >99% of cellular weight Percent of Total Cell Weight Number of Types of Each Molecule Water 70 1 Inorganic ions 1 20 Sugars & precursors 3 200 Amino acids & precursors 0.4 100 Nucleotides & precursors 0.4 200 2 50 0.2 ~200 22 ~5000 Lipids & precursors Other small molecules Macromolecules (proteins, acids & polysachharides) nucleic Basic course, CDFD: Molecules of Life, 23-Aug-2007 Water distribution on the Earth Total water 1,360,000,000 km³ Oceans 1,320,000,000 km³ 97.2 % Glaciers and ice caps 25,000,000 km³ 1.8 % Ground water 13,000,000 km³ 0.9 % Fresh water in lakes, 250,000 km³ inland seas and rivers 0.02 % Water vapour 0.001 % 13,000 km³ Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic properties of water: + Because of the unequal distribution of charge, water molecules attract each other, and that is the reason why they form drops! - As water transpires off the leaves the cohesion pulls more water up through the vessels. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic properties of water: • It is the only natural substance which is found in all the three states- gas, liquid and solid at the temperatures normally found on the earth. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic properties of water: • Anomalous properties enormously important in maintaining the ecosystem of the Earth. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic properties of water: • It has very high surface tension- also the molecular basis of capillary action= allows through roots of plants, and tiny blood vessles T = surface tension (J/m² or N/m) θ = contact angle ρ = density of liquid (kg/m3) g = acceleration due to gravity (m/s²) r = radius of tube (m) For a 1m wide tube, the water would rise a unnoticable 0.014mm. However, for a 1cm wide tube, the water would rise 1.4mm, and for a capillary tube with radius 0.1mm, the water would rise 14cm, or around 6 inches. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic properties of water: Water has high heat of vaporization: the amount of heat needed to turn a given amount of liquid water into water vapour (gas). A high heat vaporization means that in order for water to reach the gaseous state, it must absorb a great deal of heat from the surroundings. For many plants and animals, this property is the basis of a natural cooling system. Water evaporating from leaves, skin or lungs uses up heat from the organisms in the process of changing from liquid to gas. That is the reason mammals have evolved sweat glands, when the body is overheated, the glands pour watery "sweat" onto the skin, as the water evaporated, large amounts of body heat are used up and the body is cooled. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Basic properties of water: • Has high specific heat index= it can absorb lot of heat before it starts getting hot. Due to it high specific heat, water is slow to undergo changes in temperature. Much heat must be added or removed before the temperature of water changes much. The temperature of the water within living organisms tends to change more slowly than does that of the surrounding air or soil, so that the living cells are buffered somewhat against temperature fluctuations. This kind of protection is important because many biochemical reactions will take place only within a narrow range of temperatures. Basic course, CDFD: Molecules of Life, 23-Aug-2007 Miller Urey Experiment • 1953, starting material CH3, NH3, H2 and H2O • Compounds observed included nucleotide bases and amino acids Basic course, CDFD: Molecules of Life, 23-Aug-2007 Biomolecular Building Blocks • Combinations of four types methyl (-CH3), hydroxyl (OH), carboxyl (-COOH) and amino (-NH3) • Four different types of molecular building blocks: Sugars Amino acids Fatty acids Nucleotides Basic course, CDFD: Molecules of Life, 23-Aug-2007 Sugars Glucose They are important metabolically. Sugars are the major energy storage molecules for living organisms. Their carbon rings contain Fructose large amounts of energy C6H12O6 6CO2 + 6H2O releases 686 Kcal/mol Deoxyribose Ribose Basic course, CDFD: Molecules of Life, 23-Aug-2007 Cell Membrane Protects cellular components from diffusing into external environment Membrane components may: •be protective •regulate transport in and out of cell or subcellular domain •allow selective receptivity and signal transduction by providing transmembrane receptors that bind signaling molecules •allow cell recognition •provide anchoring sites for cytoskeletal filaments or components of the extracellular matrix. This allows the cell to maintain its shape and perhaps move to distant sites. •help compartmentalize subcellular domains or microdomains •provide a stable site for the binding and catalysis of enzymes. •regulate the fusion of the membrane with other membranes in the cell via specialized junctions ) •provide a passageway across the membrane for certain molecules, such as in gap junctions. •allow directed cell or organelle motility Basic course, CDFD: Molecules of Life, 23-Aug-2007 Membrane lipids Choline Phosphate Glycerol Fatty acid •Phospholipids are the principal lipids in cell membranes •They contain polar head group and hydrophobic tail Basic course, CDFD: Molecules of Life, 23-Aug-2007 Nucleotides Basic course, CDFD: Molecules of Life, 23-Aug-2007 Bases Basic course, CDFD: Molecules of Life, 23-Aug-2007 Amino Acids Genetic code specifies 20 different amino acids CH3 Basic course, CDFD: Molecules of Life, 23-Aug-2007 Chirality of Amino Acids R R C C H H N CO L- form CO N D- form Basic course, CDFD: Molecules of Life, 23-Aug-2007 Protein Structures • Primary structure – Un-branched polymer – 20 side chains (residues or amino acids) • Higher order structures – Secondary: local (consecutive) in sequence – Tertiary: 3D fold of one polypeptide chain – Quaternary: Chains packing together Basic course, CDFD: Molecules of Life, 23-Aug-2007 Primary Structure Basic course, CDFD: Molecules of Life, 23-Aug-2007 Protein Architecture • Proteins consist of amino acids linked by peptide bonds • Each amino acid consists of: – a central carbon atom – an amino group – a carboxyl group and – a side chain • Differences in side chains distinguish the various amino acids Basic course, CDFD: Molecules of Life, 23-Aug-2007 Amino Acids and Their Symbols Residue Alanine Glutamate Three- letter symbol Ala Glu One-letter symbol A E Glutamine Aspartate Asparagine Leucine Glycine Lysine Serine Valine Arginine Threonine Proline Isoleucine Methionine Phenylalanine Tyrosine Cysteine Tryptophan Histidine Gln Asp Asn Leu Gly Lys Serine Valine Arg Thr Pro Ile Met Phe Tyr Cys Trp His Q D N L G K S V R T P I M F Y C W H Mnemonic Alanine GluEtamic acid Q-tamine AsparDic acid AsparagiNe Leucine Glycine Before L Serine Valine aRginine Threonine Proline Isoleucine Methionine Fenylalanine tYrosine Cysteine tWo rings Histidine pKa 4.3 3.9 10.5 12.5 10.1 6.0 Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of 20 amino acids • Hydrophobic – Ala, Val, Leu, Ile, Phe, Pro, Met • Charged – Arg, Asp, Glu, Lys • Polar – Ser, Thr, Tyr, Asn, Gln, His, Cys, Trp Basic course, CDFD: Molecules of Life, 23-Aug-2007 Convention of Naming Side Chain Atoms Basic course, CDFD: Molecules of Life, 23-Aug-2007 Polypeptide Chain Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Glycine increases main chain flexibility. •Symmetry at the C atom •Can adopt many different conformations •Evolutionarily conserved •Occurs in tight turns Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Alanine is smallish non-polar residue •Occurs abundantly •No preference for inside or surface of the protein Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Val, Leu and Ile are branched side chains •Branching allows limited internal flexibility •Occur primarily in protein cores •“Bricks” around which functional parts are assembled Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Phe, Tyr and Trp are the aromatic side chains •All these contain one methylene group as a spacer •Side chain flexibility is restricted •Occur predominantly in the core of proteins •Tyr can form strong H-bond with its -OH group Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Met and Cys are the sulfur containing side chains •Met is rather large and flexible •Met occurs predominantly inside the core •Cys is special: it can form disulfide crosslinks and is polar Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Asn and Gln have amide in side chain •Gln has an extra methylene group, rendering the polar group flexible and reducing its interaction with main chain •H- bond donor as well as acceptor Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Asp and Glu are -vely charged at physiological pH •Althoughly chemically similar, markedly different effect on the conformation and chemical reactivity •Asp relatively rigid, and found frequently in active sites •Mostly found on protein surfaces •Can be effective chelators of metal ions Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Lys and Arg are +vely charged residues •Long and flexible •Can form salt bridges or help in catalysis Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Ser and Thr are small and aliphatic •-OH no more reactive than ethanol •Frequently form H-bond with main chain Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •Pro is imino acid •Reduces main chain flexibility drastically due to cyclization •Can often occur in cis- form Basic course, CDFD: Molecules of Life, 23-Aug-2007 Properties of Amino Acids •His is a very special residue with pKa of 6.0 •Can be uncharged or charged easily •Very suitable for catalysis, found in most active centres Basic course, CDFD: Molecules of Life, 23-Aug-2007 Chemical Similarity Reflects in Substitution Matrices Basic course, CDFD: Molecules of Life, 23-Aug-2007 Hydrophobicities Basic course, CDFD: Molecules of Life, 23-Aug-2007 Comparison of Kyte-Doolittle, Eisenberg and White Scales NAME EIS KD WHI ALA 0.62 1.80 -0.50 ARG -2.53 -4.50 -1.81 ASN -0.78 -3.50 -0.85 ASP -0.90 -3.50 -3.64 CYS 0.29 2.50 0.02 GLN -0.85 -3.50 -0.77 GLU -0.74 -3.50 -3.63 GLY 0.48 -0.40 -1.15 HIS -0.40 -3.20 -2.33 ILE 1.38 4.50 1.12 LEU 1.06 3.80 1.25 LYS -1.50 -3.90 -2.80 MET 0.64 1.90 0.67 PHE 1.19 2.80 1.71 PRO 0.12 -1.60 -0.14 SER -0.18 -0.80 -0.46 THR -0.05 -0.70 -0.25 TRP 0.81 -0.90 2.09 TYR 0.26 -1.30 0.71 VAL 1.08 4.20 0.46 Basic course, CDFD: Molecules of Life, 23-Aug-2007 Peptide torsion angles Basic course, CDFD: Molecules of Life, 23-Aug-2007 Some mostly beta architectures Basic course, CDFD: Molecules of Life, 23-Aug-2007 The Protein Folding Problem Basic course, CDFD: Molecules of Life, 23-Aug-2007