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Basic course, CDFD: Molecules of Life, 23-Aug-2007 Molecules of Life Shekhar C. Mande

Molecules of Life Shekhar C. Mande

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Molecules of Life Shekhar C. Mande. C, H, N, O, S & P make up >99% of cellular weight. Composition of Cells. Water distribution on the Earth. +. -. As water transpires off the leaves the cohesion pulls more water up through the vessels. Basic properties of water:. - PowerPoint PPT Presentation

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Page 1: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Molecules of LifeShekhar C. Mande

Page 2: 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.

Page 3: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

• C, H, N, O, S & P make up >99% of cellular weight

Percent of Total CellWeight

Number of Types ofEach Molecule

Water 70 1

Inorganic ions 1 20

Sugars & precursors 3 200

Amino acids & precursors 0.4 100

Nucleotides & precursors 0.4 200

Lipids & precursors 2 50Other small molecules 0.2 ~200Macromolecules (proteins, nucleicacids & polysachharides)

22 ~5000

Composition of Cells

Page 4: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Water distribution on the EarthTotal 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, inland seas and rivers

250,000 km³ 0.02 %

Water vapour 13,000 km³ 0.001 %

Page 5: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Page 6: Molecules of Life Shekhar C. Mande

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.

Page 7: Molecules of Life Shekhar C. Mande

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.

Page 8: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

• Anomalous properties enormously important in maintaining the ecosystem of the Earth.

Basic properties of water:

Page 9: Molecules of Life Shekhar C. Mande

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 angleρ = 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.

Page 10: Molecules of Life Shekhar C. Mande

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.

Page 11: Molecules of Life Shekhar C. Mande

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.

Page 12: Molecules of Life Shekhar C. Mande

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

Page 13: Molecules of Life Shekhar C. Mande

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

Page 14: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Sugars

Glucose Fructose

Deoxyribose Ribose

They are important metabolically. Sugars are the major energy storage molecules for living organisms. Their carbon rings contain large amounts of energy

C6H12O6 6CO2 + 6H2O

releases 686 Kcal/mol

Page 15: Molecules of Life Shekhar C. Mande

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

Page 16: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Membrane lipids

•Phospholipids are the principal lipids in cell membranes

•They contain polar head group and hydrophobic tail

Choline

Phosphate

Glycerol

Fatty acid

Page 17: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Nucleotides

Page 18: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Bases

Page 19: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Amino Acids

CH3

Genetic code specifies 20 different amino acids

Page 20: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Chirality of Amino Acids

C

CO

R

N

H

L- form

C

CO

R

N

H

D- form

Page 21: Molecules of Life Shekhar C. Mande

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

Page 22: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Primary Structure

Page 23: Molecules of Life Shekhar C. Mande

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

Page 24: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Amino Acids and Their SymbolsResidue Three- letter

symbolOne-lettersymbol

Mnemonic pKa

Alanine Ala A AlanineGlutamate Glu E GluEtamic

acid4.3

Glutamine Gln Q Q-tamineAspartate Asp D AsparDic acid 3.9Asparagine Asn N AsparagiNeLeucine Leu L LeucineGlycine Gly G GlycineLysine Lys K Before L 10.5Serine Serine S SerineValine Valine V ValineArginine Arg R aRginine 12.5Threonine Thr T ThreonineProline Pro P ProlineIsoleucine Ile I IsoleucineMethionine Met M MethioninePhenylalanine Phe F FenylalanineTyrosine Tyr Y tYrosine 10.1Cysteine Cys C CysteineTryptophan Trp W tWo ringsHistidine His H Histidine 6.0

Page 25: Molecules of Life Shekhar C. Mande

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

Page 26: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Convention of Naming Side Chain Atoms

Page 27: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Polypeptide Chain

Page 28: Molecules of Life Shekhar C. Mande

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

Page 29: Molecules of Life Shekhar C. Mande

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

Page 30: Molecules of Life Shekhar C. Mande

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

Page 31: Molecules of Life Shekhar C. Mande

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

Page 32: Molecules of Life Shekhar C. Mande

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

Page 33: Molecules of Life Shekhar C. Mande

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

Page 34: Molecules of Life Shekhar C. Mande

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

Page 35: Molecules of Life Shekhar C. Mande

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

Page 36: Molecules of Life Shekhar C. Mande

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

Page 37: Molecules of Life Shekhar C. Mande

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

Page 38: Molecules of Life Shekhar C. Mande

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

Page 39: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Chemical Similarity Reflects in Substitution Matrices

Page 40: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Hydrophobicities

Page 41: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Comparison of Kyte-Doolittle, Eisenberg and White ScalesNAME 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

Page 42: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Peptide torsion angles

Page 43: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

Some mostly beta architectures

Page 44: Molecules of Life Shekhar C. Mande

Basic course, CDFD: Molecules of Life, 23-Aug-2007

The Protein Folding Problem