Ast 248, lecture 10

AST 248, Lecture 10 Department of Physics & Astronomy 449 ESS Bldg.
Stony Brook University The Search for Intelligent Life in the Universe Abundances of the Elements

Composition of Biological Compounds I Organisms are made from long chains of monomers called polymers.
I A monomer is a molecule made from individual atoms.
I An atom is one of the approximately 100 stable elements, or which 4 are ultra-important and 2 more are moderately important.
I The number of bonds are the maximum number of covalent bonds elements can form. A covalent bond is formed when electrons areshared among atoms.
I Even though some elements can share more electrons, e.g., P, C has themost flexibility in forming moleculesof different shapes and sizes.
I Most molecules that are carbon-based are called organic molecules and canbe very complex. Elemental carbon,cabonates, CO2 and cyanides areconsidered inorganic.

Major Types of Organic Biological Molecules I Lipids (fats and oils) – although polar, are poorly soluble in water, so they are not found as individual molecules but weakly bonded aggregatesor macromolecules. They store energy and are useful in membranes.
I Carbohydrates – polar, soluble, molecules with many OH hydroxyl groups attached. Sugars are ring-like carbohydrates, polysaccharides arelinear or branched networks of carbohydrates. Carbohydrates storeenergy and provide structural support.
I Proteins – most complex macromolecules found, linear trains of amino acids. Like polysaccharides, they polymerize by releasing water.
Provide structure and act as catalysts (called enzymes).
I Nucleic Acids – Largest macromolecules found, are collections of individual nucleotides linked into linear polymers. Each nucleotideconsists of one sugar, one nitrogeneous base and one or morephosphate groups. Examples: DNA and RNA.

Isomers and Chirality I When larger groups of atoms are assembled, there may be multiple ways to bond the same number of atoms. Each of the different waysis called an isomer.
I Some isomers show handedness: these are called stereoisomers and are either left- or right-handed. They are mirror images of eachother. In general, life utilizes only one handedness (e.g., left-handedamino acids are used to make proteins).

Carbon Isomers and Chirality I Chirality is the quality that makes handedness unique.
I If less than 4 different things are linked to the central carbon, the molecule is achiral.
I If 4 different things are linked to the central carbon, the molecule is I Humans are 9:1 right-handed, but terrestrial biochemistry contains only left-handed amino acids.
I Meteorites contain amino acids in nearly equal proportions of left- and right-handed varieties. The ratio is left:right = 1.08:1, and no oneknow why. One possible explanation has to do with circularlypolarized UV light in the stellar association where the Sun formed,as is observed in the Orion nebula.
I Left-and right-handed molecules can have very different properties.
Drugs especially can be affected. Some examples are: I Orange and lemon peels get aromas from limonene, but it is left-handed in oranges and right-handed in lemons, which obviously smell different.
I The molecule carvone makes the smells of mint (left) and caraway (right).
I The drug ibuprofen, if left-handed, is 4 times as strong as the other kind.
I The sedative Darvon is an isomer of the cough medicine ingredient Novrad.
I The drug thalidomide is used to control morning sickness, but its mirror image causes birth defects.
I Ethambutol: one handedness is used to treat tuberculosis, the other causes I Naproxen: one handedness is used to treat arthritis, but the other causes liver poisoning.
I Molecular activity can also be affected by handedness. Penicillin kills only bacteria in cell walls but not the cells themselves because ofhandedness.
Building Blocks and Selectivity I The largest organic molecules are polymers, or long chains of monomers, which often containing repeating units or patterns.
I One could view monomers as lego blocks: an infinite variety are possible, but only a select few are actually used.
I Monomers tend to be simple, because otherwise it might be too difficult or take too long to form them, either deliberately or bychance.
I Examples: there are 35 isomers of C9H20 and 60 trillion isomers of I Example of selectivity: About 20 different amino acids are found in living material although virtually billions are possible to be formed inthe laboratory.
I Another example: Proteins are made of chains of about 100 amino acids. About 20 different amino acids are used. About 100,000different proteins found in living material although it is possible toform 119!/(100!19!) = 5 · 1021 combinations.
I Selectivity is extended by utilizing only a single handedness.
Kinds of polymers and their monomers: I proteins – amino acids I carbohydrates – sugars I nucleic acids – bases, sugars, phosphates I lipids – fatty acids Major Domains of Life Based on rRNA data, proposed by C. Woese Differences Between Archaea and Bacteria I Bacteria and Archaea both have 70S ribosomes, but have different ribosomal RNA (rRNA) shapes.
I Archaea have 3 RNA polymerases like eukaryotes and their ribosomes work more like eukaryotes.
I Bacteria have only 1 RNA polymerase.
I Bacteria and Archaea have different types of cell walls.
I Bacteria have cell walls containing peptiodoglycan.
I Archaea have cell walls lacking peptiodoglycan.
I Bacteria and Archae have different cell membranes.
I Bacteria have cell membranes with ester bonds.
I Archae have cell membranes with ether bonds which enclose lipids with hydrocarbons rather than fatty acids. Monolayers and histonesenhance DNA stability.
Prokaryotes Cells without nuclei Eukaryotes Cells with nuclei Major Differences: I Prokaryotes form bacteria domains eubacteria and archaea.
I Prokaryotes form single-celled organ- isms, but can cluster into colonies.
I Euacteria are enclosed by cell walls made of cross-linked peptidoglycan chains (amino acids + sugar) which maintains size and shape of cell.
I Metabolism in prokaryotes is complex and more diverse.
I Prokaryotic genome is smaller, and its DNA is not attached to histone I Most prokaryotic DNA is present in a single circular chromosome, and replication begins at a single point and proceeds around the circle inboth directions.
I Prokaryotes obtain new genes by conjugation (transferral), transformation (absorbed from environment) and transduction(transferral by viruses or phages.
I Ribosomes of eubacteria differ in molecular detail from those of eukaryotes and archaea prokaryotes.
I Chemical processses that provide energy and nutrients to cells. Without cell'spresence, these reactions would occur tooslowly to be useful. Cell's primarypurpose is to speed up these reactions.
I Metabolism requires both sources of raw materials and energy to breakdown old molecules andmanufacture new ones.
I Cells produce a large variety of products from a verylimited set of startingmaterials, utilizing adiverse array of enzymes.
I Regardless of where energy comes from, cells utilizethe same molecule (ATP,adenosine triphosphate)to store and releaseenergy. ATP iscompletely recyclable.
Alberts, Bray, Johnson, Lewis, Raff, Roberts, Walter, Garland Publishing: Taylor Francis Group Metabolic Sources Heterotroph Organism which gets its carbon by eating (animals, many microscopic organisms) Autotroph Organism which gets its carbon from CO2 in the atmosphere or dissolved in water (most plants) I Sunlight (photosynthesis) photo- I Organic (food) chemo- I Inorganic (chemicals) chemo- inorganic chemicals (e.g., Fe, S, NH3) organic compounds organic compounds organic compounds plants, photosynthetic bacteria extremophile archaea and bacteria some bacteria and archaea animals, many microbes Metabolism and the Implications for Life Cell structures are a probable basis for extraterrestrial life.
I General nature of metabolic classes implies they apply to I Any type of complex metabolism requires existence of some kind of structure that allows carbon and energy tocome together and manufacture or break down molecules.
Water plays key roles and might be universally required.
I Water is a polar solvent, opposite sides have opposite I Organic chemicals are readily available for reactions by being dissolved in water if they are polar (hydrophilic asopposed to hydrophobic).
I Water provides the medium for transporting chemicals toand within cells and trans- porting waste products away.
I Water is essential in cellular metabolic reactions, such asthe ATP-ADP cycle.

Source: http://www.astro.sunysb.edu/lattimer/AST248/lec_10.pdf