Friday, February 15, 2013

LECTURE NOTE: Introduction to Organic Molecules and Functional Group

CH3: Introduction to Organic Molecules and Functional Group
-        Functional Group
o   Heteroatoms—atoms other than carbon or hydrogen. Common heteroatoms are nitrogen, oxygen, sulfur, phosphorous, and the halogens
o   Π Bonds. The most common Π bonds occur in C—C and C—O double bonds
o   Functional group is an atom or a group of atoms with characteristic chemical and physical properties. It is the reactive part of the molecule
o   Why do heteroatoms and Π bonds confer reactivity on a particular molecule?
§  Heteroatoms have lone pairs and create electron-deficient sites on carbon
§  Π bonds are easily broken in chemical reactions. A Π bond makes a molecule a base and a nucleophile (donate electrons)
o   C—C and C—H σ bonds form the carbon backbone or skeleton to which the functional groups are bonded (R). R—Functional Group
o   Ethane has only C—C and C—H σ bonds, so it has no functional group. Ethane has non polar bonds, no lone pairs, and no Π bonds, so it has no reactive sites (alkane)
o   Ethanol has two carbons and five hydrogens in its carbon backbone, as well as an OH group (hydroxyl functional group). Ethanol has lone pairs and polar bond that make it reactive with a variety of reagents, including acids and bases (Alcohol)
-        An Overview of Functional Groups
o   We can subdivide the most common functional groups into 3 types
§  Hydrocarbons
§  Compounds containing a C—Z σ bond where Z = an electronegative elements
§  Compounds containing a C=O group
o   Hydrocarbons are compounds made up of only the elements carbon and hydrogen. They maybe aliphatic or aromatic
§  Aliphatic hydrocarbons can be divided into three subgroups
·        Alkanes have only C—C σ bonds and no functional group. Ex. Ethane (CH3CH3)
·        Alkenes have a C—C double bond as a functional group. Ex. Ethylene (CH2=CH2)
·        Alkynes have a C—C triple bond as a functional group. Ex. Acetylene (HC triple bond CH)
§  Aromatic hydrocarbons (named after the strong and characteristic odors). Ex. Benzene, the sixed membered ring and three Π bonds of benzene comprise a single functional group
·        When benzene is bonded to another group, it is called phenyl group (phenylcyclohexane)
§  Polyethylene is a synthetic plastic and high molecular weight alkane, consisting of chains of CH2 groups bonded together (no reactive site, so stable compound and not readily degrade)
o   Compound containing C—Z σ bond. The electronegative heteroatom Z creates a polar bond, making carbon electron deficient. (lone pairs on Z are available for reaction with protons and other electrophiles, especially Z=N or O)
§  Halo group (R—X) X= F, Cl, Br, I
§  Hydroxyl group (R—OH)
§  Alkoxy group (R—O—R)
§  Amino group (R—NH2, R2NH, or R3N)
§  Mercapto group (R—SH)
§  Alkylthio group (R—S—R)
o   Compounds containing a C=O group (carbonyl group)
§  The polar C—O bond makes the carbonyl carbon an electrophile, while the lone pairs on O allow it to react as a nucleophile and base. The carbonyl group also contains a pie bond that is more easily broken than a C—Z σ bond
§  Atenolol is a βblocker, a group of drugs used to treat hypertension
§  Carbonyl group (R—(CH=O)) or (R—(CR=O))
§  Carboxy group (R—(C(OH)=O))
§  COOR (R—(C(OR)=O))
§  COCl (R—(CCl=O))
o   The importance of a functional group cannot be overstated. A functional group determines all the following properties of a molecule:
§  Bonding and shape
§  Type and strength of intermolecular forces
§  Physical properties
§  Nomenclature
§  Chemical reactivity
-        Intermolecular forces – are the interactions that exist between molecules. Functional group determines the type and strength of these interactions
o   Ionic compound (extremely strong electrostatic interactions)
o   Covalent compounds (in order of increasing strength)
§  Van der Waals forces (London forces)
·        Caused by momentary changes in electron density in a molecule (the only attractive forces present in nonpolar compound)
·        When compound is not completely symmetrical, creating temporary dipole
·        The weak interaction of these temporary dipoles constitutes van der Waals forces
·        The larger the surface area, the larger the attractive force between two molecules, and the stronger the intermolecular forces
·        Polarizability is a measure of how the electron cloud around an atom responds to changes in its electronic environment
·        Larger atoms like iodine, which have more loosely held valence electrons, are more polarizable than smaller atoms like fluorine, which have more tightly held electrons.
o   More loosely, so easily induced by temporary dipoles
§  Dipole-dipole interactions – are the attractive forces between the permanent dipoles of two polar molecules
§  Hydrogen bonding – typically occurs when a hydrogen atom bonded to O, N, or F, is electro statistically attracted to a lone pair of electrons on an O, N, or F atom in another molecule
-        Physical Properties (Compound’s intermolecular forces determines many of its physical properties)
o   Boiling point (bp) – is the temperature at which a liquid is converted to gas
§  Stronger the intermolecular forces, the higher the boiling point
·        Ionic compounds have very high boiling points
·        Covalent molecules, the boiling point depends on the identity of the functional group
·        The larger the surface area, the higher the boiling point
·        The more polarizable the atoms, the higher the boiling point
·        Liquid having different boiling point can be separated in the laboratory using a distillation apparatus
o   The more volatile component (lower boiling point compound) distills first, followed by the less volatile, higher component
o   Melting point (mp) – is the temperature at which a solid is converted to its liquid phase
§  The stronger the intermolecular forces, the higher the melting point
§  Given the same functional group, the more symmetrical the compound, the higher the melting point
·        Ionic compounds have very high melting points
§  Symmetry also plays a role in determining the melting points of compounds having the same functional group and similar molecular weight, but very different shapes
o   Solubility – is the extent to which compound, called the solute, dissolves in a liquid called the solvent
§  Compounds dissolve in solvents having similar kinds of intermolecular forces
·        “Like dissolves like” (structurally similar)
·        Polar compounds dissolve in polar solvents. Nonpolar or weakly polar compounds dissolve in nonpolar or weakly polar solvent
§  Water and organic liquids are two different kinds of solvents (water is polar, organic solvents are either nonpolar or weakly polar
§  Most ionic compounds are soluble in water, but insoluble in organic solvents. To dissolve an ionic compound, the strong ion-ion interactions must be replaced by many weaker ion-dipole interactions
§  An organic compound is water soluble only if it contains one polar functional group capable of hydrogen bonding with the solvent for every five C atoms it contains
§  Acetone is so soluble in water that acetone and water are miscible—they form solutions in all proportions with each other
§  A low molecular weight alcohol like ethanol is water soluble because it has small carbon skeleton (< five C atoms) compared to the size of its polar OH group
·        Cholesterol is insoluble in water
§  The nonpolar part of a molecule that is not attracted to H2O is said to be hydrophobic
§  The polar part of a molecule that can hydrogen bond to H2O is said to be hydrophilic
§  MTBE soluble in water, 4’-dichlorobiphenyl is not soluble in water, but in organic solvent
-        Application: Vitamins
o   Vitamins are organic compounds needed in small amounts for normal cell function (A, C, D, E,K) (B1, B2, B12)
§  Vitamin A or retinol is an essential component of the vision receptors in the eyes (mucus membrane and skin)
§  Contains 20 carbons and a single OH group, making it water insoluble (soluble in any organic medium (stored in fat cells, particularly in liver)
§  Beta carotene, the orange pigment (carrots)
o   Vitamin C
§  Has six carbon atoms, each bonded to an oxygen atom that is capable of hydrogen bonding, making it water soluble
-        Application of solubility: Soap
o   Soap molecules have two distinct parts:
§  Hydrophilic portion composed of ions called polar head
§  A hydrophobic carbon chain of nonpolar C—C and C—H bonds, called nonpolar tail
§  Dissolving soap in water forms micelles, spherical droplets having the ionic heads on the surface and the nonpolar tails packed together in the interior
-        Application: The Cell Membrane
o   Structure of the cell membrane
§  The cytoplasm is the aqueous medium inside the cell, separated from water outside the cell by cell membrane
§  Phospholipids, contains a hydrophilic ion portion and hydrophobic hydrocarbon portion, in this case two long carbon chains composed on C—C and C—H bonds (a polar head and 2 nonpolar tails)
§  When phospholipids are mixed with water, they assemble in an arrangement called lipid bilayer, with the ionic heads oriented on the outside and the nonpolar tails on the inside
§  Cell membranes are composed of these lipid bilayers
o   Transport across cell membrane
§  Some ions are transported across the membrane with the help of molecules called ionophores
·        Ionophores are organic molecules that complex cations. They have hydrophobic exterior that makes them soluble in nonpolar interior of the cell membrane, and a central cavity with several atoms whose lone pairs complex with a given atom (central cavity to hold cation)
·        Two naturally occurring antibiotics that act as ionophores are
o   Nonactin
o   Valinomycin
·        Several synthetic ionophores have also been prepaed, including one group called crown ethers ( are cyclic ethers containing several oxygen atoms that bind specific cations depending on the size of their cavity)
o   Functional Group and Reactivity
§  Functional group create reactive sites in molecules
§  Electron-rich sites react with electron-poor site
§  All functional groups contain a heteroatom, a pie bond, or both, and these features make electron-deficient (electrophilic) and electron rich (nucleophilic) sites in a molecule
§  An electronegative heteroatom like N, O, or X makes a carbon atom electrophilic
§  A lone pair on a heteroatom makes it basic ad nucleophilic
§  Pie bonds create nucleophilic sites and are more easily broken than sigma bonds
§  An electron-deficient carbon atom reacts with nucleophile, symbolized as :Nu-
§  An electron-rich carbon reacts with an electrophile, symbolized as E+
-        Biomolecules – are organic compounds found in biological systems
o   Sugar, amino acids, lipids and nucleotides


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LECTURE NOTE: Estimating Evolutionary Tree

BIO155: Estimating Evolutionary Tree
-        Phylogeny or phylogenic tree is a graphical summary of this history
-        Synapomorphy is a homologous trait that is shared among certain species and is similar because it was modified in a common ancestor (are shared, derived traits)
o   A type of homology
o   Group all of living organisms into a single lineage that descended from the same common ancestor
-        Any group that includes an ancestor and all of its descendants is called a monophyletic group (or clade or lineage)
o   Genetic code helps identify that bacteria and mammals as members of the same monophyletic group, but it does not help us distinguish bacteria from eukaryotes
o   Bacteria are identified by synapomorphies such as cell walls that contain a compound called peptidoglycan; eukaryotes have synapomorphies such as nuclear envelop
o   All synapomorphies are homologous traits, but not all homologous traits are synapomorphies.
o   Synapomorphies can be identified at whatever taxonomic level
§  Populations, species, genera, and phyla
o   To understand:
§  Synapomorphies identify evolutionary branch point
§  Synapomorphies are nested, meaning that you moved through time and trace a tree from its root to its tips, each branching event adds one or more shared, derived traits (hierarchy of branching events)
o   Phylogeny inference methods that use these principles are called cladistics methods (First determine what is ancient, and what is derived)
§  Outgroup analysis – the character state in the group of interest (the ingroup) is compared to the state in a very close relative that clearly branched off earlier (the outgroup) => confirm with the fossil record
§  A phylogenetic tree inferred by clustering synapomophies in this way is called cladogram
-        Morphological similarities like the eyes and skulls evolve independently in different lineages due to convergent evolution, which occurs when natural selection favors similar structures as solutions to problems posed by similar environment
-        Reversals are common in DNA data because there are only four possible states for each base in a sequence. Other things being equal, there is a 25% chance that a reversal to the previous state will occur each time a change occurs at a particular site in DNA
-        The most efficient way to distinguish homology from homoplasy is to analyze many traits in reconstructing evolutionary relationships instead of just one or a few
-        Under parsimony, biologists consider the hypothesis of convergence as the most likely. (Two changes occur, instead of 6 in the homologous theory)
o   Octopuses and vertebrates each have a layer of light sensitive cells in their eyes; but in octopuses these cells are oriented toward the opening where light enters the eye, while in vertebrates the light sensitive cells are oriented in the opposite direction (Octopus moves the eyes back and forth, change the shape of eyeball to focus, but vertebrate depends in the muscle that change the shape of the lens
o   When parsimony is applied to phylogeny inference, the preferred tree is the one that has the least total amount of evolutionary change (least subject to homoplasy, and more reliable source of synapomorphies)
-        The phylogeny of Whales
o   Lack of posterior limbs
o   Found a fossil of relative of whales (53.5 myr ago). These whales had hind limbs and reassemble and extinct group of amphibian mammals called mesonychains
o   Choosing character: Morphology and Molecules
§  First, choose character to use as data
·        Skeletal features and other morphological characteristics
·        DNA sequence and other molecular traits
o   Finding the best tree implied by the data
§  Parsimony with a single morphological character
§  Cetaceans are close relative to ungulates
·        Ungulates – Perissodactyls (horses/ rhinos), artiodactyls (cow, deer, pig)
·        Features found in angle bone called astragalus (in artiodactyl – both end of the bone are smooth and pulley shaped
o   Shows that hippos and whales are not related
o   Whales are descended from artiodactyl ancestor
§  Parsimony with multiple molecular character
·        Milk protein gene called beta-casein
·        Site 142, most organisms seem to have G at this position from common ancestor
·        Site 192, all taxa have C except the camel
·        Site 162, cows, whales, deer and hippo have a T at this site (other artiodactyl and outgroup has C)
·        Site 166 provides only synapomorphy in these 60 bases for monophyletic group consisting of whales and hippos
·        Site 177 provides a synapomorphy for a clade consisting of whales, hippos, pigs, and peccaries, which conflict with info from site 162
o   Reversal and convergence have resulted in homoplasy (either 162 or 177 does not reflect the actual evolutionary history of artiodactyl)
o   Artiodactyl implies total of 47 nucleotide changes while whale-hippo implies 41 changes.
§  In this case, Whale-Hippo is more parsimonious
§  60 characters and 8 taxa
·        When the number of taxa in a study is relatively low—fewer than 11—a computer program can evaluate all of the possible trees (Exhaustive Search) Because it guarantees that the optimal tree implied by a particular data set will be found, the approach is called an exact method
§  Evaluating the best tree
·        Use other methods besides Parsimony: Maximum likelihood (ML) and Bayesian Markov Chain Monte Carlo (BMCMC)
o   Maximum likelihood (ML) shows how likely it will match the hypothesis (deciding how good the data is)
o   Bayesian approaches are similar to likelihood methods, except that the principle is to ask what the probability is of particular tree being correct, given the data and a model of how the traits in question change over time
o   Later on is the introduction of distance methods
o   Produce consensus tree under parsimony
o   Using statistical test o evaluate the best tree under ML and BMCMC
o   Compare the best tree under parsimony, ML and BMCMC to see how consistence they are
·        Evaluating Particular Branch: Bootstrapping
o   Not every individual can represent the entire population (If variety in population is high then less confident that sample average is reliable)
o   With trees based on ML or BMCMC analyses, you can compare tree with and without a particular branch and compute which is more likely.
§  Bootstrapping process begins by randomly selecting one of the sites and using it as the first entry in a new data set. Then it randomly selects another site which becomes the second data point in the new data set.
§  Resampling until particular branches occur in 50%, 80% or 100% of the tree estimated from the resampled data sets
§  Aunder 50%, then polytomy, or a point of uncertainty
§  Strong support for whale-hippo clade
·        Resolving conflicts
o   Need larger data set and less homoplasy
o   The presence or absence of SINE or LINE at a homologous location in the genome of two different species can be used as a trait in phylogeny inference
o   Less likely that SINE will insert itself into two independent host lineages at exactly the same location (possible but not improbable)
o   Not likely a reversal because the loss of SINE or LINE is tracable
o   No homoplasy in data set, and thus no conflicts among characters when they are mapped onto the tree
o   Found fossils of semi-aquatic ancestor that lead back to the  link between whale and hippo
-        Using Phylogenies to Answer questions
o   Classification and Nomenclature: Is there such a thing as fish?
§  The effort to name and classify species is called systematics
§  Linnaean system starts with giving each species a unique genus and species name and then groups progressively more similar species into kingdoms, classes, orders, families, and genera (phonetic approach)
§  In contrast, naming schemes that are based on evolutionary relationships are referred to as phylogenetic or cladistics approaches (tree based and branching events).
·        More specifically, only monophyletic groups, which includes all descendants of common ancestors are named
·        Paraphyletic groups, which include some but not all descendants of a common ancestor, should not be named
o   Using molecular clock ( a hypothesis)
§  There are good theoretical reasons to expect that at least some types of DNA sequences change in a clocklike fashion
§  Instead of being favor or eliminated by natural selection, these “neutral change” responds to a random process called genetic drift
§  Neutral theory of molecular evolution predicts that neutral changes in DNA should accumulate in population as rate equal to mutation rate. If the mutation rate does not change much over time and if generation times remain similar, then the number of neutral molecular differences between two taxa should be proportional to the age of their most recent common ancestors
§  By documenting the number of different neutral mutations observed in two species and multiplying by a calibration rate, representing how frequently neutral changes occur per myrs, researchers can estimate when the species diverged
§  Mutation rate to neutral alleles will vary from gene to gene, and linkage to linkage and base to base
§  Third position of codons are much more neutral than the first and second, more like a clocklike rate
§  If alleles change through natural selection, then the mutations are likely to be working in clock fashion
§  Rate of change that are calibrated for a particular gene and lineage are unlikely to work for other groups, diff in generation time and selection histories
§  Determine by fossil and geological record
o   Analyzing Phylogeography: How did Chameleons Get from Africa to India?
§  The effort to understand where organisms live and how they came to be there is called biogeography
§  Broke up of Gondwana
§  Human cause
o   Co-speciation: When new species of Aphids Form, what happens to the Bacteria that live inside their cells?
§  When natural selection occurs during these interactions and produces adaptations in both species involved, coevolution is said to take place
§  Aphids and bacteria inside them have symbiotic relationship (endosymbiosis)


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