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Chapter 4 Carbon and the molecular Diversity of Life (Carbon atoms can…

- - - - Artificial synthesis of the compound molecules extracted from living matter seemed impossible, but.....
        
        Ex 1. - Organic compounds were thought to arise only in living organisms, which were believed to contain a life force beyond the jurisdiction of physical and chemical laws.
    - - Ex 1.- In 1828, Fredrich Wohler, a German chemist, tried to make an "inorganic" salt, ammonium cyanate, by mixing solutions of ammonium ions (NH4+) and cyanate ions (CNO-).
        
        By doing so, Wohler was astonished to find that instead he had mad urea, an organic compound present in the urine of animals.
  - - - Ex 1.- The results that Miller concluded that complex organic molecules could arise spontaneously under conditions thought at the time to have existed on the early Earth.
        
        Those experiments support the idea that abiotic synthesis of organic compounds. Perhaps near volcanoes, there could be early stage in the origin of life.
    - - Because of Carbon's ability to form four bonds, this limits assortment of atomic building blocks that can be used to build an inexhaustible organic molecules.
        
        Different species of organisms, and different individuals within a species are distinguished by variations in the type of organic molecules they make.
        
        Ex 1.- The great diversity of living organisms we see on the planet (and in fossil remains) are made possible by the unique chemical versatility of the element Carbon.
- - - - In organic molecules, carbon usually forms single or double covalent bonds. Each carbon atom acts as an intersection point from which a molecule can branch off into as many as four directions
        (This enable carbon to form large, complex molecules).
        
        The electron configuration of carbon gives it covalent compatibility with many different elements.
        
        These are the four major atomic components of organic molecules.
        These valence electrons are the basis for the rules of covalent bonding in organic chemistry.( The building code for the architecture of organic molecules).
        
        Ex 1.- Carbon and its most frequent bonding partners -- Hydrogen, Oxygen, and Nitrogen.
      - A carbon atom usually completes its valence electrons by sharing its 4 electron with other atoms, so that 8 electrons in total are present.
        (Each pair of shared electrons constitutes a covalent bond).
        
        When carbon atoms form 4 single covalent bonds, the arrangement of its 4 hybrid orbitals cause the bonds to angle towards the corners of an imaginary tetrahedron.
        (Keep in mind that molecules are three-dimensional , that the shape of a molecule is central to its functions).
        
        Ethane is shaped like two overlapping tetrahedrons. In molecules with more carbons, every grouping of a carbon bonded to four other atoms have a tetrahedral shape.
        
        Molecular
        
        Structural
        
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        The bond angle of Methane (CH4) is 109.5 degrees. They are roughly the same in any group of atoms where carbon can has 4 single bonds.
        
        Molecule and Molecular shape
        A.) Methane. When carbon atom has 4 single bonds to other atoms, the molecule is tetrahedral.
        
        Molecular formula
        CH4
        
        Structural Formula
        
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        But when 2 carbons atoms are joined by a double bond as in Ethene (C2H4). The bonds from both carbons are all in the same plane. So the atoms joined to those carbons are in the same plane as well
        
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  - - - Ex 1.- Some carbon skeletons have double bonds, which vary in number and location.
        Ex 2.- The variation in carbon skeletons is one important source of the molecular complexity and diversity that characterize living matter.
      - Hydrocarbons - Organic molecules consisting of only carbon and Hydrogen.
        (Atoms of hydrogen are attached to the carbon skeleton wherever electrons are available for covalent bonding.
        
        Ex 1. - Hydrocarbons are the major components of petroleum, which is called fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago.
        
        Although hydrocarbon are not prevalent in most living organisms, many of the cells organic molecules have regions consisting of only carbon and hydrogen.
        
        Ex 1.- The molecules known as fats have long hydrocarbon tails attached to a nonhydrogen component.
        
        Neither petroleum nor fat dissolves in water; both are hydrophobic compounds because that great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages.
        
        Another characteristic of hydrocarbons is that they can undergo reactions that release a relatively large amount of energy
        
        Ex 1.- The gasoline that fuels a car consists of hydrocarbon.
        Ex 2.- The hydrocarbons of fats serve as stored fuel for plants embryos (seeds) and animals.
      - Variation in the architecture of organic molecules can be seen in Isomers.
        They are compounds that have the same numbers of atoms of the same elements but different structures. Hence different properties.
        
        Structural isomers - differ in the covalent arrangements of their atoms.
        The skeleton is straight in one compound but branched in the other.
        
        Ex 1.- Pentane, and 2-methyl butane .
        Both have the molecular formula (C5H12), but they differ in the covalent arrangement of their carbon skeletons.
        
        The number of possible isomers increase tremendously as carbon skeletons increase in size.
        (structural isomers may also differ in the location of double bonds).
        
        Cis-trans isomers are carbons that have covalent bonds to the same atom. But these atoms differ in their spatial arrangements due to the inflexibility of double bonds.
        
        Ex1. - Cis isomer: The two Xs are on the same side of the double bond
        Ex 2.- Trans isomer: The two Xs are on opposite sides of the double bond.
        
        Single bonds allow the atoms they join to rotate freely about the bond axis without changing the (Double bonds do not permit such rotation).
        
        If double bonds join two carbon atoms, and each C also has two different atoms (or groups of atoms) attached to it. Then two distinct cis-trans are possible.
        
        The subtle difference in shape between such isomers can dramatically affect the biological activities of organic molecules.
        
        Ex 1.- The biochemistry of vision involves a light-induced change of retinal, a chemical compound in the eye. It goes from cis isomer to the trans isomer.
        Ex 2.- Another example is trans fats, which we'll explain in the next chapter.
        
        Enantiomers are isomers that are mirror images of each other, and they differ in shape due to the presence of an asymmetric carbon. On is attached to four different atoms or groups of atoms.
        
        Ex 1.- L isomer and D isomer
        (Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images).
        
        The four groups can be arranged in space around the asymmetric carbon in two different ways that are mirror images.
        
        Ex 1.- Enantiomers are like your left-handed and right-handed versions of molecules. One cant be the other.
        (Only one isomer is biologically active because only that form can bind to specific molecules in an organism.
        
        The concept of enantiomers is important in the pharmaceutical industry because the two enantiomers of a drug may not be equally effective. Like ibuprofen and the asthma medication albuterol.
        
        Drug | Effects| Effective enantiomer| Ineffective enantiomer
        
        Ibuprofen | Reduces inflammation and pain | S-ibuprofen | R- ibuprofen
        
        Albuterol | Relaxes bronchial (airway) muscles, improving airflow is asthma patients | R- Albuterol | S- Albuterol
        
        Methamphetamine also occurs in two enantiomers that have very different effects
        
        Ex 1.- The first is the highly addictive stimulant drug known as "crank", sold illegally in the street drug trade.
        Ex 2.- The second one has a weaker effect. It is the active ingredient in an over-the-counter vapor inhaler for treatment of nasal congestion.
        
        The different effects of enantiomers in the body demonstrate that organisms are sensitive to even the most subtle variations in molecular architecture. (Emergent properties that depend on the specific arrangement of their atoms).
- - - - These groups may participate in chemical reactions or may contribute to function indirectly by their effects on molecular shape. (They help give each molecule its unique properties).
  - - - Ex 1.- Both are steroids , organic molecules with a common carbon skeleton in the form of 4 fused rings.
        (They only differ in the chemical groups attached to its rings.
      - The different actions of these two molecules on many targets throughout the body are the basis of gender. It produces the contrasting features of male and female vertebrates. ( the chemical groups are important because they affect molecular shape, contributing to function.
        
        Functional groups - A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules involved in chemical reactions.
        (Each has certain properties, such as the shape and charge. By doing so that causes it to participate in chemical reactions in a characteristics ways).
        
        Seven chemical groups that are most important in biological process are
        **1.Hydroxyl (-OH),
        
        Carbonyl ( C=O),
        
        Carboxyl group (-COOH),
        
        Amino groups (-NH2)
        
        Sulfhydryl group (-SH)
        
        Phosphate group (-OPO3 with a -2 charge)
        
        Methyl group (-CH3)**
        
        The first 6 groups can be chemically reactive: of these, all except the Sulfhydryl are also hydrophilic and thus increase the solubility of organic compounds in water.
        (The methyl group is not reactive, but instead often serves as a recognized tag on biological molecules).
  - - - 3 phosphate are presented in series in ATP. One phosphate may be split off as a result of a reactions with water.
        Having lost one phosphate, ATP becomes adenosine diphosphate, or ADP.
        
        Although ATP is sometimes said to store energy, it is more accurate to think of it as storing the potential to react with water.
        This reaction releases energy that can be used y the cell.