S t r u c t u r e   &   O r g a n i z a t i o n :     L e c t u r e  # 4 Vocabulary | Study Questions
The Chemistry of Life: Part 2
Objectives:
  1. Become familiar with the sources of the four most common biological elements and how they are cycled between living tissue and the environment.
  2. Understand the chemical composition (basic elements) and function of the major organic compounds of life.
  1. Carbon
    Remember: you cannot create or destroy matter, but matter cycles.
    1. Reservoir: the atmosphere (as CO2)
    2. Initially incorporated into living tissue through the process of photosynthesis.
      Photosynthesis: light energy from the sun is converted to chemical energy (in the form of carbohydrates) by taking carbon dioxide (CO2) from the atmosphere, hydrogen from water, and combining them (e.g. glucose). Simplified formula: CO2 + H20 + sunlight = carbohydrates (lecture 8).
    3. Recycled back into the atmosphere by means of respiration and decomposition.
      Carbon is returned to the atmosphere by cellular respiration (not as in breathing in and out) and decomposition (e.g. Food is eaten; ATP (a form of chemical energy) is produced in cellular respiration; CO2 is given off as a biproduct and exhaled into the atmosphere). Do plants do cellular respiration? Yes. All living things, to some degree, do cellular respiration.
      Decomposition is a specialized form of cellular respiration.
      Dr. St. Clair is a Yankees fan.
    4. Carbon serves as an ideal structural backbone for organic compounds due to its ability to form up to four separate covalent bonds.
      Carbon has 6 protons, 6 electrons: 2 in first energy level; 4 in second. Needs 4 more to become physically and chemically stable (fill outer energy level).
  2. Nitrogen
    1. Reservoir: the atmosphere (as N2)
      When raise your hands in the air and wave them like you just don't care, what you feel is 78% nitrogen.
    2. Only a very limited number of prokaryotic organisms are able to make direct use of atmospheric nitrogen in the synthesis of organic compounds. (selected species of bacteria and cyanobacteria)
      Nitrogen fixers (some specialized bacteria and cyanobacteria) are able to make direct use of atmospheric nitrogen and incorporate it into living tissues. (Agricultural soils require fertilizers, as nitrogen fixers don't survive well in highly disturbed soils.)
    3. Plants obtain nitrogen (most commonly as NO3) from the soil solution.
      You and I cannot fix nitrogen, but we need it. We need nitrogen, as in amino acids, and can only obtain it, ultimately, from nitrogen fixers: they incorporate atmospheric nitrogen into nitrate which they put into the soil. Plants can obtain nitrogen, then, from the soil, and can then by moved moved through food chains. Our best source of amino acids, in terms of abundance, is meat.
    4. Nitrogen is returned to the atmosphere by denitrification and organic decomposition.
      Denitrifying bacteria process organic nitrogen back into the atmosphere.
  3. Oxygen
    1. Reservoir: water, the atmosphere (as O2)
      Atmospheric oxygen comes from O2 and from CO2. The oxygen in the atmophere was put there by green plants (photosynthesis):
    2. Oxygen is extracted from water as a by-product of photosynthesis and is then released into the atmosphere.
    3. Most life forms use oxygen from the atmosphere for basic energy transformations (aerobic respiration).
      Why do we breathe? We (our cells) require oxygen in order to process the energy by which we live. (You can't hold your breath until you die.)
    4. Incorporation of oxygen into organic compounds occurs intially during photosynthesis. Specifically, oxygen is incorporated in combination with carbon (as CO2) during the dark reaction of photosynthesis.
      How do we get oxygen into organic molecules (carbohydrates, nucleic acids, etc..)? Photosynthesis!
    5. Oxygen is recombined with hydrogen to form water and carbon to form CO2 during respiration and decomposition.
      In your cells, you're taking in atmospheric oxygen to more efficiently process the carbohydrate end-product of photosynthesis into ATP. As you take the carbohydrate and begin to pull it apart (in your cells) through cellular respiration (to form ATP), hydrogens are released from the carbohydrate, and the oxygen you breathe recombines with that hydrogen to form what? Water.
      So: a plant pulls water apart, putting the oxygen into the atmosphere and incorporating the hydrogen into a carbohydrate. You and I then eat the carbohydrate and take oxygen in from the atmosphere. In processing the energy of the carbohydrate into ATP (cellular respiration), hydrogen is released and recombined with oxygen we breathe to form water again. (We'll get into the mechanics later: lecture 8
  4. Hydrogen
    1. Reservoir: water
      The ultimate nonliving reservoir is water.
    2. Extracted from water and incorporated into living tissue through the process of photosynthesis.
      PLANTS ARE REMARKABLE! Brainless, but remarkable: some can convert light energy into chemical energy; some can convert (from scratch) amino acids: we can't. Obviously, we couldn't live without them.
    3. Restored to water through the process of aerobic respiration.
      OK>
  5. Organic compounds of life
    For each of these we will discuss the structure and functions.
    1. Carbohydrates
      1. Chemical composition (carbon, hydrogen, oxygen)
        Maybe some others, but these are the biggies (e.g. glucose). Carboydrates are either simple or complex: simple carbohydrates are otherwise known as monosaccharides and complex carbohydrates as polysaccharides.
      2. Functions of carbohydrates
        1. Structural role
          In plants, carbohydrates are the basic structural molecule (e.g. wood: made of the complex carbohydrate cellulose, which is similar to starch, but the glucose molecules are bonded together differently).
        2. Energy role
          Carbohydrates are a great source of energy (e.g. starch: bread oatmeal, potatos, etc.. Made of glucose hooked end-to-end-to-end. We can break it down and use it. Glucose is what we begin with in cellular respiration.)
      3. Some examples
    2. Lipids
      1. Chemical composition (carbon, hydrogen, oxygen, phosphorous)
      2. Functions of lipids
        1. Structural role
          At cellular level there is a chemical boundary which is basically made up of a phospholipid bilayer. This bilayer regulates what enters and leaves the cell. All living cells have phosphlipid cell membrane.
        2. Energy role
          Fats are a category a lipids. Fat is not evil; the problem is too much fat. Fats are essential to our diet, and a wonderful energy storage molecule. Fat molecules store energy in energy rich carbon-hydrogen and carbon-carbon covalent bonds. These energy-rich bonds are in the fatty-acid chains in the fat molecules.
        3. Information role
          Biological communication is necessary to life. We, for example, are comprised of trillions of cells, making up hundreds of different tissues that must cooperate; if cells and tissues are doing their own thing, life won't work. Chemical communicators, such as hormones, function to keep things in synch. One category of hormones is comprised of lipids: steroids. Examples of steroid hormones: cholesterol, testosterone, progesterone, estrogen. These communicate chemical information (e.g. testosterone, the male hormone, produced in the testes is circulated through the blood and triggers a thickening of the voal chords, deepening the voice.)
      3. Some examples
    3. Proteins
      1. Chemical composition (carbon, hydrogen, oxygen, nitrogen, sulfur)
        The basic building blocks of proteins are amino acids. There are only 20 different amino acids, but they combine differently to form thousands of different proteins. All life-associated proteins are form from the same 20 amino acids. A polypeptide is the amino acid sequence of a protein; we often use the terms 'protein' and 'polypeptide' interchangeably. The amino acids are hooked together using condensation reactions, and broken down by hydrolysis reactions.
      2. Functions of proteins
        1. Structural role
          As complex carbohydrates are the basic structural molecule of plants, proteins are the basic structural molecule of animals. At the cellular level, proteins are an important structural element of cell membranes. At the organismal level, proteins are the basic structural molecules (e.g. You and I: muscles, ligaments, skin, hair, cartilage, bones: mostly proteins.)
        2. Motility role
          Contractile proteins (actin and myosin) are basic to our ability to move: the heart beating, hand typing, eyes reading: any movement.
        3. Information role
          Another category of hormones are protein hormones (e.g. insulin: a hormone that communicates to the cells to let the glucose in. Without insulin, cells would starve for energy (glucose). We used to use bovine insulin to aid diabetics, but now use genetically engineered human insulin).
        4. Catalyst role
          A catalyst is any chemical that speeds up (facilitates) chemical reactions. In biological systems, we use the term 'enzymes.' Almost all enzymes are proteins. When you have an enzyme to facilitate a reaction, the reaction requires less energy. Not only is less energy required, making the reaction more efficient, but less heat is given off as a biproduct of the reaction. (Too much heat would not be viable.)
        5. Transport role
          Proteins used to transport materials across the cell membrane (lecture 7).
      3. Some examples
    4. Nucleotides & Nucleic acids
      Nucleotides fall into two categories: those that operate strictly as nucleotides, and those that hook together to form nucleic acids (such as DNA and RNA).
      1. Chemical composition (carbon, hydrogen, oxygen, nitrogen, phosphorous)
        Each nucleotide cosists of three basic parts: a simple sugar, at least one phosphate group (ATP, for example, has three), and a nitrogen base (adenine, for example).
      2. Functions of nucleotides and nucleic acids
        1. Energy role
          Nucleotides of the first category (function independently as nucleotides): ATP (adenosine tri-phosphate), ADP (adenosine di-phosphate), AMP (adenosine mono-phosphate), NAD, FAD, etc..
        2. Information transmission role
          (Second category) Nucleic acids (DNA, RNA) trasmit and store genetic information. DNA is a double molecule: two nucleic acids (parallel, helical, hooked together by hydrogen bonds-the rungs of the spiral DNA ladder). (We'll get into how nucleic acids transmit genetic information in lecture 9).
        3. Information storage role
          (above)
      3. Some examples