jimtrue.com : school : BSC2010 : CH 02: Chemical Context of Life

Posted by Jim True on February 1, 2004 2:26 AM. Last Updated October 22, 2006 9:23 PM

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CH 02: Chemical Context of Life

Definitions

• Matter -- anything that takes up space and has mass.
• Mass -- amount of matter that a substance contains.
• Weight -- the force of gravity acting upon a mass.
• Atom -- smallest unit of matter with specific chemical properties.
• Element -- substance in which all atoms have the same chemical properties.
• Chemical Symbol -- written abbreviation for an element
• Molecule -- Two or more atoms linked together to form one particle.
• Compound -- Atoms of two or more elements linked together. The difference between a molecule and a compound is that a compound has to contain TWO or more DIFFERENT elements. Not all molecules are Compounds (ie. O₂, an Oxygen molecule is NOT a compound).
• Molecular Formula -- Written listing of the elements and number of atoms in one molecule.
• Structural Formula -- written diagram of the bonds and general spatial relationship between elements and atoms in a molecule. Structure dictates function; three separate compounds can have the SAME molecular formula and differing structural formulas. ie Glucose, Fructose and Galactose are all C₆H₁₂O₆, but they have very different organizations in space.
• Molecular Model -- 3-dimensional representation of the arrangement of the elements in a molecule. (See figure 2.13, p.35)
• Energy -- the Capacity to do work (put mass into motion)
• Potential Energy -- stored energy, energy that is available to do work (like a spring coiled waiting to unwind, or a ball suspended over a table waiting to fall).
• Kinetic Energy -- energy in action, work is being performed.

Examples

• Chemical Symbols: C -- Carbon, H -- hydrogen, O -- Oxygen, Na -- Sodium, K -- Potassium, Au -- Gold.
• Molecular Formulas: O₂, H₂, H₂O, CH₄
• Structural Formulas: H--H, H--O--H.

Atoms and Subatomic Particles

• Currently, atoms are known to contain over 100 different types of subatomic particles (SAP's)!
• We'll concern ourselves with only 3:
  • Proton -- SAP with a + Charge (positive)
  • Neutron -- SAP with a 0 Charge (neutral)
  • Electron -- SAP with a -- Charge (negative)
• Nucleus -- formed by protons and neutrons (means central or at the core of)
• All known elements are arranged in a special Periodic Table of the Elements; arranged together with other elements with similar properties. Tidbit: 92 naturally occuring on Earth; the remainder are created in the lab.
• Atomic Number -- number of protons in one atom.
• Atomic Mass -- Number of protons, plus the number of neutrons. Electrons have such little mass that they are ignored when calculating mass.
• Isotope -- atoms of the same element with the same number of protons, but differing numbers of neutrons.
• Radioactive Isotopes are unstable; they do not maintain nuclear integrity, ie they eject neutrons, protons and energy.
  • They can easily be tracked by their energy signatures, and after some period of time may eject protons and thus convert to a different element.
  • Many useful technological applications for radioactive isotopes.
  • Isotopes emit energy signature that interferes w/radio waves (which is how the geiger counter was invented to detect "radioactivity").
  • Isotopes typically eject protons over a specific period of time as fractions, or "half-lifes". The quantity of the isotope of Carbon, C-14 can be used to measure how long the carbon has been present.

Atoms and Energy

• Electrons in an atom represent the atoms potential energy for a particular atom. The main focus for biology will be on the electron.
• In an electrically neutral atom, the number of electrons is EQUAL to the number of electrons.
• Depending on the element, electrons are distributed around the nucleus at different distances. These electrons are CONSTANTLY in motion and can be represented as a 3-dimensional pattern, and the location in this 3-D space can be estimated.
• The nearer to the nucleus these electrons are located, the less potential energy the electrons contain; the farther away, the more potential energy.
• These different distances are called energy levels or shells. The largest elements have 7 energy levels. The Periods in the Periodic table define the Energy Levels, being 7 concentric distances, each containing a higher potential energy.
• Electrons are always in motion and we can never know precisely where they are around a nucleus. However, they tend to be found in three dimensional spaces known as orbitals about 90% of the time. See figures 2.10, p.32; 2.11, p.33
• Each orbital can have a maximum of 2 electrons; thus, electrons are "paired" within orbitals.
• Each energy level has a maximum number of orbitals it can contain.
• Thus, shells have a maximum number of electrons they can hold.
• For any element, the outermost "exposed" shell is called the valence shell, which contains one or more valence electrons.
• It is the valence electrons that give any elements its chemical properties.
• It was discovered that for an atom of any element to reach chemical stability, ie become chemically unreactive, the valence shell must fill with a certain number of electrons.
• Except for the first energy level, which is filled (reactively) stable when it contains 2 electrons, all other reach chemical stability when they contain 8 electrons. This is known as the "octet rule" or the rule of 8.
• Valence electrons give an element its chemical properties because atoms transfer or share one or more electrons in order to fill the outer shell.
• IMPORTANT -- Chemical reactions are the transfer or sharing of electrons, therefore, all chemical reactions represent energy relationships! It is this knowledge that defines how chemistry relates to biology.

Chemical Bonds

• The transfer or sharing of one or more electrons results in the formation of chemical bonds.
• Chemical bonds can either be formed or broken during chemical reactions.
• There are three main types of bonds:
  • Covalent Bond -- results from the SHARING of one or more electrons between atoms or molecules.
    • There are two types:
      • Nonpolar -- equal sharing of electrons. There is no overall charge on the molecule. ie Fats
      • Polar -- unequal sharing of electrons. Results in weakly charged ends or regions on each molecule, ie H₂O. These regions are known as "poles", created by a difference in electronegativity of the atoms within the molecules. Polar refers to a "region of charge"; and there can be multiple regions. figures 2.12, p.34, 2.13, p35
    • Most organic molecules have covalent bonds.
    • Organic molecules form the main structural components of all living things.
  • Ionic -- results from the complete transfer of one or more electrons from one atom to another.
    • Before the transfer, the number of protons = number of electrons, so there is no net charge.
    • After the transfer, charges are unequal, producing a charged particle known as an ion.
    • Anion -- ion with a negative charge, ie 'A Negative ION'.
    • Cation -- ion with a positive charge, ie 'ca + ion'
    • Ions are very important in a variety of cell functions, eg nerve impulse transmission.
    • As a result of the electron transfer, the anion is attracted to the cation by opposite charges. figure 2.14, p.35
    • Ionic bonds are very strong as solids and tend to form crystalline structures, eg NaCl, table salt, however, they are easily dissolved in polar liquids.
  • Hydrogen Bonds -- Last type of bond that is always associated with molecules that have polar covalent bonds and the element hydrogen. figure 2.16, p.36
    • When hydrogen is present in polar molecules, it typically has a weak positive charge.
    • This causes it to be weakly attracted to the negative polar regions of other molecues.
    • Do not form molecules w/Hydrogen bonds, but hydrogen bonds do give molecules their "shape" and "shape defines function".
    • Hydrogen bonds do not themselves create molecules, but are important in giving them shape, eg DNA, proteins.
• All molecules have characteristic sizes and shapes, which relate to the number of atoms, the elements in the molecule, and the types of bonds present.
• The shapes are related to the way electrons in the orbitals combine during bonding (ionic, or covalent).
• As a result, molecules have function due to their shape and also interact on the basis of shape.
• Molecules often fit precisely together to form larger structures, and when we begin looking at receptor sites on cells and enzyme shape and function, the importance of shape will become evident. figure 2.19, p.38.

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