he organization of Matter – Atoms

• All matter is composed of atoms
• All atoms have a central nucleus surrounded by electrons
  
  
  • Nucleus comprised on protons (+) and neutrons (0)
  • Elections zip around nucleus and are negative (-)
• The nucleus
  • The Atomic Number is the number of protons in the nucleus
  • Changes in the number of protons changes the element
  • Changes in the number of neutrons does not change the element – it creates an isotope
  • Example: C¹² and C¹⁴ – C¹² has 6 protons and 6 neutrons, C¹⁴ has 6 protons and 8 neutrons. Both of these carbon atoms will have the same chemistry. The only difference is that C¹² is stable while C¹⁴ is radioactive.
• Electrons
  • Electrons have virtually no mass (compared to protons and neutrons)
  • They float around the atom in distinct shell-like arrangements called orbitals
    • The first electron “shell” contains 2 electrons
    • The second electron “shell” contains 8 electrons
    • The third electron “shell” contains 8 electrons
    • There are many more electron shells, but we will not be addressing them
    • These shells are illustrated in the below graphic of the periodic table. Notice how the first row contains two elements, Hydrogen and Helium, corresponding to the two electrons in each shell. The next row contains eight electrons, corresponding to the eight electrons in the next electron shell.

    

  • In a typical atom, the number of protons = number of electrons. When this is not so, it creates an ion

The organization of Matter – Chemical Bonds

Molecular bonds depend upon the arrangement of electrons. There are two types of molecular bonds that we will be looking at, covalent bonds and ionic bonds

Covalent Bonds

	Atoms are most stable when they have a full electron shell. In order to accomplish this, they must share electrons

Ionic Bonds

	Some atoms have a very strong or very weak attraction to electrons The atoms with a very strong attraction to electrons can “steal” an electron from the atom with a very weak attraction to electrons Compounds formed in this way are called salts.

Hydrogen Bonds

Often when atoms share electrons in a covalent bond, the sharing is not equal. The electrons tend to aggregate nearer to one atom than to the other atom. This creates what is known as a dipole. In a molecule with a dipole, one end has a higher concentration of electrons than the other end. The end with more electrons has a partial negative charge while the other end has a partial positive charge. Water, as will be discussed below, has a strong dipole. A hydrogen bond is formed when the negative end of one molecule becomes oriented to and semi-attached to the positive end of another. Hydrogen bonds are fairly weak, but many of them in series, as seen in DNA, can be quite strong. Molecules with a dipole are known as polar or hydrophilic molecules, those without a dipole are known as non-polar or hydrophobic molecules.

Hydrophilic Interactions	Hydrophobic Interactions

Water

Some properties of water

• Ubiquity – Water is plentiful – about 75% of earth is covered with it. Water makes up any where from 70 to 90+% of the body weight of living things. At most temperatures on the surface of the earth water is a liquid. In this state water is an excellent solvent and because there is so much of it available on the earth’s surface water is home (oceans, lakes and rivers) to much of life. The water cycle is one of the most important biogeochemical processes. You may also what to review some general facts about water.
• Structure of water. H₂O as a liquid
  • Water is a polar molecule and can bond both to itself and to other water molecules by weak attractions called hydrogen bonds. Each water molecule can bond with as many as 4 others (See Figure 1). Figure 1 – Note that only three of the possible four hydrogen bonds are shown.
  • Hydrogen bonds make water an excellent solvent. The hydration shells of water molecules which form around both positive and negative ions as they dissolve, keep these ions in solution by eliminating their ionic attraction. See Figure 2 below. Figure 2 – Water dissolving NaCl (table salt)
  • Hydrogen bonding is responsible for the unusual thermal properties of water including:
    • Water’s high specific heat capacity. Specific heat is defined as the amount of heat energy needed to raise the temperature of one gram of a substance 1°C. Since it takes much more energy that normal to break all the hydrogen bonds in liquid water, water resists rapid temperature fluctuations, adding stability to earth’s environments where liquid water is plentiful.
    • Water has a very high heat of vaporization. The heat of vaporization is defined as the energy needed to change the phase of a liquid to a gas. Again, because of the number and relative strength of water’s hydrogen bonds, it takes a great deal of energy to break a molecule free of its liquid partners. Heat of vaporization causes a cooling effect because as the warmer molecules evaporate from your skin they take the heat energy with them, leaving you cooler.
    • Water also has a high heat of fusion. This is the amount of heat necessary to melt (or freeze) 1.00 mole of a substance at its melting point
  • Capillary action involves two properties of water, cohesion and adhesion.
    • In cohesion water’s hydrogen bonds make liquid water self-sticky. This stickiness makes water bead up more on a surface than other substances. See Figure 3. Figure 3 – Surface Tension causes water to bead
    • Water is also highly adhesive. This property of water gives it the ability to literally climb the wall of any container it is in. The top of the water column assumes a u-shape called a meniscus. See Figure 4. Figure 4 – Adhesion creates a meniscus in a pipette
    • When the container happens to be the woody walls of xylem in a plant, both adhesion and cohesion of water molecules produce a force called capillary action. As water evaporates (Transpiration) from the air sacs within the spongy layer of a plant leaf, the meniscuses in these air spaces become more concave increasing the tension on the water columns in the xylem. Along with capillary action this force, described below, helps move water (against the force of gravity) from the root up to the leaves of a mighty tree. (See TACT forces in Wallace)
  • Surface Tension, the force produced by the difference in hydrogen bonding at water’s surface verses its interior, is able to create the illusion that a body of water has a skin. Insects are light enough that they can literally walk on water. Without the natural surfactant (soapy material) produced in our lungs water’s high surface tension could actually collapse them, cutting off our air supply. Learn about complications resulting from the lack of surfactants in premature babies at the Merck Manual site (look for “Respiratory Distress Syndrome”).
  • Structure of Ice. Ice (solid water) has a regular bonding arrangement between the molecules of water which actually increases the distance between molecules in certain directions. The result is that ice is not as dense as liquid water at 4°C. Therefore ice FLOATS. This is beneficial to bottom dwellers in lakes, rivers and oceans. You figure out why.
  • Water acts as both an acid and a base
    • Acid release H⁺
    • Base accepts H⁺
    • We define the pH of a solution as the negative logarithm of the hydrogen ion concentration.
      • at pH 7.0, a solution is neutral
      • at lower pH (1-6), a solution is acidic
      • at higher pH (8-14), a solution is basic

More fun facts about water

• Campbell’s Guide to Water
• SemNet: Properties of Water
• USGS Water Science for Schools
• Detergent Chemistry Properties of Water – Kiwi Web

Acids and Bases

• Water can ionize (dissociate into charged particles)
  • H₂0 < > H⁺ + OH^-
• In pure H₂0 (distilled water):
  • [H⁺] = [OH^-]
  • Dissolved solutes can change relative [H⁺] and [OH^-]
• Acids increase [H⁺] by donnating H⁺
  • HCl —–> H⁺ + Cl^-
• Bases decrease [H⁺] in solution by accepting H⁺
  • NaOH < > Na⁺ + OH^-
    • Remember H₂0 < > H⁺ + OH^-
    • OH^- combines with H⁺ thereby lowering the [H⁺]
  • NH₃ (ammonia) dissolved in water
    • NH₃ + H⁺ < > NH₄
• pH is a measure of the relative concentration of H⁺ in solution
  • pH = -log[H⁺] where [H⁺] means the molar concentration of hydronium ions, M = moles / liter
    • Each change in pH is a 10 fold increase or decrease
  • when pH is less than 7, the solution is acidic
  • when pH is greater than 7, the solution is basic

Redox Reactions in Biology

• Reduction-Oxidation Reactions
  • Gain of electron = reduction
  • Loss of electron = oxidation
    • Electrons can be transferred completely
    • Electrons can just shift position to be closer to one atom than another
  • Redox reactions are the most common chemical reactions in biology
  • Reduction of carbon was a key step in chemical evolution
    • Carbon is the most versatile molecule found in biological tissues
      • Each carbon atom can form four bonds with other molecules
      • Carbon atoms form the skeleton of organic molecules
        • Carbon atoms can be linked in many arrangements
        • A wide variety of molecular shapes is possible
        • Functional groups added to carbon skeleton impart a variety of chemical  reactivities to carbon molecules
    • Reduction of CO2 by H2 forms H2CO, which is used as a building block to form organic compounds (compounds containing at least one C–C bond)

In summary, redox reactions primarily involve the transfer of electrons between two chemical species. The compound that loses an electron is said to be oxidized, the one that gains an electron is said to be reduced. There are also specific terms that describe the specific chemical species. A compound that is oxidized is referred to as a reducing agent, while a compound that is reduced is referred to as the oxidizing agent. Confusing, ain’t it?

The Molecules of Life

Most biologically important molecules are polymers – long chains of similar repeating sub units

• Polymer formation occurs via condensation – water is freed
• Polymers are broken apart via hydrolysis – water is used up

There are four classes of important and common molecules: carbohydrates, lipids, proteins, and nucleic acids

Polysaccharides

• Polysaccharides are formed from linking various monosaccharides together
• Polysaccharides are used in structure and in energy storage
• Polysaccharides are commonly known as “sugars” and “carbohydrates”
• Examples: glucose, sucrose, starch, cellulose

Lipids

• Lipids are technically not polymers, they are either a combination of glycerol and fatty acids or a steroid
• Lipids are used in energy storage, membrane structure, insulation
  • Saturated – all single bonds – solid at room temperature
  • Unsaturated – one or more double bonds – liquid at room temperature
• Steroids – No fatty acid component – 4 carbon rings 6-6/6-5
• Examples: Hormones, cholesterol, cell membrane components cholersterol, a steroid
  
• Phospholipids
  • Phosphate on third -OH group of glycerol
  • Have a polar head
  • Increased hydrophilicity – can form spheroid structures called micelles

  Phospholipid	Micelle

Proteins

• Proteins are polymers formed from linking various amino acids
• Amino acid structure: NH₃ – C – COOH
• Amino acids differ due to the presence of a side chain attached to the central carbon atom. This is known as the R group
  
• The structure of the R-group determines the chemical properties of the amino acid
  • The polar uncharged amino acids (Serine, Threonine, Glutamine, Asparagine, Tyrosine, Cysteine) are hydrophilic and can form hydrogen bonds
  • The nonpolar amino acids (Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline) are hydrophobic and are usually found in the center of the protein. They also found in proteins which are associated with cell membranes.
  • The electrically charged amino acids (Aspartic Acid, Glutamic Acid, Lysine, Arginine, and Histidine) have electrical properties that can change depending on the pH.
  • Cystein can form covalent disulfide bonds
  • Proline had a unique structure and causes kinks in the protein chain
• When two amino acids are joined together, the bond formed is called a peptide bond
  
• Proteins have many different levels of organization
  • Primary Structure The sequence of amino acids in the polypeptide chain
    • The sequence of R groups determines the properties of the protein
    • A change of a single amino acid can alter the function of the protein
      • Sickle cell anemia – caused by a change of one amino acid from glutamine to valine
  • Secondary Structure Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid. R groups are NOT involved.
    • Two common examples are the alpha helix and the beta pleated sheet

Alpha Helix	Beta Pleated Sheet

• • Tertiary Structure The 3-D structure resulting from folding of 2^o structural elements
    • Stabilized by bonds formed between amino acid R groups
    • Forms many shapes, such as globular compact proteins and fibrous elongated proteins

• • Quaternary Structure Relationship among multiple polypeptide chains forming a protein
    • 3-D structure due to interactions between polypeptide chains
    • R- group interactions, H bonds, ionic interactions
    • assembled after synthesis

Hemoglobin – an example of a four-subunit protein

Nucleic Acids

• There are three components to a nucleotide: a pentose sugar, a phosphate group, and a nucleotide base

• Nucleic acids are polymers formed from linking of various nucleotides. The below image is of DNA nucleotides

• Nucleic acids are used in the storage and transfer of genetic information
• Examples: DNA – four bases in double helix, RNA – four bases in single strand

Note: the carbons of the ribose sugar of DNA and RNA are numbered as illustrated below:

• Carbon #3 (denoted as the 3′ Carbon) contains an -OH group
• Carbon #5 (denoted as the 5′ Carbon) is where the phosphate group attaches

When a DNA or RNA polymer is created, the bond is formed between the 3′ -OH group and the 5′ phosphate group. Hold onto this – you’ll need it later when we talk about DNA and RNA in more detail