Basic Principles of Biological Chemistry 40-79 PDF

Ions & Isotopes The atomic mass of an element is rarely an even number This is due to isotopes. Example: In carbon, there are a lot of C-12, a couple C- 13, and a few C-14 atoms. When you average out all of the masses, the average atomic mass = 12.011. Since you never really...

Ions & Isotopes The atomic mass of an element is rarely an even number This is due to isotopes. Example: In carbon, there are a lot of C-12, a couple C- 13, and a few C-14 atoms. When you average out all of the masses, the average atomic mass = 12.011. Since you never really know which C atom you are using in calculations, you should use the mass of an average C atom. Radioactive Decay Radioisotope is an isotope that has an unstable nucleus and becomes more stabilized by spontaneously emitting energy and particles. Radioactive Decay is the loss of neutrons over time from an unstable isotope. Isotope C-14 does not last forever. Eventually it loses those extra neutrons and becomes C-12. Decay happens regularly like a clock. For carbon, the decay happens in a couple of thousand years. For P-32, decay happens in days to weeks. Common half life elements Energy Levels of Electrons An ELECTRON’S ENERGY LEVEL is the amount of energy required by an electron to stay in orbit. Just by the electron’s motion alone, it has kinetic energy. The electron’s position in reference to the nucleus gives it potential energy.  Energy Levels of Electrons An energy balance keeps the electron in orbit and as it gains or loses energy, it assumes an orbit further from or closer to the center of the atom. http://www.fastbleep.com/biology-notes/40/1089 Energy Levels of Electrons The electrons cannot choose any orbit they wish. They are restricted to orbits with certain energies. Electrons can jump from one energy level to another, but they can never have orbits with energies other than the allowed energy levels.  Energy Levels of Electrons http://www.fastbleep.com/biology-notes/40/1089 Electron Orbitals Electrons are found in clouds that surround the nucleus of an atom. Those clouds are specific distances away from the nucleus and are generally organized into shells or orbitals. The higher the atomic number, the more electrons and shells an atom will have.  Electron Orbitals The cloud that is found closest to the nucleus is called the 1s orbital. Slightly further away from the nucleus is the 2s orbital. So, the 1s orbital with its 2 electrons is the first “shell.” http://www.chem.fsu.edu/chemlab/chm1046course/orbitals.html Electron Orbitals After the 2s orbital comes the 2p orbital. Unlike the s orbitals, p orbitals are shaped like two opposite pointing balloons. 3 different 2p orbitals: 2px, 2py, and 2pz. Each 2p orbital holds 2 electrons. The 2s orbital and the three 2p orbitals contain 8 electrons. (The second “shell.”)  Electron Orbitals Next comes the 3s orbital. Similar in shape to the 1s and 2s orbitals, and also holds 2 electrons. Next comes 3p orbitals: 3px, 3py, 3pz. As we keep going, it gets goofy, so we’ll leave that for your chemistry class. http://www.chem.fsu.edu/chemlab/chm1046course/orbitals.html Electron Orbitals Electron Shells and Orbitals The Octet Rule: In general, atoms are most stable when they have 8 electrons in their outer-most shell. (That’s the s+p orbitals) The exception is the first shell which is most stable with TWO electrons (1s orbital). If you know the Atomic Number and Mass Number of an element and the maximum number of electrons in each electron shell you can draw a diagram of the element, and figure out whether electrons fill s or p orbitals. Electron Shells and Orbitals Example: Sodium (Na) Atomic # = 11 Mass # = 23 11 Protons and therefore 11 electrons. Protons + Neutrons is 23, and there are 11 Protons there must be 12 Neutrons. 2 electrons in the 1s orbital (1st shell), 2 electrons in the 2s orbital, 6 electrons in the 2p orbitals (2nd shell), and 1 electron in the 3s orbital.  Electron Shells and Orbitals http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/eleorb.html Practice Question Chlorine has a Mass Number of 35.5 and an Atomic Number of 17. This means an atom of Chlorine has x Protons and therefore x electrons. Since the number of Protons + Neutrons is 35 and there are x Protons there must be y Neutrons. Draw the orbitals.  Answer 1s Atomic # = # of protons 2s 17 protons Energy 17 electrons 2p 2p 2p Atomic Mass = # of protons + # of neutrons 3s 18 Neutrons 3p 3p 3p Chemical Bonds Principles for Atoms to Interact An atom will not react with other atoms when its outermost electron shell is completely full. This atom is inert. An atom will react with other atoms when its outermost electron shell is partially full. This atom is reactive. Types of Chemical Bonds Intramolecular (within a molecule) Covalent Ionic Intermolecular (between molecules) Hydrogen ionic vs covalent vs hydrogen Ionic and covalent bonds are intramolecular bonds, (they exist inside the molecule. These bonds deal with the exchange of electrons. Hydrogen bonds are intermolecular bonds, meaning they bond two separate molecules. Covalent Bonds Chemical bonds formed by the sharing of one or more electrons (typically a pair) between atoms. Covalent bonds are the strongest type of chemical bond and are created between atoms with similar electronegativity. Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons.  Covalent Bonds In general electronegativity increases as you move to the right of the periodic table and up the periodic table. http://edtech2.boisestate.edu/kilnerr/502/jigsaw.html Covalent Bonds Each electron shell has a maximum number of electrons, and each atom "wants" to max out its electrons in each shell. Noble gases are the most stable elements because their electron shells all carry the maximum number of electrons. They don’t easily form covalent bonds with other atoms. Helium (He), Neon (Ne), Argon (Ar), Krypton (Kr), Xenon (Xe), Radon (Rn) Fluorine is the most electronegative element. Covalent Bonds When two or more atoms have the same electronegativity, a true covalent bond is formed. Whenever two atoms of the same element bond together, a non-polar covalent bond forms Example - H2 When one of the atoms is just a bit more electronegative than the other, a polar covalent bond is formed. This means that the electrons spend a little bit more time around the more electronegative atom than the other, resulting in a slightly negative charge at one end, and a slightly positive charge at the other. Example - H20 Covalent Bonds A molecule of water (H2O) Covalent Bonds Covalent bonds are not as common within the processes of life because it takes a lot of energy to break them apart, making them too inefficient to work with. Depending on the number of shared electron pairs, a covalent bond is characterized as a single bond, a double bond, triple bond, etc. Ionic Bonds Ionic bonds are a type of electrostatic bond between two atoms that are weaker than covalent bonds, but usually stronger than hydrogen bonds. Electronegativity plays a big role here. Ionic bonds are an association between two ions that have opposing charges. Typical participants in an ionic bond are a metal and a non-metal, such as sodium and chlorine. Sodium and chlorine combine to create sodium chloride, or common table salt. Ionic Bonds Electron shells "want" to have the maximum number of electrons. That's when they're at their most stable energy state. When an atom missing only a single electron from its top orbital comes into contact with an atom that only has one electron in its top orbital, the "wanting" atom "steals" an electron from the other atom, thereby stabilizing its orbital. The orbital of the other atom is stabilized too, as it no longer has a lone electron in it’s outer orbital  Ionic Bonds http://www.nicerweb.com/bio1152/Locked/media/ch02/ionic_bond.html Ionic Bonds The consequence is that it now has one more electron than it has protons, making it negatively charged. The "victim" of the stolen electron correspondingly has a positive charge. In electromagnetic theory, opposites attract, so the atoms are forced to hang around each other until they get broken up by a force such as heat. Ionic compounds dissolve easily in water and other polar solvents. In solution, ionic compounds easily conduct electricity. Ionic vs Covalent bonds Hydrogen Bonds Polar molecules, such as water molecules, have a weak, partial negative charge at one region of the molecule (the oxygen atom in water) and a partial positive charge elsewhere (the hydrogen atoms in water). Molecules that H-bond: H2O NH3 HF Alcohols Any molecule in which H is attached directly to a very electronegative atom that has a lone electron pair. Hydrogen Bonds and Water When water molecules are close together, their positive and negative regions are attracted to the oppositely-charged regions of nearby molecules. The force of attraction, shown here as a dotted line, is called a hydrogen bond. Each water molecule can hydrogen bond to four others. http://macrotomicro.blogspot.ca/2011/04/hydrogen-bonding.html Hydrogen Bonds The hydrogen bond has only 5% or so of the strength of a covalent bond. However, when many hydrogen bonds can form between two molecules (or parts of the same molecule), the resulting union can be sufficiently strong as to be quite stable. Multiple hydrogen bonds: hold the two strands of the DNA double helix together hold polypeptides together in such secondary structures as the alpha helix and the beta conformation help enzymes bind to their substrate help antibodies bind to their antigen Chemical Reactions The reaction of two or more elements together results in the formation of a chemical bond between atoms and the formation of a chemical compound. Chemical Equations When a chemical reaction occurs, it can be described by an equation. This shows the chemicals that react (called the reactants) on the left-hand side, and the chemicals that they produce (called the products) on the right-hand side. The chemicals can be represented by their names or by their chemical symbols. Chemical Equations For example, hydrogen gas (H2) can react with oxygen gas (O2) to form water (H20). The chemical equation for this reaction is written as:  Chemical Equilibrium Because atoms are neither created nor destroyed in a reaction, a chemical equation must have an equal number of atoms of each element on each side of the arrow (i.e. the equation is said to be “balanced” or in EQUILIBRIUM). http://www.mikeblaber.org/oldwine/chm1045/notes/Stoich/Equation/Stoich01.htm Next Lecture…. The Structure and Properties of Water