Basic chemistry for general biology Electrons and orbitals, and how bonds make happy atoms
A review (I hope) Atoms are composed of three elementary particles: protons, electrons, and neutrons Protons (H+) Mass equal to 1 atomic mass unit (amu) Charge of +1 Important the terms Hydrogen and Proton I will often use interchangeably!! Neutron (n) Mass nearly equal to 1 amu No charge Electron (e-) Virtually massless Charge of -1
The nucleus The nucleus is made of protons and neutrons held together The presence of protons results in the nucleus having a positive charge The number of protons indicates the identity of an atom The number of neutrons, is generally not important in basic biology (unless you choose to study things like nuclear medicine or biophysics)
Protons The number of protons dictates one of the most important chemical properties of an atom: its ability to attract and hold onto electrons Changing the number of protons affects this property in specific and measurable ways Each variation in number of protons results in a different specific element
The elements Atomic elements have specific and unique chemical properties because of the number of protons Increasing the number of protons increases the amount of positive charge in the nucleus (as well as the size, and ultimately, the stability of the nucleus) This has a direct effect on the number of electrons required to balance out the charge of the nucleus, which has a direct effect on the total size of an atom
Affected by number of protons in nucleus This, in turn, determines the number of electrons Protons, despite being the same charge, are held in the nucleus Electrons, all being the same charge are dispersed around the nucleus They are all equally attracted to the nucleus, but the closer they get to the nucleus, the more they are pushed away by the other electrons Atomic size
Electrons and orbitals Electrons exist in specific orbitals that radiate outward from and around the nucleus They are negative (-) and nearly massless, but are attracted to the pull of the (+) charged nucleus Atoms electrons are arranged in shells, each of which is organized into orbitals Each orbital can hold only up to a specific number of electrons
The periodic table and the Octet Rule The first row, or period, on the Periodic Table has one shell with one orbital (called 1s). It holds a total of 2 electrons. The second period means atomic size has been increased by the addition of a second shell, with two orbital levels. The first orbital (called 2s) holds up to 2 electrons. The second (called 2p) holds up to six more. 2s must be full before any 2p are occupied. Before any level 2 orbitals are used, level 1 must be full. Before any p level electrons are used, the s in the same level must be filled first The same rule applies for all period 3 elements as well (3s, 3p). Additional rules apply for all periods after 3, but their orbital structures do not figure into this course.
Orbital arrangements in space
Orbital Diagram A period two arrangement of electron orbitals. Each (blue) orbital holds two electrons each, for a total of 8 possible electrons.
The Octet rule For periods 2 and 3, when the electrons of one electron shell add to 8, no more electrons can be put into that shell If more electrons were added, they would have to go into a 3 rd shell The Noble Gases are a family of elements all having full outer shells
Octet Rule and Atomic Size Protons pull electrons, so as the number of protons increases there is more pull on electrons, so the electrons that are present are pulled in more tightly But as electron number goes up past the octet limit, another shell is added so atomic radius increases
Valence The outermost electron orbitals (orbitals, not necessarily shells) are referred to as Valence orbitals By rule, the innermost orbitals must always be full. The outermost, or valence orbitals do not have to be The electrons present in these outermost orbitals are often diagramed using Lewis Dot Structures
Lewis dots and orbitals Although simplistic, Lewis Dot Structures are used to depict the position of electrons within the valence orbitals of an element A full orbital has two dots A half-full orbital has one dot An empty orbital is not shown
The Period Table
Electronegativity A measure of the relative ability of the nucleus of one atom (which is positive because of its protons) to attract electrons This is affected by: Number of protons Atomic radius Having more protons increases the attractive strength of the nucleus, but having more electrons makes the entire atom bigger
To be more electronegative, have as many protons as you can with as small an atomic radius as you can Atoms with mostly full valence orbitals and a small radius tend to be very electronegative Elements with mostly empty valence orbitals or bulky elements are less electronegative So
Why? Bromine has more protons than Fluorine or Chlorine, so its nucleus is more attractive (stronger) than either Fluorine or Chlorine BUT it has one more layer of electrons around it than Chlorine, and two more than Fluorine, so even though the pull is greater, it is weakened by having a much larger atomic radius. Fluorine has the most protons relative to atomic radius, and is the most electronegative element
Reactivity Elements react with other elements based on electronegativity Atoms want full valence orbitals, and the best way to accomplish that is to either gain or lose electrons Very electronegative atoms satisfy their need for full valence orbitals by taking electrons from less electronegative atoms Weak electronegative atoms satisfy their need by donating electrons to more electronegative atoms
Bonding The exchange of electrons between atoms as they attempt to achieve stable electron configurations (full valence orbitals) results in bonding In general, electrons are either totally given from one atom to another, or two atoms may share electron pairs Structures created by the exchange of electrons between atoms are molecules
Excited atoms Excited atoms are not happy atoms, they have a higher energy state that makes them unstable They want to form bonds, because bonding allows them to release energy and achieve a ground state Atoms will react and interact with other atoms continually as long as products have less energy than reactants
Why react? Atoms react with other atoms if they are in an excited state. Forming bonds releases energy to the environment (as heat) The opposite is true to break bonds between atoms: energy (heat) must be applied
Reaction basics Assuming two excited atoms without outside help (we ll discuss this outside help later) When two atoms are going to react with one another, we call them reactants The reason they react is to release energy as long as a reaction is energy releasing, it will occur spontaneously Such reactions are exothermic
Reaction basics No chemical reaction without an initial input of energy This is called activation energy This can be as simple as simply bringing two reactants together (physically doing so is still work and therefore requires energy) Heat applied can begin a reaction process Striking a match is the activation energy required to begin combustion of the wood
Exothermic reactions What makes this reaction exothermic? Where did the difference in energy go?
Endothermic reactions Why is this reaction endothermic? Where did the energy go?
More reaction basics Consider the following reaction A + B AB + energy (heat) Assuming infinite quantities of A and B, the reaction will progress towards AB forever Is this reaction exothermic? Why? The reverse is also true: AB + energy A + B Because here energy is used to drive the reaction towards A + B, this reaction requires the input of energy, and is endothermic
Endo and Exothermy Any chemical reaction is reversible under the right conditions! As such, the proper way to write any biochemical reaction would be this way: A + B AB + energy In biochemistry, many reactions are reversible. The important aspect is how much energy is required to reverse them some are practical, others are not
Equilibrium Consider a chemical reaction as a balance, with the as a kind of fulcrum. A + B AB + energy A and B react to release energy but where did that energy come from? A and B had that energy as potential energy. When they react, that energy is transformed into kinetic energy, which can be felt as heat. As A and B continue to react and release heat, a point is reached where there is more total energy on the AB side More energy on the AB side drives the reaction back towards A + B This back and forth continues on and on until an equilibrium is reached
Direction of reactions in biology Consider the following reaction: ATP ADP + P i + energy Which direction will it go if I Add energy Remove ADP + P i Remove P i Add ATP Do nothing
Bonding The exchange of electrons between atoms as they attempt to achieve stable electron configurations (full valence orbitals) results in bonding In general, electrons are either totally given from one atom to another, or two atoms may share electron pairs Structures created by the exchange of electrons between atoms are molecules
Thermodynamics of bonding Atoms rarely exist in a free (unattached) state Atoms are not happy when they have orbitals that are not full Atoms are happy and relaxed when they do have full orbitals (called their ground state ) Having full orbitals means a lower energy state
Bonding Energy Review Atoms form bonds to release excess energy, which can be detected as heat (as in thermo ) Bond formation is exothermic, that is, energy releasing Water freezing into ice gives up its energy to the environment This applies to any bond, especially covalent and Hydrogen To break a bond requires the input of energy Bond breaking is endothermic Melting ice requires the input of heat-energy from an external source Likewise, this applies to any bond type
Ionic bonds When two atoms of very different electronegativity interact, the more electronegative atom may entirely remove an electron from the weaker atom The result is that both atoms become charged The atom gaining an electron now has more negative charges than positive, and is a negative ion (anion) The atom losing an electron now has more positive charges than negative, and is a positive ion (cation) Opposite charges may attract, and this attraction between anion and cation is called an ionic bond All salts are ionic All ionic bonds are easily dissolved by water
Covalent bonds When two atoms of more similar electronegativity (they only are equal if they are actually the same element!) interact, they may instead share electrons by forming hybrid orbitals between the two nuclei Formation of a hybrid orbital means the two atoms are now sharing an electron pair by forming a single full orbital from any of their formerly half-full orbitals This sharing of an electron pair is called a covalent bond
End of review