The Chemical Context of Life Elements of Life Atoms, Molecules & Compounds Chemical Bonds Structure and Function Chemical Reactions

Organic Chemistry Chemistry is fundamental to understanding life Reactions at the molecular level based in rules of bonding and reactions “run” the machinery of life Chemicals are required for growth, defense, development and many other reactions in living organisms

Figure 2.1 The hierarchy of biological order from atom to organism

Organic Chemistry (Continued) You must understand the elements within living things and understand how they combine to form the four basic organic compounds A knowledge of how atoms bond and atomic structure is crucial Let’s look at the main elements found in living things

Table 2.1 Naturally Occurring Elements in the Human Body

Atomic Bonding Remember that atoms bond based on the number of unpaired electrons in their valence or outer shell. Each filled shell has a specific number of electrons (1 st shell 2, Second shell 8) There can be two electrons in each orbital. Each orbital fills one electron at a time. Carbon has four unpaired electrons, within four orbitals.This gives it four bonding sites and makes it a versatile compound for living things

Valence Numbers The valence number is the number of unpaired electrons in the outer shell You should know at least the first ten most common elements in living things and their valence numbers Normally, unpaired electrons will bond with electrons of other elements to fill the outer shell It is how atoms bond (angles, electronegativity, types of bonds) that determine a compound’s characteristics

Figure 2.10 Electron configurations of the first 18 elements

Energy Levels of Electrons The more distant an electron is from the nucleus the more potential energy it stores Energy levels are the different states of potential energy that electrons have in an atom Electrons may absorb energy and move to a higher level or fall to a lower level and release energy This is important in one complex reaction we will study-photosynthesis

Figure 2.9 Energy levels of an atom’s electrons

Compounds Remember also that a compound will usually have emergent or different properties than the individual properties of the elements that make it up.

Figure 2.2 The emergent properties of a compound Sodium + Chlorine = Table Salt Emergent Properties in a compound

Types of Bonds in Living Things There a number of strong and weak bonds in living things You should be familiar with ionic and covalent bonds already, but we will review them. There are also weak bonds important to some molecules and solutions in living things.

Covalent Bonds Covalent bonds are strong bonds that occur when electrons are shared. Examples of covalent bonds are on the following slides A type of bond called a polar covalent bond occurs when an atom that has a high electronegativity pulls atoms of other elements closer to itself than is normal (Example: water)

Figure 2.12 Covalent bonding in four molecules

Ionic Bonds Ionic bonds occur when electrons are stripped from one atom and transferred to another (Sodium and Chlorine is an example when salt forms) This causes each atom to become either a cation (atom with a + charge) or an anion (atom with a – charge) Ionic compounds those formed by ionic bonds

Figure 2.14 Electron transfer and ionic bonding

Important Weak Bonds Van der Waals interactions form weak bonds and only occur when the atoms are very close to one another They are due to the fact that electrons are in motion all the time and cause some charge to occur in even nonpolar covalent bonds.

Hydrogen Bonds Hydrogen bonds form between molecules of polar covalent compounds when there is a very slight difference in charge between two of them. They are a relatively weak bonds, but give water some of its more unique properties.

Figure 2.16 A hydrogen bond

Atoms, bonds and Shape When atoms bond to one another, the positions of their orbitals determine the molecular shape Sometimes orbitals can mix or hybridize in specific ways to give a molecule a specific shape

The Shapes of Biological Molecules The shapes of biological molecules determine their function Enzymes and neurotransmitters are examples of molecules whose shapes are crucial to their functions Receptors on the neuronal cell membrane “fit” specific neurotransmitters which then cause the neighboring neurons to fire

Figure 2.18 Molecular shape and brain chemistry

Molecular Mimics If a particular molecule, say from a drug, is similar to that of a molecule in the body, it can occupy receptors for that molecule in the body and affect it Example: Endorphins are our brain’s pain and pleasure chemicals Drugs like morphine and heroin can occupy the same receptors as these, causing powerful reactions in the brain

Figure 2.19 A molecular mimic

Chemical Reactions Chemical reactions make or break the bonds between atoms and molecules If bonds are broken, energy is released Energy is used to make bonds Reactants are what go in Products are what come out Chemical equilibrium is the point where relative concentrations of reactants and products stop changing

Unnumbered Figure (Page 38) Chemical reaction between hydrogen and oxygen