Biology 121 Lectures 2.1 & 2.2

Biology 121Lectures 2.1 & 2.2 Organic Molecules Functional Groups Chemical Reactions

Organic? That means ‘healthy’, right? • The term “organic” has developed a vernacular meaning in our language, causing many people to associate organic with the terms “healthy” and “natural”.

Organic? Aren’t those kind of dangerous? • In chemistry, the term organic maintains its original meaning. As you’ll find, in the scientific context, some organics are healthy, but many are synthesized in the lab, so they aren’t “natural” – and they aren’t necessarily healthy!

Organic? What does that mean? • Organic chemistry is the study of organic molecules. What organic molecules all have in common is… • Carbon! • More specifically, C and H.

Organic means C and H • So CO2 is generally not considered an organic molecule, but CH4 is. • CH4 = organic • CO2 = inorganic • C6H12O6 = organic • H2O = inorganic

Categorizing Organic Molecules • The compounds in the human body are organic -- we are a carbon-based organism. • Organic compounds are the building blocks of life. • There are 4 majorcategories: • Carbohydrates • Lipids • Proteins • Nucleic acids

Categorizing Organic Molecules • Keep in mind the nature of C bonds. C-C and C-H bonds are very nonpolar. • H2O is a very polar molecule, and our bodies are 60-70% water. We are a very polar environment, and simple hydrocarbons would not fare well in our tissues! • Biologically important carbon molecules need other atoms like O and N that are more electronegative to add polarity to the molecules.

Why Carbon? • C has characteristics which make it a good choice for this very central role in biology.

Nature of Carbon Bonds - Variety • C has 4 valence e- • C can form 4 covalent bonds to satisfy a full valence shell. • An example of a satisfactory arrangement is CH4, commonly known as methane. Methane is one of the simplest organic compounds. • These 4 covalent bonds yield lots and lots of possible combinations

Nature of Carbon Bonds - Variety • C’s 4 covalent bonds are very strong, but are still breakable by cells • Normal biological methods can break and reform these bonds • C bonds allow rotation to form lots of shapes and conformations

Nature of Carbon Bonds - Variety • C can form single, double or triple bonds • Here are 3 similar molecules, but C is single, double or triple-bonded. Butane Butene Butyne

Categorizing Organic Molecules • For any given pair of ions, there was ONE possible arrangement to make an ionic compound. • In covalent bonds, any unpaired e-in the carbon shell can bond with ANY other atom with unpaired e- . The possibilities are endless, so there are many more types of organic molecules, and they can become incredibly large and complex, even when there are only C and H bonding.

Categorizing Organic Molecules • Simple organic molecules contain just C and H = hydrocarbons • But more complex organic molecules contain C and H, but also O, S, P, and N and other elements • With all this complexity, we’re going to need some sort of system to categorize the myriad organic compounds into recognizable groups.

Categorizing Organic Molecules • Start simple. Study the bonding patterns of compounds that consist of ONLY C and H. • Add on polarity with other atoms, such as O, onto our C framework, noting how the compound changes. • Functional groups • With that system in place, we’ll go on to consider carbohydrates, lipids, proteins and nucleic acids

IUPAC Nomenclature • As we scrutinize and categorize organic compounds, we’ll name them based on their bonding. Naming is also referred to as “nomenclature”. • Naming compounds allows us to develop a common language, so that we can discuss compounds easily. • It’s helpful if we all use the same naming system. IUPAC is the chemistry organization responsible for setting naming rules. Even in biology, we follow their guidelines.

Start With the Simplest Carbons • To begin, we’ll consider molecules that ONLY contain C and H. • Hydrocarbons • First, we’ll consider only hydrocarbons that have all single bonds. • Alkanes

Start With the Simplest Carbons • Start with 8 alkanes, listing C number, name, and structure. • Each compound has an ”-ane” ending, because they are alkanes. • The prefix for each compound is assigned based on its C number. • 1 C is meth- • 8 Cs is oct- • have formula CnH2n+2

“Straight” carbon chains • We call hydrocarbons that have all the Cs arranged linearly (in a straight line) “straight chain” hydrocarbons. • As the ball and stick models to the right indicate, they actually aren’t “straight” at all, that’s because of the tetrahedral shape of the individual C atoms. They aren’t straight for the same reason water isn’t straight. • Flexible, can bend and rotate

Double Bond  Alkene • Cs can bond through more complex patterns than just single bonds, forming double and even triple bonds with one another. • If there is at least one double bond in a hydrocarbon, we call it an alkene. Its prefix stays the same, but the ending is now –ene. • All have formula CnH2n • Must lose 2 H to form a double bond • Double bond is more rigid, no rotating around double bond ethane ethene

If there is at least one triple bond in a hydrocarbon, we call it an alkyne. Its prefix stays the same, but the ending is now –yne. All have formula CnH2n-2 Lose 2 more H to form a triple bond. Triple bond is also rigid, no rotating around triple bond Triple Bond  Alkyne ethane ethene ethyne

Double and Triple Bonds – fewer Hs • Ethane = C2H6 • Add a double bond, remove two Hs. Ethene = C2H4. • Add a triple bond, remove two more Hs Ethyne = C2H2 ethane ethene ethyne

Double and Triple Bonds • C-C single bonds in alkanes are movable. The Cs can spin with respect to one another, causing the Hs to spiral like spokes on a wheel. • In ethene and ethyne the C-C double and triple bonds cannot move, so the Hs are stuck in one place. ethane ethene ethyne

Start With the Simplest Carbons • Learning Goal: Be able to name molecules based on the IUPAC guidelines for C1 through C8 compounds

Name That Molecule

Name That Molecule 3 C, one triple bond = propyne C3H4 6 C, all single bonds = hexane C6H14 8 C, one double bond = octene C8H16 5 C, all single bonds = pentane C5H12

Hydrocarbons can have many structures • Straight chain • All Cs bonded together in one line (even if bent due to rotation around bonds) • Can be very long (25+ Cs)

Hydrocarbons can have many structures • Branched chain • Main chain has one or more Cs attached as a side chain • Named according to the longest continuous chain • Branched propane • Branched heptane • Branched decene

Naming Branched Chains • The trick for branches, is to name the molecule based on the number of the longest C chain, and treat the branch as an “accessory”. So the bottom compound is a “heptane”, with a 3C branch off of the middle C.

Naming Branched Chains • The real name of this compound is 4-propyl-heptane. We will not be covering IUPAC rules of naming such complicated molecules, you simply need to know this as a branched heptane for now.

3. Ring Structures • It is also possible for a chain of C to bend around so that the end C bonds with the first C, forming a ring. • Rings can be as small as 3 C, but 5 and 6 C rings are the common sizes we’ll see in biology. • To name such compounds, add “cyclo” to the front. So a 6C ring with all single bonds is called cyclohexane. • Lose 2 H to make the C-C bond to close the ring. • Some rotation around bonds, but less flexible than chains.

Rings • Notice that when a hydrocarbon turns into a ring, you need to remove two Hs to accommodate the extra C-C bond - just like adding a double bond. • Notice, also, that the ring structure holds the Hs rather rigidly in place, they aren’t free to spiral anymore - just like adding a double bond. • Can have single, double, triple bonds, branches, more rings, etc.

Benzene – a special ring • Benzene, C6H6 is a very special molecule in chemistry. It has an unusual bonding arrangement which puzzled chemists for years. A rather simple representation (which suits us just fine) is to think of benzene as a 6-cabon ring with alternating single and double bonds. • Benzene is not found in the human body (it is actually a carcinogen), but there are many derivatives of benzene -- compounds which contain a benzene ring -- found in nature. They are called “aromatics” because they have pleasant aromas, you’d find them in rose oil, for example.

Chain, Branched and Ring Hydrocarbons • Learning Goal: For carbon chains between 1 and 8 carbons long, including straight-chain, branched and rings, be able to name molecules based on the IUPAC guidelines

What’s missing from these structures? • Now that we’re such good chemists, we’re going to need to understand some common shortcuts • Leave Hs off, assume maximum Hs whenever they’re omitted • C at every corner unless something else is indicated cyclopentane heptane

More Name That Molecule! 2 C, straight chain, only single bonds = ethane 4 C, ring, only single bonds = cyclobutane 5 C, straight chain, only single bonds = pentane 5 C, branched chain, only single bonds = branched butane

More Name That Molecule! 2 C, straight chain, only single bonds = ethane 4 C, ring, only single bonds = cyclobutane 5 C, straight chain, only single bonds = pentane 4 C, branched chain, only single bonds = branched butane

More Name That Molecule! 7 C, branched chain, only single bonds = branched heptane 5 C, ring, single bonds = cyclopentane 8 C, straight chain, double bond = octene 4 C, straight chain, double bond = butene

Isomers – same formula, different structure • Because C is such a ‘flexible’ atom it can bond in many different arrangements. • Even for simple hydrocarbons, you can have two different molecules with the same molecular formula • different spatial arrangements in space • For example, C4H10 can be a straight chain OR branched. • If we needed to distinguish which of these two isomers we wanted, we would need to expand the molecular formula, as in the figures to the right. • Important because different structures have different functions

Isomers – same formula, different structure 3 types of isomers – • Structural – same formula, different bond arrangement • Geometric – same formula and bonds, but held in different positions • Requires a double bond • Enantiomers – same formula, same bonds, but held in different arrangement around a central C. • Requires 4 different groups on C (chiral) • Non-superimposable mirror image

How Many Structural Isomers are Possible for the Alkanes? No memorization necessary!

Drawing Structural Isomers • Different isomers often have different names – don’t worry about this in Biol 121 • Learning Goal: For a given molecular formula of a hydrocarbon, be able to draw a stated number of different structural isomers

Sample Problems • Draw 2 structural isomers of C4H10. • Any rings, double or triple bonds? • Compare no. of Cs and Hs • Draw straight chain • Reduce chain by 1C and add 1C branch(es) • Move branch around first half of chain • Reduce chain by 2C and add 2 1C branch(es) • Move branch around first half of chain • Reduce chain by 2C and add 2C branch(es) • Move branch around first half of chain • Draw rings, rings with branches, etc.

Sample Problems • Draw 2 structural isomers of C4H10.

Sample Problems • Draw 6 structural isomers of C7H16. • Draw 4 structural isomers of C7H14.

Two More Types of Isomers • In addition to the structural isomers we have already discussed, there are two more special situations where we need to be able to distinguish between similar, but different, molecules. • Geometric isomers occur around double bonds • Enantiomers occur every time a carbon has 4 different atoms attached to it

2. Geometric Isomers • A special type of situation exists around double bonds. Remember that single bonds can rotate like wheel spokes. But double bonds are held firmly in space. • In the example molecule on this page, di-chloro-ethene, the green chlorine atoms can either be attached to the same sides of the double bond, or to opposite sides. • When atoms are on the same side, they are cis. When they are on different sides, they are trans. These are different geometric isomers, because the chlorines cannot rotate around the double bond from one side to another. • For di-chloro-ethane, the chlorine atoms are free to rotate from one side to another, there are no geometric isomers to worry about for that molecule.

2. Geometric Isomers • Need to have a double bond so no rotation • Groups held in different positions • Each C must have 2 different groups attached. • If one C has 2 of same group, not isomers Not geometric isomers

3. Enantiomers • Enantiomers have same bonds, but 4 different groups arranged differently around a central C. • C in middle, hold one atom at top & rotate to make match. No match  enantiomers

enantiomers not enantiomers 3. Enantiomers • If can rotate to match  not enantiomers • If no possible match  enantiomers • If enantiomers, central C is a chiral C. • 4 different groups attached to C • Black sphere is a chiral C in bottom enantiomer pair

Biology 121 Lectures 2.1 & 2.2