Carbon & The Molecular Diversity of Life Note this is the third portion of the Biochemistry Unit. It is quite possible that your students know a bit of this, so use it as you see fit. It would be very appropriate to have them view the companion screencast prior to and outside of class and spend time simply answering questions. A good deal of this information will be “prior knowledge” for the AP Biology exam. BUT, be sure to emphasize the points that are unique to AP Biology as pointed out throughout these speaker notes.

Carbon: The Backbone of Life Living organisms consist mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Note this is the third portion of the Biochemistry Unit. It is quite possible that your students know a bit of this, so use it as you see fit. It would be very appropriate to have them view the companion screencast prior to and outside of class and spend time simply answering questions. A good deal of this information will be “prior knowledge” for the AP Biology exam. BUT, be sure to emphasize the points that are unique to AP Biology as pointed out throughout these speaker notes.

Carbon: Organic Chemistry Carbon is important enough to have it’s own branch of chemistry called Organic chemistry Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms with O, N and P among others thrown in from time to time. Remind students that while carbon has six total electrons, two of them are in the 1st Energy level, leaving the other 4 electrons in the 2nd Energy level which is the valence level, thus only these 4 valence electrons are capable of forming bonds. Also remind them that carbon forms covalent bonds.

Experimental Design: The origin of life on this planet The Miller-Urey experiment demonstrated the abiotic synthesis of organic compounds. Water (H2O), methane (CH4),  ammonia (NH3), and hydrogen  (H2) were all sealed inside a sterile array of glass tubes and flasks connected in a loop, with one flask half-full of liquid water and another flask containing a pair of electrodes. Historical note: Originally, Miller reported that 11 amino acids were formed. After his death in 2007, the Professor Jeffrey Bada, himself Miller's student, inherited the original equipment from the experiment when Miller died in 2007. Based on sealed vials from the original experiment, scientists have been able to show that although successful, Miller was never able to find out, with the equipment available to him, the full extent of the experiment's success.

Experimental Design: The origin of life on this planet The liquid water was heated to induce evaporation, sparks were fired between the electrodes to simulate lightning through the atmosphere and water vapor, and then the atmosphere was cooled again so that the water could condense and trickle back into the first flask in a continuous cycle.

Experimental Design: The origin of life on this planet Within a day, the mixture had turned pink in color, and at the end of two weeks of continuous operation, Miller and Urey observed that as much as 10–15% of the carbon within the system was now in the form of organic compounds.

Experimental Design: The origin of life on this planet Two percent of the carbon had formed amino acids that are used to make proteins in living cells, with glycine as the most abundant. Nucleic acids were not formed within the reaction. But the common 20 amino acids were formed, in various concentrations. 23 amino acids exist, but only 20 are commonly found in living systems.

Carbon has 4 valence electrons, thus makes 4 bonds With four valence electrons, carbon can form four covalent bonds with a variety of atoms This ability makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape Most likely prior knowledge if your students have had a Chemistry I course.

“CNOPS” can combine together to make double and triple covalent bonds However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons Why is this important? Because the shape of a molecule dictates its reactivity, thus its function! Shape (or the “Big People” word conformation) matters! Use a puzzle piece, or lock and key analogy with students to explain why the shape of a molecule is tied so closely to its function.

No need to memorize these! No need to memorize, simply an illustration of how the shape of the molecule changes as additional –CH2 subunits are added vs. losing a pair of H’s each time an additional C-C bond is added to form a double or triple bonds.

Carbon Skeletons Vary Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Again, no need to memorize! Just know that carbon can make ringed compounds as well as linear chains.

Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy ATP is in their near future. Again, probably prior learning.

Fats Nucleus Fat droplets 10 m (a) Part of a human adipose cell A three carbon backbone (glycerol) has long chains of hydrocarbons to form a triglyceride…more about that in the next portion of this unit. No need to go into too much detail at this time. 10 m (a) Part of a human adipose cell (b) A fat molecule

Isomers Isomers are compounds with the same molecular formula but different structures, thus different properties. Structural isomers have different covalent arrangements of their atoms Cis-trans isomers have the same covalent bonds but differ in spatial arrangements Enantiomers are isomers that are mirror images of each other & rotate light differently The dreaded and ever so confusing “I” words: ion, isotope and isomer. Make sure that students can articulate the differences! Ions can be monatomic or polyatomic, but either way they have gained (negative ion, anion) or lost an electron (positive ion, cation). Isotopes have a different number of neutrons, but the same number of protons and electrons—carbon-12, carbon-13 and carbon-14 are excellent examples. Isomers have the same chemical formula (#’s of C’s and H’s and O’s, etc.) but a different arrangement of said parts, thus function differently.

More detail than you need, but cool none the less! Linear vs. branched arrangements of the carbon skeleton. Different shapes result in different functions or physical properties!

More detail than you need, but cool none the less! No need to memorize, just interesting! A nice opportunity to reinforce that the prefix trans- means “across” as in “transmembrane proteins” . In this case, across (opposite sides of) the double bond. These two molecules will exhibit different properties.

More detail than you need, but cool none the less! My personal favorite! Enantiomer literally means “opposite form”. Some curious student is bound to ask, “What’s the deal with the L-isomer vs. the D-isomer. Well, this is more than you probably want to know, but…An aqueous solution of one form of an optical isomer rotates the plane of polarization of a beam of polarized light in a counterclockwise direction (levorotatory), vice-versa for the (+) (dextrorotatory) optical isomer.  

More detail than you need, but cool none the less! Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Usually only one isomer is biologically active Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Glucose, for example has 32 isomers, 16 L and 16 D. Not all are sweet!

Note the mirror imaging Effective Enantiomer Ineffective Enantiomer Drug Condition Pain; inflammation Ibuprofen S-Ibuprofen R-Ibuprofen The pharmacological importance of enantiomers. Not all enantiomers are created equal. Now, that same student asks “Why are these R & S as opposed to D & L?” This is also more than you ever wanted to know, but…The symbol R comes from the Latin rectus for right, and S from the Latin sinister for left. D & L works well for carbohydrates and amino acids, but the naming system didn’t translate well to more complex molecules. So, a new system was developed. The resulting nomenclature system is sometimes called the CIP system or the R-S system. Albuterol Asthma R-Albuterol S-Albuterol

Functional Groups A few chemical groups are key to the functioning of molecules Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules While a student shouldn’t memorize these functional groups, it is helpful if they recognize them.

Functional Groups Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties This is just an introduction. Emphasize that structure relates to function and with each subtle molecular change, the IMFs are affected, thus molecular function is affected.

Hydroxyl STRUCTURE NAME OF COMPOUND EXAMPLE FUNCTIONAL PROPERTIES Alcohols (Their specific names usually end in -ol.) NAME OF COMPOUND (may be written HO—) EXAMPLE • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. FUNCTIONAL PROPERTIES Students may be confused. OH- is known as “the hydroxide ion” in inorganic chemistry and signifies a base, which is all they know at this point. They may or may not know that the OH group attached to a carbon skeleton forms an alcohol. Emphasize the polarity of an alcohol which is exactly why alcohols are water soluble. Ethanol • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

Carbonyl STRUCTURE NAME OF COMPOUND EXAMPLE FUNCTIONAL PROPERTIES Ketones if the carbonyl group is within a carbon skeleton NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. FUNCTIONAL PROPERTIES Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). Don’t stress over the names “aldehyde or ketone”, but rather emphasize that “moving” the -C=O group, alters the properties and reactivity of the molecules. Acetone Propanal

Carboxyl • Acts as an acid; can donate an H+ because the STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND EXAMPLE • Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar: FUNCTIONAL PROPERTIES Ah, this has many, many names thanks to inorganic and organic chemists that can’t get along! The carboxyl group terminology is in most biology books, as in “carboxylic acids” which we’ll see again as we build amino acids. The “acetyl” group as it is often known in inorganic chemistry. Acetic acid Nonionized Ionized • Found in cells in the ionized form with a charge of 1– and called a carboxylate ion.

Amino • Acts as a base; can • Found in cells in the STRUCTURE Amines NAME OF COMPOUND EXAMPLE • Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): FUNCTIONAL PROPERTIES Students should already know that “ammonia”, the NH3 molecule is a weak inorganic base. Emphasize that this is the “amine” portion of amino acid fame. Glycine Nonionized Ionized • Found in cells in the ionized form with a charge of 1.

Sulfhydryl • Two sulfhydryl groups can • Cross-linking of cysteines STRUCTURE Thiols NAME OF COMPOUND (may be written HS—) EXAMPLE • Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. FUNCTIONAL PROPERTIES • Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. Not one of the more popular throughout the course, but handy to know once we get to protein structure as it relates to the formation of disulfide bridges. Cysteine

• Contributes negative Phosphate STRUCTURE Organic phosphates NAME OF COMPOUND EXAMPLE • Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates). FUNCTIONAL PROPERTIES Here’s a biggie! Students should know the phosphate ion from Chemistry I. Furthermore they should already know it has a -3 charge. In ATP we have three of those -3 ions stacked next to each other which is a great deal of negative ion-negative ion repulsion! Glycerol phosphate • Molecules containing phosphate groups have the potential to react with water, releasing energy.

• Addition of a methyl group STRUCTURE Methylated compounds NAME OF COMPOUND EXAMPLE • Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. FUNCTIONAL PROPERTIES An easy one! They should know methane from Chemistry I, so simply remove an H atom to make the methyl functional group. Don’t skip past the DNA + gene expression comment on this slide. It’s important later in the course! • Arrangement of methyl groups in male and female sex hormones affects their shape and function. 5-Methyl cytidine

ATP: An Important Source of Energy for Cellular Processes One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups They most likely know this molecule’s general structure from their Biology I course. Emphasize yet again that breaking a bond requires energy (as in removing one of those phosphates) while bond formation releases energy.

Final Thoughts The versatility of carbon makes possible the great diversity of organic molecules Variation at the molecular level lies at the foundation of all biological diversity It’s all about carbon!

Created by: René McCormick National Math and Science Dallas, TX