1. 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.

2. 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.

3. 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.

4. 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 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.

5. 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.

6. 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.

7. 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.

8. 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.

9. “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.

10. 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.

11. 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.

12. 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.

13. 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

14. 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.

15. 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!

16. 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.

17. 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.  

18. 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!

19. 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

20. 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.

21. 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.

22. 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.

23. 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

24. 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.

25. 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.

26. 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

27. • 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.

28. • 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

29. 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.

30. 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!

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