AP Biochemistry


Every objective will NOT necessarily be covered during class time; you will be independently responsible for some of them.

  1. Diagram how polymers are constructed from monomers, and how polymers are deconstructed into monomers
  2. Associate dehydration synthesis and hydrolysis reactions with endergonic vs. exergonic reactions, anabolism vs. catabolism, release vs. consumption of free energy, positive vs. negative delta-G, spontaneous vs. non-spontaneous
  3. For each of the four classes of biomacromolecule, name the polymer, monomer, monomer-to-monomer bond, primary elements, functions in living things, and list major examples
  4. For each of the four classes of biomacromolecule, diagram basic molecular structures
  5. Explain at least one example of structure determining function from each of the four classes of biomacromolecule
  6. Explain the importance of the nonpolarity of lipids to their functions in living things
  7. Connect the structure of a phospholipid to its tendency to self-organize into bilayer structures
  8. Classify nucleic acid bases as purine or pyramidine, and double ring or single ring
  9. Explain the location and importance of hydrogen bonding between nucleic acid strands
  10. Explain the importance of varying R-group structures to overall protein structure
  11. Define the four levels of protein structure, and explain protein structure at each level depends upon the level “beneath” it
  12. Define protein denaturation and connect it to the levels of protein structure
  13. Explain an example of how directionality influences the structure and function of a polymer
  14. Define metabolism
  15. Distinguish between kinetic and potential energy, and classify whether the chemical energy stored in molecules is kinetic or potential in nature
  16. Identify the first and second laws of thermodynamics
  17. Explain how a living thing is an open rather than a closed system
  18. Synthesize the concepts of entropy, free energy, and open systems to explain how organisms maintain their high level of organization despite constant transfers of energy, and how doing so does not violate the second law of thermodynamics
  19. Identify the terms in the equation for Gibbs Free Energy as potential or kinetic
  20. Examine a graph of free energy over the course of a reaction to classify the reaction as endergonic or exergonic
  21. Define catalysis, catalyst, enzyme, substrate, and active site
  22. Explain and graph how enzymes increase the rate of a reaction, identifying delta-G and activation energy on the graph
  23. Explain the connection between enzyme shape and structure, and enzyme specificity and function
  24. Explain the induced fit model of enzyme activity, and how it differs from the lock-and-key model
  25. Connect the concepts of enzyme specificity and three-dimensional structure to the effects of changing environmental conditions (temperature, pH, salinity) on enzyme function
  26. Interpret data regarding the change in concentration of substrate and/or product over time to draw conclusions about enzyme activity
  27. Synthesize concepts from evolution and enzyme chemistry to explain why enzyme optimal conditions are typically a close match to an organism’s environment
  28. Explain how cofactors and coenzymes affect enzyme function
  29. Contrast how competitive vs. noncompetitive inhibitors and reversible vs. nonreversible inhibitors affect enzyme function
  30. Contrast allosteric vs. active sites on an enzyme
  31. Explain how feedback inhibition can be used to regulate enzyme activity
  32. Give examples of how the properties of water are important to life on Earth*
  33. Explain how the properties of water arise from its molecular structure, polarity, and affinity for hydrogen bonding*

  • = self-study

Enduring Understandings

Enduring Understandings are the College Board's AP Biology course concepts that you need to know for the AP exam. Below, you'll find those Enduring Understandings relevant to this unit. Numbering and lettering matches the document linked from the main page of this website.
Every Enduring Understanding will NOT necessarily be covered during class time; you will be independently responsible for some of them.

A. Growth, reproduction and maintenance of the organization of living systems require free energy and matter.
1. All living systems require a constant input of free energy.
  • a. Life requires a highly ordered system.
  • b. Order is maintained by constant free energy input into the system.
  • c. Loss of order or free energy flow results in death.
  • d. Increased disorder and entropy are offset by biological processes that maintain or increase order.
  • e. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time.
  • f. Order is maintained by coupling cellular processes that increase entropy (and so have negative changes in free energy) with those that decrease entropy (and so have positive changes in free energy).
  • g. Energy input must exceed free energy lost to entropy to maintain order and power cellular processes.
  • h. Energetically favorable exergonic reactions, such as ATP -> ADP, that have a negative change in free energy can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change.
3. Organisms must exchange matter with the environment to grow, reproduce and maintain organization.
  • a. Molecules and atoms from the environment are necessary to build new molecules.
  • d. Living systems depend on properties of water that result from its polarity and hydrogen bonding.

A. Interactions within biological systems lead to complex properties.
1. The subcomponents of biological molecules and their sequence determine the properties of that molecule.
  • a. Structure and function of polymers are derived from the way their monomers are assembled.
  • b. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions.
  • c. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein.
  • d. In general, lipids are nonpolar; however, phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids.
  • e. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Illustrative examples include: cellulose versus starch.
  • f. Directionality influences structure and function of the polymer.
  • g. Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5' to 3').
  • h. Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers.
  • i. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.

B. Competition and cooperation are important aspects of biological systems.
1. Interactions between molecules affect their structure and function.
  • a. Change in the structure of a molecular system may result in a change of the function of the system.
  • b. The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme.
  • c. For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzyme's active site.
  • d. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites on the enzyme.
  • e. Other molecules and the environment in which the enzyme acts can enhance or inhibit enzyme activity. Molecules can bind reversibly or irreversibly to the active or allosteric sites, changing the activity of the enzyme.
  • f. The change in function of an enzyme can be interpreted from data regarding the concentrations of product or substrate as a function of time. These representations demonstrate the relationship between an enzyme's activity, the disappearance of substrate, and/or presence of a competitive inhibitor.

Textbook Reference

This is the part of your textbook that covers the material for this unit.
Ch. 2-3 and 6. (You are independently responsible for Ch. 2, and the beginning of Ch. 3)

Relevant Files

Here, you'll find files for this course. Copies of lecture notes will go here, as will others.
- Part 1 (Biochemistry)
- Part 2 (Enzymes)


These connect to materials on other teachers' websites that you may find helpful. Generally speaking, I put links to helpful review materials - like video lectures summarizing the material - towards the top, and links to interesting extensions towards the bottom.
Biochemistry Self-Tests
Common Elements Self-Quiz
Acids, Bases, Salts Self-Quiz
Chapter 2 Self-Test 1
Chapter 2 Self-Test 2
Chapter 2 Self-Test 3
Matter and Energy Self-Quiz
Atoms Self-Quiz
Molecules Self-Quiz
Chemical Bonds Self-Quiz
Macromolecules Self-Quiz
Vocabulary Self-Quiz
Molecules Games 1
Molecules Games 2
Macromolecules Games
Chapter Rags-To-Riches Game
Chapter Challenge Board Game
Nature of Matter Jumble
Vocabulary Game
Carbohydrates Quiz Bowl 1
Carbohydrates Quiz Bowl 2
Nucleic Acid Quiz Bowl
Lipids Quiz Bowl
Protein Quiz Bowl 1
Protein Quiz Bowl 2
Chemicool Periodic Table - MIT
Chemistry Review Problems - Halloran
Chemistry Tutorial Introduction - The Biology Project, Univ. of Arizona
Biochemistry Problem sets -The Biology Project, Univ. of Arizona
John Kyrk animation of pH
John Kyrk animation of water
John Kyrk animation of amino acids and protein folding
Macromolecule Tutorial
Why is Water Necessary? Article
Fold-it- Free downloadable game/puzzle that challenges you to fold proteins!
Concord Consortium Molecular Workbench http://mw.concord.org/modeler/
Tutorial on Macromolecules
Mathmol Hypermedia Textbook - NYU
Online simulation on Enzymes- allows you to change different aspects of reaction and watch for changes in product formation
Free Energy animation: Simple animation illustrating the free energy changes & activation energy needed in a reaction.
Conformational Change animation: Simple animation illustrating the conformational changes in an enzyme-mediated reaction.
Enzyme animation: Simple animation illustrating how an enzyme speeds up biochemical reactions.
Allosteric Inhibition animation: Simple animation illustrating allosteric control of an enzyme.
Biochemical Pathway animation: Simple animation illustrating a biochemical pathway with the enzyme-directed transformation of pyruvate to ethanol.
Biochemical Pathway animations: Good narrated animations on the concept of biochemical pathways & feedback inhibition of enzymes.
Enzyme animations: Simple animations showing enzyme function & factors that affect enzyme function.
Enzyme animations: Clear, simple animations showing enzyme function & factors that affect enzyme function.