Learning Objectives For Test 1

Chapter 1, The Chemical Basis of Life

1.1    What is Biochemistry?

(skipped)

1.2  Biological molecules

Identify functional groups that are present in a given biomolecule.  1

Recognize the structures of the four basic biomolecules.  3, 4, 9, 11, 18

Know what a residue is.

Describe the three major kinds of biological polymers.  7

1.3  Energy and metabolism

Determine the oxidation state of an atom in a compound.  31, 32

Recognize whether entropy increases or decreases for a given change.  21, 22,

Understand the meanings of enthalpy, entropy, and free energy and how they are related.  23

Predict whether a process will be spontaneous or not using the change in free energy, given by equation , ΔG, given by ΔG = ΔHTΔS.  25, 26

1.4  The origin and evolution of life

Describe the difference between prokaryotes and eukaryotes.

Give evidence that suggests that a phylogenetic tree should have one trunk.

Describe the Miller-Urey experiment, and its significance.

SKIP this one:  Suggest how eukaryotes may have formed.

Chapter 2, Aqueous Chemistry

2.1  Water molecules form hydrogen bonds

Know which elements form hydrogen bonds.  2, 3,

Describe the different types of noncovalent forces acting on biological molecules.  4, 5, 6, 14

Describe how water dissolves ionic and polar substances.  9

Explain how replacing some of a molecule’s hydrogen atoms with fluorine atoms may increase the ease with which the molecule crosses a cell membrane.  44

2.2  The hydrophobic effect

Explain the cause of the hydrophobic effect.

Sketch an amphiphile, a micelle and a bilayer.  17, 18, 19, 25, 24

Describe diffusion through a vesicle.

2.3  Acid-base chemistry

Given pH, predict pOH, and vice versa.  33, 34, 35

Calculate the pH of a solution of a strong acid or base.

Given pKa values for acids, predict which acid will be the most ionized.  39, 40, 49, 41, 43, 45

Use the Henderson-Hasselbalch equation to calculate the pH of a solution and to prepare a buffer.  51

Given pKa values, predict which species predominate at a given pH.

Chapter 4, Protein Structure

4.1  Proteins are chains of amino acids

For each of the 20 standard amino acids, sketch it and give its name and three-letter abbreviation.  3

Given the abbreviations of a string of amino acids, sketch that string, showing the dipeptide bonds.  12, 13, 14

Use pKa’s to predict the charge of a protein.  1, 5, 6

Explain why more than one protease is needed for sequencing proteins.  41, 42

Describe the four levels of protein structure.

4.2  Secondary structure:  the conformation of the peptide group

Describe the constraints on polypeptide conformation.

Relate the α helix and ß sheet to hydrogen bonding.

Explain the difference between the two types of ß sheets.

4.3  Tertiary structure and protein stability

Know what a domain is, and recognize one.

Know which chemical interaction is mainly responsible for a protein’s tertiary structure, and describe the less significant interactions.  22, 24, 25

State where the information is stored that determines a protein’s shape when it folds.  31

SKIP:  Describe three things that can happen to a protein when it misfolds.

Recognize protein modifications.

4.4  Quaternary Structure

Describe protein quaternary structure using two systems (terms and Greek letters).  16

4.5 Tools and Techniques:  Analyzing Protein Structure

List the two methods by which a protein’s tertiary and quaternary structure is commonly determined.

Account for the order of elution of proteins in size exclusion chromatography and in ion exchange chromatography.