Midterm II Study Guide for Chemistry W 109C
(Gainer, Summer 2017)
Exam questions are based on topics that we covered in lecture, in the reading, and in assigned
practice problems, and in Mastering Chemistry. The below list of topics, while not necessarily
all inclusive, is meant as a study guide to help aid you as you study. The exam will focus on the
three chapters indicated below. However, it will be assumed that you have a thorough
understanding of the material covered previously in this class as well as in Chem 109A and 109B.
Amino Acids, Peptides and Proteins
-aminocarboxylic acids as a special group of amino acids
General structure of -aminocarboxylic acids
D, L nomenclature
R, S nomenclature
Names (incl. 3-letter abbreviations), structures, and properties of:
glycine,
alanine,
valine,
leucine,
isoleucine,
serine,
threonine
cysteine,
methionine,
aspartic acid,
glutamic acid,
asparagine,
glutamine,
histidine,
proline,
phenylalanine,
tyrosine,
tryptophan,
arginine,
lysine.
Acid-base properties of amino acids
Approximate pKa values of the various functional groups present on amino acids
You do not need to know any specific pI or pKa values.
Calculation of pI in amino acids and peptides (no more than three ionizable groups)
Separation of amino acids/peptides by electrophoresis and isoelectric focusing
Separation of amino acids by TLC and ion-exchange chromatography
Visualization of amino acids with ninhydrin (including mechanism)
Synthesis of amino acids from carboxylic acids via the Hell–Volhard–Zelinsky reaction
Synthesis of amino acids from -keto acids via reductive amination
Synthesis of amino acids from alkyl halides via N-phthalimidomalonic esters
Synthesis of amino acids from aldehydes using the Strecker method
Mechanistic details of the Hell–Volhard–Zelinsky reaction
Mechanistic details of the reductive amination process
Resolution of racemic mixture of amino acids with aminoacylase enzyme
Formation and the structure of the peptide bond
Biological functions of peptides
Chemical synthesis of peptides: the solution phase vs. solid phase synthesis
Chemical synthesis of peptides: protection strategies for the N-terminus
Chemical synthesis of peptides: activation strategies for the C-terminus
Merrifield solid-phase peptide synthesis: the big picture
Mechanism of C-terminal activation with DCC
Chemistry of the formation and cleavage of disulfide bonds; the amino acid cystine
Determination of the presence and location of disulfide bonds in a peptide
Analysis of amino acid composition of peptides and proteins
Determination of the N-terminal amino acid with phenylisothiocyanate
Full and Partial cleavage of peptides with acid
Partial cleavage of peptides and proteins with cyanogen bromide
Partial enzymatic hydrolysis with trypsin and chymotrypsin
Action and specificity of carboxypeptidases
Deduction of peptide sequences based on above analytical methods
α-Helix and -sheet as two common secondary structure elements in proteins
Interactions responsible for the formation of secondary, tertiary and quaternary structures
Catalysis
Reasons for biocatalysis in living cells
Reaction coordinate diagrams, favorable and unfavorable reactions
Reaction enthalpy, entropy, and free energy
The concept of the transition state and activation energy
Lowering the energy of transition state as a mean of catalysis
Changing the reaction mechanism as a mean of catalysis
Mechanism of anhydride formation
Intramolecular reactions, effective molarities
Chemical mechanisms of catalysis: principles and examples of:
Acid–base catalysis
Covalent catalysis (nucleophilic catalysis)
Metal ion catalysis
Electrostatic catalysis
Hallmarks of specific and general acid catalysis
Principles enzymatic catalysis
Benefits of catalysis in biological systems
Identification and mechanism of catalytic triad in serine proteases
Understanding roles the amino acid residues and cofactors play in enzymatic catalysis
Understanding the various mechanisms seen in enzymatic catalysis
Determinants of substrate specificity (e.g. in chymotrypsin)
Stereoselectivity of catalyzed reactions (e.g. by alcohol dehydrogenase)
Vitamins and coenzymes
Structures of the following compounds, as well as the chemistry and mechanisms of
their associated coenzymes:
Niacin, nicotinamide, flavin, thiamin, biotin, lipoate,
pyridoxal phosphate,
Structure of pyruvate
Redox chemistry of NAD+/NADH and NADP+/NADPH
Redox chemistry of FAD/FADH2
Chemistry of thiamine pyrophosphate as electron sink
Role and mechanisms of thiamine pyrophosphate in pyruvate decarboxylase reaction
Role of biotin in carboxylation reactions
Importance of ATP and Mg2+ in enzymes that use biotin
Chemistry of and coenzymes used in pyruvate dehydrogenase