2025 CHEM 5620 - Protein Chemistry: Final Exam Study Guide
Here are 9 key topics to focus on for your upcoming midterm exam. The exam will consist of 25
multiple-choice questions (4 points each) and 4 open-answer questions (25 points each), and you
should be able to complete them within 2 hours. One double-sided letter-sized sheet of notes
may be brought to the exam.
1. Protein Biosynthesis and Unnatural Amino Acid Incorporation
• Components required for translation: mRNA, tRNA, rRNA, ribosomes, aminoacyl-tRNA
synthetases
• Stages of translation: initiation, elongation, termination
• Genetic code expansion and unnatural amino acid (UAA) incorporation
• Orthogonal tRNA/aminoacyl-tRNA synthetase systems
• Site-specific incorporation of unnatural amino acids into proteins and applications
2. Ubiquitination and Protein Degradation in the Context of Auxin Signaling
• Mechanism of ubiquitination (E1, E2, E3 enzymes)
• 26S proteasome structure and function
• Auxin Receptor Mechanism in Plants: 1) Auxin, a plant hormone, regulates gene
expression by promoting the degradation of transcriptional repressors known as Aux/IAA
proteins. 2) The F-box protein TIR1 functions as an auxin receptor and is part of the
SCFTIR1 E3 ubiquitin ligase complex. 3) In the presence of auxin, TIR1 binds to Aux/IAA
proteins, leading to their ubiquitination and subsequent degradation by the 26S
proteasome. This degradation releases the repression on auxin-responsive genes,
facilitating various aspects of plant growth and development.
3. Enzyme Catalysis Fundamentals and Directed Evolution of Enzymes
• Definition and general properties of enzymes
• Activation energy and transition state theory
• Gibbs free energy (ΔG) and reaction spontaneity
• Directed Evolution of Enzymes: 1) Principles and methods (e.g., error-prone PCR,
DNA shuffling, continuous directed evolution) 2) Applications in developing enzymes
with novel or enhanced properties (activity, specificity, stability)
• Case study: Evolution of TurboID from ancestral biotin ligase BirA via
directed evolution, and its applications.
4. Molecular Chaperones and Protein Folding Diseases
• Role of molecular chaperones in protein folding and proteostasis.
• Molecular chaperones as facilitators of protein evolution (e.g., chaperonin-assisted
directed evolution of enzymes).
• Protein misfolding-associated degenerative diseases and disease
mechanisms: Alzheimer’s, Parkinson’s, Huntington’s, and prion diseases.
Here are 9 key topics to focus on for your upcoming midterm exam. The exam will consist of 25
multiple-choice questions (4 points each) and 4 open-answer questions (25 points each), and you
should be able to complete them within 2 hours. One double-sided letter-sized sheet of notes
may be brought to the exam.
1. Protein Biosynthesis and Unnatural Amino Acid Incorporation
• Components required for translation: mRNA, tRNA, rRNA, ribosomes, aminoacyl-tRNA
synthetases
• Stages of translation: initiation, elongation, termination
• Genetic code expansion and unnatural amino acid (UAA) incorporation
• Orthogonal tRNA/aminoacyl-tRNA synthetase systems
• Site-specific incorporation of unnatural amino acids into proteins and applications
2. Ubiquitination and Protein Degradation in the Context of Auxin Signaling
• Mechanism of ubiquitination (E1, E2, E3 enzymes)
• 26S proteasome structure and function
• Auxin Receptor Mechanism in Plants: 1) Auxin, a plant hormone, regulates gene
expression by promoting the degradation of transcriptional repressors known as Aux/IAA
proteins. 2) The F-box protein TIR1 functions as an auxin receptor and is part of the
SCFTIR1 E3 ubiquitin ligase complex. 3) In the presence of auxin, TIR1 binds to Aux/IAA
proteins, leading to their ubiquitination and subsequent degradation by the 26S
proteasome. This degradation releases the repression on auxin-responsive genes,
facilitating various aspects of plant growth and development.
3. Enzyme Catalysis Fundamentals and Directed Evolution of Enzymes
• Definition and general properties of enzymes
• Activation energy and transition state theory
• Gibbs free energy (ΔG) and reaction spontaneity
• Directed Evolution of Enzymes: 1) Principles and methods (e.g., error-prone PCR,
DNA shuffling, continuous directed evolution) 2) Applications in developing enzymes
with novel or enhanced properties (activity, specificity, stability)
• Case study: Evolution of TurboID from ancestral biotin ligase BirA via
directed evolution, and its applications.
4. Molecular Chaperones and Protein Folding Diseases
• Role of molecular chaperones in protein folding and proteostasis.
• Molecular chaperones as facilitators of protein evolution (e.g., chaperonin-assisted
directed evolution of enzymes).
• Protein misfolding-associated degenerative diseases and disease
mechanisms: Alzheimer’s, Parkinson’s, Huntington’s, and prion diseases.
