Study-Unit Description

Study-Unit Description


TITLE Fundamentals and Applications of Biological Chemistry 2

LEVEL 02 - Years 2, 3 in Modular Undergraduate Course



DESCRIPTION 1. Nucleosides, Nucleotides and Nucleic acids
- 1.1 Nucleoside and nucleotide structure: purine and pyrimidine bases, the phosphodiester and N-glycosidic bonds;
- 1.2 DNA and RNA structure: deoxyribonucleotides, the DNA double helix, the role of noncovalent interactions in complementary base pairing and the higher structure of nucleic acids, thermal and acid-base disruption of the double helix;
- 1.3 Nucleotide biosynthesis: de novo synthesis of purine and pyrimidine bases, salvage pathways, deoxyribonucletide synthesis;
- 1.4 Nucleotide biotechnology: techniques of genetic engineering, DNA editing, hybridization and its applications, PCR, DNA mapping, restriction mapping, DNA sequencing, Maxam/Gilbert method, Sanger method.

2. Amino acids and proteins
- 2.1 Structure of amino acids: different classes of amino acid side groups, amino acids and pH;
- 2.2 Higher structure of polypeptides and proteins: formation and structural geometry of the peptide bond, structure and role of noncovalent interactions in helices, sheets, turns, loops and coiled coils, tertiary structure;
- 2.3 Amino acid and protein biosynthesis, catabolism and turnover;
- 2.4 Protein physicochemistry: proteins and pH, point of zero charge, side group effects, effect of pH on protein charge and solubility, the Florey-Huggins theory, thermodynamics of the hydrophobic effect;
- 2.5 Protein stability: Chemical stability (deamidation, racemisation, proteolysis, oxidation, beta-elimination, disulfide exchange), physical stability (denaturation, aggregation, precipitation, adsorption);
- 2.6 Analytical techniques in protein chemistry: protein purification by centrifugation, salting out, dialysis and chromatography (gel filtration, ion exchange and affinity), separation of proteins by electrophoresis (PAGE, SDS-PAGE, IEF, 2-D electrophoresis), ultracentrifugation and density gradient centrifugation, evaluation of protein purification, protein sequencing (Edman degradation, enzymatic, disulfide bond analysis, protein synthesis (Merrifield method);
- 2.7 Case study of proteins I - Enzymes: Thermodynamics, kinetics and mechanisms of enzyme reactions: the Michaelis-Menton equation, Lineweaver Burke, Dixon and Eadie-Hofstee plots; kinetics of competitive and noncompetitive inhibition, allosterism, cooperativity, and hysteresis;
- 2.8 Case study of proteins II – Monoclonal antibodies: Gross and fine structure of antibody molecules; heavy chains and light chains, constant and variable regions, hypervariable regions, chemistry of antigen-antibody binding (affinity vs avidity, calculation of Ka by Scatchard analysis and nonlinear regression; the immunological importance of Ka), monoclonal antibodies, immunoassays.

Study-unit Aims:

The aim of this study-unit is to provide students with an understanding of how principles of physical, organic and analytical chemistry are applied in the field of biological chemistry of nucleotides, amino acids and proteins.

Learning Outcomes:

1. Knowledge & Understanding:
By the end of the study-unit the student will be able to:

- Name the major purine and pyrimidine bases and identify amino acid and one-carbon metabolites that contribute to the synthesis of these ring structures;
- Integrate the terminology and defining structural features that distinguish different classes of nucleotide metabolites;
- Compare and contrast the structure of DNA and RNA, explaining the difference between the constituent bases, sugars, nucleosides and nucleotides;
- Describe the double-stranded, helical, and antiparallel chain structure of DNA;
- Define and explain the roles of Van der Waals forces, charge-charge interactions, hydrogen bonds, and hydrophobic interactions in nucleic acid architecture;
- Describe the biosynthesis of the purine and pyrimidine nucleotides;
- Summarize folate metabolism and explain its connection to nucleotide metabolism;
- Describe the principles, methods, and applications of Northern, Southern, Western blot, PCR, and DNA sequencing;
- Describe how recombinant DNA technology is used to clone and express genes;
- List and name the 20 amino acids that commonly occur in proteins and classify them according to chirality, polarity, size, and charge;
- Describe the bonds and forces that contribute to the conformation of proteins;
- Define ketogenic and glucogenic amino acids, and list them as exclusively ketogenic, glucogenic, or both;
- Integrate amino acid synthesis with specific precursors from glycolysis, citric acid cycle and the pentose phosphate pathway;
- Explain the role of transamination reactions in amino acid synthesis;
- List, discuss, and evaluate the major techniques used in separating proteins;
- Describe the major enzyme classifications and the basic type of reaction catalyzed;
- Explain how an enzyme functions as a catalyst in lowering the activation energy of reactions;
- Propose a thermodynamic explanation of why enzymes cannot alter the equilibrium of reactions;
- Explain the induced fit (conformational changes) model of enzyme catalysis;
- Explain Michaelis-Menton kinetics, define initial velocity (Vo) and explain the effect of substrate concentration on enzyme velocity for a single subunit enzyme;
- Compare and contrast the different types of enzyme inhibitors.

2. Skills:
By the end of the study-unit the student will be able to:

- Examine and determine the charge on a small peptide at a given pH;
- Discriminate between primary, secondary, tertiary, and quaternary protein structure;
- Apply the Michaelis-Menton equation to calculate velocity, maximum velocity (Vmax) and the Michaelis-Menton constant Km;
- Draw a Lineweaver-Burke plot, defining Vmax and Km and use the plot to evaluate types of inhibition.

Main Text/s and any supplementary readings:

- Lehninger Principles of Biochemistry, David L. Nelson and Michael M. Cox, 5th ed., 2008.
- Biochemistry, Jeremy M. Berg, John L. Tymoczko and Lubert Stryer, 6th ed., 2007.
- Biochemistry, Donald Voet and Judith G. Voet, 4th ed., 2011.
- Essential biochemistry, Charlotte W. Pratt and Kathleen Cornely, 2nd ed., 2011.

STUDY-UNIT TYPE Lecture and Tutorial

Assessment Component/s Assessment Due Resit Availability Weighting
Classwork SEM1 No 15%
Examination (2 Hours) SEM1 Yes 85%

LECTURER/S Claude A. Farrugia

The University makes every effort to ensure that the published Courses Plans, Programmes of Study and Study-Unit information are complete and up-to-date at the time of publication. The University reserves the right to make changes in case errors are detected after publication.
The availability of optional units may be subject to timetabling constraints.
Units not attracting a sufficient number of registrations may be withdrawn without notice.
It should be noted that all the information in the description above applies to study-units available during the academic year 2020/1. It may be subject to change in subsequent years.