Amino Acids & Protein Structure

Understand how to distinguish amino acids based on the chemical properties of their side chains, i.e. whether the side chain is acidic or basic, hydrophobic or hydrophilic.

Be able to distinguish L and D amino acids. (All naturally occurring proteins from living organisms consist of L amino acids.)

Have a good familiarity with the ionization states of amino acids including an understanding of amino acid titration curves and the isoelectric point.

Understand how steric considerations of peptide bonds play a role in determining protein structure.

Be able to distinguish primary, secondary, tertiary, and quaternary protein structure articulate the significance of the (limited) reversibility of protein denaturation.

Be prepared to describe the basic organic chemistry reactions in peptide bond formation and hydrolysis of peptide bonds.

Be able to describe how 'salting out' methods of protein precipitation work.

Recognize the various types of post-translational modifications of proteins.

Understand and contextualize various protein functions at the cellular, tissue, physiological levels including enzyme activity, transport & storage, structure, immunity, and signalling.

Point to several examples of structural proteins, transport proteins, signalling proteins, and proteins involved in immunity.

Coordination Chemistry

Be prepared to define a coordination complex and describe its components.

Understand what distinguishes a coordinate covalent bond.

Be able to distinguish monodentate and polydentate ligands.

Be familiar with chelating agents and the process of chelation.

Have a basic sense of how the inner-outer hybrid model involving d orbital hybridization explaining coordination complex structure has been superseded by crystal field and ligand field theory.

Be able to account for d-orbital splitting in ligand field theory and explain why coordination complexes are often intensely colored.

Understand the role that complex ion formation can play in affecting the solubility of weak electrolytes.

Be prepared to describe the importance of coordination chemistry to many biochemical processes.

Oxygen Transporters

Be able to describe the structure of the heme prosthetic group.

Understand the role of hindrance in the heme environment for reversible oxygenation.

Be prepared to describe the tertiary structure of myoglobin.

Know how to compare and contrast the oxygen dissociation curves of myoglobin and hemoglobin.

Understand how the multi-subunit structure of hemoglobin functions in cooperative binding and how cooperative binding facilitates oxygen transport physiologically.

Beyond understanding the consequences of the Bohr and Haldane effects, be able to describe their mechanisms in terms of the effect of conformational changes on specific residues.

Comprehend the mechanism by which DPG decreases oxygen affinity in hemoglobin.

Know how to describe the variations in structure and behavior with the hemoglobin isoforms hemoglobin F and hemoglobin S.

Enzymes

Be able to apply the induced fit model in describing how substrate binding in the active site of an enzyme occurs.

Have a good sense of the mechanisms of enzyme activity as they relate to active site chemical structure as well as the roles of cofactors and coenzymes.

Understand how feedback regulation of enzyme catalysis occurs and the types of inhibition of enzyme activity.

Understand enzyme kinetics, especially the nomenclature and basic problem solving methods of the Michaelis-Menton model.

Understand how to describe the kinetic properties of allosteric enzymes.

Be able to point to a few specific examples demonstrating regulation of enzymes by covalent modification or proteolytic activation.

Zymogens

Beginning with enteropeptidase, be capable of describing the activation of pancreatic digestive enzymes.

Understand the mechanism in blood clotting of the conversion of fibrinogen into fibrin and subsequent cross-linking of fibrin to form a hard clot.

Understand the distinction between the intrinsic and extrinsic coagulation cascades.

Connective Tissue Proteins

Be able to provide a good, basic description of the structure of collagen.

Understand the rationale and mechanism for the hydroxylation of proline and lysine in collagen formation.

Be able to describe the mechanism of procollagen peptidase in collagen fiber formation.

Have a sense of the chemistry involved in the formation of desmosine crosslinks in elastin.

Understand the function of proteoglycans and be able to describe their structure.

Carbohydrates

Be able to describe the structure of carbohydrates and name the mono- and disaccharides which are prominent in the biochemistry.

Gain familiarity with the basic carbohydrate nomenclature including the D,L system and terms such as 'aldose', 'furanose', or 'anomeric carbon'.

Be able to appropriately apply the terms epimer and animer.

Understand the hemiacetal formation mechanism of the cyclicization of glucose and why unequal amounts of the two anomers of glucopyranose are formed.

Understand how to read Fischer and Haworth projections depicting the stereochemistry of carbohydrate ring structures.

Know which monosaccharides combine to form sucrose, lactose, and maltose.

Distinguish glycogen, amylose, amylopectin, and cellulose.

Understand the structure and purpose of glycoproteins and proteoglycans.

Be able to describe how the basic mechanism of glycosidic bond formation works in the context of hemiacetal to acetal conversion.

Understand the purposes of carbohydrates as fuel, biosynthetic precursors, in cell-cell recognition, and as structural components at the tissue level.

Nucleic Acids

Understand the structure of a nucleotide. Be able to distinguish deoxyribonucleotides and ribonucleotides.

Be able to characterize purines and pyrimidines and name the five bases, knowing which occur in DNA and RNA.

Be familiar with the general organic mechanism of phosphodiester bond formation in the polymerization of nucleoside triphosphates in DNA and RNA lengthening.

Understand the structure of the DNA as a helix of two complementary antiparallel strands joined by base pairing.

Be familiar at a basic level with how the A-form, B-form, and Z-forms of DNA are distinguished.

Be able to describe the processes of DNA denaturation and renaturation (annealing).

Understand why RNA is less stable under basic conditions than DNA.

In clear, basic terms, demonstrate the ability to describe the building up of the DNA superstructure in eukaryotic chromatin beginning with the formation of nucleosomes.

Understand the varieties of RNA (mRNA, tRNA, rRNA, snRNA and scRNA) in terms of their structural and functional differences.

Recall the important adenosine derivative, 3'-5'-cyclic adenosine monophosphate, cAMP and its importance as a second messenger involved in passing signal transduction events from the cell surface to internal proteins.

Lipids

Understand that the definition of the category of lipids is not strictly structural but relies on solubility.

Be able to draw the structure of a fatty acid, glycerol, and a triglyceride molecule. Understand the acyl substitution dehydration pathway of formation of a tryglyceride molecule from glycerol and three fatty acids.

Be able to explain why saturated fats have higher melting points than unsaturated fats.

Understand the structure of soaps and detergents and how they function.

Be able to distinguish the structure of phospholipids from triglycerides in general terms as well as distinguish a few different varieties of phosopholipids from each other including lecithin and sphingomyelin. Understand how their behavior underlies the properties of cell membranes.

In basic terms, understand why the terpenes usually have a number of carbon atoms that is a multiple of 5.

Be able to draw the generic structural formula for steroids. Be able to name several examples of steroids and describe their functions.

Recognize the eicosanoid lipids: the prostaglandins, thromboxanes, and leukotrienes.

Bird's Eye View

Be able to reproduce the outlines of Physics, General Chemistry, Organic Chemistry, and Biology at the main topic level.

Knowledge Mapping

Psychology & Sociology

Critical Analysis and Reasoning

Remember the five main types of Verbal Reasoning questions.