Lecture 2

• The 20 amino acids and their corresponding three-letter and one-letter abbreviations can be grouped according to the chemical properties of their side chains.
• Protein secondary, tertiary, and quaternary structures can be distinguished.
• The properties of the principal types of secondary structure, including the α helix, the β sheet, and the reverse turn, can be described.
• The hydrophobic effect serves as the primary driving force for folding of polypeptide chains into globular proteins.
• The nucleation-condensation model of protein folding is preferable to a random sampling model.
• Proteins have a wide range of shapes and sizes, and their structure determines their function.
• Proteins contain a wide range of functional groups to perform different chemistry.
• Proteins are linear polymers (polypeptides) built of monomer units called amino acids which are linked end-to-end through peptide (or amide) bonds.
• Proteins can interact with one another and other macromolecules to form complexes.
• Some proteins are rigid while others are flexible.
• Amino acids are linked together by peptide bonds, and proteins are linear, not branched.
• Proinsulin is cleaved to form mature insulin and the C-peptide.
• Insulin Lispro (rapid) does not form hexamers and insulin Glargine (long-acting) forms more stable hexamers.
• Proinsulin is cleaved in two locations to form mature insulin (A & B chains) and releasing the C peptide (connecting peptide).
• Synthetic insulin only has the A & B chains.
• Altering specific amino acids in the insulin chain results in a faster or slower acting insulin.
• Insulin peaks about 45 minutes after high carbohydrate meal.
• Lucy Letby was charged with 7 murders and 15 attempted murders.
• Serum C-peptide values can distinguish between injected and endogenous insulin.
• The sequence of amino acids in a protein is referred to as its primary structure, which defines its folding into three-dimensional structure (tertiary structure) and thus function.
• Only L amino acids are used in proteins.
• Proteins are linear polymers composed of amino acids.
• Knowing the amino acid sequence of a protein is essential to defining its function.
• Prion diseases can be transmitted through direct contact or eating tissues rich in PrPsc.
• Amyloids are very stable, resistant to degradation, cause damage to brain tissue, and their function is not clear but there is evidence for importance in sleep and memory.
• CASP is the Critical Assessment of Structure Prediction where research groups compete to predict structures.
• Amino acid sequence determines 3-dimensional structure of the protein.
• Post-translational modifications, or PTMs, confer new capabilities to proteins.
• Transition between native PrPc and PrPsc (pathological) results in aggregation of the primarily beta sheet structure.
• The protein-only model for prion disease transmission is based on the assumption that the local structures that are sampled can be found in known protein structures.
• Alphafold does a better job than other predictions in the CASP competition.
• Collagen, blood coagulation proteins, enzyme regulation, and membrane proteins are examples of proteins with important PTMs.
• AlphaFold is the best folding program, developed by DeepMind, an Alphabet subsidiary.
• Changes in amino acid sequence can lead to changes in protein structure and function.
• Amino acid sequence comparisons reveal evolutionary relationships between proteins.
• Theoretical Diversity with n residues there can be 20 n different protein sequences.
• For 100 residues there can be 20 100 different proteins.
• Histidine is ionizable and often an important residue in protein function and catalysis.
• These are dipolar ions also called zwitterions.
• Glycine allows close contact between polypeptide chains.