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What is the primary difference between an alpha helix and beta sheet in terms of hydrogen bonding? A) Alpha helix has no hydrogen bonds B) Alpha helix has hydrogen bonds within the same chain (i to i+4), beta sheet between adjacent strands C) Beta sheets have no hydrogen bonds D) Both have identical hydrogen bonding patterns

A typical transmembrane helix consists of approximately: A) 5-10 amino acids B) 100-200 amino acids C) 50-100 amino acids D) 15-25 amino acids 

Variable regions in multiple sequence alignments often represent: A) Sites tolerating diversity (surface loops) B) Catalytic sites C) Strictly conserved structural cores D) Transmembrane domains

What does the “Small Molecules” tab in a PDB entry provide information about? A) The molecular weight and isoelectric point of the protein chain B) Details of non-protein ligands, cofactors, or drug molecules bound to the protein structure, including their chemical structure and ID  C) A summary of all mutations introduced into the protein during crystallization D) The solvent content and crystal packing parameters of the structure

The aliphatic index is an indicator of: A) Protein charge B) Thermal stability C) Protein size D) Enzymatic activity

High proline content affects: A) Protein charge B) Backbone flexibility C) Extinction coefficient D) Molecular weight only

A researcher has a protein sequence with no homologous structures found in the PDB and all template searches return sequence identities below 15%. Which modelling approach is most appropriate? A) Homology modelling using the closest available template regardless of identity B) Ab initio (de novo) modelling, since no reliable template exists and the structure must be predicted from physicochemical principles alone C) Molecular docking, as it can predict structure without any template D) Comparative modelling using UniProt annotations as a structural reference

When you open a protein entry on the RCSB PDB website (e.g., 1HHO), what key information is displayed on the “Structure Summary” tab? A) Only the raw FASTA sequence of the protein with no structural details B) A general overview including the protein name, organism, experimental method, resolution, and a 3D molecular viewer C) A list of all chemical reactions the protein catalyzes D) The complete genome sequence of the organism the protein belongs to

In a high-quality protein structure, what percentage of residues should fall in the most favored regions of a Ramachandran plot? A) 50% or more B) 70% or more C) 90% or more D) 100% exactly

Essay Questions: There are 7 essay questions available for you to answer any 5 of your choice or all questions if answered correctly . Each question is 4 points if answered correctlyList the primary lymphatic organs and the secondary lymphatic organs (4points)