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Mechanical Force and Biomolecules Lecture 2: Overview of biomolecular structure

Mechanical Force and Biomolecules Lecture 2: Overview of biomolecular structure. Ribose vs. Deoxyribose. Throughout: images from online version of “Biochemistry” by Berg, Tymoczko, and Stryer. Sugar phosphate backbone. Nucleic acids: bases. DNA: A, G, T, C RNA: A, G, U , C.

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Mechanical Force and Biomolecules Lecture 2: Overview of biomolecular structure

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  1. Mechanical Force and BiomoleculesLecture 2:Overview of biomolecular structure

  2. Ribose vs. Deoxyribose Throughout: images from online version of “Biochemistry” by Berg, Tymoczko, and Stryer

  3. Sugar phosphate backbone

  4. Nucleic acids: bases DNA: A, G, T, C RNA: A, G, U, C

  5. Two chains with complementary sequences will basepair, and coil around each other to form a double helix Watson-Crick Basepairing joins 2 chains

  6. The double helix is anti-parallel and asymmetric

  7. Double-helix is asymmetric (major and minor groove); each groove has unique pattern of H-bonding- permits bp-specific binding to grooves (e.g. by other N.A., protein)

  8. Single-stranded nucleic acids can fold into complex structures This is a Ribozyme- an RNA structure that can act as an enzyme, and catalyze reactions

  9. Proteins

  10. Amino acids are chiral From Berg et al, Biochemistry (NCBI books website)

  11. Peptide bonds link amine to carboxylate

  12. Simple aliphatic: Glycine: R = Hydrogen Alanine: R = methyl Small, so not much h-phobic effect Side chains 2

  13. Larger Aliphatic; Large h-phobic effect 6

  14. Proline: also aliphatic, but not averse to H2O Cyclization makes poly-proline chains very rigid 7

  15. Aromatic rings Tyr: reactive hydroxyl Trp and Tyr: strongly absorb UV light (commonly used to quantify protein concentration) 10

  16. Hydrophilic due to hydroxyl group 12

  17. Cysteine Sulfur can form covalent di-sulfide bonds; important for labelling! 13

  18. Basic side chains: (+) charge, hydrophilic pK = 6.5 (His), 12.0 (arg), 10.0 (Lys) 16

  19. Acidic 20

  20. Large variety in physical properties of amino acids leads to a large variety of protein structures.Typically, these are classified in a hierarchy of:Primary = a.a. sequenceSecondary = local folded structuresTertiary = Globular arrangement of chainQuaternary = Association of multiple chains

  21. Secondary structure: Alpha helix (typically right-handed) Amine at position n H-bonds with CO at position n+4

  22. Anti-parallel Secondary: Beta sheet Parallel

  23. Tertiary structure: Arrangement of local motifs into compact, globular structure:

  24. Quaternary structure: Arrangement of multiple chains into a multi-meric complex

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