1 / 40

Monomers and Polymers

Monomers and Polymers. Andy Howard Biology 555, Fall 2018 28 August 2018. Bilayers create a close approximation of a 2-D environment. Kinetics of reactions Rates of diffusion, etc. All very different from what you find in solution, which is an inherently three-dimensional phenomenon.

courtneycole
Download Presentation

Monomers and Polymers

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Monomers and Polymers Andy HowardBiology 555, Fall 2018 28 August 2018

  2. Bilayers create a close approximation of a 2-D environment • Kinetics of reactions • Rates of diffusion, etc. • All very different from what you find in solution, which is an inherently three-dimensional phenomenon Biology 555: Monomers & Polymers

  3. Interior of protein resembles an organic solvent • Energetically unfavorable to bury charge • Charged amino groups very different properties in interior of protein vs exterior Biology 555: Monomers & Polymers

  4. Configuration vs Conformation • Configuration refers to the arrangement of atoms around non-rotating bonds or chiral centers • Configurations can only be changed by breaking covalent bonds • cis-trans isomers • L-D stereoisomers of proteins • Molecules with the same atomic composition but different configurations may have entirely different chemistry! Biology 555: Monomers & Polymers

  5. Configuration Biology 555: Monomers & Polymers

  6. Conformation Biology 555: Monomers & Polymers

  7. Differences in Conformation involve Rotations around Freely Rotating Bonds • gauche and anti- stereoisomers • eclipsed or staggered • a particular conformation will be more or less energetically favorable • particular conformations will have particular chemical properties Biology 555: Monomers & Polymers

  8. Torsion and Dihedral Angles Biology 555: Monomers & Polymers

  9. Biological Monomers are Generally Chiral Molecules • i.e. lack planes or centers of symmetry • Organic chemistry has conventions to describe absolute configurations • Sugars described with respect to chiral centers • Biopolymers constructed of only one enantiomer of a particular monomer • In amino acids the chiral center is the so-called alpha-carbon • Main-chain sequence of atoms: N-C-C-N-C-C…,where the non-alpha carbon is the carbonyl carbon Biology 555: Monomers & Polymers

  10. Macromolecules can have many different conformations • Typically only one is functional:it’s called the native conformation • Described in terms of the torsion angles (J) around each freely rotatable bond • J ranges from -180- 180 degrees • eclipsed gauche J = 0 • staggered anti J = 180 degrees • dihedral angles are the complement of the torsion angles Biology 555: Monomers & Polymers

  11. Proteins made of amino acids • 20 common ones • All L form except glycine (not chiral) • D-amino acids rarely seen;exceptions have specific functional roles • Some AA’s modified post-translationally • Proteins require cofactors to function • Metal ions, small organic molecules Biology 555: Monomers & Polymers

  12. AA’s can be hydrophobic or hydrophilic • Vary in degree of hydropathy • One can measure from the partition coefficient of an amino acid in an organic solvent(octanol closely mimics interior of protein) • Gives estimate of relative effect on thermodynamic stability of molecule Biology 555: Monomers & Polymers

  13. Shape of side chains important • Aromatic rings in Phe, Trp, Tyr bulky and tend to interact with each other • Planes tend to line up perpendicular to each other in the interior of globular proteins • Benzene molecule line up similarly in solution • Entropy driven i.e. more ways to stack perpendicularly than parallel Biology 555: Monomers & Polymers

  14. Special case: proline • Proline isn’t an amino acid: it’s an imino acid • Hindered rotation around bond between amine N and alpha carbon is important to its properties • Tends to abolish helicity because of that hindered rotation Biology 555: Monomers & Polymers

  15. The simplest amino acids • Glycine • Alanine These are moderately nonpolar methyl Biology 555: Monomers & Polymers

  16. Valine Isoleucine Leucine Branched-chain aliphatic aas Seriously nonpolar isopropyl Biology 555: Monomers & Polymers

  17. Serine Threonine Hydroxylated, polar amino acids hydroxyl Biology 555: Monomers & Polymers

  18. Aspartate Glutamate Amino acids with carboxylate side chains carboxylate methylene Biology 555: Monomers & Polymers

  19. asparagine glutamine Amino Acids with amide side chains amide Note: these are uncharged! Don’t fall into the trap! Biology 555: Monomers & Polymers

  20. Cysteine Methionine Sulfur-containing amino acids sulfhydryl Two differences:(1) extra methylene(2) methylated S Biology 555: Monomers & Polymers

  21. Lysine Arginine Positively charged side chains Guani-dinium Biology 555: Monomers & Polymers

  22. Phenylalanine Tyrosine Aromatic Amino Acids phenyl Biology 555: Monomers & Polymers

  23. Histidine: a special case • Histidine imidazole Biology 555: Monomers & Polymers

  24. Tryptophan: the biggest of all • Tryptophan indole Biology 555: Monomers & Polymers

  25. The Peptide bond • Amino acids condensed by dehydration synthesis • Carboxyl + amino => C-N bond. • i.e. flanked on both sides by -carbons • Formation not spontaneous => need ribosomes • Hard to reverse => need hydrolytic enzymes Biology 555: Monomers & Polymers

  26. The Peptide Bond Biology 555: Monomers & Polymers

  27. Peptide bonds have double bond character • Bond lengths less than normal C-N bond lengths • Resonance structure • Effectively rigid and planar • Barrier of ~13 kJ mol-1 between cis and trans forms • Cis-form highly disfavored because of steric hindrance (except for proline) • There is a small dipole moment across the peptide bond (-ve end carbonyl oxygen) Biology 555: Monomers & Polymers

  28. Double-bond character of peptide Biology 555: Monomers & Polymers

  29. The peptide bond and restrictions on protein conformation • Bond between -carbon and the carbonyl carbon called  • Bond between -carbon and the amino group called  • Entire peptide bond plane rotates so certain values of  and  cannot be achieved because of steric hindrance Biology 555: Monomers & Polymers

  30. The result: planarity! • This partial double bond character means the nitrogen is sp2 hybridized • Six atoms must lie in a single plane: • First amino acid’s alpha carbon • Carbonyl carbon • Carbonyl oxygen • Second amino acid’s amide nitrogen • Amide hydrogen • Second amino acid’s alpha carbon Biology 555: Monomers & Polymers

  31. Rotations and flexibility • Planarity implies  = 180º,where  is the torsion angle about N-C bond • Free rotations are possible about N-C and C-C bonds • Define  = torsional rotation about N-C • Define  = torsional rotation about C-C • We can characterize main-chain conformations according to ,  Biology 555: Monomers & Polymers

  32. Ramachandran angles G.N. Ramachandran Biology 555: Monomers & Polymers

  33. Preferred Values of  and  • Steric hindrance makes some values unlikely • Specific values are characteristic of particular types of secondary structure • Most structures with forbidden values of  and  turn out to be errors Biology 555: Monomers & Polymers

  34. How far from 180º can w vary? • Remember what we said about the partial double bond character of the C-N main-chain bond • That imposes planarity • In practice it rarely varies by more than a few degrees from 180º. Biology 555: Monomers & Polymers

  35. Secondary Structure •  & secondary structures arise from  and  based steric hindrance • If a sequence consists of AA's with similar allowed  and 's  & secondary structures may arise independent of details about bonding • Trans conformation • Fully extended AA chain - no intramolecular bonding • Other secondary structures stabilized by hydrogen bonds Biology 555: Monomers & Polymers

  36. Ramachandran plots • Allowed regions of  and  "phase space" for a particular amino acid shown on Ramachandran plots (different side chains) • Can be defined in terms of hard sphere boundaries or energy cost to enter particular regions Biology 555: Monomers & Polymers

  37. Ramachandran Plot for Poly-L Alanine Contours of vDW interaction energies Dark allowed Cross-hatched possible Blank areas not allowed P=polyproline C=collagen helix 310 &  helices left & right  helices, parallel, anti-parallel sheets Biology 555: Monomers & Polymers

  38. Ramachandran Angles in Proteins Biology 555: Monomers & Polymers

  39. Ramachandran plot • Cf. figures in text • If you submit a structure to the PDB with Ramachandran angles far from the yellow regions, be prepared to justify them! Biology 555: Monomers & Polymers

  40. Structure of Nucleic Acids • polynucleotide chains highly flexible • range of allowed conformations much greater than for polypeptide chains • because number of torsion angles in back-bone greater • some restrictions, e.g. sugar pucker • The  angle around the glycosidic bond is restricted to be between -180º and -90º for the anti comformation and -90º and 190º for the syn conformation Biology 555: Monomers & Polymers

More Related