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Calling names

Calling names. ALK ANE S ALK ENE S ALK YNE S CYCLO - ALK YL -. Cycloalkanes with Side Groups. Bonding in ethane. CH 3 -CH 3. Bonding in ethylene. CH 2 =CH 2. Bonding in acytylene. CH=CH. Cis and Trans Isomers. Double bond is fixed Cis/trans Isomers are possible

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Calling names

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  1. Calling names • ALKANES • ALKENES • ALKYNES • CYCLO- • ALKYL-

  2. Cycloalkanes with Side Groups

  3. Bonding in ethane CH3-CH3

  4. Bonding in ethylene CH2=CH2

  5. Bonding in acytylene CH=CH

  6. Cis and Trans Isomers • Double bond is fixed • Cis/trans Isomers are possible CH3 CH3 CH3 CH = CH CH = CH cistrans CH3

  7. isomers butane methyl propane • Structural – chain • Structural - position • Structural – function • Stereo - geometrical • Stereo - optical 2methylhexane 3methylhexane cis trans

  8. alkan-OL alkan-AL alkan-ONE

  9. Amino Acids and Proteins Types of Proteins Amino Acids The Peptide Bond

  10. Amino Acids • Building blocks of proteins • Carboxylic acid group • Amino group • Side group R gives unique characteristics R side chain I H2N—C —COOH I H

  11. Amino Acids as Acids and Bases • Ionization of the –NH2 and the –COOH group • Zwitterion has both a + and – charge • Zwitterion is neutral overall NH2–CH2–COOHH3N–CH2–COO– + glycine zwitterion of glycine

  12. + + pH and ionization H+OH- H3N–CH2–COOH H3N–CH2–COO–H2N–CH2–COO– Positive ion zwitterion Negative ion Low pH neutral pH High pH

  13. Most Amino Acids Have Non-Superimposable Mirror Images What is the exception?

  14. D vs L Alanine

  15. Examples of Amino Acids H I H2N—C —COOH I H glycine CH3 I H2N—C —COOH I H alanine

  16. Types of Amino Acids Nonpolar R = H, CH3, alkyl groups, aromatic O Polar ll R = –CH2OH, –CH2SH, –CH2C–NH2, (polar groups with –O-, -SH, -N-) Polar/Acidic R = –CH2COOH, or -COOH Polar/ Basic R = –CH2CH2NH2

  17. Classification of Amino Acids by Polarity Acidic Neutral Basic Asp Asn Arg Ser POLAR Tyr His Cys Gln Thr Lys Glu Gly Ala Ile Phe Trp NON- POLAR Met Val Leu Pro Polar or non-polar, it is the bases of the amino acid properties. Juang RH (2003) Biochemistry

  18. Nonpolar R groups ISOPROPYL

  19. PolarR groups.

  20. Polar R groups

  21. Alanine(Ala / A) Arginine(Arg / R) Aspartic acid(Asp / D) Asparagine(Asn / N) Cysteine(Cys / C) Glutamic acid(Glu / E) Glutamine(Gln / Q) Glycine(Gly / G) Histidine(His / H) Isoleucine(Ile / I) Leucine(Leu / L) Lysine(Lys / K) Methionine(Met / M) Phenylalanine(Phe / F) Proline(Pro / P) Serine(Ser / S) Threonine(Thr / T) Tryptophan(Trp / W) Tyrosine(Tyr / Y) Valine(Val / V) 20 “standard” amino acids used by cells in protein biosynthesis This information will be available on information sheets provided with the final exam, If needed

  22. ala arg asn asp cys gln glu gly his ile leu lys met phe pro ser thr trp tyr val 20 “Standard” Amino Acids

  23. Essential Amino Acids • 10 amino acids not synthesized by the body • arg, his, ile, leu, lys, met, phe, thr, trp, val • Must obtain from the diet • All in dairy products • 1 or more missing in grains and vegetables

  24. Formation of Peptide Bonds by Dehydration 1 COOH COOH NH2 NH2 2 O 2 1 NH2 CN COOH H Amino acids are connected head to tail Dehydration -H2O Juang RH (2004) BCbasics

  25. H O I  H2N—C —COH I H gly CH3 O I  HN—C —COH I I H H ala Peptide Linkage H O I  H2N—C —C — I H glyala CH3O I  N—C —COH I I H H Dipeptide

  26. Peptides • Amino acids linked by amide (peptide) bonds Gly Lys Phe Arg Ser H2N- end -COOH end Peptide bonds (N-terminus) (C-terminus) name: Glycyllysylphenylalanylarginylserine Symbol: GlyLysPheArgSer Or: GKFRS

  27. What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

  28. Tripeptides possible from one each of leucine, glycine, and alanine Leu-Gly-Ala Leu-Ala-Gly Ala-Leu-Gly Ala-Gly-Leu Gly-Ala-Leu Gly-Leu-Ala

  29. Tripeptide containing glycine, cysteine, and alanine Source: Photo Researchers, Inc.

  30. Write the three-letter abbreviations for the following tetrapeptide: Focus Attention on the Side Group Alanine(Ala / A) Leucine(Leu / L) Cysteine(Cys / C) Methionine(Met / M)

  31. Proteins • Proteins are sequences of amino acid residues • Amino acid: carbon atom (C), amino group (NH3),carboxyl group (COOH), variable sidechain (20 different types) • Amino acids are linked with the peptide bond • Protein structure: • Primary – sequence of amino acids • Secondary – local 3D arrangement of amino acids • Tertiary – 3D structure of a complete protein • Quaternary – 3D structure of functional protein (complex)

  32. Types of Proteins Type Examples • Structural tendons, cartilage, hair, nails • Contractile muscles • Transport hemoglobin • Storage milk • Hormonal insulin, growth hormone • Enzyme catalyzes reactions in cells • Protection immune response

  33. Proteins Vary Tremendously in Size • Insulin - A-chain of 21 residues, B-chain of 30 residues -total mol. wt. of 5,733 • Glutamine synthetase - 12 subunits of 468 residues each - total mol. wt. of 600,000 • Connectin proteins - alpha - MW 2.8 million! • beta connectin - MW of 2.1 million, with a length of 1000 nm -it can stretch to 3000 nm!

  34. Four Levels of Protein Structure • Primary, 1o • the amino acid sequence • Secondary, 2o • Local conformation of main-chain atoms (F and Y angles) • Tertiary, 3o • 3-D arrangement of all the atoms in space (main-chain and side-chain) • Quaternary, 4o • 3-D arrangement of subunit chains

  35. HIERARCHY OF PROTEIN STRUCTURE 1. 2. 3. 4. Tertiary

  36. Secondary Structure • The two most common regular (repetitive) 2˚ structures are: • a-helix • b-sheet • Both use hydrogen bonding between N-H & C=O of peptide group as primary stabilizing force.

  37. Helices (1) Cter Nter Hydrogen bonds: O (i) <-> N (i+4)

  38. The b-strand N-H---O-C Hydrogen bonds “Real b-strand is twisted” Extended chain is flat

  39. Pleated sheet

  40. Tertiary Structure • Specific overall shape of a protein • Cross links between R groups of amino acids in chain Ionic H-bond Disulfide Hydrophobic H-bond

  41. Figure 22.26: Permanent waving of hair

  42. Building the Hemoglobin Protein

  43. Urey/Miller Experiment Figure 2 – 09

  44. Urey/Miller Experiment Figure 2 – 09

  45. Replication DNA is the genetic material within the nucleus. DNA The process of replication creates new copies of DNA. Transcription RNA The process of transcription creates an RNA using DNA information. Nucleus Translation Protein The process of translation creates a protein using RNA information. Cytoplasm Central Dogma

  46. DNA Double Helix-Held Together with H-Bonds

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