Semester 1: Biochemistry Proteins, Carbohydrates,  Week 1
Contact us: <ul><li>Julie:  [email_address] </li></ul><ul><li>Jenesha:  [email_address] </li></ul>
Proteins <ul><li>L-amino acids : </li></ul><ul><li>Zwitterions  = physiologic pH </li></ul><ul><li>Buffer  = pKa ± 1 </li>...
Hydrophobic Amino Acids <ul><li>Aliphatic :  VAGLIP </li></ul><ul><ul><li>Valine (Val) </li></ul></ul><ul><ul><li>Alanine ...
Hydrophobic Amino Acids <ul><li>Aromatic :  Form Your Wheel </li></ul><ul><ul><li>Phenylalanine (Phe/F) </li></ul></ul><ul...
Hydrophilic Amino Acids <ul><li>Polar/Uncharged : 3 Serene Gluttonous Asians </li></ul><ul><ul><li>Threonine (Thr) </li></...
Hydrophilic Amino Acids <ul><li>Acidic/Negative : Gluteus = Ass </li></ul><ul><ul><li>Glutamate (Glu)  ← (Glutami n e = Gl...
Protein Structure <ul><li>Primary :  amino acid sequence </li></ul><ul><ul><li>Peptide bond = amide linkage between carbox...
Protein Structure <ul><li>Secondary : </li></ul><ul><ul><li>Alpha-helix :  (E.G., alpha-Keratin) </li></ul></ul><ul><ul><u...
Protein Structure <ul><li>Tertiary structure : 3D folding </li></ul><ul><ul><li>Domains of functionality </li></ul></ul><u...
Collagen <ul><li>Tough and fibrous; in skin, hair, and nails </li></ul><ul><li>Triple  α -helix (R=Proline/Hydroxyproline)...
Protein Structure
Protein Structure <ul><li>Quaternary Structure : </li></ul><ul><ul><li>>2 tertiary structures combine as subunits </li></u...
Prions <ul><li>Normal cell surface proteins gone bad </li></ul><ul><li>Normal protein gene:  PRNP (chromosome 20) </li></u...
Spongiform Encephalopathies <ul><li>Alzheimer's  (Xmemory) </li></ul><ul><li>New variant Creutzfeldt-Jakob's  (Xmotor) </l...
Stereochemistry <ul><li>Achiral :  superimposable mirror images with four groups </li></ul><ul><li>Chiral :  bound to four...
Carbohydrates <ul><li>D-glucose : </li></ul><ul><li>4 chiral centers </li></ul><ul><li>Diastereomer w/ D- galactose : </li...
Mutarotation :  equilibrium between alpha and beta forms Anomeric :  linear = non-chiral, ring's C1 = chiral (E.G., fructo...
Bonds to Know <ul><li>Maltose/Amylose : alpha(1-4) </li></ul><ul><li>Lactose/Cellulose : beta(1-4) </li></ul><ul><li>Sucro...
Love, Julie  and  Jenesha
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Biochem1: Week 1

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Semester 1 - Biochemistry - Week 1

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Biochem1: Week 1

  1. 1. Semester 1: Biochemistry Proteins, Carbohydrates, Week 1
  2. 2. Contact us: <ul><li>Julie: [email_address] </li></ul><ul><li>Jenesha: [email_address] </li></ul>
  3. 3. Proteins <ul><li>L-amino acids : </li></ul><ul><li>Zwitterions = physiologic pH </li></ul><ul><li>Buffer = pKa ± 1 </li></ul><ul><li>pI = </li></ul><ul><li>pKa average </li></ul>
  4. 4. Hydrophobic Amino Acids <ul><li>Aliphatic : VAGLIP </li></ul><ul><ul><li>Valine (Val) </li></ul></ul><ul><ul><li>Alanine (Ala) </li></ul></ul><ul><ul><li>Glycine (Gly) </li></ul></ul><ul><ul><li>Leucine (Leu) </li></ul></ul><ul><ul><li>Isoleucine (Ile) </li></ul></ul><ul><ul><li>Proline (Pro) </li></ul></ul>
  5. 5. Hydrophobic Amino Acids <ul><li>Aromatic : Form Your Wheel </li></ul><ul><ul><li>Phenylalanine (Phe/F) </li></ul></ul><ul><ul><li>Tyrosine (Tyr/Y) </li></ul></ul><ul><ul><li>Tryptophan (Trp/W) </li></ul></ul><ul><li>Sulfur : Musky Crap </li></ul><ul><ul><li>Methionine (Met) </li></ul></ul><ul><ul><li>(Cysteine (Cys)) ←( Hydrophilic) </li></ul></ul>
  6. 6. Hydrophilic Amino Acids <ul><li>Polar/Uncharged : 3 Serene Gluttonous Asians </li></ul><ul><ul><li>Threonine (Thr) </li></ul></ul><ul><ul><li>Serine (Ser) </li></ul></ul><ul><ul><li>Glutami n e (Gln) </li></ul></ul><ul><ul><li>Asparagi n e (Asn) </li></ul></ul>
  7. 7. Hydrophilic Amino Acids <ul><li>Acidic/Negative : Gluteus = Ass </li></ul><ul><ul><li>Glutamate (Glu) ← (Glutami n e = Gln) </li></ul></ul><ul><ul><li>Aspartate (Asp) ← (Asparagi n e = Asn) </li></ul></ul><ul><li>Basic/Positive : Hiss! Lyse! Argh! </li></ul><ul><ul><li>Histidine (His) </li></ul></ul><ul><ul><li>Lysine (Lys) ← (pKa = 7) </li></ul></ul><ul><ul><li>Arginine (Arg) </li></ul></ul>
  8. 8. Protein Structure <ul><li>Primary : amino acid sequence </li></ul><ul><ul><li>Peptide bond = amide linkage between carboxyl group and next amine (mostly trans configuration) </li></ul></ul><ul><ul><li>Quick note: </li></ul></ul><ul><ul><ul><li>Configuration = must break bond to change (cis vs. trans, D vs L, R vs S) </li></ul></ul></ul><ul><ul><ul><li>Conformation = molecular motion to change form (chair vs. boat) </li></ul></ul></ul>
  9. 9. Protein Structure <ul><li>Secondary : </li></ul><ul><ul><li>Alpha-helix : (E.G., alpha-Keratin) </li></ul></ul><ul><ul><ul><li>Few bulky (Ile, Val) or tiny (Pro, Gly) R's </li></ul></ul></ul><ul><ul><ul><li>3.6 residues/turn </li></ul></ul></ul><ul><ul><li>Beta-sheet : (E.G., Fibroin of silk) </li></ul></ul><ul><ul><ul><li>Backbone H-bonds = perpendicular between sheets </li></ul></ul></ul><ul><ul><ul><li>Not regular, repeating pattern. </li></ul></ul></ul><ul><ul><li>Random-coil : </li></ul></ul><ul><ul><ul><li>Not random configuration </li></ul></ul></ul><ul><ul><ul><li>Usually functional portion of protein </li></ul></ul></ul>
  10. 10. Protein Structure <ul><li>Tertiary structure : 3D folding </li></ul><ul><ul><li>Domains of functionality </li></ul></ul><ul><ul><li>Types: </li></ul></ul><ul><ul><ul><li>Globular : H2O soluble (E.G., Pepsin) </li></ul></ul></ul><ul><ul><ul><li>Fibrous : (E.G., Collagen) </li></ul></ul></ul><ul><ul><li>Bonds: </li></ul></ul><ul><ul><ul><li>Hydrophobic (interior) </li></ul></ul></ul><ul><ul><ul><li>Salt bridges (exterior) </li></ul></ul></ul><ul><ul><ul><li>Disulfide links </li></ul></ul></ul><ul><ul><ul><li>Van der waals </li></ul></ul></ul><ul><ul><ul><li>Side-chain H-bonds </li></ul></ul></ul>
  11. 11. Collagen <ul><li>Tough and fibrous; in skin, hair, and nails </li></ul><ul><li>Triple α -helix (R=Proline/Hydroxyproline) </li></ul><ul><ul><li>Needs Vitamin C (or suffer from Scurvy) </li></ul></ul><ul><li>Cysteine (strong, covalent disulfide) bonds </li></ul><ul><ul><li>Less cysteine = curlier hair!! ← (unimportant) </li></ul></ul><ul><li>4 protofibrils ->microfibril->macrofibril->hair </li></ul>
  12. 12. Protein Structure
  13. 13. Protein Structure <ul><li>Quaternary Structure : </li></ul><ul><ul><li>>2 tertiary structures combine as subunits </li></ul></ul><ul><ul><li>Disulfide bonds are RARE </li></ul></ul>
  14. 14. Prions <ul><li>Normal cell surface proteins gone bad </li></ul><ul><li>Normal protein gene: PRNP (chromosome 20) </li></ul><ul><li>Normal protein: Prpc </li></ul><ul><li>Prion (mutated protein): Prpsc (scrapie) </li></ul><ul><li>Infective post-mortem </li></ul><ul><li>Diseases: </li></ul><ul><ul><li>Creutzfeldt-Jakob disease (Mad Cow; Xmotor ) </li></ul></ul><ul><ul><li>KURU (from cannibalism) </li></ul></ul>
  15. 15. Spongiform Encephalopathies <ul><li>Alzheimer's (Xmemory) </li></ul><ul><li>New variant Creutzfeldt-Jakob's (Xmotor) </li></ul><ul><li>Fatal Familial Insomnia </li></ul><ul><li>(Amyloid) Parkinson's (tremor, Xmotor ) </li></ul>
  16. 16. Stereochemistry <ul><li>Achiral : superimposable mirror images with four groups </li></ul><ul><li>Chiral : bound to four or more unique groups; implies stereoisomers (same formula but different bond placements; Z/cis vs E/trans) </li></ul><ul><li>Enantiomers : non-superimposable mirror images with same properties but rotates light differently (D vs. L) </li></ul><ul><li>Diastereomers : non-mirror image stereoisomers (D-glucose vs. D-galactose) </li></ul>
  17. 17. Carbohydrates <ul><li>D-glucose : </li></ul><ul><li>4 chiral centers </li></ul><ul><li>Diastereomer w/ D- galactose : </li></ul>
  18. 18. Mutarotation : equilibrium between alpha and beta forms Anomeric : linear = non-chiral, ring's C1 = chiral (E.G., fructose) Anomers
  19. 19. Bonds to Know <ul><li>Maltose/Amylose : alpha(1-4) </li></ul><ul><li>Lactose/Cellulose : beta(1-4) </li></ul><ul><li>Sucrose : alphaDGlu-betaDFru </li></ul><ul><li>Amylopectin : alpha(1-4); branches: alpha(1-6) </li></ul><ul><li>Also know that all monosaccharides are reducing sugars because of OH on C1 (hemiacetal) </li></ul>
  20. 20. Love, Julie and Jenesha

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