Imported Notes

• Proteins

  Mediate almost every process of the cell
• Proteins


  • They are the most abundant biological macromolecule
  • They occur in all cells and in all cell parts
  • Great variety of proteins
  • They are the molecular instruments through which genetic information is expressed
• Cells

  Produce a wide variety of proteins using only 20 amino acids
• Enzymes


  The most varied and specialized proteins
• In every living organism, proteins are constructed from a common set of 20 amino acids
• Amino acids

  • Each has a side chain with distinctive chemical properties
  • May be regarded as the alphabet through which the language of protein structure is written
• Amino acids in proteins

  They are joined with a characteristic linear sequences through a common amide linkage, the peptide bond
• Primary structure of proteins

  The amino acid sequence
• For study, individual proteins can be separated from the thousands of other proteins present in a cell, based on their differences in their chemical and functional properties arising from their distinct amino acid sequences
• Purification of individual proteins for study is essential as proteins are central to biochemistry
• Amino acid sequences are a key resource for understanding the function of individual proteins and tracing broader functional and evolutionary relationships
• Proteins


  They are polymers of amino acids, where each amino acid is joined by a covalent bond
• Proteins can be hydrolyzed to their constituent amino acids by a variety of methods
• Twenty amino acids are commonly found in proteins
• Asparagine was discovered first


  1806
• Threonine was discovered last


  1936
• Amino acids

  • They have a carboxyl group and an amino group bound to an alpha carbon
  • Side chains, or R groups, are what varies in amino acids
• There are more than the 20 common amino acids
• Amino acid identification

  • Each amino acid is identified by a three and one letter code
  • The one letter code was devised by Margret Oakly Dayhoff, one of the founders of bioinformatics
  • The other letter code is an attempt to reduce the size of data files
  • It was designed to be easily memorized
• Amino acid one letter codes

  • CHIMSV - first letter is unique and used as symbol
  • AGLPT - first letter not unique, used symbol of most common
  • RFYW - letters phonetically suggestive
  • DNEQ - letters found within or suggested by their names
  • Lysine assigned K
• Alpha carbon


  • For amino acids, the additional carbons in the R group are commonly designated beta, gamma, delta, epsilon, etc preceding from the alpha carbon
  • In heterocyclic R groups, like lysine, the numbering system is also used
• Alpha carbon


  • For all amino acids, except glycine, the alpha carbon is bonded to four different groups
  • This makes the alpha carbon a chiral center
  • The four bonds gives a tetrahedral arrangement
  • The four different groups occupy two unique spatial arrangements and have two stereoisomers, or enantiomers
  • They are all optically active
• D, L system

  • Special nomenclature developed to study the absolute conformation of the four subsitituents of the alpha carbon
  • Based on the absolute conformation of the 3 carbon sugar glyceraldehyde, a convention proposed by Emil Fischer in 1891
• For all chiral compounds, stereoisomers related to L-glyceraldehyde are labeled L and those related to D-glyceraldehyde are labeled D
• L and D

  • Historically used to signify levorotatory (rotating to the left) or dextrotatory (rotating to the right)
  • Not all L-amino acids are levorotatory
  • L and D only refer to the absolute configuration of the substitutents, not the optical properties
• RS system


  Describes systemic nomenclature of organic chem and more precisely describes the configuration of molecules with more than one chiral center
• The amino acid residues in proteins are almost all L stereoisomers
• D stereoisomers in proteins

  • Less than 1% are found in D conformation
  • Introduced to a protein by an enzyme catalyzed reaction that occurs after protein synthesis (translation)
• In most chemical reactions, there is a racemic mixture of D and L isomers
• Cells are able to specifically synthesize the L isomers of amino acids because the active sites of enzymes are asymmetric, causing the reaction they catalyze to be stereospecific
• Nonpolar aliphatic amino acids

  • Glycine, Gly, G
  • Alanine, Ala, A
  • Proline, Pro, P
  • Valine, Val, V
  • Leucine, Leu, L
  • Isoleucine, Ile, I
  • Methionine, Met, M
• Aromatic amino acids

  • Phenylalanine, Phe, F
  • Tyrosine, Tyr, Y
  • Tryptophan, Trp, W
• Polar amino acids

  • Serine, Ser, S
  • Threonine, Thr, T
  • Cysteine, Cys, C
  • Asparagine, Asn, N
  • Glutamine, Gln, Q
• Positively charged amino acids


  • Histidine, His, H
  • Arginine, Arg, R
  • Lysine, Lys, K
• Negatively charged amino acids

  • Aspartic acid, Asp, D
  • Glutamic acid, Glu, E
• Lambert-Beer law


  Relates the fraction of incident light absorbed by a solution at a given wavelength to the thickness of the absorbing layer (path length) and the concentration of the absorbing species
• Tryptophan absorbs light at 280nm
• Spectrophotometry


  Measurement of light absorption is used to detect and identify molecules and to measure their concentration in solution
• Lambert-Beer law

  I0 is the intensity of the incident light, I is the intensity of the transmitted light, I/I0 is the transmittance, Epsilon is the molar extinction coefficient, c is the concentration of the absorbing species, l is the path length of the light absorbing sample
• Absorbance


  The expression log(I0/I), it is directly proportional to the concentration of the absorbing solute