Biochemistry protein

• Protein


  A naturally-occurring, unbranched polymer in which the monomer units are amino acids
• Proteins are the most abundant molecules in cells after water - account for about 15% of a cell's overall mass
• Elemental composition of proteins

  • Carbon (C)
  • Hydrogen (H)
  • Nitrogen (N)
  • Oxygen (O)
  • Sulfur (S)
• The average nitrogen content of proteins is 15.4% by mass
• Proteins also contain Iron (Fe), phosphorus (P) and some other metals in some specialized proteins
• Amino acid


  An organic compound that contains both an amino (-NH2) and a carboxyl (-COOH) group attached to the same carbon atom
• Amino acids


  • The position of the carbon atom is Alpha (a)
  • The -NH2 group is attached at the alpha (a) carbon atom
  • The -COOH group is attached at the alpha (a) carbon atom
  • The R = side chain varies in size, shape, charge, acidity, functional groups present, hydrogen-bonding ability, and chemical reactivity

  
• There are over 700 amino acids known
• Standard amino acids


  • 20 standard amino acids based on common "R" groups

  
• Groups of standard amino acids based on R-group properties

  • Non-polar amino acids
  • Polar neutral amino acids
  • Polar acidic amino acids
  • Polar basic amino acids

  
• Non-polar amino acids


  1. groups are non-polar, hydrophobic (insoluble in water), located in the interior of proteins

  
• Polar neutral amino acids

  1. groups are polar but neutral

  
• Polar acidic amino acids

  1. groups contain carboxyl group

  
• Polar basic amino acids

  1. groups contain amino group

  
• Nomenclature of amino acids

  Common names, three letter abbreviations, one letter symbols

  
• Non-polar amino acids

  • Alanine (Ala, A)
  • Valine (Val, V)
  • Leucine (Leu, L)
  • Isoleucine (Ile, I)
  • Proline (Pro, P)
  • Phenylalanine (Phe, F)
  • Tryptophan (Trp, W)
  • Methionine (Met, M)

  
• Polar neutral amino acids

  • Serine (Ser, S)
  • Threonine (Thr, T)
  • Cysteine (Cys, C)
  • Tyrosine (Tyr, Y)
  • Asparagine (Asn, N)
  • Glutamine (Gln, Q)
  • Histidine (His, H)

  
• Polar acidic and basic amino acids

  • Aspartic acid (Asp, D)
  • Glutamic acid (Glu, E)
  • Lysine (Lys, K)
  • Arginine (Arg, R)

  
• Essential amino acid

  A standard amino acid needed for protein synthesis that must be obtained from dietary sources - adequate amounts cannot be synthesized in the human body
• Essential amino acids

  • Arginine*
  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine
  • Phenylalanine
  • Threonine
  • Tryptophan
  • Valine

  
• Arginine is required for growth in children and is not essential for adults
• Chirality


  19 of the 20 standard amino acids contain a chiral center - molecules with chiral centers exhibit enantiomerism (left- and right-handed forms)

  
• The amino acids found in nature as well as in proteins are L isomers, while bacteria do have some D-amino acids</b>

  
• Rules for drawing Fischer projection formulas for amino acid structures

  • The -COOH group is put at the top
  • The R group is placed at the bottom position of the carbon chain vertically
  • The -NH2 group is placed in a horizontal position
  • Positioning -NH2 on the left - L isomer
  • Positioning -NH2 on the right - D isomer

  
• Zwitterion


  An ion with + (positive) and - (Negative) charges on the same molecule with a net zero charge
• Amino acids in solution exist in three different species (zwitterions, positive ion, and negative ion) - Equilibrium shifts with change in pH
• Isoelectric point (pI)

  The pH at which the concentration of Zwitterion is maximum - net charge is zero
• Cysteine

  • The only standard amino acid with a sulfhydryl group (-SH group)
  • The sulfhydryl group allows cysteine to dimerize to form cystine via a covalent disulfide bond

  
• Peptide

  An unbranched chain of amino acids bonded together
• Peptide bond


  The covalent bond between amino acids in a peptide
• Types of peptides based on length

  • Dipeptide (2 amino acids)
  • Oligopeptide (10-20 amino acids)
  • Polypeptide (large number of amino acids)
• Peptide nomenclature


  The C-terminal amino acid keeps its full name, all other amino acids have names ending in -yl, the sequence begins at the N-terminal

  
• Peptides that contain the same amino acids but in different order are different molecules (constitutional isomers) with different properties
• Biochemically important small peptides

  Hormones, neurotransmitters, antioxidants
• Examples of small peptide hormones

  • Oxytocin
  • Vasopressin
• Examples of small peptide neurotransmitters

  • Met-enkephalin
  • Leu-enkephalin
• Glutathione


  A tripeptide antioxidant (Glu-Cys-Gly) that protects cells from oxidizing agents
• Protein


  A peptide in which at least 40 amino acid residues are present
• Several proteins with >10,000 amino acid residues are known, common proteins contain 400-500 amino acid residues, and small proteins contain 40-100 amino acid residues

  
• Monomeric protein

  Contains one polypeptide chain