5 Proteins (book)

• Berzelius suggested the name "protein".
• There are 20 amino acids that make up proteins, and they all gave the same basic structure, except for R group or the side chain they have.
• Proteins are the building blocks of the cell which constitute the majority of its dry mass.

  • They are the product of nucleic acid transcription and translation
  • Expresses the ultimate impact of the data processed and produced by nucleic acid
• Martin and Synge developed chromatography, a technique which is now widely used to separate proteins
• Mann, Aebersold, Yates, and others developed effective methods for the use of mass spectrophotometry to identify proteins in complex mixtures, and exploited the availability of complete genome sequences
• Proteins are biochemical molecules made up of covalently linked amino acid residues and carboxyl groups combined by peptide bonds.
• Amino acid are the basic building blocks of proteins

  • They have and amino group bonded directly to the alpha-carbon, referred to as alpha-amino acids
• Alpha-amino acid has a carbon atom, called an alpha carbon, C' bonded to a carboxylic acid, –COOH group; an amino, –NH2 group; hydrogen atom; and an R group that is unique to each amino acid
• Amino acids are grouped accordingly based on the nature of their R group
• Amino acids are connected to other amino acids by an amide bond, referred as a peptide bond.
• Peptides are continuous connection of several amino acids by an amide bond
• Polypeptides are long linear chains formed by combination of amino acids
• Essential amino acids are the amino acids you need through your diet, because your body cannot make them
• Non-essential amino acids are those that can be synthesized by the body and need not be provided by your diet
• Primary structure of protein is the simplest level of structure of proteins that shows a linear sequence of amino acids.

  • e.g., Insulin
• Secondary structure of protein applies to local folded proteins that occur inside a polypeptide due to atom interactions

  • e.g., alpha-helix and beta-pleated sheet
• Tertiary structure of protein is the 3D framework of the polypeptide; structure is mainly due to interactions between R classes of amino acid sequence of the protein

  • e.g., Hydrophobic interactions, hydrogen bonds, and sulfur bridges
• Quaternary structure of protein refers to association of two or more polypeptides into a multi-subunit complex or the assembly of individual polypeptides into a larger functional cluster

  • e.g., Hemoglobin
• The function of a protein depends on its 3D structure

  • each are specific and determined by the sequence of amino acids in its polypeptide chain
• All molecules of any proteins species have a single conformation (or the native state), which is the molecule's most stable folded form
• Proteins fold into a conformation of the lowest energy
• Energetic factors determine the ultimate folded structure or conformation employed by any polypeptide chain
• Fibrous proteins are those with thread-like shapes, they tend to have structural or mechanical functions; water-insoluble
• Globular proteins are those with spherical shapes, they operate as enzymes, carry proteins, or antibodies; water-soluble
• Simple proteins are proteins that contain only amino acid residues
• Conjugated proteins contain amino acid residues + other organic or inorganic components referred to as the prosthetic group
• Conjugated proteins

  • Nucleoproteins - nucleic acids [viruses]
  • Lipoproteins - lipids [fibrin, serum lipoproteins]
  • Glycoproteins - carbohydrates [gamma globulin, mucin]
  • Phosphoproteins - phosphate groups [casein]
  • Hemoproteins - heme [hemoglobin, myoglobin, cytochromes]
  • Metalloproteins - iron [ferritin, hemoglobin] or zinc [alcohol dehydrogenase]
• A newly synthesized polypeptide chain must undergo folding and often chemical modification to produce desired protein.
• Denatured proteins loses its higher-order structure, but not its primary sequence; usually non-functional
• Denaturation is the loss of structural integrity with associated loss of activity
• Heat and UV light disrupts hydrogen bonds and ionic attractions by making molecules vibrate too violently; produce coagulation, as in cooking an egg.
• Organic solvents disrupts hydrogen bonds in proteins and probably form new ones with the proteins
• Strong acids/bases also disrupt hydrogen bonds and ionic attractions.

  • Prolonged exposure = hydrolysis of proteins
• Detergents disrupt hydrogen bonds, hydrophobic interactions, and ionic attractions
• Heavy metal ions form bonds to thiol groups and precipitate proteins as insoluble heavy metal salts
• Renaturation is a process where protein often refolds spontaneously into its original confirmation when the denaturing solvent is removed.
• Error in protein plating can cause harm to cells and even to whole tissue as aggregates are created
• Chaperone protein is a unique protein that supports the protein folding in a living cell

  • simply creates the folding process more effective and safer
  • some attaches to partially folded chains and assists them to fold along the most substantial favorable pathway
  • other creates isolation compartments in which single polypeptide chains can fold in the crowded cytoplasm conditions without the fear o4f forming aggregates
• Abundant proteins with many secondary structures may need assisted folding to avoid aggregation of unfolded proteins
• Chaperonins functions mainly to prevent the aggregation of unfolded protein