Biochem Midterm

• Protein


  Naturally occurring, unbranched polymer in which the monomer units are amino acids
• Protein


  • Contains 40 and up amino acids
• COOH


  Acid part, put at the top of the Fischer projection, attached to alpha carbon
• NH2


  Basic part, basis of L and D isomer, attached to alpha carbon
• R group or side chain


  Unique in every amino acid, located at the bottom of Fischer projection
• Amino acids


  • 20 standard amino acids
  • 19 are chiral
  • Glycine is the only amino acid that is not chiral
• Zwitterion


  An ion with + (positive) and - (Negative) charges on the same molecule with a net zero charge
• Isomeric Peptides


  Peptides that contain the same amino acids but present in different order are different molecules
• Cysteine


  The only standard amino acid with a sulfhydryl group (-SH group)
• Cystine


  Two cysteine residues linked via a covalent disulfide bond
• Peptide Nomenclature

  • End in -yl, replacing the -ine or -ic acid ending
• Enkephalins


  Pentapeptide neurotransmitters produced by the brain, bind receptor within the brain, help reduce pain
• Glutathione


  Protects cellular contents from oxidizing agents such as peroxides and superoxides, regulates the oxidation-reduction process
• Simple proteins


  A protein in which only amino acid residues are present
• Conjugated protein


  A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure
• Types of conjugated proteins

  • Lipoproteins (contain lipid prosthetic groups)
  • Glycoproteins (contain carbohydrate groups)
  • Metalloproteins (contain a specific metal as prosthetic group)
• Protein structure levels


  • Primary Structure (order and sequence of amino acids)
  • Secondary Structure (backbone - alpha-helix, beta-pleated)
  • Tertiary Structure (3D structure, interactions)
  • Quaternary Structure (combination of 2 or more subunits)
• Interactions stabilizing protein structure

  • Disulfide bond (between two cysteine groups)
  • Electrostatic interactions (between charged side chains)
  • H-Bonding (with O, N or F)
  • Hydrophobic interactions (between non-polar side chains)
• Types of amino acids

  • Non-polar (hydrophobic/water-fearing)
  • Polar (hydrophilic/water-loving)
  • Polar acidic (with carboxyl group)
  • Polar basic (with amino group)
• Alpha-Keratin


  Provide protective coating for organs
• Collagen


  Most abundant proteins in humans (30% of total body protein), organic component of bones and teeth
• Myoglobin


  An oxygen storage molecule in muscles
• Hemoglobin


  An oxygen carrier molecule in blood, transports oxygen and specialized protein because it is composed of elements with additional component of Iron (Fe)
• Protein functions

  • Catalytic (enzymes)
  • Defense (immunoglobulins/antibodies)
  • Transport (bind small biomolecules)
  • Messenger (transmit signals)
  • Contractile (actin and myosin)
  • Structural (confer stiffness and rigidity)
  • Transmembrane (have channels)
  • Storage (bind and store small molecules)
  • Regulatory (act as sites for receptor molecules)
  • Nutrient (particularly important in early life)
• Hydrolysis


  Results in the generation of an amine and a carboxylic acid functional groups
• Nucleic Acids


  Polymers in which repeating unit is nucleotide
• Nucleotide components


  • Pentose Sugar (monosaccharide)
  • Phosphate Group (PO43-)
  • Heterocyclic Base (total 5 bases)
• Heterocyclic bases

  • Uracil (U, found only in RNA)
  • Thymine (T, found only in DNA)
• Sugar-phosphate groups


  Referred to as nucleic acid backbone
• Base composition


  %A = %T and %C = %G
• Complementary bases


  A=T and G=C
• Ribonucleic acid (RNA)


  Nucleotide polymer in which each monomer contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil
• Deoxyribonucleic acid (DNA)


  Nucleotide polymer in which each monomer contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine
• Replication


  DNA molecules produce exact duplicates of themselves
• Topoisomerase (DNA Gyrase)


  Removes the supercoiled part of the DNA
• Helicase


  Breaks the hydrogen bonds
• Single strand binding (SSB) proteins


  Stabilizes the strands, preventing it from getting back together
• DNA primase


  Creates RNA primer (RNA primer starts or initiates the action)
• DNA Polymerase III


  Adds nucleotide to the sequence
• Lagging strand


  Causes fragments known as Okazaki fragment