unit one

• enzymes serve as catalysts, increasing the rates of chemical reactions
• structural proteins -- physical support and shape
• motility proteins -- contraction and movement
• regulatory proteins - control and coordinate cell function
• transport proteins - move substances into and out of cells
• signaling proteins - communication between cells
• receptor proteins - enable cells to respond to chemical stimuli from the environment
• defensive proteins - protect against disease
• storage proteins - reservoirs of amino acids
• all proteins are polymers with common structural characteristics
• Only 20 kinds of amino acids are used in protein synthesis. No two different proteins have the same amino acid sequence. Every amino acid has the same basic structure
• L amino acids are not used to build proteins
• which of the non-polar amino acids is the only amino acid that does not have separate L and D isomers?

  Glycine
• Glycine does not have separate L and D isomers because the R group is just an H, meaning it is achiral
• nonpolar amino acids: in the center of the protein, interact with each other and not with aqueous surroundings. predominant in transmembrane domain
• polar and ionic amino acids: outer edges of protein structure - interact with water
• amino acids are linked together stepwise into a linear polymer by dehydration (or condensation) reactions. As the three atoms comprising the H2O are removed, a covalent C-N bond (a peptide bond) is formed
• which of these represents an important distinction between a polypeptide and a protein?

  (a.) there is no difference. the terms are interchangeable.

  (b.) "protein" implies function while "polypeptide" is a structural term.

  (c.) proteins are always made of multiple polypeptides.

  (d.) a polypeptide has multiple protein subunits

  b. protein implies function, while polypeptide is a structural term
• multimeric proteins consist of multiple polypeptide. e.g. dimers, trimers, tetramers
• both covalent bonds and noncovalent interactions are needed for a protein to adopt its proper shape or conformation. these same bonds and interactions are required for polypeptides to form multimeric proteins. the interactions involve carboxyl, amino and R groups of the amino acids, called amino acid residues once incorporated into a polypeptide
• in the cell

  noncovalent: reversible

  covalent: non reversible, require specific rxns and enzymes to break
• the primary structure of a protein is a sequence of amino acids linked together by peptide bonds, forming a polypeptide
• secondary structure: local regions of the resulting polypeptide can then be coiled into an alpha-helix or beta pleated sheet
• regions of secondary structure associated in a specific manner to form the tertiary structure, which describes the final folding of the polypeptide
• the quaternary structure describes the association of two or more polypeptides as they interact to form a functional multimeric protein
• the importance of primary structure

  • primary structure is important genetically because the sequence is specified by the order of nucleotides in the corresponding messenger RNA
  • primary structure is always read from N terminus to C terminus (the same order the polypeptide was assembled)
• secondary structure

  • the secondary structure of a protein describes local regions of structure that result from hydrogen bonding between NH and CO groups along the polypeptide regions
  • these result in two major patters, the alpha helix and beta sheet
• the alpha helix

  • the alpha helix is spiral in shape, consisting of the peptide backbone, with R groups jutting out from the spiral
  • a hydrogen bond forms between the NH group of one amino acid and the CO group of a second amino acid that is one turn away from the first
  • the amino acid on one turn is attached to an amino acid on the next
  • often have hydrophobic R groups on outside of the helix, embedded in the center of the protein and form transmembrane domains
• the beta-sheet

  • the beta-sheet is an extended sheetlike conformation with successive atoms of the polypeptide chain located at peaks or troughs
  • can be parallel or anti-parallel
  • flat stretches of polypeptides that line up along each other
• proline is referred to as the helix breaker because it lacks the hydrogen atom needed for hydrogen bonding
• tertiary structure

  • reflects the unique aspect of the amino acid sequence because it depends on interactions of the R-GROUPS
  • neither repetitive nor easy to predict
  • results from the sum of hydrophobic residues avoiding water, hydrophilic residues interacting with water, the repulsion of similarly charged residues, and attraction between oppositely charged residues
• fibrous proteins have extensive regions of secondary structure, giving them a highly ordered, repetitive structure

  e.g. fibroin produces silk and is made predominantly of beta-sheets
• many alpha helices that intertwine =

  coiled coil
• • most proteins are globular proteins that are folded into compact structures
  • each type of globular protein has its own unique tertiary structure
  • most enzymes are globular proteins
  • secondary structure is a combination of alpha-helices and beta-sheets, not one or the other
• • the quaternary structure of a protein is the level of organization concerned with subunit interactions and assembly
  • the term applies specifically to multimeric proteins
  • some proteins consist of multiple identical subunits; others such as hemoglobin, contain two or more types of polypeptides
  • the bonds and forces maintaining quaternary structure are the same as those responsible for tertiary structure
• which component of DNA is responsible for the acidic part of nucleic acid?

  the phosphate group
• nucleic acids are of paramount importance to the cell because they store, transmit, and express genetic information

  • they are linear polymers of nucleotides
• protein domains

  • some monomeric proteins
  • multiple functions
  • commonly regulatory or catalytic
  • one polypeptide but two distinct structural domains
• nucleotides with one phosphate group can be thought of as nucleoside monophosphates

  • adenosine diphosphate (ADP) has two phosphate groups and adenosine triphosphate (ATP) has three
• • nucleic acids are linear polymers of nucleotides linked by a 3'-5' phosphodiester bridge, a phosphate group linked to two adjacent nucleotides via two phosphoester bonds
  • the polynucleotide formed by this process has a directionality with a 5' phosphate group at one end and a 3' hydroxyl group at the other
  • nucleotide sequences are conventionally written in the 5' to 3' direction