Proteins

• How are peptides obtained?

  Proteolysis of proteins and direct synthesis
• How are peptides formed?

  Amino acids bound by condensation and the peptide bond can be broken by hydrolysis
• How can we count and name peptides?


  Start from amino terminus and end at the carboxyl terminus. When naming you can use the full amino acid names , three letter code or Letters
• What are properties of peptides?

  Is not ionized but presents partial charges , is a resonance hybrid of two canonical structures (planar) and therefore is more stable and less reactive (rigid bond).
• What are the types of rotations that occur on the peptide bond?

  Phi: Around the alpha carbon-amide nitrogen bond

  Psi: Around the alpha carbon - carbonyl carbon bond

  (substituents are usually trans) (In a fully extended peptide both phi and psi are 180)
• What is a Ramachandran plot?

  A plot with the distribution of the angles found in a proteins and it shows common pattern
• What is the alpha helix?


  a secondary structure present in alpha keratins and in many globular proteins
• How to identify a left or right-handed helix?

  look at one loop (one section) and if its from left-right then its right handed. IF its from right to left then left handed
• What are parameters of the helix?

  N = number of monomers in a full turn (3.6aa)

  P = distance between two equivalent points (5.4Å)

  D = How helix moves in respect to each monomers (1.5Å)
• What does it mean if P is small?

  If p is small then there is more space
• What is the backbone structure?

  All c=o and N-H of peptide bonds are involved in a hydrogen bond at 4 aa of distance. Only amino acid and carboxyl terminus are not involved in hydrogen bonds. Hydrogen bonds are parallel with the helix axis.
• What are characteristics of the side chains in the alpha chain?

  The R point out and are perpendicular with helical axis

  Restrictions due to R will depend on: Electrostatic repulsion , volume of adjacent R , presence of proline
• How does proline affect the alpha helix chain?

  Acts as an alpha helix breaker because the rotation around the N-C alpha bond is impossible. Can also form cis peptide bonds (most present in Beta turns). Proline isomerase is the enzyme responsible for the reaction.
• What are alpha keratins?


  Filament forming protein produced by the skin
• What are the characteristics of alpha keratins?

  Rich in ala ,leu , arg and cys

  Two right-handed alpha-helix form a left-handed coiled coil bound by disulphide bonds

  Dimers align to form a protofilament also bound by disulphide bonds
• What are the characteristics of the beta sheet?

  Present in B keratins and in many globular proteins , pleated sheet , side chains point out from the sheet alternating in up and down direction. Held by its bonds between C=O and N-H of different strands
• What are the arrangements of the B sheets?

  Antiparallel: Sheets run opposite, resulting in linear H bonds (strong)

  Parallel: Sheets run in same direction, resulting in bent H bonds.
• What are the characteristics of B keratins?

  Main component of feathers , silk

  Piled together in a compact way

  Ala and Gly are abundant in B keratins
• What are characteristics of B turns?

  Strands in B sheet change direction

  A 180 turn is obtained over 4 aa

  Turn is stabilized by a Hydrogen bond from a carbonyl oxygen to amide protein three residues down

  Pro in position 2 and gly in position 3
• What are the characteristics of collagen?

  Most abundant in nature , present in bones and cornea

  Sequences: triplets of glycine-x-y where x and y are frequently proline or hydroxyproline
• What is the structure of alpha chains?

  A left handed helix , Pro and Oh-pro are responsible for the turns , inner diameter of the helix is so small only the H or. gly fits into it
• What are the parameters of the alpha chains?

  N = 3 aa

  P = 9.3 Å

  d = 3.1 Å
• What is the structure of tropocollagen?

  Super helix with three strands folded in a right handed way. Bound together by H bonds between Co and NH from backbone of different chains (only gly)
• What are characteristics of the collagen fiber?

  Units of collagen (tropocollagen) pile up to form fiber and bound by covalent cross-links involving hydroxy-lysine
• What are proteins?

  Polymeric macromolecules comprising one or more polypeptide chains (>50 aa)
• What are conjugated proteins?

  proteins that derive part of their function from prosthetic groups. They have cofactors (Functional non-amino acid molecules) and prosthetic groups
• What is a holoprotein?

  Apoprotein + prosthetic group
• What are the functions of proteins?

  Catalysis , transport , structural and motion
• What are the characteristics of globular proteins?

  Quite compact , no knots in protein folding and 70% of polypeptide with some kind of secondary structure
• How do secondary structures combine?

  To form motifs and domains (a defined part of the protein)
• What are the forces in the tertiary structure?

  Tertiarys tructure is stabilized by many weak interactions. Disulfide bonds between two cysteines.
• What are the hydrophobic forces in tertiary structure?

  Apolar R are in the inner core of proteins and in membrane proteins also in the surface in contact with lipids.
• How are structure and function related in proteins?

  FUnction of proteins can be carried out by amino acids of the polypeptide chain and cofactors
• What is a structure and function of myoglobin?

  A monomeric oxygen binding proteins. Polypeptide chain (153aa) forms a globin domain with a prosthetic group (heme - iron)
• How does globin bind to oxygen?

  Heme (prosthetic group). The globin provides a chemical microenvironment and so heme can facilitate oxygen binding.
• How does the structure of heme allow for oxygen binding?

  Includes a histidine which stabilizes oxygen binding as well as hydrophobic amino acids which prevent Fe oxidation
• How can we protect heme from CO binding?

  CO binds to heme with more affinity than oxygen so the globin fraction diminishes CO affinity for heme
• How can protein structure be altered?

  Proteolysis or degradation (breaking peptide bonds) , modification of amino acids (phosphorylation) and changes in spatial arrangement
• How can a protein be denatured?

  heat or cold

  Extreme Ph

  Organic solvents

  chaoropic agents

  hydrochloride
• What happens when a protein is heated?

  weak forces of the protein can be altered bby moderate stress and melting the properties of protein change (Tm)