Proteins

Cards (147)

  • 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)