LM1 proteins Flashcards
describe a peptide bond
condensation reaction of the alpha carboxyl group of one amino acid with the alpha amino group of another
what is an amino acid residue
an amino acid that is part of a polypeptide chain
how are peptide chains named
from the n-terminus to the c-terminus
why are the n and c termini always charged
n-terminus is always positively charged as pH<pKa>pKa</pKa>
why is rotation around the C-N bond in a peptide bond limited?
due to the double bond nature of the resonance hybrid form peptide group bonds are therefore planar
describe the conformation of a peptide bond
they have some double properties so they are planar and their conformation is restricted to either cis or trans but the cis conformation is less favorable due to steric clashes
what amino acid may have both cis and trans peptide bonds
proline
what is the phi angle
the bond between nitrogen and the alpha carbon
what is the psi angle
the bond between the alpha carbon and carboxyl carbon
why is rotation around bonds restricted
steric clashes between main and side chain atoms
what is the Ramachandran diagram
shows possible combinations of phi and psi angles when steric clashes between atoms are absent or minimized
define protein conformation
3D shape
define native conformation
each protein folds in to a single stable shape
What does the biological function of a protein depend on
its native conformation
describe the alpha helix
each C=O residue (n) forms a hydrogen bond with residue n+4 amide. The helix is stabilised by many hydrogen bonds which are nearly parallel to the axis
what are some distinctive features of an alpha helix
all C=O groups point towards the c-terminus
3.6 amino acids per turn
right handed helices are most abundant
define beta strands
polypeptide chains that are almost fully extended
define a beta sheet
multiple beta strands arranged side by side and are stabilised by hydrogen bonds between C=O and N-H on adjacent strands
describe hydrogen bonding in parallel beta sheets
the NH group is hydrogen bonded to the CO group of one amino acid on the adjacent strand
whereas the CO group is hydrogen bonded to the NH group on the amino acid two residues away
Describe the hydrogen bonding in antiparallel beta sheets
the hydrogen bonds are nearly perpendicular to the chain
describe the side chains on beta chains
side chains project alternately above and below the plane of the beta strands, one surface of a beta sheet may consist of hydrophobic side chains and then can interact with other hydrophobic residues
what is the purpose of loops and turns
they connect alpha helices and bet strands and allow a peptide chain to fold back on itself to make a compact structure
describe loops
often contain hydrophilic residues and are found on protein surfaces
describe turns
loops containing 5 residues or less often containing glycine
what is a super secondary structure (motif)
recurring protein structures
give examples of super secondary structures
helix loop helix
coiled coil
helix bundle
beta alpha beta unit
hairpin
beta meander
greek key
beta sandwich
beta barrel
describe globular proteins
usually water soluble compact and roughly spherical
describe fibrous proteins
provide mechanical support and often assembled into large cables or threads
for example alpha keratin and collagen
describe a reverse turn
a CO group of residue i is hydrogen bonded to the NH group of i+3 residue to stabilise the turn
define domain
independently folded compact units in proteins 25-300 residues in size and illustrates the evolutionary conservation of protein structure
define primary structure
sequence of amino acids joined by an amide bond
define secondary structure
alpha helices and beta strands stabilised by hydrogen bonds
define tertiary structure
3 D structure
define quaternary structure
made of more than one polypeptide subunit
what is a heptad repeat
found in alpha keratin - where every 7th amino acid is repeated e.g. leucine
define denaturation
loss of native 3D protein structure and results in a loss of biological function
What can denaturation be caused by
increase in temperature
extreme pH - leads to a lot of repulsion as side chains are either protonated or deprotonated
denaturing substances such as urea or guanidium chloride
what substance can reduce disulfide bridges
beta mercatoethanol
define nucleation
preference for native structure drives folding
