BCH- Week 3 Flashcards
What are the four levels of protein structures?
primary- linear sequence
secondary- alpha helix and n=beta sheets
teritary- folded into motifs and domain due to noncovalent interactions
quaternary- assembly of distinct polypeptides into multisubunit structures
What are the three themes of protein structure?
1- the 3D structure must me flexible enough to function properly
2- 3D structure must be stable enough to not convert into another conformation
3- the exposed amino acids must be compatible with the environment where protein is
What make up the primary structure and how is it formed?
primary structure consist of amino acids joined enzymatically in condensation reaction and teh polypeptide chain formed has directionality and the peptide bonds that join the amino acids are polar and uncharged bonds that experience resonance
What are the angles found in the primary sequence that allow peptide bond rotation
the phi is rotation ranging from -180 to +180 around bond linking amide to alpha carbon
the psi is rotation ranging from -180 to +180 around bonds linking carbonyl to alpha carbon
the omega rotation is restricted to 180
What are the characteristics of alpha helices in secondary structure
they are stable coils of proteins which are formed by the intra strand H-bonds forming between peptide backbone and these H-bonds form between negative dipole of carboxyl group of one amino acid with the positive dipole of amino group of another amino acid 4 residues away
How is the hydrogen bonding in beta sheets different from alpha helices
the hydrogen bonding links neraby or distant proportions of polypeptides to beta strands forming beta sheets and the hydrogen bonding will still occur between carbonyls and amines in peptide backbone and the strands may run parallel or antiparallel or mixed directionality and larger amino acids prefer beta sheets because there is more room for them
Why is proline not found in alpha helices, and if found thne at the end of the sequence?
that is becaise it is very rigid and doesn’t allow proper phi and psi angle to form in the coil and also because there is no H present on nitrogen of peptide bond to form H-bond
What is a beta turn, also known as reverse turn
a 4-residue segment that allows peptide chains to teun 180 degrees and is found on surface of globular proteins and the H-bonds in here form between carbonyl oxygen and amine hydrogen of peptide backbone
what are the noncovalent interactions found in teritary structure
electrostatic interactions- salt bridge between charged groups on different amino acids
hydrogen bonding- interaction between amino acids between the partial charges on hydrogen and partial negative charge on other atoms
hydrophobic interactions- grouping of non polar amino acids
What are some common motifs?
coied coil, helix bundle, beta-alpaha-beta unit, hairpin, greek key, and beta barrel, and zinc finger
proteins with similiar functions can have similiar domains
how do chaperons help with protein folding
they will prevent teh aggregation of newly sunthesized and unfolded proteins by binding to exposed hydrophobic regions
what are some types of protein structures
globular proteins, fibrous proteins, and transmembrane proteins
what makes the antibody distinict
the variable regions
what is teh fate of protein that fold incorrectly
either degraded by proteasome or lysosome or aggregate and result in disease
What is teh difference between the PrP^c and PrP^sc
they are both stable prion proteins but the correct one that is supposed to be the result of the folding is the PrP^c form which consist of alpha helices and when it gets misfold it be becomes PrP^sc which consist of beta sheets and if this misfold form aggregate with the PrP^c, it will cause the normal one to also misfold in to PrP^sc
