Final Flashcards
what is electronegativity
a measure of the force of an atoms attraction for electrons it shares in a chemical bond with another atom
a compound that contains both an amino group and a carboxyl group
amino acid
what gives identity to an amino acid
the R group
pKa value of the carboxylate group
2.3
pKa value of the amino group
9.5
what determines the 3D conformation of a protein
its primary structure
hemoglobin associated with sickle cell anemia is an example of what
how a change in just one amino acid in a proteins primary structure can alter biological function
where does free rotation occur in the secondary structure of a protein
- between the alpha carbon and amino nitrogen
- between the alpha carbon and carboxyl carbon
Why is there no rotation around the omega (ω) bond in a peptide?
the bond between the carbonyl oxygen and the amide nitrogen has partial double bond character due to a small electric dipole
where do all R groups point from the alpha helix
outward; they are found on the outside of the helical spiral
where does each carbonyl oxygen of the peptide bond to
forms a hydrogen bond with the amide hydrogen (N–H) of the fourth amino acid ahead in the sequence.
what stabilizes an alpha helix
the hydrogen bonds that run parallel to the axis
what amino acids are common in alpha helices
alanine, leucine and methionine
which amino acid is known as a helix breaker
proline
how does proline disrupt an alpha helix
creates a bend due to its cyclic structure and has no amino hydrogens for bonding
which amino acids would cause steric crowding due to the proximity of bulky side chains
ser, val, leu, ile, thr, cys and asn
where do the C=O—-H-N bonds lie in an alpha helix
parallel to the helical axis
where do the C=O—-H-N bonds lie in an beta pleated sheet
between adjacent sheets and perpendicular to the direction of the sheet
alpha helices and beta pleated sheets are apart of what structure
secondary
when do beta turns occur
when the peptide forms a tight loop with the carbonyl oxygen forming a hydrogen bond with the amide proton of the amino acid 3 positions down the chain
what amino acids are commonly found in beta turns
glycine and proline
why is proline common in beta turns
the cyclic amino acid produces a bend or kink in the amino acid sequence
why is glycine common in beta turns
small and easily adaptable to the steric constraints of the turn
types of supersecondary structures
beta-alpha-beta
alpha-alpha
beta-meander
greek key
beta-barrel
