Lecture 9: The Structure of Proteins Flashcards
the sequence of amino acids is specified by the __ sequence encoding the protein
gene
amino acid polymers of less than 50 amino acids are called __
peptide
a peptide bond is formed between which two groups in a peptide chain?
carboxyl group of the first and the amino group of the second
the H and R groups are opposite the ___ in a peptide bond to avoid steric clash
o in the carbonyl
the equilibrium of making a peptide bond favours the ___ side
left (hydrolysis)
why does the peptide equilibrium favour the hydrolysis rather than synthesis?
because the synthesis requires free energy
the alpha carbon can always be identified because it has the ___ attached to it
R group
each amino acid in a peptide chain is called a __
residue
every peptide chain begins with a ___ residue and ends in a __ residue
amino, carboxyl
the amino acid at the beginning of the chain is called the __
amino / N terminus
the amino acid at the end of the chain is called the __-
carboxly / C terminus
the geometry of an aa about a peptide bond is __
planar
what makes the peptide bond rigid? (not free to rotate)
resonance from the carboxyl makes the bond not purely single and therefore unable to freely rotate
the psi and phi bonds flank the ___ of each amino acid
alpha carbon
what bonds are free to rotate in amino acids?
the phi and psi bonds
the phi bond forms between the alpha carbon and the
amino group
the psi bond forms between the alpha carbon and the
carbonyl group
what does a Ramachandron plot show?
the permissible phi and psi bond angles allowed in a polypeptide backbone
the range of permissible angle combinations reflect the ___ and ___structure of proteins
secondary and tertiary
the polypeptide structure will have inherent __ and ___ within the constraints dictated by the permissible angles
flexibility and mobility
the secondary structure of proteins is stabilized by __ bonds between N and carboxyl groups in linear squence
H bonds
due to combination of bond angles and H bonding effects, certain aa segments ____ form secondary structures
spontaneously
what are the 3 types of secondary structures?
aplha helix , beta sheets, turns and loops