3 - 3D structure - 2ary structure Flashcards
why do peptide bonds have partial double bond character
resonance
what kind of rotation do amide bonds have
limited
what is the C=O distance in amide like relative to in typical carbonyl
LONGER
what is the C-N distance in amide like relative to typically
SHORTER
do peptide bonds have an electric dipole
yes but small
towards C=O from NH
what are the 2 main configurations of peptide bonds and what is most common
trans or cis (with respect to alpha carbon) - mostly trans
which aroms are all in a plane
6 atoms around the C-N peptide bond
how many m in an A
10^-10m
what are Phi (φ) and psy(ψ)
torsions describing rotation around alpha carbon bonds
what is Phi (φ)
bond from N to alpha carbon
what is psy(ψ)
bond from alpha carbon to C=O carbon
how many atoms define a torsion
4 - central 2 + 2 on other side
when are Phi (φ) and psy(ψ) defined as 0
when the two peptide bonds are flanking the alpha carbon when in same plane (atoms 1 and 4 are cis)
is 0,0 allowed conformation
no (steric hindrance)
which coordinates of phi (φ) and psy(ψ) are in the extended chaine
around 180 each
is it - or + if its a CW rotation of bond in back relative to bond in front
+
is it - or + if its a CCW rotation of bond in back relative to bond in front
-
which area of the ramachandran plot is beta sheet
top left
what is the x axis for ramachandran plot
Phi (φ)
what is the Y axis for ramachandran plot
psy(ψ)
what does blue mean on ramachandran plot
fully allowed conformation
what does green mean on ramachandran plot
at limit of unfavorable interaction
what is glycines ramachandran plot like and why
lots of allowable areas because there is no beta carbon so lots of flexibility
also asymmetrical because it is achrial
is phi or psy(ψ) more restricted in proline
Phi (φ) more restricted than psy(ψ) (Phi (φ) is between N-C which is in the cyclic side chain)
what are the phi (φ) and psy(ψ) in regular secondary structure
repeating angles for sequential amino acids, often similar angles
what are the phi (φ) and psy(ψ) in irregular secondary structure
non repeating angles
what are the H bonds like in regular secondary structure
stable forms have repeating H bonding patterns
what are the main types of regular secondary structures and another type
common: alpha helix beta sheet
also there are collagen helices
what are the types of irregular secondary structures
beta turns, coils, loops
where are alpha sheets usually in the ramachandran plot
more on the lower left
is alpha helix left or right handed
right
where are the H bonds in alpha helix
C=O of residue (i) to NH of residue (1+4)
which NH and C=O residues do not H bond
first 4 NH and last 4 C=O
where are the side chains in alpha helices
projecting away from core
how many residues per turn in alpha helix
3.6
how many A per turn in alpha helix
5.4
where is phi (φ) and psy(ψ) in alpha helix
near (-57, -47)
what stabilizes the atoms in the helix backbone (they are packed densely in the core)
van der waals and hydrogen bonding
how many residues apart in the alpha helix interact favourably (like close by in helix)
r groups 3-4 residues apart
what direction is the helix dipole
negative C terminal and positive N terminal
which a.a. are often found at the N terminus and why
negative ones (Asp, Glu) because of charge complementarity
which a.a. are often found at the C terminus and why
positive ones (Arg, Lys) because of charge complementarity
which direction is the dipole in the NH bond
H towards N (N is more negative)
which direction is the dipole in the C=O bond
C towards O (O is more negative)
what are the types of beta sheets
parallel, antiparallel, mixed
where is phi (φ) and psy(ψ) in parallel beta sheets
is it more or less extended
near (-120, +120) (less extended)
where is phi (φ) and psy(ψ) in antiparallel beta sheets
is it more or less extended
near (-140, +140) (extended)
what causes the formation of beta sheets (allows them to stay too)
H bonds between strands
are beta strands only from the same 1ary structure
yes but also can also come from different peptides
what does the H bonding pattern look like in antiparallel beta sheets
parallel couplets (2 then space, 2 then space…)
what does the N to C pattern look like in antiparallel beta sheets
they are oriented opposite to eachother
how can you determine N-C directionality
NRO is N-C
what does the N to C pattern look like in parallel beta sheets
they are oriented in same direction (N to C in both . directions)
what does the H bonding pattern look like in parallel beta sheets
they are not parallel, they are more diagonal looking
does antiparallel or parallel have more pronounced pleats
parallel (-120, +120) (not as extended)
does antiparallel or parallel have less pronounced pleats
anti parallel (-140, +140) (extended)
does antiparallel or parallel travel more distance
anti parallel (-140, +140) (extended)
does antiparallel or parallel travel less distance
parallel (-120, +120) (not as extended)
and beta sheets form between two subunits in a quaternary structure
yes-they dont need to have to follow eachother within primary sequence
are beta sheets planar
why or why not
no, they typically twist into saddle shapes or barrels
where are irregular 2 structures on the ramachandran plot
all different, not concentrated to a single location
what kind of structure are beta turns
irregular 2ary
what characterizes beta turns
backbone H bond
when are beta turns used
to change direction in polypeptide (180 turns), like connecting antiparallelbeta strands
what are types of beta turns
type 1 and type 2
what amino acids are most common in beta turns and why
proline (good for turning)
glycine (good for flexibility)
what are the phi (φ) and psy(ψ) in beta turns
they vary
what is the difference with type 1 and 2 beta turns (general and specific)
diff geometry
type 2 always have glycine as 3rd residue
what is always constant in beta turns
type 2 always have glycine as 3rd residue
why does type 2 beta turns always have glycine as 3rd residue
it is the only thing that can adopt a (80, 0) geometry
where is the (80,0) in the ramachandran plot (glycine(
right and middle
which amino acids are most found in alpha helices
ala
glu
met
which amino acids are least found in regular structures
glycine and proline
what kind of structure is ala found in most
alpha helix
what kind of structure is glu found in most
alpha helix
what kind of structure is met found in most
alpha helix
what kind of structure is glycine found in most
irregular + collagen helix
what kind of structure is proline found in most
irregular + collagen helix
