test 2: protein structure Flashcards
covalent bonds are present in what protein structure level
primary
what bonds do secondary protein structure have
covalent and hydrogen bonds
what bonds are more prevalent in tertiary and quaternary protein structuer
hydrophobic effect
what is significant about covalent bonds in protein strucutre
- shows in amino acid sequence
- location of s-s bonds
H bonds
- interaction of amino acids close to each other
- form specific patterns
hydrophobic effect level
- 3d structure of polypeptide
quat - arrangement of multiple folded molecules
what % of DB character does a peptide bond have
40
what are the characteristics of a peptide bond
- planar
- no rotation around peptide bond
- cis/ trans isomerism
what isoermism are peptide bonds
- nearly 90% are trans
- 10% are cis
why is trans configuration better than cis
steric hinderance and interactions
in peptide bond where can rotation occur
around the alpha carbon but there is no rotation at all
what does a ramachandran plot show
- sterically allowed alpha and beta angles for a polypeptide chain
- limited amount of allowed configurations
2nd protein structure is found where
- local segments of biopolymers
- proteins and nucleic acids (DNA/ RNA)
- local conformations
what is an example of a secondary protein structure
- alpha helix
- beta strnad
- beta bend
- collagen triple helix
- loops and turns
what bonding is present in secondary
- H bonding between backbone amide NH of one AAand the carbonyl of another
who proposed the alpha helix
linus pauling
what bonds are present in alpha helix
- h bonds between n and n+4 residue
where do R groups poin on alpha helix
outward, perpendicular to the axis
what are some characteristics of alpha helix structure
- h bonds are parallel
- pitch = 5.4 angstrom
- 3.6 residue/ turn
1.5 Rise/AA - right hand
-charged AA - dipole polarity
how is alpha helix dipole polarity
- all c=O grpups point toward C and give dipole with + N, (-) C termini
how can you make a stable alpha helix
- end C term with a charged AA to neutralize
which protein has predominantly alpha helices
myoglobin
what does proline do to alpha helix
- detabilizes the alpha helix that why it is not found
do alpha helices like bulky things
no
what are the alpha helix detablilizers
- proline
- bulkiness
- R groups to large( tryptophan and tyrosine)
- too small (glycine)
what is an amphipathic helics
hydrophonic residues on one side
- hydrophi8llic resides on opposite sides
what is keratin
-key structural material in hair skin and nails
- coiled coil
- 2 amphipathic alpha helices
what amino acid is kertatin rich in
- cys to form s-s bonds
what does a perm do
- reduce s-s bonds–> 2RSH ; then reoxidize to s-s
why is keratin important
used to detect heavy metal poisoning
what are B strands
polypeptide chain almost fully extended found in B sheets
what is a beta sheet
multiple b strands arranged side by side
what are charactersitcs of B strands and B sheets
- h bonds occur between aa on adjacent stands and perp to the strand direction
- side chains R-gps alternate in pointing above and below plane perp to b bonds and stands
do beta sheets like bulky
yes they do
what is an antiparallel b sheet
stand runs in opposite direction
parallel
run in the same N to C direction
what is the beta sheet structure
- zig zag
- 6-12 residue
- repeat 2AA
distance 7A - may be amphipathic
what is silk fibroin
antiparallel B sheets of Gly-ser-gly
what does ala do in a silk fibroin
interlocksw/ ala from another sheett
what is collagen
- main sturctural protein in the extracellular matrix in connective tissues
- most abundant protein in mamels
where is collagen present
- bone matrix
- tendonds
-cartilage - blood vessesl
what is the repeating AA in collagen
G-P-P
proline helix
where are the gly residues located in collagen
- invariant
- central axis of triple helix, other can’t fit
does interchain H bonds occur in collagen
no
what helps stabilize the helix
- interchain H bonds w/ Hydroxypro
what is osteogenesis imperfecta
- mutation in a gene for collagen
- gly is substituted for another AA
- prevents normal production of collagen
- leads to brittle bones
to form hydroxypro what is required
O2 and ascorbic acid(vitamin c)
what is scurvy
vitamin c deficiency
- lack of hydroxypro
- not enough interchain h bonding
- tweaking collagen
how are collagen fibrils strengthened
- interchain lysine-lysine
interaction hydroxypyrindium covalent cross links
increase in cross links =
less eslatic collagen= more brittle bones = sign of old age
why are loops and turns important
- allow chain reversal
- found on the surface of globular protein
