Midterm Flashcards
name the greek letters in order for the additional carbons in an amino acid
alpha, beta, gamma, delta, epsilon, zeta, eta, theta, phi, chi, psi, omega
what is a zwitterionic
charged form ion but charges make atom neutral
what determines the charged forms of aa
sidechain properties and pH of medium
what is the L form of aa
co, r, n
what is the d form of aa
n, r, co
what form of aa is almost found exclusively in naturally occurring proteins
L-form
is glycine chiral
no due to no side chain
what are some functions of proteins
enzymes, motor proteins, structural or cytoskeletal proteins, transport proteins, electron transfer, cell signaling, chaperones, storage proteins
proteins are diversified with what type of interactions
covalent and non covalent
what is primary structure
the linear amino acid sequence of the polypeptide chain
what is the secondary structure
the local structure of linear segments of the polypeptide backbone atoms without regard to conformation of the side chains
what is tertiary structure
the overall 3D arrangement of all atoms in a single polypeptide chain
what is quaternary structure
the arrangement of separate polypeptide chains (subunits) into the functional protein
what creates the peptide bond
condensation of the carboxyl group of aa 1 and amino group aa 2 which form an amide bond
what are some factors of the peptide bond
resonance, partial double bond, shorter than single bond but longer than double bond
where is the partial dipole in peptide bond
N in amino group and O in carboxyl group
polarity is important for the blank of a folded protein
stability
the peptide plane is
planar
what are the six atoms in the peptide plane
C alpha, carbon, O, N, H and C alpha
where is the limited rotation in the primary structure
around the peptide bond, due to resonance
what bonds are single and free to rotate
N-Ca and Ca-C
what atoms are in the psi angle
Ca-C
what atoms are in the phi angle
N-Ca
what are dihedral angles
phi and psi
omega angle directs what
the orientation of the sidechains between two consecutive aa in a peptide
180 degree for omega
trans
0 degree for omega
cis
which is more energetically favorable, trans or cis
trans due to less steric henderance
when do you see cis
when proline involved
what is ramachandran plot based on
close contacts between atoms based on their van der waals radii
the ramachandran plot shows
conformations of phi and psi that are sterically favorable or unfavorable
how do secondary structures form
repetition of similar phi and psi angles
what are the three common types of secondary structures found in proteins
alpha helices, beta strands, beta sheets
what is the other category of secondary structures
turns, loops and connections
what is a common element of secondary structures
h bonds
what is the basis of secondary structure
get as many carbonyl O and amide NH to b paired
what is the most prevalent type of secondary structure
alpha helice
how many residues per turn in alpha helice
3.6
dihedral angles are what in alpha helices
same or similar
what is the pitch of the alpha helix
5.4 A per turn of helix
what is the angstrom per residue of 100 degree rotation in alpha helice
1.5
how are the side chains viewed in the alpha helix
staggered, outside of helix
carbonyl oxygens point to what is alpha helix
to c terminus
R groups point to what in the alpha helix
N terminus
what aa are good helix formers
A, E, L , M
what aa are bad helix formers
P, G, Y, S
alpha helical structures are stabilized by
h-bonding within the main chain atoms
what makes the alpha helix the most stable secondary structure
repetitive H-bonding pattern
how do the H bond in the alpha helix
carbonyl O, h bonded with H of NH four residues away
how many atoms are joined in H bond of main chain in alpha helix
13
what is helix propensity
tendency of aa to be in a helix
what determines helix propensity
H-bond, hydrophobic interactions, sidechain interactions with helix, lower energy value indicates higher probability
what causes dipole in single peptide
polarity of NH and CO
what aligns the dipole of each peptide approximately parallel to the helical axis
H-bonds
what s the degree that aa residues are plotted around the spiral of alpha helix
100 degree
where are helices located and why
outer surface of globular proteins with hydrophobic inside and hydrophillic outside
what part of helix can bind to DNA
n term
a number of enzymes have their active site close to what on helix
N term of helix
explain helix capping
the n and c ends that have un-bound due to H bond only binding every four
so if you have 12 residues how many h bonds in main chain of alph
4 h bond but leaves four empty at both c and n term
what do you call the last unoccupied N and C term with helix capping
C1, C2, and very end is Ccap and Ncap
in alpha helix how many aa for one spiral
3.6
describe aa distribution in spiral of helix
hydrophobic on one side and charged on the other
what are the different types of alpha helices
alpha (3.6), 3.10, pi (4.4)
feature of 3.10 helix
narrower in diameter, longer in length, tighter turn
feature of pi helix
wider in diameter, shorter in length, wider turn
describe h bonds in 3.10 helix
between i and i+3
where can you see 3.10 helix
beginning or end of alpha helix with a single turn
what leads to potential steric interference in 3.10 helix
side chain
collagen contains what secondary structure
alpha helix, (3), twist around each other
how is collagen alpha helix stabilized
inter-chain H bonding
what is PPII
poly-proline helices
feature of PPII
4-8 residues long, more flexible, more exposed to solvent
what is a beta strand
a continuous stretch of aa residues in Beta conformation
features of beta strand
peptide bonds of adjacent residues point in opposite directions, alternate side chain point in opposite directions
beta strands associate with
beta sheet
average length of beta strand
6 residues
what are the three perpendicular features in beta strands
direction of backbone, direction of h bond bw strand, direction of side chain above and below plane sheet
where does the h bond go in beta sheets
c=o and h-n
why can beta sheets contain strands that are not local
h-bond between different segment of a polypeptide
what are the different types of h bond in beta sheets
antiparallel, parallel, mixed
feature of parallel beta sheet
h bond not parallel, not perpendicular to strand, 3.2 A per residue translation, less stable than anti, must have more than 4 strands to improve stability, equal space of h bond
what are the side chains like in parallel beta sheet
hydrophobic, buried in protein
since h bonds angled in parallel beta sheet, what happens to dipole
only 1/3 of peptide dipole aligns parallel to strand
Features of H bond of antiparallel beta sheet
shorter connection bw adjacent strands and connection is on same side, H bonds parallel and perpendicular to strand but not equally spaced
features of antiparallel beta sheet
3.5 A residue translation, uneven spaced h bond pattern, narrowly spaced bond pairs alternate with widely spaced bond pairs, stable even with two strands
what is an example of beta sheets that have different morphology
beta barrel
example of beta barrel protein
GFP, green fluorescent protein
hairpin
backbone enters the same end of the sheet that is left, small,
crossover
the backbone enters the opposite end, longer,
different types of crossover
right vs left
which crossover is more prevalent
right
feature of beta bulge
h bonds between two residues on one strand opposite a single residue on the other strand, slight bend in beta sheet
when does beta bulge happen
between antiparallel strands, between a narrow pair of hydrogen bonds
function of beta bulge
compensating for the effects of a single residue insertion or deletion within beta structure, providing the strong local twist required for form closed beta barrel structures
a turn causes direction change of polypep by what degree
180
where do turns occur
surface of the molecule
loops between anti parallel beta strands referred to
beta hairpins, hairpin bends, beta turns
turns contain about how many residues
2
in a turn what are the residues
i and i+3
feature of type 1 turn
antiparallel beta sheet, pro is second residue
feature of type 2 turn
antiparallel beta sheet, residue three glycine
difference between type one and two
180 flip in residue two
feature of gamma turn
only 3 residues
feature of omega turn
main chain to side chain h bond, cause chain reversal, found in metal binding locations
what is the main driving force of protein folding
pack hydrophobic side chain in the inside and hydrophilic surface
how to create hydrophobic core
main chain should be neutralized by forming H bonds between the amide N and carbonyl O
super secondary structures are also known as
motifs
motifs contain
more than one secondary structural element, 2 or 3 consecutive secondary structures and arrange themselves with specific geometry even with completely different sequences
motifs can have what type of roles
structural or functional
examples of super secondary structures
alpha-alpha, beta-beta, beta-alpha-beta
example of alpha-alpha unit
helix-turn-helix
feature of helix turn helix
two helices, lie antiparallel connected by short loop, helices are roughly perpendicular to each other, sequence specific interactions with DNA
how does helix turn helix work with DNA
second helix binds to major groove of DNA (recognition helix) and first helix stabilizes the interaction (stabilization helix), interact with H bond and hydrophobic of protein sidechain and DNA bases
feature of helix turn helix with three helices
regulate developmental gene expression, third helix interacts directly with DNA, stabilized by salt bridges and H bonds
describe winged helix turn helix
dna binding motif, wings are small beta sheets, 3 helices and 3 beta, H1S1S2H2H3S3S4H4
feature of winged HTH
3rd helix makes contact with the major groove of DNA, wings bind to minor groove
features of helix hairpain helix (HhH)
contain two alpha helices with hydrophobic residues in helix that pack the two helices, gly and pro in the hairpin
binding DNA and HhH
non-sequence specific DNA interaction, binds to DNA with hairpin, positive charge on loop bind to phosphate backbone
describe EF hand
loop has 12 residues and has polar and hydrophobic aa for binding with metal ion
how does metal bind in EF hand
carboxyl side chain, main chain groups and bound solvent
describe three helix bundle
helix 2 and 3 antiparallel to each other, helix 1 tilted at 30 degree angle, hydrophobic residues are buried in interior
describe four helix bundles
interfaces consist of hydrophobic residues and polar side chains are present on the exposed surfaces
coiled coils function as
oligomerization domains
coiled coils typically consist of
two or more alpha helices that wrap around each other with a superhelical twist
coiled coils may interact with each other to form
homotypic oligomers
coiled coils may interact with other coiled coil domains to form
heterotypic oligomers
coiled coil structures are characterized by the
heptad repeat pattern (7 pattern)
coiled coil motif features
hydrophobic residues inside and interact with different helices
example of coiled coil
leucine zipper
how does leucine zipper work
monomers held together in a dimer in the zipper region, basic region bind to DNA in major groove
where are globin folds found
myoglobin, hemoglobin, phycocyanins
feature of globin fold
eight alpha helices, helices form pocket for active site which binds to heme group, the last two helices are antiparallel
what is a lone helix
small proteins (peptides) often consist of a single structural element, can form pores in the membrane, similar to 3.10 helix, amphipathic helix
beta hairpin motifs contain
antiparallel beta strands connected by a loop
what is in a propeller blade
six motifs made up of 4 stranded anti parallel sheet connected by a loop from strand 4 to first motif to strand one of second motif
feature of greek key motif
folding of 4 adjacent antiparallel beta strands
what is the topology of a greek key
-1,-1, +3 or +1,+1, -3
do all four beta stands have to fall within the same beta sheet of greek key
no could be 4,0 or 3,1
only up to two beta sheets though
describe jelly roll barrel
nonlocal structure in which four pairs of antiparallel beta strands are wrapped in 3d to form a barrel shape
feature of jelly roll
loops crossing over on top and bottom of barrel, antiparallel when strands next to each other, consecutive greek key motifs wrapped around barrel
feature of beta barrel
antiparallel, last strand joined by H bond with first strand closing barrel, has one open end and one close end, hydrophobic inside
feature of beta sandwhich
two separate beta sheets pack together face to face, end strands of each sheet not H bonded to one another
feature of orthogonal beta sandwhich
beta sheets are folded on themselves, two sheets make an angle of 90 degree
feature of aligned beta sandwhich
antiparallel beta strands, sheets surround a central hydrophobic core, single disulfide bond bridges the two sheets, angles vary from 20 to 50 degree
feature of beta helix
beta strands wind around the structure forming a helical topology, 2 or 3 sheets
how many coils for 2 sheet beta helix
3 complete coils, 2 parallel beta sheets
how many residues in the loop of beta helix
2
membrane proteins contain what secondary structure
either all alpha or beta structures
what secondary structure are more common for membrane proteins
alpha helices due to intra strand H bonds
feature of beta alpha beta
parallel beta strands connected by alpha helix
why b-a-b composed of parallel or mixed sheets
parallel sheets create longer region of chain which cross over and the cross over create alpha helix, usually right which go above plane
b-a-b aka
a/b fold
what are the three types of b-a-b
TIM barrel, rossman fold, horseshoe fold
feature of packing helice and sheet of b-a-b
hydrophobic core, alpha pack up against beta shield hydrophob inside, loop regions vary in length
the loop linking the c terminal end of the 1st beta strand to the N tem end of helix is involved in
binding of ligands or substrates
binding crevices of a/b motif are formed by
loop regions that do not contribute to structural stability
feature of a/b barrel
alpha helices outside, hydrophobic side chains inside, +1x, +1x…
feature of TIM barrel
closed a/b barrel, 8 beta strands and 8 helices, beta inside and alpha outside, parallel beta sheet
what does TIM barrel stand for
triose isomerase
TIM barrel is always associated with
an enzymatic function
where is the active site in the TIM barrel
C-term end of the eight parallel beta strands of the barrel
feature of double wound a/b folds
open twisted sheet, not closed, central twisted wall of parallel or mixed b sheet, start in middle then go from one side to other
what are the types of double wound a/b folds
classic and reverse
what is a classic doubly wound a/b fold
starts in the middle
what is a reverse doubly wound a/b fold
starts on one end
function of doubly wound a/b folds
bind nucleotides
feature of rossman fold
a/b open twisted sheet, parallel or mixed b sheet with a helices on both sides, b strands vary from 4 to 10, BABAB motif, involves two motifs
rossman fold binds what dinucleotides
NAD/NADP, FAD
feature of a/b horseshoe fold
tandem repeats of 20 to 30 aa, no closing in structure, one side of sheet faces helices (hydrophobic) and other side exposed to solvent
a/b horseshoe fold used in
proteins involved in cell adhesion, virulence, DNA repair, RNA splicing
what amino acid present in horseshoe
leucine,
features of Zn finger motif
30 residues, 4 ligands bind Zn atom, antiparallel beta hairpin motif followed by helix and loop region which bind to DNA seq and non seq specifically
finger region in zinc finger motif consist of
linker region between last cys and the first his is 12 aa long
classic zing fingers bind to DNA in tandem along
the major groove
feature of a+b folds
folds include alpha and beta secondary structure but are mixed
3D structure is stabilized by
multitude of specific interactions b/w various chemical groups
can different primary sequences give rise to similar tertiary folds
yes
3D structure is more highly conserved than
primary structure
can a protein by composed of single or multiple domains
both
can a domain fold independently of rest of protein
yes
for multi domain proteins, tertiary structure describes the
association of the polypeptide within each domain
feature of domains
all or mostly alpha, all or mostly beta, can be alpha/beta, alpha + beta
mosaic proteins
different domains in same polypeptide
how are domains attached
covalently through loops of varying length
disulfide bonds or metal ligands (S-M) features
single domain and monomeric, distorted helix clusters, distorted beta barrels
oligomer
protein assemblies with more than one polypeptide
subunit/ monomer
single polypeptide in oligomer
how do monomers assembly
spontaneously and specific
homomultimers
copies of same polypeptide chain associate non-covalently, symmetric, subunit coded by same gene
heteromultimers
different polypeptide chains, each subunit coded by different gene, each subunit can have a similar/different fold
similar fold despite sequence differences hints what
gene duplication event
oligomers form through what interactions
H bonds, van der waals, salt bridges, disulfides, metal ion binding, buried water molecules
what indicates the strength of binding in oligomer
the amount of surface area buried
an assembly with more area and a predominance of hydrophobic interactions indicate
tight binding assemblies
a smaller buried area and polar interactions indicate
weaker complexes that have to dissociate often for biological function
why is oligomerization important
for optimized biological performance, higher order structures can facilitate the allosteric cooperativity resulting in increased catalytic efficiency
can each subunit of oligomer have independent reactions
yes
active sites can be formed from
two monomers
assembly of biomolecules into quarternary structures provide
enhanced, multiple, or novel functional and structural roles
protein folding structure determined by
primary sequence
what else can stabilize protein structures
post translational modifications
3D structure is stabilized by
efficiently packing atoms into the protein interior
what are some chemical interactions that stabilize polypeptides
covalent bond, disulfide bond, salt bridge, h-bond, van der waals, long-range electrostatic interactions
what chemical interaction has the smallest distance that stabilizes polypeptides
covalent
what chemical interaction has the largest distance that stabilizes polypeptides
van der waals
post translational modification increases the
functional diversity of the proteome
what are the different types of post translational mods
phosphorylation, glycosylation, ubiquitination, s-nitrosylation, methylation, n-acetylation, lipidation, proteolysis
phosphorylation
protein kinase on aa with OH, protein folding
glycosylation
covalent addition of sugar, cell attachment to extracellular matrix and protein ligand interactions
methylation
add methyl group on arg or lys
acetylation
lys residues within n term tail are acetylated for regulating gene expression
