Chapter 4-Three Dimensional Structure of Proteins Flashcards
native conformations
3D shapes of proteins with biological activity
primary structure
- the order in which the amino acids in a protein are linked by peptide bonds
- the 1D first step in specifying the 3D structure of a protein
secondary structure
- the arrangement in space of the backbone atoms in a polypeptide chain
- alpha helix and beta pleated sheets
- contain repetitive interactions resulting from hydrogen bonding between the N-H and the carbonyl group of the peptide
- contains domains or supersecondary structures
tertiary structure
-3D arrangement of all the atoms in the protein (including those in the sedition and in prosthetic groups)
prosthetic groups
portions of proteins that do not consist of amino acids
subunits
individual parts of the larger molecule
quaternary structure
interaction of several polypeptide chains in a multisubunit protein
what does the primary structure of a protein determine?
the 3D structure, which determines the properties
hemoglobin is associated with what disease?
sickle cell anemia
sickle cell anemia
- RBC can’t bind oxygen efficiently
- RBC lack sickle shape
- stem from a change in one amino acid residue
domain
aka supersecondary structure
-specific clusters of secondary structural motifs in proteins
what type of bonds in secondary structure?
hydrogen
Ramachandran angles
used to designate rotations of the C-N (phi) and C-C (psi) bond
alpha and beta pleated sheets are found in what structure
secondary
alpha helix
- one of the most frequently encountered folding patterns in the protein backbone
- rodlike
- one polypeptide chain
beta pleated sheets
- one of the most important types of secondary structure, in which the protein backbone is almost fully extended with hydrogen bonding between adjacent strands
- can give 2D array
- can involve 1+ more polypepetide chains
why are alpha helices and beta sheets considered periodic structures?
they feature repeats at regular intervals
Alpha helices are stabilized by
- hydrogen bonds parallel to the helix axis within the backbone of a single polypeptide chain
- hydrogen bonding is linear
There are ____ residues for each turn of the helix
3.6
pitch (linear distance between corresponding points on successive turns) is ____ A
5.4A
1A= 10-8cm=10-10m
Disruptive forces in alpha helices
- Proline: creates bend in the backbone b/c of its cyclic structure
- strong electrostatic repulsion
- steric replusion: caused by bulky side chains
in alpha helices, where do side chains lie?
outside the helix
describe the peptide backbone in the B sheet
- completely extended
- hydrogen bonds can be formed between different parts of a single chain that is doubled back on itself or between different chains
Hydrogens bonds are ______ to the direction of the protein chain in beta pleated sheets and ______ in the alpha helix
perpendicular; parallel
Three10 helix
three residues per turn and 10 atoms in the ring formed by making the hydrogen bond
B-Bulge
- common non-repetive irregularity found in antiparallel beta sheets
- occurs between two normal B structure hydrogen bonds
- involves 2 residues on one strand and 1 on another
what does a reverse turn often mark?
a transition between one secondary structure to another
reverse turn
parts of proteins where the polypeptide chain folds back on itself
motif
repetitive super secondary structure
what molecule is frequently encountered in reverse turns?
glycine: the single hydrogen of the side chain prevents crowding
list the super secondary structure
- beta alpha beta
- alpha alpha
- beta meander
- greek key
beta alpha beta
two parallel stands of B sheets are connected by a stretch of alpha helices
alpha alpha unit
- aka helix turn helix
- consists of two antiparallel alpha helices
- energetically favorable contacts exist between the side chains in the two stretches of helix
B meander
-antiparallel sheet is formed by a series of tight reverse turns connecting stretches of polypeptide chain
greek key
-antiparallel sheet doubles back on itself in a pattern
protein sequences that allow for B meander or greek key can often be found arranged into a B-barrel in
the tertiary structure of the protein
can motifs predict biological function?
no; they are found in proteins and enzymes with very dissimilar functions
type 1 reverse turn
residue 3 the side chain lies outside the loop
any amino acid can be there
type 2 reverse turn
side chain of residue 3 has been rotated 180 degrees
residue 3 now on inside of loop
glycine must be residue 3
proline residue normally occupies what residue on the reverse turn
2
collagen
- component of bone and connective tissue
- consists of three polypoetide chains wrapped around eacahother in a triple helix
- either X-Pro-Gly or X-Hyp-Gly
- every third position must be Gly (inside the helix)
proline and hydroxyproline can constitute up to 30% of the residues in
collagen
how is hydroxyproline formed?
from proline by a specific hydroxylating enzyme after the amino acids are linked together
tropocollagen
- triple helical molecule
- 300nm long and 1.5nm diameter
- held together by hydrogen bonds
- each strand contains 800AA residues
T/F: amount of cross linking increases with age
true
collagen is both intramolecularly and intermolecularly linked by covalent bonds formed by
reactions of lysine and histidine residues
Scurvy
- result of fragile collagen (when proline is not hydroxylated to normal extent)
- bleeding of gums and skin discoloration
- deficient in Vitamin C
fibrous proteins
proteins whose overall shape is that of a long, narrow rod
globular proteins
- proteins whose overall shape is more or less spherical
- water soluble
- compact structures
- complex tertiary and quaternary structures
characteristics of tertiary structure
- 3D arrangement of all atoms
- side chains (arrangement of atoms inside and position)
- position of prosthetic groups
secondary and tertiary structure depends on ______ interactions
non-covalent
information about the location of disulfide links combined with primary structure gives
complete covalent structure of a protein
what two molecules lack disulfide bonds, but have metal ions? what metal ion?
myoglobin and hemoglobin; Fe(II) as part of a prostethic group
list the forces that stabilize the tertiary structure of proteins
- metal ion coordination
- hydrophobic interactions
- disulfide bond
- electrostatic interaction
- side chain hydrogen bonding
xray crystallography
experimental method for determining the 3D structure of proteins using crystals
NMR
method for determining the shape of proteins in a solution
depends on H atoms
myoglobin
- globular protein
- 153 AA residues
- heme group
- compact structure (interior atoms close together)
- 8 alpha helices; no beta sheets
- 2 polar histidine residues on inside that interact with heme group and oxygen
heme
- iron-containing cyclic compound found in cytochromes, hemoglobin and myoglobin
- consists of metal ion Fe(II), protroporhrin ring
porphyrin part consists of
4 five membered rings based on pyrrole structure
4 rings linked by bridging methane groups
Fe(II)
- 6 coordination sites (4 sites occupied by nitrogen of pyrrole; 1 by nitrogen atoms in imidazole side chain of histidine residue F8; 1 by oxygen)
- forms 6 metal ion complexation bonds
the presence of what is required for myoglobin to bind to oxygen
heme
E7 histidine
streakily inhibits oxygen from binding perpendicularly to the heme plane; lies by binding site of oxygen
why does oxygen have imperfect binding to the heme group?
- more than 1 molecule can bind to the heme
- affinity of heme for CO2 is greater than oxygen (but is forced to bind at an angle)
- too perfect binding would defeat purpose of having the oxygen-carrying proteins
combination of both heme and protein is needed to bind
O2; without protein the iron of heme can be oxidized to Fe(III) and won’t bind oxygen
denaturation
unraveling of the 3D structure (3level) of a macromolecules caused by breakdown of noncovalent interactions
reduction of disulfide bonds causes
extensive unraveling of 3 structure
how can proteins be denatured?
- heat
- change in pH
- binding of detergents
- urea & guanidine hydrochloride
- B mercaptoethanol
describe how heat causes denaturation
increase in temp, favors vibrations, energy of these vibrations disrupt the structure
describe how change in pH causes denaturation
at either extreme, charges are missing and so the electrostatic interactions that normally stabilize the protein are reduced
describe how binding of detergents causes denaturation
ex) SDS
- disrupt hydrophobic interactions
- if charged can disrupt electrostatic interactions
describe how urea & guanidine hydrochloride causes denaturation
- they form hydrogen bonds with the protein that are stronger than those within the protein
- disrupt hydrophobic interactions
describe how B mercaptoethanol causes denaturation
-reduces disulfide bridges to two sulfhydryl groups
dimers
molecules with two subuntis
oligomer
aggregate of several smaller units; bonding can be covalent or non
allosteric
property of a multisubunit proteins such that a conformational change in one subunit induces a change in another
how to chains of quaternary structure interact with eachother
electrostatic interactions, hydrogen bonds and hydrophobic interactions
hemoglobin
- allosteric protein
- tetramer (4 polypeptide chains, 2alpha/2beta that are identical)
- alpha chain: 141 residues
- beta chain: 153 residues
- heme
- four molecules of oxygen bind to 1 hemoglobin
binding of oxygen to hemoglobin exhibits
positive cooperativity
postive cooperativity
cooperative effect where by binding the first ligand to an enzyme or protein causes the affinity for the next to be higher (i.e.: once one O is bound it is easier for the next to bind)
oxygen binding curve of myoglobin
hyperbolic (rises quickly then levels off)
oxygen binding curve of hemoglobin
sigmodial (S shaped curve); characteristic of cooperative interactions
myoglobin has a higher percentage of _______ that hemoglobin at any level
saturation
function of myoglobin
oxygen storage
function of hemoglobin
oxygen transport; must be able to bind and release oxygen easily
alveoli of lungs
where hemoglobin must bind oxygen for transport, O2 pressure 100torr
so hemoglobin is 100% saturated with oxygen
capillaries of active muscle
O2 pressure 20torr; less than 50% saturation
aka hemoglobin gives up oxygen here easily because need is great
in the bound (oxygenated) form of hemoglobin the B chains are
much closer to each other than that of the deoxygenated
What other molecules affect the affinity of hemoglobin for oxygen by alterating the proteins 3D shape?
H+ and C02 (bind to hemoglobin)
Bohr effect
- the effect of H+
- in actively metabolizing tissue (lower pH), hemoglobin releases oxygen and binds both CO2 and H+
- in the lungs (higher pH), hemoglobin hemoglobin releases CO2 and H+ and binds to oxygen
- in the presence of H+ and CO2, the oxygen binding capacity of hemoglobin decreases
2,3-bisphosphoglycerate (2,3-BPG)
- binds to hemoglobin in blood
- binding to hemoglobin is electrostatic
- lowers oxygen binding capacity when bound to hemoglobin
fetal hemoglobin
- fetus obtains oxygen from bloodstream of mom via placenta
- has high affinity for oxygen
why does fetal hemoglobin have a higher oxygen binding capacity?
- presence of two polypeptide chains (HbF & HbA)
- HbF binds less strongly to BPG than HbA
role of hydrophobic interactions
-protein folding into 3D shape `
what makes hydrophobic interactions favorable?
- spontaneous
- entropy (S) increases when reactions occur
what diseases are caused by acculmulation of protein deposits from incorrect folding of hydrophobic regions?
Alzheimers
Parkinsons
Huntingtons
chaperones
prevents a protein from associating with another protein which it shouldn’t or itself in negative ways
AHSP
globin chaperone that binds to alpha global (excess) and keeps it from aggravating with itself and delivers it to the B-globin
thalassemia
damaged red blood cells from excessive alpha chain aggravates
Prion diseases
- cause of mad cow
- cause of creutzfeldt jakobs
- comes about when normal form of PrP folds into PrPsc
what are prions
natural glycoproteins found in cell membrane of nerve tissue
abnormal prions have
more beta sheets
