Protein structures (primary, secondary, tertiary, etc.) Flashcards
Why would a protein want to have a quaternary structure (subunits)?
1) Error frequency in translation
2) Ease of folding of small vs. large polypeptide chains
3) Signalling/communication (“division of labor”, regulatory functions…)
4) Use of same subunit in different multi‐subunit proteins/complexes
Do all proteins have quaternary structures?
no, only proteins that have more than one polypeptide chain (subunits) have quaternary structure
also most proteins with a MW greater than 100kD is most likely comprised of subunits
subunits in quarternary structures are held together by what types of bonds/
non covalent interactions, salt bridges, van der waal’s, hydrogen bonds, and hydrophobic interactions
What are oligomers?
proteins with more than one subunits, if identical they are called protomers
if you have two identical subunits you call them?
dimers (2 protomers)
What happens if there are two non identical subunits?
the efficiency of the enzyme is detrimentally affected b/c the reaction would depend on the diffusion of the intermediate to the second subunit and there might be other enzymes in the cell that would compete for the intermediate
How is cn rotational symmetry classiified?
by a single rotational axis
What is the meaning of quasi equivalent?
subunits that are not strictly equivalent in environment
What is tertiary structure of proteins?
3D arrangement of secondary structures and side chains
What two methods can be used to determine tertiary structure?
x-ray crystallography or NMR spectroscopy
Which amino acids are hydrophobic and what does it mean when it comes to interactoins?
F, I, L, M, V, W
hydrophobic interactions usually drive these into the interior
Which amino acids are uncharged polar? where are they located in a peptide
H, N, Q, S, T Y
located either in or exterior but when interior they are usually bonded with a Hydrogen
Which amino acids are charged polar? where are they located?
D, E, K R
located mostly on the exterior but if interior will either be in a salt bridge or involve in a specific function such as catalysis, metal ligation etc.
These are very unstable internally if they don’t interact w/another species
If uncharged residues are found interior what type of bond will they have?
predominantly be H bonded
Are hydrogen bonds stronger in a non-polar environment or an aqueous solution?
stronger in non-polar
what is. domain?
a region of polypeptide or protein that fold independently of each other and are functioning units that are connected by polypeptide segments
How can we classify domains?
using the CATH classification
C-class overall secondary-structure of the domain
A- architecture - high structural similarity but no evidence of homology
T-topology/fold - large-scale grouping of topologies which share particular structural features
Homologous superfamily: demonstrable evolutionary relationship
What is the dominant secondary structure seen in fibrous proteins?
coiled coil structure and it is the basic building block of fibrous proteins
What gives keratin its fibrous nature?
the alpha helix.
the fundamental building block of keratin is the two chain coiled coil, where two alpha helices twist around each other.
What are protofilaments?
part of the keratin structure - two chain coiled coil comes together w/another two chain coiled coil in a staggered arrangement and form protofilaments
a bunch of protofilaments for what?
protofibril
Keratin is a component of what?
hair, nails, horn, feathers, porcupine quills etc.
What is the differences between type I and type II alpha helices in keratin? What do they do together?
Type I: acidic, right handed structure
Type II: basic, right handed structure
Type I and Type II twist around each other to form the coiled coil structure. and become a combined left handed structure
What motif do you look for in any protein primary structure to see if it has a twisted coil-coil structure associate w/it?
-look for a 7 amino acid sequence (a, b, c, d, e, f, g) that repeats one after another. this heptad repeat can extend over hundred residues
in position a (1) and position d (4) are usually hydrophobic amino acids ( Leu, Ile, Val, etc) the residues in the e and g positions are generally charged
What is a pseudorepeat?
when some keratin repeats do not have hydrophobic residues at site a or site d
Why are residues in a and d in the keratin pseudo-repeat usually hydrophobic?
residues a and d ffrom the two strands in the coil-coil interact with each other due to helix alignment and are buried at the helix helix interface due to hydrophobic effect
e and g are charged and can form ion ion interactions or salt bridges
Alpha keratin is rich in what type of residues?
cys residues = disulfide bridges
why is one form of keratin as in hair flexible and springy while the other form as in the horn, hard and inflexible?
due to its chemical composition of different forms
Springy characteristic: low concentration of Cys and more hydrogen bonds
Stiffness:
cysteine forms disulfide bonds and more cystine and more disulfide bonds decrease springiness and increase hardness
How do amyloid fibrils form?
from globular soluble proteins
What are amyloid fibrils?
important fibrous protein involved in bovine spongiform encephalopathy (BSE = mad cow disease) and other prion diseases
-alzheimer’s disease and transthyretin amyloidosis
How do amyloid fibrils contribute to diseases like mad cow and other prion disease?
normally globular soluble proteins become deposited as stable insoluble plaques in the extracellular space of the brain or eye
in prions, the alpha helix globular protein becomes beta sheet fibril
in transthyretin beta sheet globular protein becomes beta sheet fibril
What is the role of transthyretin (amyloid fibrils)?
thransthyretin is a transpor protein
in the serum and cerebrospinal fluid that carries hormone thyroxine and retinol-binding protein in bloodstream
What mutation causes transthyretin to cause amyloidosis?
single point mutation from Valine to Methionine and unfolding of c and d strands leads to fibril development
What is the structure of amyloid fibrils of transthyretin? How does it differ from keratin?
twisted beta sheets, each around 10 amino acids long. Has a repeat unit of 24 beta strand and each repeat unit is 4 transthyretin molecules. Unlike keratin, there are no consensus sequences
collagen is comprised of how many polypetide chains?
3 polypeptide chains termed alpha chains that form LEFT HANDED HELICES
-the 3 LEFT HANDED helices in turn form a coiled-coil RIGHT HANDED structure (tropocollagen)
How are the triple helical tropocollagen elements in collagen cross linked?
via lysine side chains
collagen is found where?
bone cartilage teeth skin blood vessels
provides strong stress bearing material