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Protein Structure I


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What are the degrees of freedom in peptide groups?
the alpha-C - C' bond and (psi angle)
the alpha-C - N bond (phi angle)
Why are the degrees of freedom important?
They allow for protein folding
What causes secondary structure?
The need for the neutralization of the main chain polar groups via H-bonds

This would allow the hydrophobic regions to settle into the interior
What are comp's of secondary s(x)?
What is the structure of alpha-helix
peptide backbone w/side chains radiating out
How is it stabilized?
by h-bonds btw.C'=0 bond of residue n and the NH residue of n+4
What is the average length of alpha-helix?
approx 10 residues = 3 helical turns
What is almost always observed? R-handed or L-handed alpha-helixes
What is the net dipole moment for a-helix?
partial positive at amino term
partial negative at carbox term
What does this favor?
bonding of negatively charged groups (phophate)
Why is proline bad for a-helices?
side chain bonded to the N = No H-bonding!!!!
what are the two ways beta strands can interact to form a pleated sheet?
paralled and anti-parallel
What characterizes anti-parallel
narrowly h-bond pairs that alternate w/widely spaced pairs
What characterizes parallel
evely spaced h-bonds that bridge the B-strands at an angle
loop regions are generally at the _______ of the molecule at when exposed to solvent have lots of ________ and ___________ residues
surface; charged and hydrophilic
What do loop regions freq. form?
binding sites
active sites
What things are the helix-turn-helix motif specific for?
DNA binding (seen in transcription factors)
Calcium binding
Why does the B-a-B motif exist and what type of B-sheet is it specific to?
because two adjacent B-sheets must be joined at opposite edges

parallel b-sheet
What is the fundamental unit of tertiary s(x)
The domain
What is a domain?
An area of a polypeptide that can fold independently
What are the groups of domains
What is the globin fold
short a-helices connected by loops; packed together to form a hydrophobic core.
What are coiled-coils?
Two right handed a-helices forming a left-handed supercoil
What are they used for?
the basis for many fibrous proteins
How often do the patterns of the side chains repeat?
Every 7 (Heptad Repeat)
What compounds contain coiled-coils
fibrinogen, collectins, RNA/DNA binding proteins, spectrin and dystrophin
beta-domain structures resemble a?
What is their general s(x)?
hydrophobic core made up of side of B-strands. surface has loop regions
What do alpha/beta domains consist of?
central parallel or mixed B-sheet;
surrounded by a-helices;
binding crevices formed by loops
What is the s(x) of the TIM barrel
twisted parallel b-sheets AND
a-helices connecting opposite sides of the b-sheets
What is the s(x) of the rossman fold?
open twisted B-sheet surrounded by alpha-helices
Where is this seen?
NAD+ binding domain of lactate dehydrogenase
Where is a leucine-rich motif commonly seen
at ribonuclease inhibitors
What 4 interactions stabilize tertiary structure?
1.Disulfide bonds
2.Hydrophobic interactions
4.Ionic interactions
What are inactive enzymes called?
zymogens (proenzymes)
How does N-linked glycosylation work?
Attachment of oligosacc. group to Asn side chain, ensures proper folding because of recognition by chaperones
How does 0-linked glycosylation work?
Attachment of oligosacc. group to either Ser or Thr
What is the function of carboxyglutamate residues?
Binding of Ca++

Inv. in blood clotting and bone structure
What two non-standard A.A.'s are important in the structure of collagen?
Hydroxyproline, hydroxylysine
What does scurvy result from?
Insufficient hydroxyoxylation of collagen due to vit. C defic.
What are the usual sites for phosphorylation?
OH groups of Ser, Thr, and Tyr

sometimes Asp, His, and Lys
What is the function of the acetylation of the amino terminal end of polypeptides?
Makes them more resistant to degradation
the formation of disulfide bonds requires an __________ environment
What is the f(x) of disulfide bonds?
Stabilize 3-D structure (ex. alpha and beta chains of insulin linked by disulfide bonds)
Where do cis-proline peptides occur?
In tight bends of polypeptide chains
What enzyme catalyzes cis-trans proline isomerization?
peptidyl prolyl isomerases
How do lipids tether proteins to the membrane?
By embedding the hydrophobic portion in the membrane and covalently attaching to the protein via its polar group
What lipid can attach to the N-terminus?
Myristoyl group
What groups attach to the C-terminus?
phosphatidylinositol and farnesyl
What A.A. side chain binds palmitoyl groups?
What A.A. side chain is sulfonated in a post-translational modification?
Where do disulfide bonds occur in eukaryotic cells? in bacteria?
endoplasmic reticulum (rough)
periplasmic space
What side chains are particularly suited for binding metal?
His, Cys, Asp, Glu
What are zinc fingers and what is the function of zinc in that structure?
A class of DNA-transcription factors, zinc stabilizes the DNA-binding region
What is the structure of myoglobin?
Single polypep. chain (153 AA's), very compact (primarily alpha-helices),
What type of AA's are seen in the interior of myoglobin?
all non-polar residues
What is the exception for that?
Two histidines are present inside
What is the structure of heme?
protoporphyrin w/a central iron atom
How does oxygen enter myoglobin given that heme is buried deep inside?
"rapid molecular flexing" of the amino acid side chains
What is the structure of hemoglobin?
Tetrameric; 4 heme groups ass. w/2 alpha-chains and 2 beta-chains
When 02 binds to hemoglobin what is the result?
A change in conformation; some ion pairs are broken, some new ones formed
What is collagen?
A right-handed superhelix formed by 3 parallel, very extended left-handed helixes.
What is the common 3-AA sequence?
What holds the 3 chains together?
hydrogen bonds btw. proline C=0 and glycine N-H
What is the purpose of hydroxyproline in collagen?
Promotes water-mediated H-bonds that stabilize the structure
What causes osteogenesis imperfecta?
Substitution of a single larger R-group for Gly in each alpha-chain.
What largely dictates the folding pattern of proteins?
the AA sequence
What is the Cystic Fibrosis Transmembrane Regulator do?
Ion channel spec. for Cl-
What causes cystic fibrosis?
A deletion of Phe at position 508
At do proteins denature at extreme pH
1.Because groups in non-ionized form (such as Met and Tyr) will be able to ionize if they unfold in the extreme pH, so they start the unfolding process
2.Salt bridges are disrupted
How do Urea and Guanidinium denature proteins?
By breaking inherent H-bonds

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