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1.) Tertiary protein structure is stabilized by many types of interactions, which of the
following is an example one such interaction?
a. Hydrophobic interaction between alanine and glutamine R groups.
b. Disulfide bridge between two methionine residues.
c. Hydrogen bond between asparagine R group and water surrounding.
d. Ionic interaction between aspartate and tyrosine R groups.
e. All of the above.
1.) Alpha Helix. ( about ¼ of all amino acids)
 H-Bonds form between (C=O/NH) of residue n and (C=O/NH) of residue n+4.
 ___ ____ residues per turn, 5.4 angstroms per turn, 100° apart.
 1.5 Angstroms between each residue
 The alpha helix is (right handed/left handed).
 R- groups side chains project (outward/inward)? circle
 Has a diplole amino terminus has a partial _________ – carboxyl terminus has a
partial ___________.
 R groups interact with other R groups ________ residues down the helix.
 Hydrogen bonding is intramolecular/intermolecular (circle).
Question? What two amino acids are not usually found in alpha helices and why?
Beta strand -> forms beta sheets.
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Two types, ______ and _______
Between these two the hydrogen bonding angle is slightly different.
R groups project in opposite directions.
Maximizes _______________ within the main chain
Hydrogen boding is intermolecular/intramolecular (circle)
_________ angstroms between each residue
2.) Turn / loop: regions of protein that link 2° structural elements together. Often exposed
to the hydrophilic solvent, will contain more hydrophilic residues.
a. Beta turn = 4 ammio acid hairpin turn that connects 2 ______ beta strands. C=O
on (n) interacts with N-H on (n+4)
Turns often contain proline and glycine, why ?
3.) Question: Beta-Sheets often have one side facing the surface of the protein and one
side facing the interior, giving rise to an amphiphillic sheet with one hydrophobic
surface and one hydrophilic surface. From the sequences listed below pick the one that
could form a strand in a amphiphillic beta-sheet.
a. A-L-S-C-D-V-E-T-Y-W-L-I
b. T-L-N-I-S-F-Q-M-E-L-D-V
often contain proline and glycine, why ?
4.) Question: Which of the two would form a more stable alpha helix? And what is the
overall charge of each peptide?
i.)
A-V-R-M-W-V-E-L-S
ii.)
R-K-R-W-Q-K-R-M-P-W
3° Tertiary: 3D folding of 2° structure
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Motif: ______________________ ; stable arrangement of 2 or more secondary
structural elements + connecting regions e.g. beta barrel, beta alpha beta loop.
Domains (two types functional and structural): _
___________________________; Can also be a unit of function. Eg. DNA binding
domain, antigen binding domain.
4° Quaternary: arrangement in space of 2 or more subunits.
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Suunits can function __ ___________ or _________
Each subunit is an ______________ poly peptide chain.
Motifs
I.
Helical Motifs
a. Important rule -> helices pack together according to the ____________ theory
determined by Francis Crick.
i. This model suggest that when helices pack together they do so in a
slightly _____fashion – _____varies between ______________.
ii. This allows the side chains to pack closely together and allows each side
chain in the hydrophobic core to interact with _________ of the adjacent
helix -> stabilizing and strengthening the _____________ interactions.
1.) ____________ -> 2 right handed __________ intertwined and coil around each
in a left handed fashion (aka supercoil)
i. Characteristic ___ amino acid repeat (___________) -> every 4th (D)
position is a ___________(which is __________)
 Usually labeled a-g
ii. Approx ____ angstroms between ________
iii. Hydrophobic Leu of adjacent helices pack together every _______ turn ->
forming a _________ core.
iv. The (A) position is also _________ and assist in forming the
_____________
v. _________ are also important for the formation of coiled-coil -> residues
__ and _ often interact with such salt bridges.
vi. Motif is Often found in fibrous proteins
2.) _______________ -> 4 helices with their helical axis almost parallel to each
other, but slightly tiled.
i. Side chains are arranged so that the ___________ are buried between
the helices and the ___________ chains are on the outer surface of the
bundle -> creating a hydrophobic core.
ii. α- helices are arranged in an anti-parallel fashion -> two types.
 1.) ___________ -> example: Cytochrome b2
 2.) ___________ -> example : Human Growth Hormone
 OR it can be 2 helices from 2 different polypeptide chains
(subunits) that come together to from a 4 helical bundle.
3.) _________ -> an all ___________ motif which is found in a lot of different
proteins including myoglobin the first protein structure that was determined.
i. 8 – alpha helices In a bundle arraignment -> helices are labeled A-H
4.) Globin fold example Myoglobin -> Oxygen binding protein found in muscle.
i. It is one subunit (Single polypeptide chain) and contains a ________ with
coordinates an _______atom Fe2+.
ii. Iron has 6 coordination sites 4 come from Nitrogen in the Heme, and 1
from a His residue. 1 coordination site is open to allow oxygen to bind.
iii. Has a _________ core with the exception of _________which coordinate
Iron unequally -> There is a _____________ group attached directly to
the iron center, and a ________ group on the opposite face, not
_________ to the iron.
iv. This distal His not bounded to the iron has important function like
forming hydrogen bonds with the bound oxygen allowing stronger
binding.
Alpha/Beta Motifs: Most frequent of all the domains -> contains a central beta sheet
surrounded by alpha-helices. Commonly found in enzymes as well as proteins that bind and
transport metabolites.
i.
ii.
iii.
iv.
In alpha/beta motifs -> binding crevices are formed by the loop regions -> which
do not contribute to the structural stability but participate in binding and
catalytic activity.
Beta strands are orientated in a _________ fashion.
Can form large metabolic enzyme complexes, which have several active cavities,
where the _________ of enzyme subunit is the _______ to the next enzyme
subunit -> shields the substrate from the _________ and shuttles it to the next
enzyme. (assembly line)
Two main types
a. Closed Barrel-> Forms a barrel with all the connecting alpha helices on
the outside of the helix
i. Active site: is formed by the loops connecting the _________ end
of beta strand to the ___________end of the alpha helix.
ii. Closed alpha/beta barrels have _ alpha helices and _ beta sheets.
iii. Usually core of the barrel is filed with large ____________
residues such as -> _____________________
iv. Example: triosephoshpate isomerase.
b. ______________ -> Has helices on both sides of the sheet
i. Variable/Non-Variable (circle) number of alpha beta sheets
ii. Active site : formed by a crevice at C-end of β-sheet
All Beta-Motifs
1. Beta Barrel -> anti parallel/parallel (circle) beta strands form a barrel like structure.
a. Functionally diverse
b. Number of beta strands is variable/non-variable (circle correct choice).
c. The core of the barrels are generally lined with hydrophobic/hydrophilic (circle
correct choice) residues.
d. Beta barrels are generally very robust/flexible (circle correct choice).
T/F -> Beta Barrels undergo large conformational change during ligand binding.
2. Three main types of motifs
a. ____________-> Simplest form of anti-parallel beta strands forming a closed
barrel. Each beta strands is simply connected to the next by a short loop region.
i. Beta strands are amphipathic -> alternating hydrophilic/hydrophobic
residues.
ii. This group generally binds _________ ligands inside a large
__________cavity.
iii. Example -> Retinol-binding protein (RBP) -> single polypeptide chain
involved in biding vitamin A (retinol) a hydrophobic alcohol.
1. Features: beta barrel is wrapped around the retinol molecule. Its
hydrophobic end is packed inside the core of the barrel aligned
with mostly hydrophobic ________ residues.
2. Hydrophilic tail (-OH) of the retinol is exposed to the _________
b. ___________ -> Formed when one of the of the connections of 4 antiparallel B
strands is not a hairpin connection.
c. ___________
3. Beta-Propeller -> example: Neuraminidase
a. Not a simple barrel but instead, __________beta-sheets formed by ___________
beta strands are arranged like the blades of a six-bladed propeller.
b. Active site is formed by the___________ connecting the _________ end of the
beta strand to the __________ end of the adjacent beta strand, on _________ of
the propeller.
c. ___________ identical beta-propeller subunits come together to form a homotetrameric super-barrel.