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.
 ___3.6 ____ 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 positive – carboxyl terminus has a
partial negative.
 R groups interact with other R groups 3-4 residues down the helix.
 Hydrogen bonding is intramolecular/intermolecular (circle).
Question? What two amino acids are not usually found in alpha helices and why?
Proline – destablilizing kinks, not freely able to rotate around the phi angle, nitrogen hydrogen
not available.
Glycine – r group is small and too flexible, destabilizes the helices.
2.) Beta strand -> forms beta sheets.
 Two types, ______ and _______
 Between these two the hydrogen bonding angle is slightly different.
 R groups project in opposite directions.
 Maximizes H-bonding within the main chain
 Hydrogen boding is intermolecular
 3.5 angstroms between each residue
3.) 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)
4.) 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
Correct answer is b. Beta-sheets R groups are alternating from the top to the
bottom of the sheet.
often contain proline and glycine, why ?
5.) 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
Number 2 – lots of positive charged towards the n terminus – bad interactions bw side chains.
Peptide #1 is likely to form a more stable helix since all of the residues in
helix #2 are large and bulky which could lead to steric hinderance between
side chains. Furthermore, there are large residues with the same charge 34 residues apart , which will lead to electrostatic repulsion of side chains.
3° Tertiary: 3D folding of 2° structure


Motif: recurring structural pattern ; stable arrangement of 2 or more secondary
structural elements + connecting regions e.g. beta barrel, beta alpha beta loop.
Etc.. also called supersecondary structure.
Domains (two types functional and structural): _ distinct structural unit of a
polypeptide_; Can also be a unit of function. Eg. DNA binding domain, antigen
binding domain.
A single polypeptide chain can form two or more units that are independently stable and could
fold separately = domains. Single polypeptide chain can have more than one domain. Eg.
Troponin C has two Ca2+ domains.
4° Quaternary: arrangement in space of 2 or more subunits.


Subunits can function __cooperative___________ or ___independent______
Each subunit is an individual/separate poly peptide chain.
Motifs
I.
Helical Motifs
a. Important rule -> helices pack together according to the “knobs in holes” theory
determined by Francis Crick.
i. This model suggest that when helices pack together they do so in a
slightly tiled fashion – tilt varies between 17° – 22° degrees.
ii. This allows the side chains to pack closely together and allows each side
chain in the hydrophobic core to interact with 4 residues of the adjacent
helix -> stabilizing and strengthening the hydrophobic interactions.
1.) Coiled-coil motif -> 2 right handed alpha helices intertwined and coil around
each in a left handed fashion (aka supercoil)
i. Characteristic 7 amino acid repeat (heptamer) -> every 4th (D) position is
a Leucine (which is hydrophobic)
 Usually labeled a-g
ii. Approx 10.4 angstroms between leucines.
iii. Hydrophobic Leu of adjacent helices pack together every second turn ->
forming a hydrophobic core.
iv. The (A) position is also hydrophobic and assist in forming the
hydrophobic core.
v. Salt bridges are also important for the formation of coiled-coil -> residues
e and g often interact with such salt bridges.
vi. Motif is Often found in fibrous proteins
2.) 4 Helix bundle domain -> 4 helices with their helical axis almost parallel to each
other, but slightly tiled.
i. Side chains are arranged so that the hydrophobic side chains are buried
between the helices and the hydrophillic side 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.) Globin Fold -> an all alpha helix 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 heme group
with coordinates an Iron 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 non-polar core with the exception of 2 His residues which
coordinate Iron unequally -> There is a proximal histidine group attached
directly to the iron center, and a distal histidine group on the opposite
face, not bonded 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 parallel fashion.
Can form large metabolic enzyme complexes, which have several active cavities,
where the product of enzyme subunit is the substrate to the next enzyme
subunit -> shields the substrate from the solvent 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 C-Terminal end
of beta strand to the N-Terminal end of the alpha helix.
ii. Closed alpha/beta barrels have 8 alpha helices and 8 beta sheets.
iii. Usually core of the barrel is filed with large hydrophobic residues
such as -> Val, Ile, Leu.
iv. Example: triosephoshpate isomerase.
b. Open Twisted sheet -> Has helices on both sides
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. Up-Down -> 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 hydrophobic ligands inside a large
hydrophobic 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 Phe residues. Hydrophilic tail (-OH) of
the retinol is exposed to the solvent.
b. Greek Key -> Formed when one of the of the connections of 4 antiparallel B
strands is not a hairpin connection.
c. Jelly Roll
3. Beta-Propeller -> example: Neuraminidase
a. Not a simple barrel but instead, six smaller beta-sheets formed by four antiparallel beta strands are arranged like the blades of a six-bladed propeller.
b. Active site is formed by the loops connecting the C-Terminal end of the beta
strand to the N-Terminal end of the adjacent beta strand, on one side of the
propeller.
c. Four identical beta-propeller subunits come together to form a homo-tetrameric
super-barrel.