1. Read the following slides by “Day 12”

2. Proteins are long chains of amino acids, but the chain isn’t just extended and flopping around. Rather, it is “folded” into a specific 3-dimensional shape/structure:
A protein’s amino acid SEQUENCE determines its STRUCTURE
A protein’s STRUCTURE determines its FUNCTION

3. Overview of Protein Structure: Flexibility of the Polypeptide Chain
So far we have covered protein SEQUENCE
Next we will cover protein STRUCTURE
Later we will cover protein FUNCTION
Overview of Protein Structure:
Flexibility of the Polypeptide Chain

4. Remember that amino acids are joined by peptide bonds:
Fig 3-13 from Lehninger

5. The peptide bond has partial double bond character:
The peptide bond has resonance structures (shown above), due to partial sharing of two pairs of electrons.
Therefore: C-N bond is shorter than C-N bond of a simple amine;
O has d- charge, N has d+ charge (there is an electric dipole);
peptide bond does not rotate
Fig 4-2 from Lehninger 5th ed.

6. The peptide bond does not rotate: it exists
in either the trans or cis configuration O O H R H O H C N C C N C N C C C C N R R R H O
O and H are in cis positions surrounding the peptide bond
O and H are in trans positions surrounding the peptide bond
How can you tell which is trans and which is cis?
Look at the positions of the oxygen and hydrogen of the amide functional group (containing the peptide bond).
Figure 3.25, Biochemistry, by Berg, Tymoczko, Stryer, 5th ed.

7. The peptide bond does not rotate: most peptide bonds are in the trans configuration because the cis configuration is sterically unfavorable. O O H R H O H C N C C N C N C C C C N R R R H O
99.95% of peptide bonds % of peptide bonds
for amino acids other for amino acids other
than proline exist in trans than proline exist in cis
configuration configuration
no steric clashes; R groups steric clashes between
are spaced far apart R groups (indicated by
orange semi-circles)
Figure 3.25, Biochemistry, by Berg, Tymoczko, Stryer, 5th ed.

8. Peptide bonds next to proline are different from other peptide bonds (the reason is on next slide):
X-Pro peptide bond– refers to the peptide bond on the N-terminal side of a Pro residue; X represents any amino acid.
Example: – Lys – Pro – Ala –
Lys is on N-terminal side or Pro
Ala is on C-terminal side or Pro
Peptide bond between Lys and Pro is the X-Pro peptide bond
Pro-X peptide bond– refers to the peptide bond on the C-terminal side of a Pro residue; X represents any amino acid.
Example: – Lys – Pro – Ala –
Peptide bond between Pro and Ala is the Pro-X peptide bond

9. X-Pro peptide bonds: energies of the trans and cis forms are
relatively balanced because steric clashes occur in both forms C O C C C C N C H C N C N C C C C N C O C H O O
94% of X-Pro bonds exist in trans configuration
6% of X-Pro bonds exist in cis configuration (higher percentage than for other peptide bonds!)
Figure 3.26, Biochemistry, by Berg, Tymoczko, Stryer, 5th ed.

10. How can you tell which is trans and which is cis for an X-Pro peptide bond?
Look at the positions of the oxygen and Pro side chain surrounding the peptide bond. C O C C C C N C H C N C N C C C C N C O C H O O
O and C of Pro side chain are in cis positions surrounding the peptide bond
O and C of Pro side chain are in trans positions surrounding the peptide bond
Figure 3.26, Biochemistry, by Berg, Tymoczko, Stryer, 5th ed.

11. Consider the atoms surrounding the peptide bond:
The peptide bond is between C and N.
There are a total of 4 atoms bonded directly to the C and N.
These 6 atoms are in the same plane
because the peptide bond cannot rotate (it’s similar to a double bond). 1 6 4 2 5 3
Like a double bond, can’t rotate. 1 6 4 2 5 3
For comparison:
a carbon-carbon double bond can’t rotate. Therefore, the 6 atoms form a plane.
Fig 1-15 from Lehninger

12. This ball-and-stick model gives a more realistic picture of how the six atoms of the peptide group form a plane:
This square indicates the plane formed by the 6 atoms.
Notice how the R groups (purple spheres) are not in the plane. O R H C Ca N N Ca C H R O
Peptide bond is like a double bond, can’t rotate.
Fig 4-2 from Lehninger

13. To view the peptide plane with a sense of 3 dimensions, go to the website below and follow the instructions:
Select the Jsmol option, then select Peptides from the menu on the right.
Click the Tripeptide button and select one of the boxes to color the peptide as you wish.
Select the last box to highlight the peptide planes.
Rotate the molecule with your mouse, and zoom in by holding down the shift key while moving the mouse.
Which 6 atoms form each plane?

14. A polypeptide chain is like a series of these planes which are connected at their corners (see squares/planes on figure below). Ca
Since the peptide bonds can’t rotate, bond rotation occurs only at the corners (Ca) of adjacent planes, by rotation of the single bonds on either side of each Ca.
Fig 4-2 from Lehninger

15. f and y are called dihedral angles or torsion angles
Rotation of the single bonds on either side of Ca is indicated by the circular arrows: O H C Ca N N C Ca H O
f (phi) = the angle formed by rotation of N-Ca bond
y (psi) = the angle formed by rotation of Ca-C bond
f and y are called dihedral angles or torsion angles
Fig 4-2 from Lehninger

16. Determining the values of f and y:
each angle can range from
-180o to +180o
Figure 3.27, Biochemistry, by Berg, Tymoczko, Stryer, 5th ed.

17. Ramachandran plot for a peptide made entirely of L-Ala residues
Not all values of f and y are allowed, due to steric hindrance. In other words, if certain angles are adopted, atoms would be bumping into each other. A Ramachandran plot shows the allowed values for the dihedral angles.
Ramachandran plot for a peptide made entirely of L-Ala residues
Dark blue:
fully allowed
angles
Lighter blue:
allowed angles, but less favorable
Tan region: angles that are not allowed due to steric hindrance
Fig 4-3 from Lehninger

18. On a Ramachandran plot, would the allowed regions be bigger or smaller for an L-Trp polypeptide (compared to the L-Ala polypeptide on previous slide)? Would the allowed regions be bigger or smaller for an L-Gly polypeptide?
Think about proline– which dihedral angle (f or y) for a Pro residue will be greatly restricted in its allowed conformations? Why?

19. Protein Secondary Structure
Protein structure can be described hierarchically. Proteins are viewed as having different levels of structure with progressively greater complexity.
The four levels, from simplest to most complex, are:
Primary structure (Abbreviated as “1o structure”)
Secondary structure (Abbreviated as “2o structure”)
Tertiary structure (Abbreviated as “3o structure”)
Quaternary structure (Abbreviated as “4o structure”)

20. Primary Structure– a description of all covalent bonds linking the amino acid residues (includes peptide bonds and disulfide bonds). Therefore, the primary structure of a protein is simply its amino acid sequence, written from N-terminus to C-terminus, with any disulfide bonds or other covalent bonds indicated.
Every protein has a different primary structure. (Millions of combinations of the 20 amino acids are possible and the length of the chain can vary from hundreds to thousands of amino acids.)
Example– the primary structure of the protein hemocyanin is shown here:
(An unusual covalent bond exists between a specific Cys and His– this bond is part of the primary structure and is indicated.)
Ala-Ile-Ile-Arg-Lys-Asn-Val-Asn-Ser-Leu-Thr-Pro-Ser-Asp-Ile-Lys-Glu-Leu-
Arg-Asp-Ala-Met-Ala-Lys-Val-Gln-Ala-Asp-Thr-Ser-Asp-Asn-Gly-Tyr-Gln-
Lys-Ile-Ala-Ser-Tyr-His-Gly-Ile-Pro-Leu-Ser-Cys-His-Tyr-Glu-Asn-Gly-Thr-
Ala-Tyr-Ala-Cys-Cys-Gln-His-Gly-Met-Val-Thr-Phe-Pro-Asn-Trp-His-Arg-
Leu-Leu-……… (404 residues total)

21. 1. a-helix– the amino acid chain coils loosely, like a spring
Secondary Structure– the 3D spatial arrangement of amino acid residues that are adjacent in the primary structure. (You can think of secondary structure as regions of “local” structure formed by neighboring residues when the chain folds back on itself.)
We can categorize the local 3D spatial arrangements adopted by the amino acid chain into four main categories (or 4 types of 2o structural elements):
1. a-helix– the amino acid chain coils loosely, like a spring
2. b-strand– the amino acid chain is extended with the backbone forming a slight zig-zag pattern
3. b-turn– the chain wraps around sharply, forming a 180o turn
4. random coil and/or loop– no specific structural pattern
Suppose the line below represents a protein of 300 amino acids (its N and C-termini are labeled):
Below, sections of this amino acid chain have folded into two a-helices and two b-strands:
Here the chain has formed a b-turn: N C N C N C

22. Tertiary Structure– the overall 3-dimensional arrangement of all atoms in
a protein. (You can think of tertiary structure as the “global” structure adopted by the entire amino acid chain as it folds back on itself.)
The amino acid chain is folded back on itself, so that the a-helices and b-strands interact with each other, and an overall three-dimensional structure/shape is formed—this “global” structure is the protein’s tertiary structure.
Suppose the amino acid chain from the previous slide (containing a-helices and b-strands) is wrapped up into “a ball”:
b-strands are normally depicted as arrows, so the above protein structure can be represented like this: N
the tertiary
structure C N C

23. Quaternary Structure
Some proteins, in their functional form, are composed of more than one amino acid chain. When this is the case, each amino acid chain is called a subunit of the protein. These subunits always associate with each other in a specific spatial arrangement. That spatial arrangement is the protein’s quaternary structure. (Note that proteins composed of a single amino acid chain do not have quaternary structure.)
Example– Suppose a specific protein has four subunits, and each
cylinder at the right represents one folded subunit. When the subunits
associate, the way they are arranged next to each other in 3D space is
this protein’s quaternary structure (shown at the right).
You can imagine a variety of other possible
quaternary structures for these four subunits, such as those shown below. But normally the subunits will only be arranged in one way, and that particular way is that protein’s quaternary structure.

24. Residues 2773 to 2790 of the octopus protein hemocyanin form an alpha-helix.
This is a description of the _______ structure of this protein.
The first 6 residues of the sweet potato enzyme polyphenol oxidase are Ala-Pro-Ile-Gln-Ala-Pro-….
This is a description of the _______ structure of this protein.

25. The four common types of secondary structure:
a-helix
b-strand
b-turn
random coil and/or loop (no specific structural pattern)
Next we will study these structural elements one at a time.

26. This diagram of an a-helix illustrates two important structural features:
the backbone coils into a right-handed helical shape
the side chains stick out all around the “outside surface” of the helix
left-handed right-handed
helix helix
green spheres
represent
side chains
ribbon
represents
backbone
Fig from Biochemistry, 5th ed., by Berg, Tymoczko, and Stryer.
Box 4-1 from Lehninger

27. This figure shows a ball-and-stick model of an a-helix.
All the atoms of the backbone are shown, but the side chains are shown simply as purple spheres. N
One turn of the helix:
5.4 Å per turn
(0.54 nm per turn)
3.6 residues per turn C
Fig 4-4 from Lehninger

28. The dihedral angles of all residues in an a-helix are approximately:
f = -60o
y = -45o to -50o
This region represents a-helices
Fig 4-3 from Lehninger

29. is a sterically favorable structure for the amino acid chain.
This realistic space-filling model of an a-helix illustrates three structural features:
It doesn’t look like a spring– you can’t easily see the backbone coiling into
the helical shape.
The side chains protrude all around the outside surface of the helix– this
is a sterically favorable structure for the amino acid chain.
The helix is not hollow– the “center” is “filled” by the atoms of the
backbone.
Looking down the
helix from one end:
purple spheres
represent
side chains
gray atoms are
backbone atoms
green spheres
represent
side chains
blue and white
atoms are
backbone atoms
Fig from Biochemistry, 5th ed.,
by Berg, Tymoczko, and Stryer.
Fig 4-4

30. a-helices are stabilized by hydrogen bonds that occur between every “residue i” and “residue i+4” all along the length of the helix.
Each hydrogen bond is between the carbonyl oxygen of “residue i” and the amide hydrogen of “residue i+4.”
Suppose the amino acid chain of an a-helix was uncoiled, as shown below. We could then easily map out the locations of the hydrogen bonds by numbering the residues. Two of the hydrogen bonds are indicated below:
from residue i+1 to i+5
from residue i to i+4 N C
i i i i i i+5
(This pattern would continue down the helix: bond between i+2 and i+6; bond between i+3 and i+7; etc.)
Fig from Biochemistry, 5th ed., by Berg, Tymoczko, and Stryer.

31. Hydrogen bonds stabilize the structure of an a-helix.
Here the backbone of the amino acid chain is shown coiling into an a-helix, and the hydrogen bonds are shown in green. If you count carefully, you can see that they occur between every residue i and i+4. N H O O N H N H O O N H N H O
N-H of residue i+4 O N H N H
C=O of residue i O N H
Important Features to Note:
The hydrogen bonds are roughly parallel to the axis of
the helix.
Hydrogen bonds occur all the way up and down the
entire length of the helix.
The hydrogen bonds are between atoms of the
backbone (not atoms of the side chains).
The combined effect of all the hydrogen bonds gives
the helix considerable stability. O N H O N H O N H O N H N H N
Fig of Denniston, Topping, & Caret,
General, Organic, and Biochemistry, 4th ed.

32. Consider the peptide below
Consider the peptide below. If it were to form an a-helix, which residue(s) would form backbone hydrogen bonds to Phe?
Asp-Val-Arg-Ile-Lys-Glu-Phe-Cys-Ser-Leu-Asn-Thr-Asp-Trp

33. Factors Affecting a-Helix Stability:
1. Electrostatic repulsion or attraction between successive residues
with charged R groups. (residues i and i+1)
Examples: Which would favor helix stability and which would not?
Glu next to Glu (pH 7)
Arg next to Asp (pH7)
Lys next to Lys (pH 7)
2. Bulkiness of adjacent R groups. (residues i and i+1)
Two bulky residues adjacent to each other will destabilize
the helix due to steric hindrance.
Example: Trp at ‘i’ and Phe at ‘i+1’ destabilize the helix.
3. Interaction of R groups spaced 3 residues apart.
R groups spaced 3 residues apart are above/below each
other in 3D space, so they are positioned well for
interaction. (residues i and i+3)
Example: Side chains of Asp100 and Arg103 in this helix
interact favorably, forming an ion pair and stabilizing the helix.
(a pair of oppositely charged ions is often called a “salt bridge”)
Arg103
Asp100
Fig 4-5, Lehninger, 4th ed.

34. 3. Continued… (i and i+3)
Another example: Aromatic R groups spaced 3 residues apart interact via the hydrophobic effect and stabilize the helix. Since aromatic groups are flat, they stack like pennies and their p-orbitals interact (p-p interactions).
4. Occurrence of Pro and Gly residues.
Pro destabilizes a helix and is rarely found in helices because:
(a) All f angles in a helix must be ~60o, but rotation of f is limited for Pro Pro won’t be able to adopt a proper f angle, and this incorrect f angle in the helix causes a destabilizing kink/bend in the helix.
(b) Pro has no H attached to its N, so it cannot H-bond with the C=O that
is 4 residues away in the helix.
Gly destabilizes a helix because:
Gly has only hydrogen for a side chain (very small). Therefore, Gly residues have more conformational freedom than other residues. Due to this conformational flexibility, Gly residues tend to adopt other structures, rather than a-helices. f

35. d- d+ C 5. Interaction between amino acid residues
at the ends of the helix and the electric dipole
of the helix.
There is a dipole moment associated with
each peptide bond (due to resonance structures).
These dipoles are connected through the H-bonds
up and down the length of the helix.
The result is a net dipole along the entire helix:
d+ at N-terminus, d- at C-terminus
Therefore, negative side chains at N-term stabilize the
helix, and positive side chains at C-term stabilize the
helix (also: negative side chains at C-term destabilize;
positive side chains at N-term destabilize). N H O O N H N H O O N H N H O O N H N H O N H O N H O N H O N H O N H d+ N H N
Fig of Denniston, Topping, & Caret,
General, Organic, and Biochemistry, 4th ed.

36. Asp-Val-Arg-Ile-Lys-Glu-Phe-Cys-Ser-Leu-Asn-Thr-Asp-Trp
Assume that this peptide forms an a-helix.
1. How would helix stability be affected by the fact that Lys is next to Glu?
2. The Arg could form a salt bridge with the ______.
3. Are the Phe and Trp in positions that will allow their hydrophobic aromatic rings to stack and participate in the hydrophobic effect?
4. There is an Asp at the N-terminus of this helix. How will this affect helix stability?

37. Assume that two a-helices are oriented next to each other in the 3-dimensional structure of a certain protein. These helices are only a portion of the polypeptide chain, so the chain continues on at the end of each helix. (In other words, there isn’t a free a-amino or free a-carboxyl group at the end of each helix.)
Which orientation would be more stable? Why? N C A B

38. Work through the alpha helix tutorial available here:
Select the Jsmol option, then select Alpha helix from the menu on the right.
Click the “X” buttons in order as you carefully read the information on the right. As you go, rotate the molecule with your mouse, and zoom in by holding down the shift key while moving the mouse.
Notice that the backbone of the polypeptide chain forms the helical shape. Where are the side chains located? Which functional groups and atoms form the stabilizing hydrogen bonds? Can you locate the N-terminus and C-terminus of the helix?

39. Read the following slides by “Day 13”

40. This diagram of a b-strand illustrates two important structural features:
the backbone is extended but has a slight zig-zag (pleated) conformation
the side chains stick out, alternating “above and below” the strand
ribbon
represents
backbone
purple spheres
represent
side chains
View from the edge of the strand

41. Here the amino acid chain is shown in order to show the locations of all atoms, and to show how the backbone adopts the zig-zag conformation:

42. The dihedral angles of all residues in a b-strand are approximately:
f = -90o
y = +150o
This region represents b-strands
Fig 4-3 from Lehninger

43. Multiple b-strands always occur side by side, forming a structure called a b-sheet.
Suppose the line below represents the amino acid chain of a protein and each arrow represents a b-strand. (Arrow always drawn so that it points from N-terminus of the protein to C-terminus.) N C
The chain can wrap around so the b-strands are side by side and running in opposite directions. The two b-strands are then forming an
antiparallel b-sheet. N C
Or the chain can wrap around so the b-strands are side by side and running in the same direction. They are then forming a parallel b-sheet. N C

44. The “pleats” of one b-strand line up with those on the
Another representation of a b-sheet is shown below. This figure emphasizes three structural features of b-sheets:
The “pleats” of one b-strand line up with those on the
neighboring b-strand
The side chains on one b-strand line up with those on the
On a given b-strand, the side chains alternate between protruding out on one side of the sheet (toward you) and protruding out on the other side of the sheet (away from you). Thus, the front surface of the sheet is “coated” in side chains, and the back surface is also “coated” in side chains.

45. Larger b-sheets are common
Larger b-sheets are common. For example, this is a representation of a three-stranded b-sheet: N C

46. Each b-strand is depicted as an arrow, pointing from N to C.
This diagram shows three b-sheets stacked on top of each other, a common occurrence in protein structures.
Each b-strand is depicted as an arrow, pointing from N to C.
In this case, neighboring strands are arranged in an antiparallel fashion. (Side chains are not shown in this diagram.)
Fig 4-14 from Lehninger

47. The side chains stick out, alternating “above and below”
This diagram represents two b-sheets stacked on top of each other. Each blue pleated sheet represents a b-sheet, and the R groups represent said chains. It illustrates two points:
The side chains stick out, alternating “above and below”
the plane of each b-sheet
When two sheets are stacked, their side chains are in
contact, interacting with each other
Side chains (R) alternate between pointing above and pointing below the plane of each b-sheet.
Fig from McMurry & Castellion, Fundamentals of
General, Organic, and Biological Chemistry, 4th ed.

48. The figure below shows two stacked b-sheets, but in more detail than the diagram on the previous slide. The side chains of the sheets protrude above and below the plane of each sheet. The sheets are closely stacked so the side chains of one sheet interlock with those of the neighboring sheet. This close contact allows van der Waals interactions between the side chains.
Top b-sheet
The interlocking side chains (colored black)
Bottom b-sheet

49. Go to the following website to view 3 stacked b sheets in a protein called silk fibroin (the web material secreted by spiders is composed of this protein):
Zoom in by holding down the shift key while moving the mouse. Rotate the structure and look for interlocking side chains as shown below.
Top b-sheet
The interlocking side chains (colored black)
Bottom b-sheet

50. b-sheets are stabilized by hydrogen bonds that occur between neighboring b-strands in the sheet.
Each hydrogen bond is between a carbonyl oxygen of one b-strand and an amide hydrogen of the neighboring b-strand. (The hydrogen bonds are between atoms of the backbone, not atoms of the side chains.) N C N C
An antiparallel b-sheet; hydrogen bonds shown in red.

51. A parallel b-sheet. Hydrogen bonds shown in red.
Note that the hydrogen bonds are at a slight angle relative to those in an antiparallel b-sheet (on previous slide). N C C N

52. Another view of the hydrogen bonds that stabilize an ANTIPARALLEL b-sheet. (Hydrogen bonds shown as blue dashed lines.)
(Hydrogen bonds between backbone C=O and N-H of adjacent strands) N C C N N C
Fig 4-6 from Lehninger

53. Another view of the hydrogen bonds that stabilize a PARALLEL b-sheet
Another view of the hydrogen bonds that stabilize a PARALLEL b-sheet. (Hydrogen bonds shown as blue dashed lines.)
(Hydrogen bonds between backbone C=O and N-H of adjacent strands)
Note the hydrogen bonds
are at a slight angle. N C N C N C
Fig 4-6 from Lehninger
(tilted)

54. A single b-strand won’t exist alone. Why?

55. N ____ - ____ - ____ - ____ C
We will do this exercise in class:
Come up with the sequences for two 4-residue b-strands that will form an “amphipathic” parallel b-sheet. An amphipathic b-sheet has one surface that is polar (polar R groups on that surface) and one surface that is nonpolar (nonpolar R groups on that surface). Use what you have learned about the positions of the side chains in a b-sheet to ensure that the sheet is amphipathic.
N ____ - ____ - ____ - ____ C
Purple spheres on “back” surface of sheet represent polar side chains;
yellow spheres on “front” surface represent nonpolar side chains.
Note: On one of the Problem Set questions you will examine a realistic molecular model of an amphipathic beta-sheet.

56. Secondary vs. Tertiary Structure
Remember: 2o structure is local structure, 3o structure is global structure.
The residues making up an a-helix are always near each other in the primary structure (so an a-helix is an element of 2o structure).
The residues making up a b-sheet can be distant from each other in the primary structure (so a b-strand is an element of 2o structure, but a b-sheet is really an element of 3o structure).
There could be a very long loop connecting the two strands that interact to form a b-sheet.
Figs 4-4, 4-6 from Lehninger

57. b-Turns: Allow the amino acid chain to make a 180o turn.
Formed by four residues.
Stabilized by a hydrogen-bond between backbone C=O of
1st residue and N-H of 4th residue (see figure). R
Commonly occur between
two b-strands of an
antiparallel b-sheet, as shown
here: C
(always) 4 3 C 2 N 1 R R
b-turn N
(more common)
Fig 4-7 from Lehninger

58. Gly and Pro are commonly found in b-turns because:
Gly has only H as its R-group, so it is small and flexible. This enables the chain to make a tight turn without steric hindrance.
X-Pro peptide bonds form the cis configuration more often than other peptide bonds, and a cis peptide bond enables the chain to make a tight turn. (6% of X-Pro peptide bonds are cis; only 0.05% of other peptide bonds are cis.)
A b-turn that contains Pro
X-Pro
X-Pro
Figs 4-8, 4-7 from Lehninger

59. Some amino acids are accommodated better than
others in different types of secondary structures.
Note the trend for Gly and Pro.
Fig 4-10, Lehninger, 4th ed.

60. Work through the beta strand tutorial available here:
Select the Jsmol option, then select Beta strand from the menu on the right.
Click the “X” buttons in order as you carefully read the information on the right. As you go, rotate the molecule with your mouse, and zoom in by holding down the shift key while moving the mouse.
Notice that the backbone of the polypeptide chain forms the strands. Where are the side chains located? Which functional groups and atoms form the stabilizing hydrogen bonds? Can you locate the N-terminus and C-terminus of each strand? Is the sheet parallel or antiparallel?
If your computer has Java, carfully examine the 3D rendering of a
4-stranded beta sheet available here:
After the molecule stops spinning, you can rotate it with the mouse and change the rendering using the buttons at the right. Try to answer the same questions as above for the tutorial.

61. To see a complete protein structure containing alpha helices and beta strands go to this website:
Select the Jsmol option, then select Lysozyme from the menu on the right.
The protein is first shown as a simple “ribbon diagram” so that the helices and strands are easy to identify. Whenever an arrow is used to represent a beta strand, the arrow head points from N- to C-terminus. How many strands are forming the beta sheet? Are the neighboring strands arranged in a parallel or antiparallel fashion? Can you locate two beta turns in the beta sheet?
Click the “spheres” button to show ALL the atoms. This shows a “space-filling” model which gives a realistic representation of the overall shape of the protein molecule.

62. To see an example of 3 beta sheets stacked on top of each other, go to this website:
Click the “cartoon” option at the right to see a simple “ribbon diagram.” You should be able to identify 3 beta sheets stacked on top of each other.
How many beta strands form each of the sheets? The side chains are not shown in a ribbon diagram, but can you determine where they would be located?
If your computer has Java, examine the 3D rendering of a beta turn available here:
After the molecule stops spinning, you can rotate it with the mouse and change the rendering using the buttons at the right. How many residues form the turn? Where is the stabilizing hydrogen bond located (which residues, atoms, functional groups, are involved?)