Summary The Three-dimensional Structure of Proteins
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Course
Molecular And Cell Biology (MCBG2039A)
Institution
University Of The Witwatersrand (wits)
Book
Biochemistry
These notes are a comprehensive summary of chapter 6: The 3-D Structure of Proteins. The topics include:
The Secondary Structure: Regular Ways to Fold the Polypeptide Chain.
Fibrous Proteins: Structural Materials of Cells and Tissues.
Globular Proteins: Tertiary Structure and Functional Diversit...
IIA: Molecular Processes- The primary level of Protein Structure
FULL Summary Biochemistry, ISBN: 9781292267203 Biochemistry
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University of the Witwatersrand (wits)
Molecular And Cell Biology (MCBG2039A)
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Secondary Structure: Regular Ways to Fold the Polypeptide Chain
Theoretical Descriptions of Regular Polypeptide
Structures
In the early 1950s, Pauling and collaborators
postulated several principles of secondary protein
structures that any such structure must obey:
1. Bond angles and lengths should be like those for
respective free amino acids
2. No atoms should approach one another more
closely than allowed by their van der Waals radii
3. The amide group must remain planar
4. Some kind of noncovalent bonding is necessary to
stabilize a regular folding. Noncovalent bonds
(particularly hydrogen bonds) stabilize folding
processes and products
Steric hindrance can occur due to the overlap of
any atoms in the structure
α-helix β-sheet
𝟑𝟏𝟎 -helix
TJW Notes
,α Helices and β Sheets
• Of the several possible secondary structures for polypeptides, the most frequently observed are the α helix
and the β sheet.
• All of the protein secondary structures shown satisfy the criteria listed earlier.
• In each structure the amide group is planar, and all amide protons and carbonyl oxygens (except a few
near the ends of helices, or edges of sheets) are involved in hydrogen bonding.
• The arrangement of the main-chain hydrogen bonds in the a helix orients the amide N–H and C=O groups
such that the dipole moments for each of these polar bonds align and give rise to a helical dipole moment
(also called a “macrodipole”).
• In effect, the N-terminus of the helix has partial (+) charge character, and the C-terminus has partial (-)
charge character.
α Helix
→ Its center consists of backbone atoms, closely packed together.
→ The hydrogen stabilize the helix and are nearly parallel to the helix axis.
→ Side chains radiate out from helix axis
→ Helix may have distinct hydrophilic and hydrophobic faces
TJW Notes
, β Sheets
→ β sheet: stabilized by inter-chain H bonds; side
chains alternate sides of the sheet
→ A β sheet is composed of two or more β strands
with main-chain hydrogen bonds between adjacent
β strands.
→ There are two ways in which b strands can be
oriented in a β sheet:
⤷ two β strands arranged such that the N-terminus
to C-terminus orientations of the two strands are
in opposite directions ~ antiparallel
⤷ the arrangement with both strands oriented in
the same direction is called ~ parallel
→ In addition to the helices and sheets described
above, there is one more regularly repeating
conformation that is commonly observed in protein
structures—the so-called polyproline II helix.
→ This particular conformation was not predicted on
theoretical grounds because it does not satisfy
Pauling’s requirement for hydrogen bonding.
→ This structure does not have stabilizing hydrogen
bonds between main-chain groups, and it is left-
handed.
→ Roughly a third of the amino acid residues found in
this conformation are prolines, leading to the
designation “polyproline II helix. ”
→ Glycine is also often found in this helix, as are,
albeit to a much lesser extent, several other amino
acids.
TJW Notes
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