Secondary Structure Flashcards
2^(o)=
Local spatial alignment of amino acids
Usually repeated structures.
Examples:
a-helix
β-sheets
loops or random coil
turns
Secondary structure
occurs…
due to
regularly spaced
hydrogen bonds
Sub-Structure=
= Secondary Structure = 2^(o)
structure
The attempt to analyze sub-structure…
- within
the tertiary structure of a polypeptide has
revealed some common patterns. - α helix and β pleated sheet are the most
common secondary structure.
Other less distinct secondary structures:
- b “turn”:
Sharp bend composed
of 3-4 amino acid
residues
- “Loop”:
Larger regions that include less sharp bend or turns
Four levels of architecture in proteins:
- the alpha helix (a-helix) is one
common form of secondary structure - much like the coils of a telephone cable* protein helices are always right-handed(look down the helix in this figure)
- due to the hydrogen bonding networkin an alpha helix, this structure is stable
Secondary Structure: a-helix
- Three-dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape
- Held by H bonds between the H of –N-H group and the –O of C=O of the fourth amino acid along the chain
- Looks like a coiled “telephone cord”
t the helix is stabilized by…
H bonds between atoms in the backbone.
(NOT R group bonds)
Secondary Structure – Triple Helix
- Three polypeptide chains woven together
- Glycine, proline, hydroxyproline and
hydroxylysine - H bonding between –OH groups gives a strong structure
- Typical of collagen, connective tissue, skin,
tendons, and cartilage
Coiled Coils:
higher order structure of alpha-helices (supersecondary structure)
ex: Collagen.
Major structural component in many proteins, some
globular proteins contain mostly…
a-helices, connected by turns.
(i.e., hemoglobin: 70% a-helices)
Some Interesting a-Helices:
- small DNA binding helices
- membrane – spanning helices
- amphipathic helices
- coiled Coils
DNA Binding:
- ana-helix fits perfectly into the major
groove of double stranded DNA. - many DNA binding proteins use
particular a-helices to specifically
recognize a DNA sequence.
Membrane Spanning:
- contains hydrophobic amino acids
in the central region to allow the
protein to cross a bi-layer
membrane
Helical Wheels:
- a tool to visualize the position
of amino acids around an
alpha-helix - allows for quick visualization
of whether a side of a helix
posses specific chemical
properties - example shown is a helix that
forms a Leucine-Zipper
Amphipathic Helices
Amphipathic: hydrophilic & hydrophobic
- these helices posses
hydrophilic amino acids
on one side and hydrophobic
residues on the other. - in some cases these a-helices can
be used to associate a protein to
a membrane.
a-Helix Breakers:
Most amino acids like to be in an a-helix.
Notable exceptions: GLYCINE
PROLINE (imino Acid)
- proline residues often serve as ‘
a-Helix Breakers’ - often found at the boundaries of a-Helices and in turns
The a - helix:
the helix content of proteins
differs markedly
Four levels of architecture in proteins: (b-sheet)
- the beta sheet (b-sheet) is another common form of secondary structure* much like the pleats of an accordion
- beta sheets can join very distant parts of the protein together
- due to the hydrogen bonding network, beta sheets are very stable
Secondary Structure
the Beta Pleated Sheet:
- Polypeptide chains are arranged
side by side - Hydrogen bonds form between
chains - R groups of extend above and
below the sheet - Typical of fibrous proteins such
as silk
The b-pleated sheet is formed from…
two or more extended chain structures, sometimes called strands, where each residue is rotated by 180° with respect to the preceding one.
The b-pleated sheet strands can be arranged…
next to one another to optimize linear hydrogen bonds between them such that their NC directions run Parallel or Antiparallel to one another.
Parallel beta sheet…
Hydrogen bonding pattern is evenly spaced out
Anti-parallel b structure:
Hydrogen bonding patterns: 2 H-bonds closetogether, then a gap, then 2 H-bonds, and so on
Protein structure: beta-sheets:
- the basic unit of abeta-sheet is called abeta-strand
- repeating unit like thealpha helix
- beta-sheets can formvarious higher-level
structures, supersecondary structure such as a betabarrel
The Beta-Sheets:
- strands of amino acids held…
together in sheets by INTER-STRANDH-Bonding
- bonding between backbone >C=O and >N-H on different strands
- strands of the b-sheets tends to be twisted and inclinated in a b-barrel
- the R-groups lie perpendicular to the sheets; stick out on either face of the sheet
In a b-barrel…
amino acids side chains inside the barrel are very
often b-branched or hydrophobics
Beta-Sheets and DNA:
- an alpha-helix is of appropriate size
to fit in the major groove of DNA - beta sheets fit very well into the
minor groove of DNA double helices - beta-sheets can also used in DNA
binding but less commonly
Secondary structure of proteins: (structural properties)
The structural properties of silk are due to beta pleated sheets.
– The presence of so many hydrogen bonds makes each silk fiber stronger than steel.
