Secondary Structure

Question 1

2^(o)=

Answer 1

Local spatial alignment of amino acids

Usually repeated structures.

Examples:

a-helix
β-sheets
loops or random coil
turns

Question 2

Secondary structure
occurs…

Answer 2

due to
regularly spaced
hydrogen bonds

Question 3

Sub-Structure=

Answer 3

= Secondary Structure = 2^(o)
structure

Question 4

The attempt to analyze sub-structure…

Answer 4

• within
  the tertiary structure of a polypeptide has
  revealed some common patterns.
• α helix and β pleated sheet are the most
  common secondary structure.

Question 5

Other less distinct secondary structures:

Answer 5

• b “turn”:

Sharp bend composed
of 3-4 amino acid
residues

• “Loop”:

Larger regions that include less sharp bend or turns

Question 6

Four levels of architecture in proteins:

Answer 6

• 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

Question 7

Secondary Structure: a-helix

Answer 7

• 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”

Question 8

t the helix is stabilized by…

Answer 8

H bonds between atoms in the backbone.

(NOT R group bonds)

Question 9

Secondary Structure – Triple Helix

Answer 9

• 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

Question 10

Coiled Coils:

Answer 10

higher order structure of alpha-helices (supersecondary structure)

ex: Collagen.

Question 11

Major structural component in many proteins, some
globular proteins contain mostly…

Answer 11

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

Question 12

DNA Binding:

Answer 12

• ana-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.

Question 13

Membrane Spanning:

Answer 13

• contains hydrophobic amino acids
  in the central region to allow the
  protein to cross a bi-layer
  membrane

Question 14

Helical Wheels:

Answer 14

• 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

Question 15

Amphipathic Helices

Answer 15

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.

Question 16

a-Helix Breakers:

Answer 16

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

Question 17

The a - helix:

Answer 17

the helix content of proteins
differs markedly

Question 18

Four levels of architecture in proteins: (b-sheet)

Answer 18

• 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

Question 19

Secondary Structure
the Beta Pleated Sheet:

Answer 19

• 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

Question 20

The b-pleated sheet is formed from…

Answer 20

two or more extended chain structures, sometimes called strands, where each residue is rotated by 180° with respect to the preceding one.

Question 21

The b-pleated sheet strands can be arranged…

Answer 21

next to one another to optimize linear hydrogen bonds between them such that their NC directions run Parallel or Antiparallel to one another.

Question 22

Parallel beta sheet…

Answer 22

Hydrogen bonding pattern is evenly spaced out

Question 23

Anti-parallel b structure:

Answer 23

Hydrogen bonding patterns: 2 H-bonds closetogether, then a gap, then 2 H-bonds, and so on

Question 24

Protein structure: beta-sheets:

Answer 24

• 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

Question 25

The Beta-Sheets:
- strands of amino acids held…

Answer 25

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

Question 26

In a b-barrel…

Answer 26

amino acids side chains inside the barrel are very
often b-branched or hydrophobics

Question 27

Beta-Sheets and DNA:

Answer 27

• 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

Question 28

Secondary structure of proteins: (structural properties)

Answer 28

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.