α-helix

Examples of α-helix in the following topics:

• Protein Structure

  • The most common forms of secondary structure are the α-helix and β-pleated sheet structures and they play an important structural role in most globular and fibrous proteins.
  • In the α-helix chain, the hydrogen bond forms between the oxygen atom in the polypeptide backbone carbonyl group in one amino acid and the hydrogen atom in the polypeptide backbone amino group of another amino acid that is four amino acids farther along the chain.
  • The R groups (the side chains) of the polypeptide protrude out from the α-helix chain and are not involved in the H bonds that maintain the α-helix structure.
  • The α-helix and β-pleated sheet form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone.
  • Certain amino acids have a propensity to form an α-helix, while others have a propensity to form a β-pleated sheet.

• Secondary & Tertiary Structure of Large Peptides and Proteins

  • The other diagrams display a ball & stick model and a ribbon that defines this α-helix.
  • Using the dihedral angle terminology noted above, a perfect α-helix has Φ = -58º and Ψ = -47º.
  • In natural proteins the values associated with α-helical conformations range from -57 to -70º for Φ, and from -35 to -48º for Ψ.
  • Using this terminology, the alpha-helix is a 3.613 helix.
  • Unlike the other common amino acids, rotation about the α C-N bond in proline is not possible due to the structural constraint of the five-membered ring.

• Initiation of Transcription in Prokaryotes

  • Four of these subunits, denoted α, α, β, and β', comprise the polymerase core enzyme.
  • Each subunit has a unique role: the two α-subunits are necessary to assemble the polymerase on the DNA; the β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent "recently-born" mRNA molecule; and the β' binds the DNA template strand.
  • The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site.

• Summary of Formulas

  • α is preconceived.
  • α = probability of a Type I error = P(Type I error) = probability of rejecting the null hypothesis when the null hypothesis is true.
  • If there is no given preconceived α, then use α = 0.05.

• Decision and Conclusion

  • A systematic way to make a decision of whether to reject or not reject the null hypothesis is to compare the p-value and a preset or preconceived α (also called a "significance level").
  • A preset α is the probability of a Type I error (rejecting the null hypothesis when the null hypothesis is true).
  • If α > p-value, reject Ho.
  • If α ≤ p-value, do not reject Ho.

• Diastereoselection in Reactions with Chiral Enolates

  • These Z-enolates are expected to favor 1,2-syn diastereoselectivity of the newly created α & β chiral centers, as noted earlier.
  • However, the 1,4-diastereoselectivity (α':β) is not consistent.
  • The 1,4-anti-selectivity shown in reactions 6 and 7 is predicted by the transition state model, but the 1,4-syn-selectivity and 1,3-anti selectivity (α':α) in reaction 5 is anomalous.
  • Again, strong facial selectivity is displayed for bonding at the re-face of the enolate as drawn, with both the new 1,2- (α:β) and 1,4- (α':β) diastereoselectivities being syn, as expected.
  • The exceptional and unusual 1,3-anti selectivity (α':α) shown by the Z-enolate is noteworthy.

• The Favorskii Rearrangement

  • Treatment of α-halogenated ketones, having acidic α'-hydrogens, with nucleophilic bases often leads to a skeletal rearrangement known as the Favorskii rearrangement.
  • Here the unsymmetrical cyclopropanone opens to favor the less substituted α-carbon, reflecting the carbanion stability order: 1º > 2º > 3º .
  • In this case cleavage of the cyclopropanol at the more substituted α-carbon probably reflects the inductive effect of the THPO substituent.

• Summary of the Hypothesis Test

  • Compare the preconceived α with the p-value, make a decision (reject or do not reject Ho), and write a clear conclusion using English sentences.
  • Notice that in performing the hypothesis test, you use α and not β. β is needed to help determine the sample size of the data that is used in calculating the p-value.
  • If the power is too low, statisticians typically increase the sample size while keeping α the same.

• Practice: One-Way ANOVA

  • State the decisions and conclusions (in complete sentences) for the following preconceived levels of α .

• Type I and II Errors

  • The threshold for rejecting the null hypothesis is called the α (alpha) level or simply α.
  • The Type I error rate is affected by the α level: the lower the α level, the lower the Type I error rate.
  • It might seem that α is the probability of a Type I error.
  • Instead, α is the probability of a Type I error given that the null hypothesis is true.