CH 17: Amino Acids, Peptides, and Proteins

How are disulfide bonds formed and broken?

Formed by oxidation of thiol groups (-SH) to create disulfides (-S-S-); they can be reduced back to thiols.

Can an amino acid exist as an uncharged compound?

No, an amino acid can never exist as an uncharged compound.

What is the purpose of disulfide bonds in proteins?

Disulfide bonds contribute to the overall shape of proteins.

Which charged amino acids does the resin in ion-exchange chromatography bind to?

Negatively charged resin binds selectively to positively charged amino acids.

What is the primary structure of a protein?

The sequence of amino acids in the chain and the location of disulfide bridges.

How is an amino acid sequence read?

The structure is read from the N-terminus to the C-terminus end.

What is quaternary protein structure?

Individual polypeptide chains called subunits assembling into (more than one polypeptide chain called) an oligomer.

What role do porphyrin rings play in hemoglobin?

They bind to oxygen and carbon dioxide molecules.

What property does thin layer chromatography separate amino acids by?

It separates amino acids based on their relative polarity.

What are the main types of secondary structures found in globular proteins?

α-helix coils and β-pleated sheets

At what pH does the amino group of an amino acid become protonated?

The amino group gets protonated at lower (more acidic) pH.

How is the pI calculated for amino acids without ionizable R-groups?

It is the average of the pKa values of the amino and carboxyl groups.

What characterizes the tertiary structure of proteins?

It is defined by primary structure. The three-dimensional arrangement of all atoms in the protein.

At what pH does the carboxyl group of an amino acid get deprotonated?

The carboxyl group gets deprotonated at higher (more basic) pH.

How do amino acids differ from one another?

Amino acids differ from each other by the R group attached to the α-carbon.

What determines the configuration (D or L) of an amino acid?

• The position of the amino group on the α-carbon

  • On the Fischer projection, the amino group on the right side means it is the D configuration.

  • On the Fischer projection, the amino group on the left side means it is the L configuration.

What is the isoelectric point (pI) of an amino acid?

The pI is the pH at which the amino acid has no net charge.

What factors determine the choice of secondary structure in proteins?

Regional planarity of each peptide bond, the maximization of hydrogen bond engagement, and adequate separation of R groups.

What chemical reaction converts an α-keto carboxylic acid into an amino acid?

Reductive Amination

How do R-groups protrude in an α-helix?

R-groups extend outward from the α-helix, pointing away from the helical backbone.

How much double-bond character is in peptide bonds?

40%

How does electrophoresis separate amino acids?

Electrophoresis separates amino acids based on their pI values.

What stabilizes an α-helix?

Hydrogen bonds between the peptide groups in the backbone.

How is the pI calculated for amino acids with ionizable R-groups?

The pI is calculated by the average of the pKa values of groups with similar charge.

What are peptides, polypeptides, and proteins made of?

Polymers of amino acids linked together by amide (peptide) bonds.

In terms of quanternary structure, what are the individual chains in a protein called?

Subunits

What is the quaternary structure of hemoglobin?

A tetramer composed of two different types of subunits, with each hemoglobin molecule containing two of each.

What influences the tertiary structure of a protein?

Stabilizing interaction which are covalent bonds, hydrogen bonds, electrostatic attraction, and hydrophobic interactions.

How are R-groups placed on the peptide bonds?

opposite sides of each other

In electrophoresis, how are individual amino acids detected?

Ninhydrin binds to the amino acids and colors it.

What reagents reacts with an α-keto carboxylic acid to form a zwitter ion?

1) H⁺ (trace acid), excess NH₃

2) H₂, Pd/C or Pt/C

What mechanism reacts with an aldehyde to form a positively charged amino acid?

Strecker Synthesis

What mechanism reacts with an α-bromomalonic ester to form a positively charged amino acid?

Gabriel Synthesis

What reagents react with α-bromomalonic ester to form a positively charged amino acid?

1) potassium phthalimide

2) X^{+ -}OR

3) R’—Br

4) HCl, H₂O and heat

What mechanism reacts with a thiol to form a disulfide?

Oxidation of Thiols

What reagents react with a thiol to form a disulfide?

1) NaOH, H₂O

2) Br₂

3) R—S^-

What are similarites and differences between α-helix coils and ß-pleated sheets?

similarities:

• α-helix coils and parallel ß-pleated sheets have their R-groups protrude outwards.

• both types are stabilized by hydrogen bonding.

differences:

• ß-pleated sheets require two strands of amino acids while α-helix coils require only one.

• ß-pleated sheets have two types of structure (parallel and antiparallel) while the α-helix coils only have one.

• The peptide groups in the α-helix coils are held together by H-bonds while the amino strands in the ß-pleated sheets are held together by H-bonds.

What is the secondary structure of a protein?

the repetitive conformations assumed by segments of the backbone of a peptide or protein

When a protein folds, what is the only covalent bond that can form?

disulfide bonds