BIOC 2580

Label the steps of tandem mass spectrometry.

• A) Electrospray ionization (sample hydrolyzed by protease into peptides)

  B) 1st Mass Spectrometer

  C) 2nd Mass spectrometer

  D) Collision cell
  E) Detector

• A) 1st Mass Spectrometer

  B) Electrospray ionization (sample hydrolyzed by protease into peptides)

  C) 2nd Mass spectrometer

  D) Detector
  E) Collision cell

• A) 1st Mass Spectrometer

  B) Detector

  C) Collision cell

  D) 2nd Mass spectrometer
  E) Electrospray ionization (sample hydrolyzed by protease into peptides)

• A) Electrospray ionization (sample hydrolyzed by protease into peptides)

  B) 1st Mass Spectrometer

  C) Collision cell

  D) 2nd Mass spectrometer
  E) Detector

• A) Collision cell

  B) Electrospray ionization (sample hydrolyzed by protease into peptides)

  C) 1st Mass Spectrometer

  D) Detector
  E) Collision cell

Answer explanation

Tandem mass spectrometry helps sequence and identify proteins.

The first step that occurs is occurs when the sample is hydrolyzed by protease into peptides (the sample is circled in a red box). The first mass spectrometer then sorts the different peptides (it appears by size). In the image, the two sizes are green and red. and selects one type to go inside the collision cell (many copies of one type/size, in the image, the green peptide is chosen). The chosen type/size will then go into a collision cell where it will be cut once in a random place (the green is cut into orange and blue). The second mass spectrometer then measures the masses of each fragment.

With trypsin, each peptide has K or R at its C-terminus resulting in a ______ charge at the peptide C-terminus

• negative
• positive
• neutral

Breakage of peptide bonds in the collision cell cuts each peptide into 2 fragments : beta-type (_-terminal fragments) and gamma-type (_-terminal fragments)

• N, beta-type and C, gamma-type

• C, beta-type and N, gamma-type

Chain flexibility arises from bond...

• bond vibration
• bond bending

• bond rotation
• bond contraction
• bond elongation

Answer explanation

Chain flexibility arises from bond rotation, not bond bending!

What amino acids prefer alpha helix folding?

• FWTC IVY

• GPNDS

• MARK ELF HQ

Answer explanation

MARK, ELF (Head)(Quarters)!

Methionine, Alanine, Arginine, Lysine, Glutamate, Leucine, Phenylalanine, Histidine, Glutamine

Conformations represent states of a molecule that can be

interconverted by ________, without breaking covalent bonds

(e.g. different shapes of a polypeptide chain)

• hydrogen bonding
• bond rotations

• bond bending

• ionic interactions

Answer explanation

For macromolecules such as proteins, we are usually concerned with conformations.

___________ can only be interchanged by breaking covalent bonds, not by bond rotation

e.g., cis- and trans- forms of molecules with a -C=C- double bond or two chiral forms of amino acids (D- and L-)

• Bond conformations

• Bond configurations

Identify the major and minor patterns of alpha and beta keratin:

• Alpha keratin; major pattern = 1.5 Å, minor pattern = 5.4 Å

  Beta keratin; major pattern = 3.5 Å, minor pattern = 7.0 Å

• Alpha keratin; major pattern = 5.4 Å, minor pattern = 1.5 Å

  Beta keratin; major pattern = 7.0 Å, minor pattern = 3.5 Å

• Alpha keratin; major pattern = 7.0 Å, minor pattern = 1.5 Å

  Beta keratin; major pattern = 5.4 Å, minor pattern = 3.5 Å

• Alpha keratin; major pattern = 7.0 Å, minor pattern = 3.5 Å

  Beta keratin; major pattern = 5.4 Å, minor pattern = 1.5 Å

Answer explanation

Alpha keratin;

major pattern = 5.4 Å

minor pattern = 1.5 Å

(Protein of hair, skin, wool)

Beta keratin;

major pattern = 7.0 Å

minor pattern = 3.5 Å

(Silk moth and spider silk)

A peptide bond is rigid, fixed in A)____-geometry, because it behaves more like a

B)____ bond than a C)____ bond

• A) cis

  B) double
  C) single

• A) trans

  B) double
  C) single

• A) trans

  B) single
  C) double

• A) cis

  B) single
  C) double

Answer explanation

▪ Normal C–N is 1.49 Å

▪ Peptide C–N is 1.32 Å

▪ Normal C=N is 1.27 Å

In a normal peptide chain, alpha-amino and alpha-carboxylate are locked in rigid planar peptide bonds. Which two bonds can rotate freely?

• Alpha-amino to alpha-carboxylate group and alpha-carbon to R group

• Alpha-carbon to alpha-amino group and alpha-carbon to alpha-carboxylate group
• Alpha-amino to alpha-carbon group and alpha-amino to alpha-carboxylate group

Answer explanation