431 – EXAM REVIEW QUESTIONS AND
ANSWERS
Ionic bonding - Answer-Bonds held together by oppositely charged atoms
Hydrophobic interactions - Answer-- Hydrophobic regions cluster together away from
water to minimize the hydration layer
- Between nonpolar amino acids which don't form H-bonds with water
- Important in protein folding
Kw - Answer-The ionization constant of water = 1.0*10^-14
Henderson-Hasselbalch equation - Answer-pH = pKa + log [A-]/[HA]
Alpha Helix - Answer-- Right handed
- Helix stabilized by H-bonds
- 3.6 residues per turn
- Both + and - charges present
- Amphipathic
Beta Sheets (Strands) - Answer-- Held together by H-bonding
- Antiparallel configuration has less bond strain
Beta Turns - Answer-- Connect the strands of a beta sheet
- Glycine is most common beta turner, so it contributes the MOST torsional strain
- Type 1 configuration has less strain
4 classes of Tertiary Structures - Answer-- Alpha-helices
- Beta sheets
- Alpha/beta tertiary
- A + B structure
4-helix Bundle - Answer-
Greek Key Fold - Answer-
Rossmann Fold - Answer-
TIM Barrel Fold - Answer-
FERM Domain - Answer-
What locks 3° structures in place and how does this work - Answer-Disulfide bonds
, 2 nearby cysteine molecules form bonds between S atoms through oxidation
Chaperone Proteins - Answer-- Form stable 3D structure
- Fix misfolded proteins
- Break up protein aggregates
- 2 types: Clamp and chamber
Luciferase Activity - Answer-- Determines if a protein is an activator or repressor
- If activator, luciferase transcribed when luciferin added, tray glows
- If repressor, luciferase NOT transcribed when luciferin added, tray DOESN'T glows
Fractionation methods - Answer-Sonication, french press, dounce homogenizer
Sonication - Answer-Lyse both prokaryotes and eukaryotes through the use of
ultrasonic waves
French press - Answer-Prokaryotes
Dounce homogenizer - Answer-Eukaryotes
Centrifugation - Answer-- After lysing cells, spin at varying speeds to form pellets
Salting Out - Answer-- Adding high salt to exploit different solubilities and form protein
aggregates
- Done after centrifugation
- Buffer exchange method
Disalysis - Answer-- Buffer exchange method
- Removes ammonium sulfate from a protein sample
- Relies on diffusion
Column Chromotography Methods - Answer-Gel filtration , HPLC, Ion exchange, affinity
Gel Filtration (Other name, how it works) - Answer-- AKA Size-exclusion
chromatography
- Separates molecules based on size
- Large molecules go through faster
- Small molecules move slower because they get trapped in the beads
HPLC - Answer-- Higher Resolution Gel Filtration
- Smaller beads leads to greater separation of proteins
- High pressure is needed
Ion Exchange Chromatography - Answer-- Separates molecules based on charge
- + beads attract - proteins and - beads attraqct + proteins
- Washed with a high salt afterwards to remove bound proteins
ANSWERS
Ionic bonding - Answer-Bonds held together by oppositely charged atoms
Hydrophobic interactions - Answer-- Hydrophobic regions cluster together away from
water to minimize the hydration layer
- Between nonpolar amino acids which don't form H-bonds with water
- Important in protein folding
Kw - Answer-The ionization constant of water = 1.0*10^-14
Henderson-Hasselbalch equation - Answer-pH = pKa + log [A-]/[HA]
Alpha Helix - Answer-- Right handed
- Helix stabilized by H-bonds
- 3.6 residues per turn
- Both + and - charges present
- Amphipathic
Beta Sheets (Strands) - Answer-- Held together by H-bonding
- Antiparallel configuration has less bond strain
Beta Turns - Answer-- Connect the strands of a beta sheet
- Glycine is most common beta turner, so it contributes the MOST torsional strain
- Type 1 configuration has less strain
4 classes of Tertiary Structures - Answer-- Alpha-helices
- Beta sheets
- Alpha/beta tertiary
- A + B structure
4-helix Bundle - Answer-
Greek Key Fold - Answer-
Rossmann Fold - Answer-
TIM Barrel Fold - Answer-
FERM Domain - Answer-
What locks 3° structures in place and how does this work - Answer-Disulfide bonds
, 2 nearby cysteine molecules form bonds between S atoms through oxidation
Chaperone Proteins - Answer-- Form stable 3D structure
- Fix misfolded proteins
- Break up protein aggregates
- 2 types: Clamp and chamber
Luciferase Activity - Answer-- Determines if a protein is an activator or repressor
- If activator, luciferase transcribed when luciferin added, tray glows
- If repressor, luciferase NOT transcribed when luciferin added, tray DOESN'T glows
Fractionation methods - Answer-Sonication, french press, dounce homogenizer
Sonication - Answer-Lyse both prokaryotes and eukaryotes through the use of
ultrasonic waves
French press - Answer-Prokaryotes
Dounce homogenizer - Answer-Eukaryotes
Centrifugation - Answer-- After lysing cells, spin at varying speeds to form pellets
Salting Out - Answer-- Adding high salt to exploit different solubilities and form protein
aggregates
- Done after centrifugation
- Buffer exchange method
Disalysis - Answer-- Buffer exchange method
- Removes ammonium sulfate from a protein sample
- Relies on diffusion
Column Chromotography Methods - Answer-Gel filtration , HPLC, Ion exchange, affinity
Gel Filtration (Other name, how it works) - Answer-- AKA Size-exclusion
chromatography
- Separates molecules based on size
- Large molecules go through faster
- Small molecules move slower because they get trapped in the beads
HPLC - Answer-- Higher Resolution Gel Filtration
- Smaller beads leads to greater separation of proteins
- High pressure is needed
Ion Exchange Chromatography - Answer-- Separates molecules based on charge
- + beads attract - proteins and - beads attraqct + proteins
- Washed with a high salt afterwards to remove bound proteins
