Mutations and Proteins

Question 1

alpha helices

Answer 1

• H bonds between every i and i+4 residue
• side chains of i and i+4 also react, hydrophillic on one side and hydrophobic on the other
• hydrophobic sides interact with membrane lipids
• look for long chains on hydrophobic AAs

Question 2

B sheet

Answer 2

• 2+ beta strands, H bonds between each strand
• every 2 residues interact, commonly AA sequence alternates hydrophilic/hydrophobic
• Porins are an example: lined with + and - side chains on inner portion to allow small, polar, charged groups through

Question 3

Reverse B turn

Answer 3

• proteins needs to reverse direction
• proline forms a kink bc of covalent bond in backbone
• glycine needed to prevent steric clash in tight turn

Question 4

irregular/random coils

Answer 4

• important for differentiating proteins based on length, location and sequence of loop
• hydrophilic usually
• tether domains, bind proteins and substrates
• lead to a specific function

Question 5

domains and motifs

Answer 5

• few secondary structures combine to make them
• motifs are short and unstable on their own
• domains can be long and stable
• 3 types: helix turn helix, zinc finger, coiled coil domain

Question 6

helix - turn- helix

Answer 6

• recognizes DNA and binds tightly, specifically to major groove
• one helix for binding and other supports

Question 7

zinc finger

Answer 7

• chain of His and Cys with any AA in between
• helix binds DNA weakly, need many of them
• zinc helps stabilize

Question 8

coiled-coil domain

Answer 8

• very stable
• characterized by heptad a b c d e f g
• a and d are hydrophobic, e and g oppositely charged
• when two domains binds, a of 1 interacts with d of another, same for e and g
• GCN4 transcription factor: 3 heptads in a coiled coil homodimer
• Flu haemagglutin - triple coiled-coil in stalk domain and 3 globular domains in head
• when flu infects its inside its own membrane. pH drops, causing coil to extend and fuse to get into host cytosol
• many viruses use this “harpoon” method; can make inhibitors against it

Question 9

Protein folding in vitro vs in vivo

Answer 9

in vitro - easy to do because alone in media. when given time, an unfolded protein could refold properly

• folding directions are in AA sequence
• in vivo: path to fold involves intermediates that can aggregate
• use chaperones to prevent this
• folding driven by hydrophobic effect but there is competition between hydrophobic mlcs in protein and others in cytosol

Question 10

Chaperones

Answer 10

• aid in protein folding in large, multidomain proteins
  1. Hsp70 class - prevent aggregation during folding by covering with hydrophobic patches
  2. Hsp60 class - place misfolded protein in cylinder with cap and give time to refold.
  3. Hsp100 class - ATP hydrolysis energy to break up harmful aggregates (Alzheimers)

drugs may stimulate chaperones that prevent aggregates for diseases like Alzheimers
or
inhibit chaperones that cancer cells are addicted to