Lecture #3 - Protein folding

Question 1

What is a super secondary structure?

Answer 1

Combining secondary structure with turns and coils

Elements of secondary structure are connected by turn or regions of less ordered structure called loops or coil make up super secondary structure

Question 2

What are the 4 common motifs of super secondary structures?

Answer 2

1. Helix-turn-helix
2. Beta hairpin
3. Greek key
4. Strand-helix-strand

Question 3

Helix-turn-helix

1. What two kinds and tell me the bullet points

Answer 3

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Question 4

Greek key

What is it? What do you think of it as?

Answer 4

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Question 5

Strand-helix-strand

Describe it in your head

Answer 5

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Question 6

Strand-helix-strand

Describe it in your head

Answer 6

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Question 7

Protein Domains and motifs

Supersecondary structure elements combine to form _____ or ______ - independently folded regions that often possess a specific binding function

Typically, a protein domain has a ______ core and the _____ parts of the protein are arranged on the surface in contact or near solvent.

Small proteins contain usually one domain, larger proteins may be ______

Answer 7

Supersecondary structure elements combine to form DOMAINS OR MOTIFS - INDEPENDENTLY FOLDED REGIONS THAT OFTEN POSSESS A SPECIFIC BINDING FUNCTION

Typically, a protein domain has a HYDROPHOBIC core and the HYDROPHILIC parts of the protein are arranged on the surface in contact or near solvent.

Small proteins contain usually one domain, larger proteins may be MULTI-DOMAINED

Question 8

Proteins can be grouped into families based on tertiary structure - three examples

Answer 8

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Question 9

Alpha domain:

1. Four helix bundle - describe 3 points about it
2. Globin fold - how many helices?
3. What’s the main point?

Answer 9

Main point: The alpha domain family is mainly alpha-helix

Question 10

A/B family

1. What’s the main point?
2. What’s inside the barrel?
3. What super secondary structure in the alpha beta barrel?
4. Three examples in this family

Answer 10

Main point: Have an alpha helix followed by a beta sheet followed by alpha helix

Question 11

Anti-parallel B family:

1. What super secondary structure?
2. One example - what is it?
3. What’s inside?
4. Main point

Answer 11

Main point: Have mainly antiparallel beta sheets

Question 12

Domains are often reused by nature and combined with what to make proteins with different functions?

Answer 12

Other domains

Question 13

Protein folding:

1. Where are they made?
2. When does it fold?
3. Where are the instructions to fold?

Answer 13

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Question 14

What’s the Afinsen Experiment in a nutshell?

Answer 14

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Question 15

Folding pathways:

1. What is it largely directed by?
2. What’s the sequence of events?

Answer 15

1. Short secondary structure segments
2. Come together, grow cooperatively to form domain
3. Domains come together (but tertiary still partly disordered)
4. Small conformational adjustments to give compact native structure

Question 16

Stabilisation of protein folding:

1. What’s it stabilised by?
2. In some proteins - what may be present?

Answer 16

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Question 17

Some protein folding assisted by what? Three types - explain them

Answer 17

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Question 18

Unfolding of proteins

1. What can lead to unfolding of proteins? (five things)

Answer 18

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