Lecture 5-7: Protein Folding Flashcards Preview

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Flashcards in Lecture 5-7: Protein Folding Deck (69)
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1

Non-covalent interactions

Short range repulsion,
van der waals interactions,
hydrogen bonds,
electrostatic forces (ion pairs and salt bridges)

2

Hydrophobic interactions

Exclusion of water plays role in the folding and stability of proteins

3

Short range repulsion

2 like charges repel each other when too close and have no attraction when far apart----affects proteins folding

4

Van der waals interactions

interacting dipoles from distinct molecules in proteins. Transient.

5

Hydrogen bonds

Weaker than covalent, but longer than covalent bonds. FON can bond w/ H.

6

Ion pairs/ salt bridge

This forms a stability for tertiary structure. Ions interacting to cancel out charge.

7

Hydrophobic effect is

when 2 nonpolar substances come together in solvent(water) and cause water to be excluded from interior of the 2 nonpolar molecules

8

Secondary structure

A helix (more flexible), B sheet (more rigid and structured). Also, omega loops can be added to give flexibility to B sheets

9

Bovine insulin

Has both interchain and intrachain disulfide interactions that comprise tertiary structure.

10

Disulfide bonds Intracellular or extracellular?

Extracellular, the cytoplasm is a reducing environment

11

Folding funnel timescale

1-rapid formation of 2 structure
2-formation of domains through cooperative aggregation(folding nuclei)
3-Formation of assembled domains (molten globule)
4-Adjustment of conformation
5-More rigid structure

12

Calmodulin

A Ca++ senior that contains 4 similar A helices, in a single polypeptide. Each unit binds a Ca++ ion

13

Alternative conformations

Context-dependent; certain protein sequences can be B sheet or A helix based on context of protein location.

14

Ex of alternative conformation

Lymphotactin; Chemokine structure or glycosaminoglycan binding structure

15

Determinants of protein folding

2 structure allows for efficient packing, folding is hierarchal (folding funnel), hydrophobic effects, context-dependent

16

Molten globule state

An intermediate conformational states btw native and fully folded states of a globular protein.

17

Characteristics of molten globule state:

1-presence of native-like content of 2 struture
2-absence of a tertiary structure (produced by packing of AA side chains
3-Compactness in overall shape of protein, w/ radius 10-30% larger than that of the native state.
4-presence of loosely packed hydrophobic core that increases the hydrophobic SA accessible to solvent.

18

Molten globule is a compact globule w/ "molten" side chain structure that is primarily stabilized by:

Nonspecific hydrophobic interactions

19

Protein folding stability is governed by:

non-covalent interactions and hydrophobic interactions

20

T/F: protein folding is a cooperative process

TRUE

21

DO proteins prefer higher or lower energy states?

Lower

22

Molten globule state is

btw native and fully folded state of globular protein

23

PRimary protein structure

AA linked by peptide bonds

24

2 structures

Polypeptide chains that can fold into: A helices, B sheets, omega loops (B turns, hairpin turns)

25

Protein 2 structure stabilizing factors:

Short range repulsion,
H bonds,
van der waals ,
ion pairs and salt bridges

26

Tertiary structure

WAter soluble proteins fold into compact structures w/ nonpolar cores

27

Tertiary structure stabilizing factors:

Disulfide bonds, hydrophobic properties

28

Quaternary structure:

Polypeptide chains can assemble into multisubunit structures

29

What determines 3D structure of proteins?

AA sequence

30

How is protein folding/unfolding cooperative?

It is an "All or none" process. Molten globule states is very short. Partial loss of folding / partial fold of structure destabilizes / stabilizes remainder of protein, Structural properties of proteins provide a clear rationale for cooperative process.