3-D Structure and Function of Proteins Flashcards Preview

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Flashcards in 3-D Structure and Function of Proteins Deck (26):
1

Proteomics

Study of large sets of proteins, often those produced by a cell

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Primary structure

Linear sequence of amino acid residues

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Secondary structure

Structures created by H-bonding between amino acid residues in peptide chain

4

Tertiary structure

Completely folded and compacted polypeptide chain

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Quaternary structure

Several polypeptides come together

6

X-ray crystallography

Technique used for determining 3-D structure of protein
Electromagnetic waves of similar size to regularity of crystal pass through crystal and create diffraction pattern

7

Protein Data Bank

Data bank through which thousands of solved 3-D protein crystal structures can be accessed

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Space-filling models

Use Van der Waals radii to illustrate overall shape and surface topography of protein
Looks like blob of balls

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Ribbon structures

Simplified model of protein (shows some aspects of secondary structure) used to show binding domains

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Ball-and-stick structures

Highly detailed model of protein that shows H-bonding and other molecular interactions
Combines aspects of space-filling models and ribbon structures

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Flexibility of proteins

Proteins don't have static, immovable structures

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Phi bond

Rotation around N-alpha C bond

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Psi bond

Rotation around alpha C-carboxyl C bond

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Ramachandran plot

Graphical representation of types of secondary structures allowed in polypeptides

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Alpha helix

Corkscrew-type secondary structure
Sidechains oriented outward from helix axis
Can be amphipathic (different sides of helix can have sidechains with different polarities)

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Beta sheets

Flat secondary structure
Stable due to interstrand H-bonding
More flexibility in bond angles than alpha helices
Amino acid sidechains point alternatively above and below the plane
Each strand in sheet has a slight right hand twist
Can be amphipathic

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2 types of beta sheets

Parallel and anti-parallel

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Loops

Segments of non-regular structure that connect proteins
Contain hydrophilic residues and are found at or near the surface of proteins

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Turns

Short loops (<5 residues)
Often cause an abrupt change in chain direction

20

Motifs

Combination of alpha helices, beta sheets, and loops to form tertiary structure of proteins

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Domains

Independently folded, compact globular units
Made up of motifs
Show structural similarity across species

22

Chemical denaturation agents

Chaotropic agents (urea, guanidinium salts)
Detergents (SDS)

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Beta-mercaptoethanol

Denatures proteins by cleaving disulfide bonds

24

Renaturation of proteins

Rare- some small proteins can spontaneously reform their native conformations, but most cannot

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Dictation of protein folding

Controlled by amino acid sequence

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Molecular chaperones

Assist in protein folding