Secondary and Tertiary Structure in Proteins Flashcards

1
Q

Genetic Code

A

How the sequence of DNA dictates the sequence of proteins - triplet code

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2
Q

quaternary structure

A
  • interactions between subunits
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3
Q

all folding orders dictated by

A

primary sequence of the protein

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4
Q

the major secondary structures in proteins

A
  1. alpha-helix
  2. beta-sheet
  3. beta-turn
  4. random coils
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5
Q

structure and function

A

closely tied to one another

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6
Q

determine the structure of proteins

A
  • use X-ray crystalography
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7
Q

X-ray crystallography

A
  • proteins must be collected at high concentrations and crystallized
  • crystals exposed to X-rays and diffracted by protein in a way determined by position of chemical bonds within the protein
  • diffraction pattern produces 3D image of density of electrons within crystal to determine protein structure. q
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8
Q

Linus Pauling’s solution of the alpha-helix

A
  • contributed to structure of DNA - the way H bonds stabilize alpha-helices in proteins
  • The Nature of the Chemical Bond
  • proposed alpha-helix and beta-sheet
  • establishes hydrophobic face that will interact with other proteins to form a leucine dimer
  • proposed triple helix -wrong!
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9
Q

alpha-helix

A
  • hydrogen bonds between C=O and NH stabilize the helix
  • one helical turn ~ 3.5 amino acids
  • two turns = 7 amino acids
    • every 7th amino acid will have R-groups on the same face of the helix - important for protein interaction
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10
Q

Beta-sheet

A
  • hydrogen bonds between C=O and NH stabilize the B-sheet
  • remaining C=O and NH can hydrogen bond with another B-sheeet creating B-pleated structures
  • flattened sheet instead of helical structure
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11
Q

anti-parallel

A
  • amino group adjacent to carboxy group of next

- more stable and found more commonly

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12
Q

parallel

A
  • all amino termini in same direction
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13
Q

ribbon structure

A
  • idealized drawings of the tertiary structures of several globular proteins (secondary structures)
  • coiled regions represent alpha helix and flat arrows indicate beta-structure
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14
Q

Barrel structure

A
  • another way of drawing alpha-helices

- alpha-helix between two beta-sheets

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15
Q

Chou-Gasman table

A
  • propensity of amino acids to form alpha-helix or beta-sheet based on proteins of known sequence and known secondary structure from x-ray crystallography
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16
Q

most likely to be found in alpha-helix

A
  • Glu
  • Ala
  • Leu
17
Q

least likely to be found in alpha-helix

A
  • Pro

- Gly

18
Q

most likely to be found in beta-sheet

A
  • Met
  • Val
  • Ile
19
Q

least likely to be found in beta-sheet

A
  • Pro

- Glu

20
Q

Absolute helix breakers

A
  • proline and glycine
21
Q

proline

A
  • not in alpha-helix due to its structure

- no H bond because tied up in ring structure.

22
Q

Chou-Fasman Rules

A
  • are used to PREDICT (not Determine) secondary structure in proteins.
23
Q

hydrophobic interactions and tertiary structure

A
  • hydrophilic outside to interact with H2O

- hydrophobic inside to not react with H2O

24
Q

Hydropathy index

A
  • help predict tertiary structure of protein also using sliding window approach
25
Q

Sliding window

A
  • Consider 5 AA next to each other
    • average hydropathy index
    • plot
  • slide down one AA
26
Q

Hydropathy plots

A
  • done for whole length of protein
  • help determine which regions are hydrophobic or hydrophilic in a given protein
  • good sliding window of 9
27
Q

bars above 0

A

interior regions of the protein as determined by crystallography

28
Q

bars below 0

A

exterior region of the protein as determined by crystallography

29
Q

A reason why you might expect a hydrophobic portion of a protein to be on the outside of a protein rather than on the inside

A
  • if a protein spans a membrane

- if a portion of the protein is involved in an INTERACTION with another macromolecule through hydrophobic interactions

30
Q

Homology modeling

A
  • constructing a model of a protein based off known AA seq and known 3D seq of related protein with similar function
  • identification of insect olfactory receptors after mammalian receptors identified
31
Q

hydropathy plots for evolutionary comparisons

A
  • to identify functional homologues