Secondary and Tertiary Structure in Proteins Flashcards Preview

GN 421 > Secondary and Tertiary Structure in Proteins > Flashcards

Flashcards in Secondary and Tertiary Structure in Proteins Deck (31):
1

Genetic Code

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

2

quaternary structure

- interactions between subunits

3

all folding orders dictated by

primary sequence of the protein

4

the major secondary structures in proteins

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

5

structure and function

closely tied to one another

6

determine the structure of proteins

- use X-ray crystalography

7

X-ray crystallography

- 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

8

Linus Pauling's solution of the alpha-helix

- 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!

9

alpha-helix

- 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

10

Beta-sheet

- 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

11

anti-parallel

- amino group adjacent to carboxy group of next
- more stable and found more commonly

12

parallel

- all amino termini in same direction

13

ribbon structure

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

14

Barrel structure

- another way of drawing alpha-helices
- alpha-helix between two beta-sheets

15

Chou-Gasman table

- 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

16

most likely to be found in alpha-helix

- Glu
- Ala
- Leu

17

least likely to be found in alpha-helix

- Pro
- Gly

18

most likely to be found in beta-sheet

- Met
- Val
- Ile

19

least likely to be found in beta-sheet

- Pro
- Glu

20

Absolute helix breakers

- proline and glycine

21

proline

- not in alpha-helix due to its structure
- no H bond because tied up in ring structure.

22

Chou-Fasman Rules

- are used to PREDICT (not Determine) secondary structure in proteins.

23

hydrophobic interactions and tertiary structure

- hydrophilic outside to interact with H2O
- hydrophobic inside to not react with H2O

24

Hydropathy index

- help predict tertiary structure of protein also using sliding window approach

25

Sliding window

- Consider 5 AA next to each other
- average hydropathy index
- plot
- slide down one AA

26

Hydropathy plots

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

27

bars above 0

interior regions of the protein as determined by crystallography

28

bars below 0

exterior region of the protein as determined by crystallography

29

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

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

30

Homology modeling

- 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

hydropathy plots for evolutionary comparisons

- to identify functional homologues