Lecutre 8

Question 1

Why do we need structural bioinformatics or databases when we already have sequences?

Answer 1

Related proteins structure is much better preserved than sequence.

Structural motifs may predict similar biological function.

Getting insight into protein folding: recovering the limited (?) number of protein folds.

Question 2

How many amino acids do we have? and what are the diffrent groups of an amino acid

Answer 2

20 naturally occuring amino acids

2 different groups:

Amino group NH2

Carboxyl group COOH

Question 3

What are the different categories of amino acids based on their side chains?

Answer 3

Size: small, large

Affinity of the water: hydrophobic and hydrophilic

Hydrophobic: aliphatic and aromatic
Hydrophilic: polar and charged

Question 4

How does the peptide formation occurs?

Answer 4

Peptide formation occurs by two amno acids joining at the OH and H and releasing water.

Question 5

What is a polypeptide?

Answer 5

Polypeptide: a linear polymer of >50 aa residues

A polypeptide, or a protein, has a well-defined 3D arrangement.

Question 6

What is a peptide?

Answer 6

Peptide: a polymer with <50 residues without a well-defined 3D structure.

Question 7

Explain the different parts of the polypeptide: N-terminus and C-terminus

Answer 7

N-terminus: the amino group of the beginning residue of a peptide/polypeptide.

C-terminus: the carboxyl group of the end residue of a peptide/polypeptide.

The sequence of aa residues (1° structure) determines its ultimate structure and function

Question 8

Explain the dihedral angles

Answer 8

Phi (ϕ): the dihedral angle along the N-Cα bond.

Psi (ψ): the dihedral angle along the Cα-C bond.

Various combination of ϕ and ψ angles allow the proteins to fold in many different ways.

Question 9

What are the different levels of protein structure?

Answer 9

4 levels:
Primary (1°) structure
Secondary (2°) structure
Tertiary (3°) structure
Quaternary (4°) structure

Question 10

Explain each level of the protein structure

Answer 10

Primary (1°) structure: Linear aa sequence of a protein

Secondary (2°) structure:Local conformation of a peptide chain: highly regular and repeated arrangement of aa residues stabilized by H-bonds between C=O group and the N-H group of different residues.

Tertiary (3°) structure:Complete 3D assembly of all amino acids of a single polypeptide chain

Quaternary (4°) structure: Association of several polypeptide chains into a protein complex, maintained by non-covalent interactions

Question 11

What maintains 2 to 4 structures?

Answer 11

Noncovalent forces

Question 12

What are the different noncovalent forces that main the 2 to 4 structures?

Answer 12

2° to 4° structures are maintained by noncovalent forces:

• Electrostatic interactions
• van der Waals forces
• H-bonding

Question 13

Explain electrostatic interaction

Answer 13

Electrostatic interactions:excess (–) charges in one region are neutralized by (+) charges in another region

Question 14

Explain van der waals forces

Answer 14

van der Waals forces:instantaneous interactions b/t atoms when they become transient dipoles

Question 15

Explain H-bonding

Answer 15

H-bonding:A special type of electrostatic interactions similar to dipole-dipole interaction involving H from 1 residue and O from another.

H-bonding patterns are a dominant factor in determining different types of protein 2° structures.

Question 16

Explain disulfide bridges

Answer 16

Disulfide bridges:Covalent bonds between the sulfur atoms of the cysteine residue

Question 17

Explain the different parts of secondary structures

Answer 17

Chief elements:

• α-helices
• β-sheets

α-Helices:

• Corkscrew conformation
• Nearly all right-handed
• Ala, Gln, Leu and Met (NOT Pro, Gly and Tyr)

β-Sheets:

• Fully extended configuration
• Can run in the same direction: parallel sheet
• Run in reverse orientation: anti-parallel sheet

Coiled coil and loops: Irregular local structures

• Coiled coil: bundle of 2+ α-helices wrapping around each other.
• Loop: sharp turns or hair-pin like structures

Question 18

What are the classifications of tertiary structures?

Answer 18

Various forms but generally classified into:

Globular proteins

Membrane proteins

Question 19

Exaplain each of the classification of the tertiary structure

Answer 19

Globular proteins:

• exists in solvents through hydrophilic interactions with solvent molecules
• overall compact structure of spherical shape with polar or hydrophilic residues

Membrane proteins:

• exists in membrane lipids and is stabilized through hydrophobic interactions with the lipid molecules.
• the exterior of the protein - very hydrophobic to be stable

Question 20

What are the two popular experimental techniques that determine the protein 3D structure?

Answer 20

2 popular experimental techniques:

X-ray Crystallography

NMR (Nuclear Magnetic Resonance) Spectroscopy

Question 21

Explain X-ray crystallography

Answer 21

• Proteins are grown into large crystals so their positions are fixed in a repeated, ordered fashion.
• The protein crystals are then illuminated with an intense x-ray beam.
• The x-rays are deflected by the electron clouds surrounding the atoms in the crystal producing a regular pattern of diffraction.

Question 22

What are the limitations of the X-ray crystallography?

Answer 22

LIMITATION: whether suitable crystals of proteins of interest can be obtained.

Question 23

Explain nuclear magnetic resonance spectroscopy

Answer 23

• Detects spinning patterns of atomic nuclei in a magnetic field.
• Protein samples are labeled with radioisotopes such as 13C and 15N
• A radiofrequency radiation is used to induce transitions b/t nuclear spin states in a magnetic field.
• Interactions between spinning isotope pairs produce radio signal peaks that correlate with the distances between them.

Question 24

What are the limitations of nuclear magnetic resonance spectroscopy

Answer 24

LIMITATION:

(1) protein size limit: must be <200 residues
(2) heavy instrumentation requirement.

Question 25

What are some exaples of molecular structure visualization forms?

Answer 25

Examples of molecular structure visualizarion forms.

A) Wireframes.

B) Balls and Sticks.

C) Space-filling spheres.

D) Ribbons.

Question 26

What are some examples of molecular graphic generators

Answer 26

Examples of molecular graphic generated by

A) Rasmol,

B) Molscript,

C) Ribbons, and

D) Grasp