Lecture 5 - Elements of Protein Structure

Question 1

In proteins and peptides, amino acids are joined together by

Answer 1

peptide bonds

Question 2

Levels of protein structure

Answer 2

Primary
Secondary
Tertiary
Quaternary

Question 3

Primary structure

Answer 3

Amino acid sequence (chain)

Question 4

Secondary structure

Answer 4

Local 3D stretch of residues

Question 5

Tertiary structure

Answer 5

(3D) structure of a complete
protein chain

Series of helices connected by loops
Global fold

Question 6

Quaternary structure

Answer 6

More than 1 protein chains packed together

Question 7

Φ phi angle

Answer 7

angle around the N–Ca bond

Question 8

Ψ psi angle

Answer 8

angle around the Ca–C’ bond

Question 9

Protein structures Begin to fold when

Answer 9

Amino acid residues emerge from the ribosomes

Fold locally then globally

Question 10

How do the protein structures fold?

Answer 10

Do it themselves

Rotate around the flexible bonds that connect them.

Some bonds can be flexible or rigid

Question 11

Main chain bonds

Answer 11

N (in peptide bond)

Cα (sidechain attached to it)

C’ (carbonyl carbon. Attached to the double bonded oxygen)

Question 12

C’

Answer 12

carbonyl carbon.

Attached to the double bonded oxygen

Question 13

Main chain bond angles:

Answer 13

Φ phi angle
Ψ psi angle

How much rotation there is around the single bonds.

0 - 180 & -180 - 0

Question 14

To figure out the orientation of a peptide and what direction its going. Look for…

Answer 14

amide nitrogen (H and Cα attached)

Question 15

Peptides move from

Answer 15

amino terminus to the carboxyl terminus

Question 16

Bond between amide nitrogen and Cα

Answer 16

Phi Φ angle

Single bond free rotation

Question 17

Bond between Cα to C’

Answer 17

Psi Ψ angle

Question 18

Residue 1

Answer 18

Phi 1

Psi 1

Question 19

When a protein is completely flat

Answer 19

All angles are 180 degrees

Question 20

Peptide bonds

Answer 20

Stiff
Rigid
Not very flexible

Question 21

Phi and Psi restrictions

Answer 21

Steric hinderance

rotate around Phi and Psi bonds, collisions can occur

Question 22

If rotate around the Phi Φ angle

Answer 22

2 oxygens will collide

o has vanderwaal radius, certain distance that can’t get any closer

Question 23

If rotate around the Psi Ψ angle

Answer 23

Amide Nitrogens (NH) will collide.

Question 24

The combination of all the rotation and twists around the flexible peptide bond leads to…

Answer 24

3D structure which in turn leads to its function.

Question 25

Amino acid sequence leads to...

Answer 25

structure

Question 26

Secondary structures

Answer 26

α helix (right hand turn) β - strand/sheet (4 main chains) Dominates tertiary protein structures. Side chains point out from helix axis

Question 27

α - helix and β - strand/sheet difference

Answer 27

Internal hydrogen bonding in helices In beta, hydrogen bonding are across main chains

Question 28

α-helix properties

Answer 28

Find amide nitrogen Find Cα (has sidechain) H bond (interaction between NH and C’) stabilizes helix and promotes helical formation. Spiral right handed Side chains point out from helix axis Dipole (NH has partial positive charge and carbonyl has negative charge)

Question 29

α-helix properties residues / turn turns d =

Answer 29

3. 6 residues/turn; 5. 4Å/turn 1.5Å/residue

Question 30

The carbonyl residue of 1 interacts with amide nitrogen (NH) of residue 5

Answer 30

Carbonyl residue = n Amide Nitrogen residue = n + 4

Question 31

α-helix Φ angle (phi) and Ψ angle (Psi)

Answer 31

``` Φ = ~ - 57 degrees Ψ = ~ - 47 degrees ```

Question 32

Helix breakers residues

Answer 32

``` Glycine Proline (restrictions. Sidechains binds to themselves) ```

Question 33

β structure

Answer 33

Extended structure that allows hydrogen bonding to occur on adjacent strands (another main chain by it) Two types of interactions within (parallel and antiparallel)- arrows always from amino (N) to carboxy end (C) Example Silk

Question 34

β - sheet

Answer 34

Contains 2+ β strands Typically 2-10 Multiple strands

Question 35

β strands

Answer 35

6 amino acid residues long on Average Can have up to 15 residues Single chain

Question 36

Parallel

Answer 36

Arrows pointing in same direction (always from amino (N) to carboxy end (C)) Hydrogen bonds on angles

Question 37

Antiparallel

Answer 37

Arrows pointing in opposite direction (always from amino (N) to carboxy end (C)) Carbonyl Oxygen pointing down and underneath amide hydrogen pointing up.(vice versa) Hydrogen bonds straight up and down

Question 38

β structure properties

Answer 38

``` Extended more than helix Pleated (main chains up and down) All strands can twist Sidechains point above and below Any stretch of protein residues that can alternate in polarity (non polar, polar) forms a beta strand (be apart of beta structure). ```

Question 39

Silk

Answer 39

``` Beta structure Model with 4 chains Sequence is Gly-Ser-Gly-Ala-Gly-Ala etc Antiparallel Flexible (because of hydrophobic interactions) Extended ```

Question 40

β turns key properties

Answer 40

hairpin like 3-4 residues high Gly Pro content 30% residues involved in turns h bond, across the turn Type I, Type II are common types more than 16 types, given Roman Numeral names