Protein Structure

Question 1

What is Å?

Answer 1

Angstrom
1Å = 1 x 10^-10 m (0.1 nm)

Question 2

How long is a peptide bond?

Answer 2

1.32 Å

CN single bond = 1.49 Å
CN double bond = 1.27 Å

Question 3

What is Da?

Answer 3

Dalton - unit of atomic mass very nearly equal to that of a hydrogen atom.

Used to express mass on the atomic scale of objects.
Used for protein molecular weight.

1 kDa = 1000 Da

Question 4

What makes planar peptide bonds stronger and less flexible?

Answer 4

Peptide bond has partial double bond character.

Question 5

List the 2 possible configurations for the planar peptide bond.

Answer 5

Trans-configuration.
Cis-configuration.

Question 6

What is a trans-configuration in terms of the planar peptide bond?

Answer 6

2 alpha carbons on opposite sides of peptide bond.

Question 7

What is a cis-configuration in terms of the planar peptide bond?

Answer 7

2 alpha carbons on same side of peptide bond.

Question 8

What configuration are most peptide bonds? Why?

Answer 8

Trans-configuration:
R-groups are on opposite sides of the chain to avoid steric (atoms in space) clashes.

Question 9

What is the exception to this?

Answer 9

Proline can be in cis configuration.

Question 10

Where does protein flexibility come from?

Answer 10

Free rotation around single bonds in a residue (the structure of each residue can be adjusted).

Question 11

What is Phi (Φ)?

Answer 11

The angle of rotation about bond between N and alpha C atom.

Question 12

What is Psi (Ψ)?

Answer 12

The angle of rotation about bond between alpha C atom and carbonyl C atom.

Question 13

The angles Φ and Ψ determine…

Answer 13

The path of the polypeptide chain (where it will fold).

Question 14

In 1963, Gopalasamudram N. Ramachandran and his co-workers recognised many combinations of phi and psi were forbidden due to…

(If confused look at PowerPoint).

Answer 14

steric collisions between atoms.

Question 15

Allowed values are visualised on a 2D…

(If confused look at PowerPoint).

Answer 15

Ramachandran plot (scale = 180 on both ends).

Top left corner = beta strands
Top right corner = left handed alpha helix
Middle left = right handed alpha helix

Question 16

What is it that limits the number of structures accessible to the unfolded polypeptide chain?

Answer 16

• Rigidity of peptide bond.
• Restricted set of allowed phi and psi
  angles.

Question 17

What are the secondary structures available to the polypeptide chain?

Answer 17

Alpha helices
Beta sheets
Reverse turns
Omega loops

Question 18

What is an alpha helix?

Answer 18

A rod-like structure consisting of a tightly coiled polypeptide chain which forms the inner part of the tube and amino acid residue groups extend outwards in a helical array.

Question 18

How many residues (n) per turn are there?

(If confused look at PowerPoint).

Answer 18

3.6

Question 19

Give the pitch distance of an alpha helix.

Pitch distance = the distance the helix rises along its axis/turn.

Answer 19

5.4 Å

Question 20

How does hydrogen bonding affect the structure of an alpha helix?

Answer 20

Stabilises the structure - the bond is almost at optimal length (2.8 Å).

Question 21

How many residues is an alpha helix?

Answer 21

Vary from 4-40 residues.

Average length of globular proteins = 10.

Question 22

How is hydrogen bonding arranged in an alpha helix?

Answer 22

So peptide C=O group of residue n points along helix towards peptide N-H group of residue n + 4.

Question 23

How many amino acid residues are there between 2 groups making up a hydrogen bond?

Answer 23

3

Question 24

What is a helical wheel? (Look at PowerPoint if confused).

Answer 24

The view of the alpha helix from above.

Question 25

Since one turn of an alpha helix is 3.6 residues long, how can each residue be plotted on a helical wheel?

Answer 25

360/3.6 = 100 degrees around a circle/spiral.

Question 26

What do helical wheel plots highlight?

Answer 26

Properties of alpha helices in regard to type of amino acid residue R-groups.

Question 27

Where are amino acids that form polar bonds most likely to be?

Answer 27

On the surface of the protein.

Question 28

How does the alpha helical content of proteins vary?

Answer 28

From 0% to 100%.

Question 29

What percentage of all soluble proteins are composed of alpha helices?

Answer 29

25%

Question 30

What percentage of residues in iron storage protein (ferritin) are alpha helices?

Answer 30

75%

Question 31

What is the form of the polypeptide chain in a beta-sheet/beta-strand?

Answer 31

It is almost fully extended.

Question 32

A beta-strand is rarely found in...

Answer 32

Isolation.

Question 33

How many polypeptide chains are beta sheets?

Answer 33

At least 2 but typically 4/5. Beta strands come together in beta sheets, there can be 10 or more.

Question 34

How are beta strands arranged? How do they appear?

Answer 34

Parallel/antiparallel/mixed. Rippled/pleated appearance.

Question 35

What is the distance between adjacent amino acid residues in a beta-strand?

Answer 35

3.5 Å

Question 36

What does hydrogen bonding do for a beta sheet?

Answer 36

Stabilises the sheet.

Question 37

How many residues are beta strands typically?

Answer 37

3-10 residues long.

Question 38

When does hydrogen bonding occur in a beta sheet?

Answer 38

Between C=O of one strand to N-H of adjacent strand. Pattern varies depending on whether adjacent strands are parallel /antiparallel.

Question 39

How are beta strands depicted?

Answer 39

As broad arrows pointing in C-terminal end direction.

Question 40

Beta sheets are important structural elements in many proteins, specifically...

Answer 40

fatty acid binding proteins.

Question 41

What is a reverse turn also known as?

Answer 41

A beta-turn / a hairpin turn.

Question 42

What stabilises the abrupt changes in direction of the polypeptide chains in beta-sheets?

Answer 42

Hydrogen bonding.

Question 43

How do hydrogen bonds form reverse turns?

Answer 43

The C=O group of residue i of the polypeptide is hydrogen bonded to the N-H group of residue i + 3.

Question 44

What are omega loops also known as?

Answer 44

Ω-loops

Question 45

Unlike alpha helices and beta sheets, omega loops don't have a structure that is...

Answer 45

regular and periodic.

Question 46

What are the structures of omega loops often like?

Answer 46

Rigid and well defined.

Question 47

Why do turns and loops often lie on the surfaces of proteins?

Answer 47

They participate in interactions with other proteins/molecules.

Question 48

What do elements of the secondary structure do with each other?

Answer 48

Link together into combinations that are very common, these form as motifs that have some stability in their own right. Motif = specific structural patterns within proteins that are evolutionarily conserved and have particular functions or roles.

Question 49

List some common motifs. (If confused, look at PowerPoint).

Answer 49

Helix-turn-helix motif Hairpin motif Greek key motif Beta-alpha-beta motif

Question 50

What is the tertiary structure? What is it made up of?

Answer 50

The overall fold of the whole protein. Any combination of alpha helices, beta sheets and omega loops.

Question 51

What should be done after the formation of the tertiary structure to obtain the active form of the protein/enzyme?

Answer 51

Post-translational modifications and/or binding of co-factors.

Question 52

Approximately 70% of the main chain is folded into 8 alpha helices. What does the rest form?

Answer 52

Loops and turns.

Question 52

Myoglobin is a single polypeptide chain of 153 amino acids. It's overall dimensions are 45x35x25 Å. What does the polypeptide chain bind to?

Answer 52

A prosthetic haem group. Prosthetic group = non-peptide compounds that mostly attach to proteins and assist them in different ways.

Question 52

What did Kendrew and his co-workers publish in 1958?

Answer 52

The first protein structure to be determined = myoglobin.

Question 53

Each type of representation of a protein highlights different features. List 3 ways proteins can be represented.

Answer 53

- Ribbon/cartoon diagram. - Wireframe/ball and stick diagram. - Space filling models (show surface residues and cross section shows core residues).

Question 54

Concanavalin (Con A) is a lectin that has a tertiary structure of 14 beta-strands. It is an all beta-sheet protein. What is a lectin?

Answer 54

Carbohydrate binding protein.

Question 55

Instead of being an all alpha helix or beta sheet protein, what are most proteins?

Answer 55

Mixtures of alpha helices and beta sheets.

Question 56

List three common tertiary structure folds. (If confused look at PowerPoint).

Answer 56

Globin fold Alpha/beta barrel Beta barrel

Question 57

All proteins fold into at least one...

Answer 57

domain.

Question 57

Many proteins have several sections that fold independently to form domains. What is a domain?

Answer 57

A region of polypeptide chain that is distinct, independently folding and region is self-stabilising.

Question 58

But some have many for example more than...

Answer 58

10.

Question 59

How do domains range in size?

Answer 59

From 30-400 amin acid residues.

Question 60

What is the quaternary structure of a protein?

Answer 60

Groups of 2 or more polypeptide chains. Homomultimer = a protein with two or more copies of the same protein monomer/subunits. Heteromultimer = a mature protein with several different protein monomers/subunits.

Question 61

Haemoglobin is a tetramer comprised of two pairs of slightly dissimilar subunits (α2β2). What is a tetramer?

Answer 61

Polymer with 4 subunits.

Question 62

Each subunit binds to a haem group, so how many oxygen molecules can haemoglobin transport?

Answer 62

4.

Question 63

What is a multimeric protein?

Answer 63

A protein composed of several subunits.

Question 64

Define protein.

Answer 64

Formed from polypeptide chain(s) of 50-2000 amino acid residues.

Question 65

The molecular weight of most proteins is between 5500 and 220,000 Da. Proteins are on the nanometre scale and their widths range 2-100nm.

Answer 65

Titin is an exception of this. The muscle protein is 34,000 amino acids. The molecular weight 3,816,030 Da. The length stetches up to 1.5 micro metres.