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Biochemistry > Protein Structure > Flashcards

Protein Structure Flashcards

Units, peptide bond, amino acid residue bonds, alpha helix, beta sheet, reverse turn, loops, tertiary structure, common folds, quaternary structure.

1
Q

What is Å?

A

Angstrom
1Å = 1 x 10^-10 m (0.1 nm)

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2
Q

How long is a peptide bond?

A

1.32 Å

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

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3
Q

What is Da?

A

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

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4
Q

What makes planar peptide bonds stronger and less flexible?

A

Peptide bond has partial double bond character.

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5
Q

List the 2 possible configurations for the planar peptide bond.

A

Trans-configuration.
Cis-configuration.

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6
Q

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

A

2 alpha carbons on opposite sides of peptide bond.

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7
Q

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

A

2 alpha carbons on same side of peptide bond.

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8
Q

What configuration are most peptide bonds? Why?

A

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

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9
Q

What is the exception to this?

A

Proline can be in cis configuration.

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10
Q

Where does protein flexibility come from?

A

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

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11
Q

What is Phi (Φ)?

A

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

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12
Q

What is Psi (Ψ)?

A

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

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13
Q

The angles Φ and Ψ determine…

A

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

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14
Q

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).

A

steric collisions between atoms.

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15
Q

Allowed values are visualised on a 2D…

(If confused look at PowerPoint).

A

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

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16
Q

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

A
  • Rigidity of peptide bond.
  • Restricted set of allowed phi and psi
    angles.
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17
Q

What are the secondary structures available to the polypeptide chain?

A

Alpha helices
Beta sheets
Reverse turns
Omega loops

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18
Q

What is an alpha helix?

A

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.

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18
Q

How many residues (n) per turn are there?

(If confused look at PowerPoint).

A

3.6

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19
Q

Give the pitch distance of an alpha helix.

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

A

5.4 Å

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20
Q

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

A

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

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21
Q

How many residues is an alpha helix?

A

Vary from 4-40 residues.

Average length of globular proteins = 10.

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22
Q

How is hydrogen bonding arranged in an alpha helix?

A

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

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23
Q

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

A

3

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24
Q

What is a helical wheel?

(Look at PowerPoint if confused).

A

The view of the alpha helix from above.

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25
Q

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

A

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

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26
Q

What do helical wheel plots highlight?

A

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

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27
Q

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

A

On the surface of the protein.

28
Q

How does the alpha helical content of proteins vary?

A

From 0% to 100%.

29
Q

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

A

25%

30
Q

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

A

75%

31
Q

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

A

It is almost fully extended.

32
Q

A beta-strand is rarely found in…

A

Isolation.

33
Q

How many polypeptide chains are beta sheets?

A

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

34
Q

How are beta strands arranged? How do they appear?

A

Parallel/antiparallel/mixed.
Rippled/pleated appearance.

35
Q

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

A

3.5 Å

36
Q

What does hydrogen bonding do for a beta sheet?

A

Stabilises the sheet.

37
Q

How many residues are beta strands typically?

A

3-10 residues long.

38
Q

When does hydrogen bonding occur in a beta sheet?

A

Between C=O of one strand to N-H of adjacent strand.

Pattern varies depending on whether adjacent strands are parallel /antiparallel.

39
Q

How are beta strands depicted?

A

As broad arrows pointing in C-terminal end direction.

40
Q

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

A

fatty acid binding proteins.

41
Q

What is a reverse turn also known as?

A

A beta-turn / a hairpin turn.

42
Q

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

A

Hydrogen bonding.

43
Q

How do hydrogen bonds form reverse turns?

A

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

44
Q

What are omega loops also known as?

A

Ω-loops

45
Q

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

A

regular and periodic.

46
Q

What are the structures of omega loops often like?

A

Rigid and well defined.

47
Q

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

A

They participate in interactions with other proteins/molecules.

48
Q

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

A

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.

49
Q

List some common motifs.

(If confused, look at PowerPoint).

A

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

50
Q

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

A

The overall fold of the whole protein.

Any combination of alpha helices, beta sheets and omega loops.

51
Q

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

A

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

52
Q

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

A

Loops and turns.

52
Q

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

A

A prosthetic haem group.

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

52
Q

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

A

The first protein structure to be determined = myoglobin.

53
Q

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

A
  • Ribbon/cartoon diagram.
  • Wireframe/ball and stick diagram.
  • Space filling models (show surface
    residues and cross section shows core
    residues).
54
Q

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?

A

Carbohydrate binding protein.

55
Q

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

A

Mixtures of alpha helices and beta sheets.

56
Q

List three common tertiary structure folds.

(If confused look at PowerPoint).

A

Globin fold
Alpha/beta barrel
Beta barrel

57
Q

All proteins fold into at least one…

A

domain.

57
Q

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

A

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

58
Q

But some have many for example more than…

A

10.

59
Q

How do domains range in size?

A

From 30-400 amin acid residues.

60
Q

What is the quaternary structure of a protein?

A

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.

61
Q

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

A

Polymer with 4 subunits.

62
Q

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

A

4.

63
Q

What is a multimeric protein?

A

A protein composed of several subunits.

64
Q

Define protein.

A

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

65
Q

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.

A

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.

Biochemistry (10 decks)

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