Lecture 5-8

Question 1

Seven essential function carried out by proteins, and an example of a protein for each?

Answer 1

Enzymatic,   e.g. trypsin
Transport,   e.g. haemoglobin
Structural,   e.g. collagen
Movement,   e.g. actin
Signalling,   e.g. insulin
Defence,   e.g. antibodies
Storage,   e.g. ferritin.

Question 2

What must happen to proteins after synthesis?

Answer 2

They must fold properly.

Question 3

What are proteins synthesised as?

Answer 3

Long unbranched chains of amino acids.

Question 4

What is a protein’s primary structure?

Answer 4

The sequence in which the amino acids are arranged.

Question 5

How many amino acids are used to make proteins?

Answer 5

20.

Question 6

What are the 4 functional groups found in 19/20 amino acids?

Answer 6

Hydrogen atom, amino group, carboxyl group, R group.

Question 7

What 5 properties do side chains vary in?

Answer 7

Size
Shape
Charge
Hydrophobicity/hydrophilicity
Chemical reactivity.

Question 8

Are there optical isomers for amino acids? If so, why?

Answer 8

All but glycine.

4 different groups attached to the central atom.

Question 9

What isomers are incorporated into proteins?

Answer 9

L-isomers.

Question 10

Why is glycine not chiral?

Answer 10

2 hydrogen atoms attached to carbon.

Question 11

At pH 7, are amino acid groups ionised? What name can you give them?

Answer 11

Yes.

Zwitterions.

Question 12

What is pKa?

Answer 12

The pH at which an ionisable group is one-half charged and one-half neutral.

Question 13

Which amino acid’s side chain has a pKa around physiological pH?

Answer 13

Histidine (pKa 6.8).

Question 14

What is the pKa of CH3COOH, and what does this mean?

Answer 14

50% molecules = CH3COOH,

50% molecules = CH3COO-.

Question 15

What type of bond joins amino acids together?

Answer 15

Peptide bonds.

Question 16

How do peptide bonds work?

Answer 16

Carboxyl group of the first amino acid reacts with amino group of the second.

Question 17

What type of reaction is the formation of a peptide bond?

Answer 17

Condensation reaction.

Question 18

What do proteins have at either end?

Answer 18

Free amino group (N terminus) at start, free carboxyl group (C terminus) at end.

Question 19

Which direction are proteins written in?

Answer 19

N->C direction.

Question 20

How would you describe the bonding in a peptide bond? What effect does this have?

Answer 20

Partial double bond character.

Rotation is restricted - peptide unit rigid and planar.

Question 21

Is the peptide unit sys or trans?

Answer 21

Trans.

Question 22

What is the rotation around Cα-C denoted as?

Answer 22

Psi (ψ)

Question 23

What is the rotation around the N-Cα denoted as?

Answer 23

Phi (φ)

Question 24

Why are most phi and psi angles not allowed?

Answer 24

Steric collisions between side chains and main polypeptide chain.

Question 25

What determines the shape of the entire protein regarding angles?

Answer 25

ψ and φ bond angles for each amino acid.

Question 26

What is the main driving force in protein folding?

Answer 26

Attaining an energetically stable structure.

Question 27

The main polypeptide chain is hydrophilic due to C=O and N-H groups. How does the protein combat this, enabling a hydrophobic core?

Answer 27

Structures must be assumed that neutralise these groups by hydrogen bonding.

Question 28

2 types of secondary structure?

Answer 28

``` Alpha helix (α-helix) Beta sheet (β-sheet). ```

Question 29

α-helices formed from how many amino acids typically?

Answer 29

5-40.

Question 30

What happens to the N-H and C=O groups in the α-helix?

Answer 30

H-bonded to one another along the axis of the helix.

Question 31

How many amino acids per turn of α-helix?

Answer 31

3.6.

Question 32

How far does each amino acid turn the α-helix?

Answer 32

100º.

Question 33

What's the vertical distance from one amino acid to the next? Therefore, what's the pitch of the helix?

Answer 33

Vertical distance = 0.15nm. | Pitch = 0.54nm.

Question 34

To what is the C=O group of amino acid n bonded to?

Answer 34

N-H group of amino acid n+4.

Question 35

Do amino acid side chains project into or out of the α-helix?

Answer 35

Project out.

Question 36

What type of plot can an α-helix be plotted on?

Answer 36

Helical wheel diagram.

Question 37

What are β-sheets formed from?

Answer 37

Non-continuous regions of the polypeptide chain. A.K.A.β-strands.

Question 38

How do the β-strands bond to one another?

Answer 38

Form hydrogen bonds between C=O groups of one strand, and N-H groups of another.

Question 39

Do β sheets always run continuously in one direction?

Answer 39

No. If all N->C, PARALLEL. | If opposite directions, ANTI-PARALLEL.

Question 40

How do hydrogen bonds change between parallel and anti parallel β sheets?

Answer 40

Hydrogen bonds evenly spaced within parallel β sheet, but narrowly spaced separated by a larger gap in anti-parallel sheet.

Question 41

What is another name for β sheets? And why?

Answer 41

β-pleated sheets. | Because Cα carbons lie successively above and below plane of sheet.

Question 42

What links secondary structures?

Answer 42

Loop regions.

Question 43

What are long loops called, and what is a key property?

Answer 43

Random coils - very flexible.

Question 44

What are short loops called, and what do they connect?

Answer 44

Hairpin loops or β turns. | Connect anti-parallel β strands.

Question 45

What are the 2 amino acids often found in loops, and why?

Answer 45

Proline - locked ring structure introduces kink to polypeptide chain. Glycine - small side chain enables it to form turns where others couldn't.

Question 46

What are parallel β-strands often connected by, and how? | Also, what is this called?

Answer 46

α-helices, by crossing β-sheet from one edge to the other. | Called β-α-β motif.

Question 47

What is a tertiary structure?

Answer 47

Association of secondary structure into complex domains.

Question 48

What is a disulphide bridge?

Answer 48

Sulphydryl on one cysteine forming a crosslink with another sulphydryl on another cysteine near to it in space.

Question 49

What benefit does cysteine's disulphide bridge confer to proteins?

Answer 49

Stabilises tertiary structure, making proteins more resistant to degradation and denaturation.

Question 50

What is a quaternary structure?

Answer 50

Multiple polypeptide chains (subunits) associating into a multimeric complex held together by electrostatic, hydrogen and van der waals bonds (sometimes disulphide bridges).

Question 51

Why is polypeptide backbone usually shown as line/ribbon?

Answer 51

Diagrams usually very complex when representing all atoms.

Question 52

How is an α-helix depicted in diagrams?

Answer 52

Spiral/cylinder.

Question 53

How are β-strands depicted in diagrams?

Answer 53

Thick arrows, pointing from N to C terminal end.

Question 54

What are the 2 major classes of proteins?

Answer 54

Globular - arranged in compact domains. | Fibrous - protein chains arranged into fibres.

Question 55

What is the typical role of globular and fibrous proteins?

Answer 55

Globular proteins usually active components of cellular machinery. Fibrous proteins usually structural role.

Question 56

3 main groups of fibrous proteins? | And how are they defined?

Answer 56

coiled-coil (e.g. keratin, myosin). β-sheets (e.g. amyloid fibres, silks). triple helix (e.g. collagens). Defined by secondary structure.

Question 57

Where are keratins found, and why?

Answer 57

Hair, nails, feathers, etc. | Mechanically durable.

Question 58

How many amino acids are repeated in α-keratin? What does this form?

Answer 58

7. (a-b-c-d-e-f-g). | Forms α-helix.

Question 59

Which 2 residues of α-keratin lie on the same side of the helix? What's notable about them?

Answer 59

a and d. | Both are hydrophobic residues.

Question 60

How are the 2 α-keratin helices associated? | What is this structure called?

Answer 60

Both twist around each other, associated by hydrophobic faces of helices. COILED-COIL.

Question 61

When 2 coiled coils in α-keratin line up with one another, how are they referred to?

Answer 61

Staggered antiparallel tetramer.

Question 62

What are staggered antiparallel tetramers the foundation of?

Answer 62

Foundation of protofilaments, which form protofibrils, forming microfibrils.

Question 63

What do long stretches of silk fibroin contain?

Answer 63

A six amino acid repeat (Gly-Ser-Gly-Ala-Gly-Ala), forming an antiparallel β-sheet.

Question 64

Where do glycine, alanine and serine side chains protrude in silk fibroin? What benefit does this confer?

Answer 64

Glycine protrudes on one side. Serine and alanine protrude on the other side. Enables β-sheets to stack into an array with alternating layers.

Question 65

Why is silk strong yet flexible?

Answer 65

Strong because stretching would require breaking of covalent bonds. Flexible because β-sheets interact via weak van der Waals bonds.

Question 66

What is the most abundant vertebrate protein?

Answer 66

Collagen.

Question 67

Nearly one third of the amino acids in collagen are which amino acid? Another 15-30% are which other amino acids?

Answer 67

``` ~1/3 = glycine. 15-30% = proline or hydroxyproline (Hyp). ```

Question 68

What's the primary amino acid sequence in collagen? | repeating tripeptide

Answer 68

Gly-X-Y. X often proline. Y often Hyp.

Question 69

Why can collagen not form an α-helix? What does it form instead?

Answer 69

Pro and Hyp residues prevent collagen from forming α-helix. | Forms loose helix instead, with around 3 residues per turn.

Question 70

Three collagen peptides wind around each other. What does this form?

Answer 70

Triple helix. (Trimer)

Question 71

What is the only residue that can fit through the centre of the triple helix? (every 3rd amino acid).

Answer 71

Gly.

Question 72

What do the Hyp and Pro residues do in collagen?

Answer 72

Confer rigidity.

Question 73

What bonds do the polypeptide chains form?

Answer 73

Inter-chain hydrogen bonds.

Question 74

What can trimers do in collagen?

Answer 74

Associate, building large, strong fibres.