Week 2

Question 1

Ribonuclease is a small protein that contains ____ linked via _____

Answer 1

8 cysteins

Linked via 4 di sulfide bonds

Question 2

T/F:

proteins fold to the lowest energy fold randomly

Answer 2

False

not random

Question 3

Within the fold of a protein, where would you find hydrophillic and hydrophobic parts?

Answer 3

Hydrophobic want to bury in the centre
Hydrophillic will be exposed to water
Expell water

Question 4

T/F:

Charged residues are only found inside the protein fold

Answer 4

False
Try to put them outside the protein fold
If they are inside they should try to be neutralized

Question 5

T/F:

It is worse to bury a charged residue than expose a hydrophobic one

Answer 5

True

Question 6

T/F:

Fibrous proteins are soluble

Answer 6

False

Insoluble

Question 7

How do type I-III collagen assemble in comparison to type IV?

Answer 7

I-III= assemble in fibrils
IV= laminar network, plates that stack on top of each other

Question 8

Describe the structure of elastin

Answer 8

Cross-linked random coiled proteins
Mesh that is oriented in a random way
Provides elasticity to tissues
Hydrophobic
Insoluble
Random coil
Permits the protein to stretch and recoil
Coils pack closely together, amino acids interact with each other

C terminals form a double di-sulfide bond
Lots of glycine, alanine, valine

Question 9

What amino acids are commonly found in collagen?

Answer 9

Glycine
Alanine
Proline (special case where proline is in a helix)

Question 10

Describe the structure of keratin

Answer 10

helical rods with globular N and C terminals (to allow them to interact with neighbouring chains)
Durable, unreactive
Hard alpha and soft alpha
Lots of cysteine and cross links through disulphide bonds

Coiled coil comes together to form protofilaments
Protofilaments form protofibrils
Lots of protofibrils packed into cells to form keratin
(curly hair= more cysteins)

Question 11

What is a coiled-coil motif?

Answer 11

Bundle of right handed alpha helixes wound into a left handed super helix

Question 12

Describe the structure of silk

Answer 12

Beta sheets
Hydrophobic (makes it feel smooth)
Alternating sequence of Gly and Ala
Sheets stacked on top of each other

Question 13

Which two types of components give spider silk its properties?

Answer 13

Fibrion= provides structure
Seracin= glue/matrix

Question 14

Who discovered the sequence of insulin?

Answer 14

Frederick Sanger

1953

Question 15

What is the first step to find the sequence of insulin?

Answer 15

Separate the chains
achieved with: extreme pH, 8M urea, 6M guanidine HCl, high sal concentration- usually ammonium sulfate. Then purify the chains

Oxidation with performic acid= prevents them reuniting again
Reducing agents= makes sure they are purified, allows them to go back once you remove them out of solution

Question 16

What is the second step to find the sequence of insulin?

Answer 16

Determine which amino acids are present

Acid hydrolysis and ion exchange chromatography
o Boiled water and 6M HCL, break all the peptide bonds
o Runs elution profile in chromatography manner
o In different pHs, there will be different peaks indicating various amino acids (provides an idea of the ratios of the amino acids)
o Quantity/composition can be conferred

Question 17

What is the third step to find the sequence of insulin?

Answer 17

3. Identify N and C terminal Residues
   o N terminal= free amino group
   o C terminal= free carboxyl group
   o These terminals can therefore react
   o Determine the sequence using DNFB
   o Helps to identify the number of distinct polypetides
   o Found that there were 2 polypeptide chains

Question 18

What is a DNFB Sanger Reagent?

Answer 18

➢ DNFB reacts with the polypeptide to form a yellow compound
➢ Run it on TLC places with standards
➢ Measure the different ratio that they can migrate on the TLC plates with different compositions of solvent and their colour as well
➢ Can quantify each

Question 19

Explain Edman’s Degradation

Answer 19

By dropping the pH you can release one amino acid at a time and analyse

Can be used to identify a protein of known sequence

Question 20

What is a negative about Edman’s Degradation?

Answer 20

Only works for up to 39 amino acids (not enough)

Question 21

How do you sequence polypeptide chains that are bigger than 39 amino acids?

Answer 21

Need to break it down into smaller constituents

Sequence N and C terminus first
Use proteases to break them into smaller constituents
determine the sequence
put them back together

Question 22

What type of technique can be used to identify post translational modifications of a protein?

Answer 22

Mass spectrometry

Question 23

How does mass spectrometry work?

Answer 23

Identify the mass

and therefore identify the amino acid composition

Question 24

Differences in amino acid sequence can be used to identify _______

Answer 24

evolutionary divergences

Question 25

What is a motif?

Answer 25

Specific arrangement of several secondary structure elements

e.g. beta-alpha-beta motif
beta-hairpin motif

Question 26

T/F:

protein synthesis is energy demanding

Answer 26

True

Question 27

Each step of protein synthesis requires ____

Answer 27

energy in the form of ATP

Question 28

There are __ amino acids with __ possible codons

Answer 28

20 aa
61 codons
= redundancy

Question 29

Which two amino acids have a single codon?

Answer 29

Methionine (Met) and Tryptophan (Trp)

Question 30

List the 5 stages of protein synthesis

Answer 30

Activation of amino acids
Initiation of translation
Elongation
Termination and ribosome recycling
Folding and post-translational processing

Question 31

Where does protein synthesis occur?

Answer 31

On free ribosomes in the cytosol

Question 32

What tells the protein where to go once it has been made ???

Answer 32

a sequence of amino acids