W1 - Intro to Proteins

Question 1

What is the unit of mass and length for proteins?

Answer 1

Mass - Da, Length - Angstrom

Question 2

What is 1 Da equivalent to?

Answer 2

Mass of 1H atom

Question 3

What is 1 Angstrom equivalent to?

Answer 3

0.1nm

Question 4

Which terminals are proteins read from and what does this direction tell us about proteins?

Answer 4

N terminus to C terminus, meaning they’re polar

Question 5

What type of reaction creates a peptide bond?

Answer 5

Condenstion

Question 6

Is a peptide bond planar?

Answer 6

Yes planar

Question 7

What are two characteristics of a peptide bond that are also the same as double bonds?

Answer 7

Distance is shorter and no rotation

Question 8

Does a trans or cis peptide bond usually form in proteins?

Answer 8

Normally trans

Question 9

What is the exception of trans/cis peptide bonds in proteins?

Answer 9

When proline is bound to another aa, there’s steric constraints due to the ring so can express both

Question 10

What is the main chain and what may it also be called?

Answer 10

Regular repeating part of polypeptide, also known as the backbone

Question 11

What is the native structure of proteins?

Answer 11

The 3D structure under physiological conditions

Question 12

How do disulphide links form?

Answer 12

Between cysteine residues, losing 2H+ and 2e-

Question 13

What happened in Anfinsen’s experiment when he added RNAse to 8M urea sol and 6M guanidine hydrochloride sol?

Answer 13

Protein denatures and unfolds into random coils

Question 14

What does beta - mercetoethanol used for in Anfinsen’s experiments?

Answer 14

Acts as a reducing agent, breaks H-bonds in protein

Question 15

What was the conclusion from the experiment that found the RNAse would renature after the Beta-m and 8M urea had been removed?

Answer 15

Primary structure has all info to correctly fold protein into final conformation

Question 16

How was the urea and Beta-m removed?

Answer 16

Using dialysis

Question 17

How many disulfide bonds in Ribonuclease A?

Answer 17

4

Question 18

What was the second conclusion made by Anfinsen?

Answer 18

The most thermodynamically stable structure of RNAse is it’s native conformation

Question 19

Where are the hydrophobic/philic residues on an aquaporin?

Answer 19

Hydrophilic inside channel - phobic external bit of channel

Question 20

What 2 things do chaperone proteins do to help proteins fold correctly?

Answer 20

Delay folding and change environment

Question 21

Why would a chaperone protein altering the cell environment be useful?

Answer 21

A busy cell environment is not ideal for folding

Question 22

What 5 things can denature a protein?

Answer 22

Heat, pH, metals, chemicals and other proteins

Question 23

Explain why the process of protein folding can be visualised as a funnel

Answer 23

As the protein is folded, the number of folding options decreases

Question 24

Give an example of a dipeptide and tripeptide

Answer 24

Asp-Phe (sweetener), Glu-Cys-Gly (antioxidant)

Question 25

How many aa is a short polypeptide? (e.g. glucagon + substance P)

Answer 25

10-40

Question 26

How many aa is a large polypeptide?

Answer 26

> 40

Question 27

The large protein, dystrophin, has how many aa?

Answer 27

3684aa (427kDa)

Question 28

Why cannot proteins renature after denaturation?

Answer 28

Tangled net of polypeptides ‘confuses’ where bonds were meant to form

Question 29

Chaperones do not contribute to the folding process, what do they do and are they specific to the protein?

Answer 29

They prevent unwanted reactions and they are generalised

Question 30

What 4 things can trigger hs proteins?

Answer 30

Temp, pH, ethanol + urea

Question 31

What amino acid is replaced with valine at position 6 in SCA?

Answer 31

Glutamate

Question 32

Glutamate is -ve, valine is neutral, what hydro- property is also swapped?

Answer 32

Glutamate is hydrophilic and this is swapped for a hydrophobic valine

Question 33

What does the hydrophobic spot from the Glu6Val mutation cause?

Answer 33

HbS molecules clump together

Question 34

CFTR channel is mutated in CF causing the aqueous layer of mucous to thin, what causes this?

Answer 34

Cl- cannot move through, so water potential isn’t maintained

Question 35

What happens when a chaperone protein is misfolded? (e.g. in mad cow disease)

Answer 35

Positive feedback loop of generating misfolded proteins which act as more dodgy chaperones

Question 36

What are amyloids?

Answer 36

Aggregates of misfolded proteins = plaques/fibrils

Question 37

What is the hypothesis involved with mad cow disease?

Answer 37

Prion hypothesis

Question 38

Are prions or amyloids infectious?

Answer 38

Prions yes, amyloids no