Amino Acids/Enzymes/Proteins etc

Question 1

What is the R group of glycine?

Answer 1

H

Question 2

How can amino acids be classified?

Answer 2

Charge, polarity, aromatic/aliphatic, acid/base properties

Question 3

What are aliphatic amino acids?

Answer 3

Amino acids with carbon chains as their side chains

Question 4

Aromatic?

Answer 4

Has a ring- often benzene

Question 5

Which amino acid shows no stereoisomerism? Why?

Answer 5

Glycine, it’s R group is only a H

Question 6

In aqueous solution, what tends to happen to non-polar AA’s?

Answer 6

The hydrophobic effect- the side chains cluster together in the interior of a protein

Question 7

Why are cysteine residues so important?

Answer 7

Their side chains have sulphydryl groups and so can form disulphide bonds

Question 8

What is KA?

Answer 8

Acid dissociation constant

=[H+][A-]/[HA]

Question 9

Larger the KA….

Answer 9

The stronger the acid

Question 10

What is the general rule regarding pK/pH values and whether it will be protonated or not?

Answer 10

pH will be protonated

pH>pK–> will be deprotonated

Question 11

If the pH is lower than the pK value, will the amino acid be protonated or not?

Answer 11

Protonated

Question 12

What are characteristics of a peptide bond?

Answer 12

In trans form, planar, has partial double bond characteristics TF cannot rotate, uncharged yet polar

Question 13

Why are peptide bonds always in trans form?

Answer 13

Due to steric interference

Question 14

Define isoelectric point

Answer 14

pH at which there is no overall net charge on the protein

Question 15

If pH is lower than the pI, will the protein be protonated or not?

Answer 15

Protonated

Question 16

If pH is higher than pI, will the protein be protonated or not?

Answer 16

Deprotonated

Question 17

Give a rough pI range for an acidic protein

Answer 17

pI

Question 18

Give a rough range of pI for a basic protein

Answer 18

High pH

pH>7

Question 19

Give characteristics of an alpha helix

Answer 19

Right handed
3.6 AA per turn
R groups of AA play no role in making the helix(lie outside of helix)
0.54nm pitch
Stabilised by H bonds between aside H and carbonyl O

Question 20

Which amino acids are helix breakers? Why?

Answer 20

Proline and Glycine

Proline S R group is so large and isn’t geometrically compatible with the α helix and forms a kink

Question 21

Give some characteristics of B sheet

Answer 21

Can be parallel OR anti-parallel OR mixed
Has multiple inter strand H bonds
Presence of H bonds stabilises structure

Question 22

In anti-parallel B sheet, which direction(s) do the strands run in?

Answer 22

One runs N terminus –> C terminus and the other goes C–>T

Question 23

How do detergents denature proteins?

Answer 23

Interfere with hydrophobic interactions

Question 24

What are amyloid fibres?

Answer 24

Misfolded, insoluble form of a protein

Question 25

At physiological pH, what form are amino acids in?

Answer 25

Zwitterion form- carboxyl is dissociated (COO-) amino is protonated (NH3+)

Question 26

Define Vmax

Answer 26

Maximal velocity- maximal obtainable rate when all active sites are saturated with substrate

Question 27

What are the units for Vmax?

Answer 27

Mol/min

Question 28

Define Km and what is it?

Answer 28

Michaels Constant- substrate concentration at half the maximal velocity. It is a measure of affinity.

Question 29

What affinity would an enzyme with a low Km have?

Answer 29

High affinity

Question 30

What affinity would an enzyme with high km have?

Answer 30

Low affinity

Question 31

How can you overcome the effects of a competitive inhibitor?

Answer 31

Increase the amount of substrate

Question 32

How would/not Vmax and Km change with the addition of a competitive INHIBITOR?

Answer 32

Vmax unaffected. Km would be affected (increased) as it would decrease the amount of available active sites Therefore require a higher [substrate] to reach Km TF Km increases

Question 33

How would/not Vmax and Km be affected with the addition of a non-competitive INHIBITOR?

Answer 33

Vmax would be affected (decreases) because binding of non-competitive inhibitor alters structure of active site and so reduces no. of free/usable active sites. TF there are less available to saturate. Km unaffected

Question 34

With Vmax/Km graphs? What are the Y and X axes?

Answer 34

(Y to the sky) | Y axis= Reaction velocity. X axis= [substrate]

Question 35

What is Michaelis Constant?

Answer 35

Km- substrate conc at half maximal velocity ([s] when half active sites are occupied)

Question 36

What is reaction velocity?

Answer 36

Speed in a certain direction

Question 37

In general terms, what effect will a non-competitive inhibitor or activator have on Vmax and Km?

Answer 37

Affects Vmax, doesn't affect Km

Question 38

In general terms, what effect will a competitive inhibitor or activator have on Vmax and Km?

Answer 38

Affect Km, won't affect Vmax

Question 39

Why will the addition of a competitive INHIBITOR increase Km?

Answer 39

Because to overcome the effect of the inhibitor you add a lot of substrate in, TF [s] increases ^

Question 40

What is the Michaelis Menten equation?

Answer 40

Vo= Vmax X [s] / Km + [s]

Question 41

What is the purpose/function of a Lineweaver Burk plot?

Answer 41

Allows for easy estimation of Km and Vmax

Question 42

What are the Y and X axes in Lineweaver Burk Plots?

Answer 42

``` Y= 1/V X= 1/[s] ```

Question 43

REMEMBER!! Regarding Lineweaver Burk plots...

Answer 43

The axes are 1 over eg 1/V. TF if Km^, the line will become steeper.

Question 44

In Lineweaver Burk plots, what is the Y intercept?

Answer 44

1/Vmax

Question 45

In Lineweaver Burk plots, what is the X intercept?

Answer 45

-1/Km

Question 46

List three ways enzymes may be regulated

Answer 46

Allosteric regulation (inhibition/activation) Covalent modification Proteolytic activation

Question 47

Difference between alpha helix and double helix?

Answer 47

Alpha helix is tertiary protein structure, double helix is two strands of DNA wound together

Question 48

How does a drop in pH denature a protein?

Answer 48

Rise in H+ ions causes change in ionisation of side chains of AA's in protein, can affect H & ionic bond formation, causing structural change to protein.