MCB Lecture 4 & 5 Amino Acids

Question 0

L and D amino acids are…

Answer 0

Optical isomers

Question 1

Describe what is meant by L and D amino acids

Answer 1

This is the different conformations around the alpha carbon

Question 2

What do the L and the D refer to?

Answer 2

The direction they rotate light
L : left
R : right

Question 3

Describe the stereochemistry of an amino acid (looking down the H – alpha-carbon bond)

Answer 3

CORN when read clockwise

Question 4

What is the name of the dihedral/torsion angles in the side chain?

Answer 4

Chi

X1, X2 etc

Question 5

What is the preffered conformation of the side chain atoms?

Answer 5

Staggered

Question 6

What are amino acids synthesised from?

Answer 6

L glyceraldehyde

Question 7

What are the acidic side chains?

Answer 7

Aspartic acid (Asp, D)

Glutamic acid (Glu, E)

Question 8

What are the basic side chains?

Answer 8

Arginine (Arg, R)
Histadine (His, H)
Lysine (Lys, K)

Question 9

What are the polar amino acids?

Answer 9

Asn
Gln
Tyrosine
Serine
Threonine

Question 10

Which are the aromatic amino acids?

Answer 10

Trp
Phe
Tyr (also polar)

Question 11

What is the ionic status of the acidic side chain?

Answer 11

Completely ionised at physiological conditions

Question 12

What is physiological pH?

Answer 12

7.4

Question 13

What do the acidic side chains often do?

Answer 13

At as chelators on metal ions

Question 14

What is the ionic status of lysine?

Answer 14

Completely ionised at physiological pH

Question 15

Which is the predominate form of histadine at physiological pH?

Answer 15

Both ionised and not are found

Question 16

What are the aliphatic amino acids?

Answer 16

Cysteine
Gly
Ala
Val
Leu
Ile
Pro
Met

Question 17

Which amino acids are highly used in enzyme active sites?

Answer 17

Histadine

Cysteine

Question 18

How is Histadine chemically ambidextrous?

Answer 18

It’s a nucleophile

It’s an electrophile

Question 19

Describe the reactivity of Asparagine and Glutamine

Answer 19

Not very reactive

Question 20

Describe the reactivity of the hydroxyls (Thr & Ser)

Answer 20

Not very chemically reaction

Question 21

Describe the reactivity of Phenylalanine

Answer 21

Very unreactive

Question 22

Describe the reactivity of Tyr

Answer 22

OH can hydrogen bond

Question 23

What is special about Trp

Answer 23

It absorbs UV and fluorescent

Question 24

Describe the reactivity of the aliphatic side chains

Answer 24

Unreactive

Question 25

What are the two possible conformations of Pro? Which is favoured?

Answer 25

Trans and cis | Trans is favoured

Question 26

Compare the reactivity of cysteine and methionine

Answer 26

Though they both have sulfur, cysteine is very reactive and methionine is very unreactive

Question 27

Inside the cell (cytosol) is a ... environment

Answer 27

Reducing

Question 28

Describe the formation of disulfide bridges

Answer 28

Oxidise, two protons released, and a bond between the two sulfurs

Question 29

In what environments will disulfide bridges be present in protein?

Answer 29

In the blood (oxidising) Inthe cell is reducing, so there will be no disulfide bridges

Question 30

What does the presence of di-sulfide bonds mean for a protein? Eg ?

Answer 30

Increased stability Eg. The disulfide bridges in insulin

Question 31

Describe the inner structure of a protein

Answer 31

No water | Hydrophobic region

Question 32

Describe the localisation of polar and non polar side chains in amino acids

Answer 32

Polar: outside | Non polar: inside

Question 33

Where are Glycine and Proline predominantly found?

Answer 33

In alpha and beta turns

Question 34

Which forces drive protein folding?

Answer 34

Van Der Waals Hydrogen bonding Electrostatic Hydrophobic force

Question 35

What is the native state of amino acids? | What is the other state?

Answer 35

Folded is native | Denatured is not the native state

Question 36

What is renaturing?

Answer 36

Protein denaturing is reversible. | After it has been denatured, if the solvent is removed, it will denature and be folded

Question 37

What is meant by protein folding is cooperative?

Answer 37

It is all or none. There is no such thing as a half folded protein

Question 38

If any part of the protein has it's interactions disturbed, ...

Answer 38

The whole protein will denature

Question 39

Describe what happens in the cases where proteins can not fold by themselves?

Answer 39

Chaperones will help them fold Chaperones prevent the proteins from folding badly whilst they are still being synthesised

Question 40

What are amyloid diseases?

Answer 40

These are diseases in which there are complexes of protein where all the protein is mis folded. Eg. Huntington, Parkinson's, Creurzfeld-Jacob

Question 41

Identify the direction of a dipole in a peptide bond

Answer 41

Up

Question 42

Describe van Der Waals interactions

Answer 42

Once the atoms get to a certain proximity, there is an attractive force Closer than this, and the electrons repulse the two atoms Further away and there is no attraction

Question 43

Describe hydrogen bonds

Answer 43

Two electronegative atoms share a hydrogen atom

Question 44

Describe hydrophobic interactions and entropy in proteins

Answer 44

Hydrophobic molecules stick together It is more favourable for the protein to fold up for that all the hydrophobic residues are together in the middle. This way, all the water molecules are released. This represents a higher level of disorder

Question 45

Which amino acid is ambidextrous in terms of bonding reactivity?

Answer 45

Histadine It is both a electrophile and a nucleophile

Question 46

Which amino acid acts as a chelator?

Answer 46

Aspartic acid and glutamic acid