MCB Lecture 4 & 5 Amino Acids Flashcards Preview

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Flashcards in MCB Lecture 4 & 5 Amino Acids Deck (47)
0

Describe what is meant by L and D amino acids

This is the different conformations around the alpha carbon

1

L and D amino acids are...

Optical isomers

2

What do the L and the D refer to?

The direction they rotate light
L : left
R : right

3

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

CORN when read clockwise

4

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

Chi
X1, X2 etc

5

What is the preffered conformation of the side chain atoms?

Staggered

6

What are amino acids synthesised from?

L glyceraldehyde

7

What are the acidic side chains?

Aspartic acid (Asp, D)

Glutamic acid (Glu, E)

8

What are the basic side chains?

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

9

What are the polar amino acids?

Asn
Gln
Tyrosine
Serine
Threonine

10

Which are the aromatic amino acids?

Trp
Phe
Tyr (also polar)

11

What is the ionic status of the acidic side chain?

Completely ionised at physiological conditions

12

What is physiological pH?

7.4

13

What do the acidic side chains often do?

At as chelators on metal ions

14

What is the ionic status of lysine?

Completely ionised at physiological pH

15

Which is the predominate form of histadine at physiological pH?

Both ionised and not are found

16

What are the aliphatic amino acids?

Cysteine
Gly
Ala
Val
Leu
Ile
Pro
Met

17

Which amino acids are highly used in enzyme active sites?

Histadine
Cysteine

18

How is Histadine chemically ambidextrous?

It's a nucleophile
It's an electrophile

19

Describe the reactivity of Asparagine and Glutamine

Not very reactive

20

Describe the reactivity of the hydroxyls (Thr & Ser)

Not very chemically reaction

21

Describe the reactivity of Phenylalanine

Very unreactive

22

Describe the reactivity of Tyr

OH can hydrogen bond

23

What is special about Trp

It absorbs UV and fluorescent

24

Describe the reactivity of the aliphatic side chains

Unreactive

25

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

Trans and cis
Trans is favoured

26

Compare the reactivity of cysteine and methionine

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

27

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

Reducing

28

Describe the formation of disulfide bridges

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

29

In what environments will disulfide bridges be present in protein?

In the blood (oxidising)

Inthe cell is reducing, so there will be no disulfide bridges

30

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

Eg ?

Increased stability

Eg. The disulfide bridges in insulin

31

Describe the inner structure of a protein

No water
Hydrophobic region

32

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

Polar: outside
Non polar: inside

33

Where are Glycine and Proline predominantly found?

In alpha and beta turns

34

Which forces drive protein folding?

Van Der Waals
Hydrogen bonding
Electrostatic
Hydrophobic force

35

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

Folded is native
Denatured is not the native state

36

What is renaturing?

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

37

What is meant by protein folding is cooperative?

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

38

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

The whole protein will denature

39

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

Chaperones will help them fold

Chaperones prevent the proteins from folding badly whilst they are still being synthesised

40

What are amyloid diseases?

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

41

Identify the direction of a dipole in a peptide bond

Up

42

Describe van Der Waals interactions

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

43

Describe hydrogen bonds

Two electronegative atoms share a hydrogen atom

44

Describe hydrophobic interactions and entropy in proteins

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

45

Which amino acid is ambidextrous in terms of bonding reactivity?

Histadine

It is both a electrophile and a nucleophile

46

Which amino acid acts as a chelator?

Aspartic acid and glutamic acid

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