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Miscellaneous > MCB Lecture 4 & 5 Amino Acids > Flashcards

MCB Lecture 4 & 5 Amino Acids Flashcards

0
Q

L and D amino acids are…

A

Optical isomers

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1
Q

Describe what is meant by L and D amino acids

A

This is the different conformations around the alpha carbon

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2
Q

What do the L and the D refer to?

A

The direction they rotate light
L : left
R : right

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3
Q

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

A

CORN when read clockwise

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4
Q

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

A

Chi

X1, X2 etc

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5
Q

What is the preffered conformation of the side chain atoms?

A

Staggered

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6
Q

What are amino acids synthesised from?

A

L glyceraldehyde

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7
Q

What are the acidic side chains?

A

Aspartic acid (Asp, D)

Glutamic acid (Glu, E)

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8
Q

What are the basic side chains?

A

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

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9
Q

What are the polar amino acids?

A 
Asn
Gln
Tyrosine
Serine
Threonine
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10
Q

Which are the aromatic amino acids?

A

Trp
Phe
Tyr (also polar)

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11
Q

What is the ionic status of the acidic side chain?

A

Completely ionised at physiological conditions

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12
Q

What is physiological pH?

A

7.4

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13
Q

What do the acidic side chains often do?

A

At as chelators on metal ions

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14
Q

What is the ionic status of lysine?

A

Completely ionised at physiological pH

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15
Q

Which is the predominate form of histadine at physiological pH?

A

Both ionised and not are found

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16
Q

What are the aliphatic amino acids?

A 
Cysteine
Gly
Ala
Val
Leu
Ile
Pro
Met
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17
Q

Which amino acids are highly used in enzyme active sites?

A

Histadine

Cysteine

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18
Q

How is Histadine chemically ambidextrous?

A

It’s a nucleophile

It’s an electrophile

19
Q

Describe the reactivity of Asparagine and Glutamine

A

Not very reactive

20
Q

Describe the reactivity of the hydroxyls (Thr & Ser)

A

Not very chemically reaction

21
Q

Describe the reactivity of Phenylalanine

A

Very unreactive

22
Q

Describe the reactivity of Tyr

A

OH can hydrogen bond

23
Q

What is special about Trp

A

It absorbs UV and fluorescent

24
Q

Describe the reactivity of the aliphatic side chains

A

Unreactive

25
Q

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

A

Trans and cis

Trans is favoured

26
Q

Compare the reactivity of cysteine and methionine

A

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

27
Q

Inside the cell (cytosol) is a … environment

A

Reducing

28
Q

Describe the formation of disulfide bridges

A

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

29
Q

In what environments will disulfide bridges be present in protein?

A

In the blood (oxidising)

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

30
Q

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

Eg ?

A

Increased stability

Eg. The disulfide bridges in insulin

31
Q

Describe the inner structure of a protein

A

No water

Hydrophobic region

32
Q

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

A

Polar: outside

Non polar: inside

33
Q

Where are Glycine and Proline predominantly found?

A

In alpha and beta turns

34
Q

Which forces drive protein folding?

A

Van Der Waals
Hydrogen bonding
Electrostatic
Hydrophobic force

35
Q

What is the native state of amino acids?

What is the other state?

A

Folded is native

Denatured is not the native state

36
Q

What is renaturing?

A

Protein denaturing is reversible.

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

37
Q

What is meant by protein folding is cooperative?

A

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

38
Q

If any part of the protein has it’s interactions disturbed, …

A

The whole protein will denature

39
Q

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

A

Chaperones will help them fold

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

40
Q

What are amyloid diseases?

A

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

41
Q

Identify the direction of a dipole in a peptide bond

A

Up

42
Q

Describe van Der Waals interactions

A

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
Q

Describe hydrogen bonds

A

Two electronegative atoms share a hydrogen atom

44
Q

Describe hydrophobic interactions and entropy in proteins

A

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
Q

Which amino acid is ambidextrous in terms of bonding reactivity?

A

Histadine

It is both a electrophile and a nucleophile

46
Q

Which amino acid acts as a chelator?

A

Aspartic acid and glutamic acid

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