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Biomolecules Flashcards

1
Q

What is Gibbs free energy?

A

The energy of the reaction available to do work, also called available energy

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2
Q

What is the equation for change in Gibbs Free Energy?

A

<G = G products - G reactants

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3
Q

What does it means by an exergonic reaction?

A

<G is negative, free energy released, favourable, spontaneous

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4
Q

What does it means by endergonic reaction?

A

<G is positive, free energy absorbed, unfavourable, not spontaneous

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5
Q

What does exothermic means?

A

<H is negative, heat is released

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6
Q

What does endothermic means?

A

<H is positive, heat is absorbed

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7
Q

What is Keq ?

A

Thermodynamic equilibrium constant for an reaction, it describes the position of the reaction at equilibrium

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8
Q

What does <G* means?

A

standard free energy change, it is a constant measured under standard conditions

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9
Q

State the equation relating <G*.

A

<G* + RTQ

  • Q: reaction quotient
  • R: universal gas constant
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10
Q

What is the biochemistry standard conditions?

A 
*:
298K
1 atm
[H+] = 10^(-7)M
{H2O} = 55.5M
Mg2+ = 1mM
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11
Q

What does “native” state of a protein means?

A

The fold with lowest free energy

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12
Q

What does the conformational freedom of a molecules depends on? Give examples with single and double bonds.

A

It depends on the bonding between the atoms.

  • single bonds: allow largely free rotations
  • double bonds: planar, very limited rotation
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13
Q

Where is the N and C terminus of a peptide?

A

N; ammonium group

C: carboxylic group

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14
Q

what is resonance?

A

it is the movement of electron between orbitals, which forms partial positive and negative bonds

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15
Q

Why is the trans form highly favoured in proteins?

A

it is highly favoured energetically due to steric hinderance (Van Der Waals repulsion) of the main chain

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16
Q

What is special about Proline?

A

Proline: Trans:Cis = 4:1

Other amino acids: Trans:Cis = 1000:1

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17
Q

what is the omega angle in amino acids?

A

C-N

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18
Q

What are the four atoms that defines the omega angle?

A

alpha C-C-N-alpha C

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19
Q

What does the omega angle describes?

A

it describes the diherdral/torsion angle between alpha C-C and N-alpha C

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20
Q

What are the values of angle of omega?

A

trans: -180 degrees
cis: 0 degrees

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21
Q

Which are the 2 single bond angles with free rotation in amino acids?

A

N-alpha C(phi) and alpha C-C(psi) as they are pure single bonds

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22
Q

What makes up a phi angle?

A

C-N-alpha C-C (not all in the same residue)

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23
Q

What makes up a psi angle?

A

N-alpha C-C-N(not all in the same residue)

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24
Q

Why are phi and psi angles so important?

A

they dictates how the polypeptide is folded up since all the conformational freedom are within them

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25
If an amino acid was found in the disallowed region of a Ramachandran plot, what has happen to it?
this residue has non-standard background angles
26
Which type of proteins can we find in naturally occurring proteins?
those made up of L-amino acids
27
What is the difference between L and D amino acids?
Look down from the H atom: L - clockwise D - anticlockwise
28
What is the chi angle?
side chain dihedral angle: R-alpha C
29
Name all the amino acids with aliphatic side chains.
``` Glycine, Gly, G Alanine, Ala, A Valine, Val, V Leucine, Leu, L Isoleucine, Ile, I Proline, Pro, P ```
30
What does aliphatic means?
Contains C and H only
31
Name all the branched amino acids.
Valine, Val, V Leucine, Leu, L Isoleucine, Ile, I Threonine, Thr, T
32
List all the aromatic amino acids.
Phenyalanine, Phe, F Tyrosine, Tyr, Y Tryptophan, Try, W
33
List all the hydroxyl-containing amino acids.
Serine, Ser, S Threonine, Thr, T Tyrosine, Try, Y
34
List the 2 sulfur-containing amino acids.
Cystine, Cys, C | Methionine, Met, M
35
Name the 3 amino acids which are basic.
Lysine, Lys, K Arginine, Arg, R Histidine, His, H
36
List down all the amino acids which is acidic or derivative of amine.
Aspartic acid, Asp, D Asparagine, Asn, N Glutamic Acid, Glu, E Glutamine, Gln, Q
37
Name the 5 methyl group containing amino acids.
``` Alanine, Ala, A Valine, Val, V Leucine, Leu, L Isoleucine, Ile, I Threonine, Thr, T ```
38
Name all the greek alphabets used in naming of amino acids. (according to their sequence)
alpha, beta, gamma, delta, epsilon, zeta, eta
39
What are the properties of D and E?
- can be completely ionised - negatively charged at pH 7.4 - very polar - often acts as chelators of metal ions
40
What is the structural differences between D and E? State their structures.
D: Glutamic acid, -CH-CH2-COOH E: Aspartic acid, -CH-CH2-CH2-COOH E has one more methylene group
41
What does the word "chelate" means?
A chelate is a chemical compound composed of a metal ion and a chelating agent. A chelating agent is a substance whose molecules can form several bonds to a single metal ion. In other words, a chelating agent is a multi-dentate ligand.
42
What is the structure of K?
K: Lysine, -CH-CH2-CH2-CH2-CH2-CH2-NH3+ | zeta amino group
43
What are the properties of K?
K: Lysine - basic - completely ionised - positively charged at physiological pH - NH3+ form dominates - very polar - NH2 form can be found at very high pH, K is now a potent nucleophile due to the presence of reactive centres
44
What is the structure of R?
R: Arginine -CH-CH20CH2-CH2-NH-C-(NH2)2
45
How does the guanidino looks like?
C+ in the middle, connected to one NH and two NH2
46
Which amino acid contains guanidino group?
R, Arginine, Arg
47
What are the properties of R?
- basic - completely ionised at physiological pH - very polar
48
When can we find the neutral form of R?
At extremely high pH
49
How does the positively charged form of R looks like?
- partial double bonds between the central C and the NH, 2x NH2 - this partial double bond is planar, and it is stabilised by resonance, charge is delocalised over the whole group
50
Where can we find imidazole ring?
Histidine, H
51
What is the structure of H?
-CH-CH2- his imidazole ring with 2 N
52
What is the special property of his imidazole ring?
It makes H chemically ambidextrous | - His can be both a H-bond donor or acceptor (electrophile, nucleophile)
53
In which type of molecules is H commonly found?
enzyme active sites
54
List the characteristics of H.
- basic - effective nucleophile in its deprotonated form, (electrophile when protonated), both states are quite common - tertiary amine, better nucleophile than primary and secondary amines - pKa ~ 7 - both states are well populated at pH7.4
55
Why is H aromatic for its resonance structure?
Presence of delocalised double bonds in the his imidazole ring
56
What is the difference between structures of N and Q?
N: Asparagine, Q: Glutamine N: -CH-CH2-CONH2 Q: -CH-CH2-CH2-CONH2
57
List the chemical properties of Q and N.
N: Asparagine, Q: Glutamine - not very chemically active - polar - H-bond donor and acceptor - Deaminate to Asp and Glu (rarely occurs) at high and low pH - resonance structure has partial double bonds, planar, similar to the peptide bond
58
Describe the structure of S and T.
S: Serine, T: Threonine S: -CH-C(OH)(H)(H) T: -CH-C(CH3)(H)(CH3) T has an extra chiral carbon
59
State the chemical properties of S and T.
S: Serine, T: Threonine - not very chemically active - polar - H-bond acceptor and donor
60
Describe the structure of F.
F: Phenylalanine | -CH-CH2-benzene ring (with all H)
61
What are the chemical properties of F?
F: Phenylalaine - non-polar - non-reactive (only reacts under extreme conditions)
62
What is the structure of Y?
Y: Tyrosine | -CH-CH2-benzene ring (With OH at the extreme end)
63
What are the chemical properties of Y?
Y: Tyrosine - largely non-polar(ring) - somewhat polar (OH) - OH can form H-bond - Hydroxyl group pKa ~ 10
64
What are the properties of W?
W: Tryptophan - largely non-polar - indole ring - largest and rarest side chain - conjugated double bonds - absorbs UV and fluorescent - Indole NH H-bond donor - electron rich negative charge transfer
65
Describe the structures of A and V.
A: Alanine, V: Valine A: -CH-CH3 V: -CH-C(CH3)(H)(CH3)
66
What are the chemical properties of A and V?
- aliphatic - no reactive groups - non-polar/hydrophobic - interact favourably with other non-polar groups
67
What are the structures of L and I?
L: Leucine, I: Isoleucine L: -CH-CH2-C(CH3)(H)(CH3) I: -CH-C(CH2-CH3)(H)(CH3) I has extra chiral centre.
68
Describe the chemical properties of L and I.
- aliphatic - no reactive groups - non-polar/hydrophobic - interact with other non-polars
69
Which type of amino acid makes up proteins?
L amino acids
70
What is a chi angle?
Side chain dihedral angle
71
What are the chemical properties of P?
P: Proline - aliphatic - no reactive groups - non-polar/hydrophobic - interact with other non-polar - cannot be H-bond donor due to the presence of imino acid instead of amino acid (No NH group) - trans: cis = 4:1 (due to steric hinderance)
72
What is the structure of G?
G: Glycine (Just the structure of amino acid which the R group is H) - 2H present, not chiral, no D or L isomers
73
What are the properties of G?
G: Glycine - No side chain (only H) - > not chiral, no D or L isomers - > less steric clashes - > much less restriction on phi and psi angles - can form right and left handed turns - no reactive groups - aliphatic - non-polar/hydrophobic
74
What are the structures of C and M?
C: Cysteine, M: Methionine C: -CH-C(SH)(H)(H) M: -CH-CH2-CH2-S-(CH3)
75
What are the properties of C?
C: Cysteine - non-polar/hydrophobic - very reactive in deprotonated form due to presence of S - thiolate: most reactive side chain (S-) - > used in enzyme active sites - Disulfide bonds can form between two Cys side chains - > can be interchain or intrachain - > a very stable bond - E.g. Insulin, Lysozyme
76
What are the properties of M?
M: Methionine - non-polar - not particularly reactive - can be air oxidised to sulfoxide

MCB (1 decks)

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