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MCB 2020 > 1.1 Amino acids and peptides > Flashcards

1.1 Amino acids and peptides Flashcards

1
Q

What is the simple definition of Gibbs free energy?

A

It is the energy of the reaction available to do work

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2
Q

What is the equation relating the change in gibbs free energy to heat and entropy?

A
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3
Q

How are spontaneous reactions defined in terms of delta G?

A

Spontaneous reactions have a negative delta G

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4
Q

What is the difference between exergonic and endergonic?

A
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5
Q

What is the difference between exothermic and endothermic?

A
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6
Q

whats up

What does the sign of delta S indicate in terms of the change in entropy?

A

􏰀Delta S is negative: less disorder

Delta 􏰀S is positive: more disorder

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7
Q

What is the equation linking delta G and delta G*?

A
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8
Q

How does the position of equilibrium relate to the change in Gibbs free energy?

A

The further away from equilibrium you start, the more work is done before you get there.

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9
Q

What are some ways through which a negative delta G can be achieved?

A
  1. Negative delta H (exothermic)
  2. Positive delta S (increase in entropy)
  3. Any combination that leaves delta G negative
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10
Q

What are the standard conditions in chemistry?

A
  1. 298 K
  2. Gases at a partial pressure of 101.3 kPa (1 atm)
  3. Reactants and products at 1 M concentrations
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11
Q

What are the standard conditions in biochemistry?

A

Same as those of chemistry but the reaction occurs in a well buffered aqueous solution at pH 7 with [H+] ion concentration 10-7 and Mg2+ = 1mM

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12
Q

If you look at the free energy equation and set all initial concentrations to 1, what happens?

A

Shows delta G is equal to delta Go when everything is at standard conditions

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13
Q

How does the free energy equation change when all concentrations are at equilibrium?

A

At equilibrium delta G=0 this means the reaction can do no more work.

This shows that delta G0 is a constant

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14
Q

What is used to predict where a reaction will be spontaneous?

A

The measure of whether a reaction will proceed spontaneously is delta G not delta Go.

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15
Q

How can the initial conditions of a reaction be altered in order to get a spontaneous reaction?

A
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16
Q

What are three ways of making unfavourable reactions go?

A
  • Remove one or more of the products at a rate much faster than it is produced so that the reaction is now kinetically driven
  • Replenish one or more of the reactants at a much faster rate than it is removed
  • Couple the unfavourable reaction with a highly favourable reaction (in the active site of an enzyme)
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17
Q

Label the blanks on this ATP molecules

A
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18
Q

What is the difference between a nucleotide and nucleoside?

A

Nucleotide = base + sugar + phosphate

Nucleoside = base + sugar

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19
Q

What causes the release of energy via ATP?

A

Energy is released upon the hydrolysis of phosphoanhydride bonds

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20
Q

Show the equation for the release of energy via ATP including delta G

A
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21
Q

How is bond energy related to bond breakage/forming?

A

Energy is required to break any bond

Energy is released when any bond forms

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22
Q

Why is energy required to break any bond?

A

The bonded state is a more stable state that’s why it required energy to break

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23
Q

Why is the ATP reaction highly exergonic?

A
  • ATP has a higher negative charge density than ADP (ATP less stable)
  • Pi is very stable: multiple resonance states exist
  • ATP phosphoanhydride bonds are relatively weak
  • ADP phosphoanhydride bonds and Pi bonds are relatively strong
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24
Q

Why is tri phosphtate less stable than di phosphate?

A

Due to charge density, are there is a great accumualtion of negative charges and more strain and repulsion

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25
Q

What are some of the roles of proteins in the body?

A
  • Catalysis
  • Transport
  • Structure
  • Motion
  • Signaling
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26
Q

What are some of the properties that make amino acids well suited to carry out a variety of biological functions?

A
  • Capacity to polymerise
  • Useful acid base properties
  • Varied physical properties
  • Varied chemical functionality
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27
Q

What is the basic structure of an amino acid?

A

The 􏰿 carbon always has four substituents and is tetrahedral.

All (except proline) have:

– an acidic carboxyl group connected to the 􏰿carbon

– a basic amino group connected to the 􏰿carbon
– a alpha hydrogen connected to the􏰿 carbon

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28
Q

Which protein isomer is found in naturally occuring amino acids?

A

L amino acids

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29
Q

Where do the D and L names for amino acids originate from?

A

Based on the rotation of plane of polarised light viewed towards the light source or based on what you could chemically synthesise them from

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30
Q

How can you determine the chirality of the alpha carbon?

A
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31
Q

What amino acid is this?

A

Alanine

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32
Q

Alanine

A

What amino acid is this?

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33
Q
A

Cysteine

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34
Q
A

Aspartate

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35
Q
A

Glutamate

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36
Q
A

Phenylalanine

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37
Q
A

Glycine

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38
Q
A

Histidine

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39
Q
A

isoleucine

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40
Q
A

Lysine

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41
Q
A

Leucine

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42
Q
A

Methionine

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43
Q
A

Asparagine

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44
Q
A

Proline

45
Q
A

Glutamine

46
Q
A

Arginine

47
Q
A

Serine

48
Q
A

Threonine

49
Q
A

Valine

50
Q
A

Tryptophan

51
Q
A

Tyrosine

52
Q
A
53
Q

Reversed prompt draw the amino acid

Cysteine

A
54
Q

Reversed prompt draw the amino acid

Aspartate

A
55
Q

Reversed prompt draw the amino acid

Glutamate

A
56
Q

Reversed prompt draw the amino acid

Phenylalanine

A
57
Q

Reversed prompt draw the amino acid

Glycine

A
58
Q

Reversed prompt draw the amino acid

Histidine

A
59
Q

Reversed prompt draw the amino acid

isoleucine

A
60
Q

Reversed prompt draw the amino acid

Lysine

A
61
Q

Reversed prompt draw the amino acid

Leucine

A
62
Q

Reversed prompt draw the amino acid

Methionine

A
63
Q

Reversed prompt draw the amino acid

Asparagine

A
64
Q

Reversed prompt draw the amino acid

Proline

A
65
Q

Reversed prompt draw the amino acid

Glutamine

A
66
Q

Reversed prompt draw the amino acid

Arginine

A
67
Q

Reversed prompt draw the amino acid

Serine

A
68
Q

Reversed prompt draw the amino acid

Threonine

A
69
Q

Reversed prompt draw the amino acid

Valine

A
70
Q

Reversed prompt draw the amino acid

Tryptophan

A
71
Q

Reversed prompt draw the amino acid

Tyrosine

A
72
Q

What is the three letter code for aspartate?

A

D and Asp

73
Q

What is the three letter code for glutamate?

A

E and Glu

74
Q

What is the letter codes for phenylalanine?

A

F and Phe

75
Q

What is the three letter code for isoleucine?

A

I and ile

76
Q

What is the three letter code for Lysine?

A

K or Lys

77
Q

What is the three letter code for asparagine?

A

N or Asn

78
Q

What is the three letter code for glutamine?

A

Q or Gln

79
Q

What is the three letter code for Arginine?

A

R or arg

80
Q

What is the three letter code for tryptophan?

A

W or trp

81
Q

What is the three letter code for tyrosine?

A

Y or Tyr

82
Q

Which amino acids belong to the non polar aliphatic R groups?

A

Glycine, alanine, proline, valine, Leucine, Isoleucine, methionine

83
Q

Which amino acids belong to the polar, uncharged R group category?

A

Serine, Threonine, Cysteine, Asparagine, Glutamine

84
Q

Which amino acids belong to the aromatic R groups?

A

Phenylalaline

Tyrosine

Tryptophan

85
Q

Which amino acids belong to the positively charged R groups? (basic)

A

Lysine

Arginine

Histidine

86
Q

Which amino acids belong to the negatively charged R groups?

A

Aspartate

Glutamate

87
Q

When is pKa equal to pH?

A
88
Q

For the acidic side chains of aspartic acids and glutamic acid, in what state do these R groups exist at physiological pH?

A

Their pKa is 4.4 so at neutral pH they are completely ionsided and negatively charged

89
Q

In what state do the basic side chains of Lysine and Arg have their R groups at physiological pH?

A

Lys has a pKa of 10 so the protonated, positively charged form dominates

Arg has a pKa of 12 so similarly completely ionised.

90
Q

What are the special properties of basic side chain Histidine?

A
  • HIghly used in enzyme active sites
  • The imidazole ring is a H bond done or acceptor (electrophile or nucleophile) and chemically ambidextrous
  • Effective nucleophile in its deprotonated form
91
Q

What are some properties of the amide side chains asparagine and glutamine?

A
  • Not very chemically reactive
  • Polar
  • H bond donor and acceptor
  • THe can remove amide group to become carboxylic acids
92
Q

What state does Tyrosine’s aromatic side chain exist at physiological pH?

A
  • The phenol form dominates above pH 10, but below it phenolate is negatively charged
93
Q

Why are the aromatic side chains responsible for UV absorbance and fluorescence properties?

A
  • The extent and geomtery of conjugated double bond systems cause spectral differences
94
Q

What properties does proline hold due to its unique geometry?

A
  • It has no NH group so its an imino acid
  • Can’t act as a backbone H bond donor
  • Limites rotation between N-Cæ angle -60o
95
Q

Compare the two sulfur containing side chains, cysteine and methionine

A
96
Q

What are some examples of disulfide bonds being seen in proteins?

A
97
Q
A
98
Q

What are the rotation properties of the peptide bonds?

A
  • The peptide bond has partial double bond character due to resonance
  • Rotation around CO-NH bond is not free, groups are co-planer
99
Q

What can be said about the size of the peptide bond?

A
100
Q

Which peptide bond isomer is favoured energetically?

A
  • The trans form is intrinically favoured energetically
  • Due to severse steric hindrance (van der Waals) repulsion of the side chain in cis
101
Q

What sort of peptied bond isomerisation is found in proline?

A

Similar steric hindrance in trans and cis but trans is still favoured for steric reasons

102
Q

Label the terminology of the peptide bond

A
103
Q

What happens when the peptide linkage is cis in nature? For bond angle

A
104
Q

Label which one is the phi and si angle

A
105
Q

Fill in the blanks about the phi angle

A
106
Q

Fill in the blanks about the psi angle

A
107
Q

Why are phi and psi so important?

A

Because assuming all peptide bonds are trans then all the conformation freedom in the backbone of the polypeptide is due to these two rotations, everything else is fixed

108
Q

Fill in the blanks about side chain dihedral angles

A

MCB 2020 (38 decks)

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