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Biocheem > Lecture 11 > Flashcards

Lecture 11 Flashcards

1
Q

What are the Polar Amino Acids?

A
  • Serine
  • Threonine
  • Tyrosine
  • Cysteine
  • Asparagine
  • Glutamine
  • Histidine
  • glycine
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2
Q

What do all the Polar Amino acids have in common?

A

They have side chains that contain an electronegative atom

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3
Q

Why are Polar Amino Acids reactive?

A

Because of the presence of functional groups

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4
Q

What are the two subgroups of polar amino acids?

A
  • Those that don’t carry a formal charge at pH 7

* Those that carry amino a formal charge at pH 7

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5
Q

What is the side chain of Glycine?

A

Just a hydrogen atom

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6
Q

Why is Glycine achiral?

A

Because the alpha carbon contains two H’s

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7
Q

What is the Polarity of Glycine?

A

Even though it is classified as a polar amino acid it is only weakly polar

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8
Q

What is the R group of Serine?

A

A CH2 group bonded to an OH

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9
Q

How many H-bonds can the side chain of Serine form?

A

Three. Two as an acceptor and one as a donor with the alcohol group

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10
Q

What is the way Serine can be modified?

A

Through Phosphorylation

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11
Q

What is the polarity and charge of serine?

A

It is polar and uncharged

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12
Q

Can the OH in Serine be deprotonated?

A

No. It it is very difficult to deprotonate the OH in serine

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13
Q

Can serine participate in H bonding interactions?

A

Yes with the polar OH group

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14
Q

What is meant by Serine can be phosphorylated?

A

The alcohol on the side chain can be used to create a phosphoester structure

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15
Q

What is the Polarity and charge of Threonine?

A

Threonine is polar and uncharged

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16
Q

What functional group does the side chain of Threonine have?

A

-OH

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17
Q

Can Threonine form H-bonds?

A

Yes. Thronine can form H-bonds with the OH on is R group

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18
Q

How can Threonine be modified?

A

It can be phosphorylated

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19
Q

Which three amino acids can be phosphorylated?

A
  • Serine
  • Threonine
  • Tyrosine
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20
Q

How many chiral carbons does Threonine have?

A

It has two chiral carbons

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21
Q

What is a Chiral Carbon?

A

A carbon that contains four different groups (not just carbon atoms)

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22
Q

Which amino acids contain Hydroxyl groups?

A
  • Serine
  • Threonine
  • Tyrosine
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23
Q

How does Tyrosine differ from Serine and Threonine?

A

It is much larger due to its aromatic group

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24
Q

Which Polar uncharged amino acid has an aromatic side chain?

A

Tyrosine

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25
Q

Why is the side chain in Tyrosine considered Amphipathic?

A

Because the aromatic ring is non-polar but the alcohol group is polar

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26
Q

What kind of interactions can Tyrosine participate in?

A

Hydrophobic interactions

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27
Q

What is the difference in the hydroxyl group in Tyrosine when compared to Serine or Threonine?

A

The hydroxyl group is weakly acidic

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28
Q

What is the pKa of the Hydroxyl group in Tyrosin?

A

10.5 pKa

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29
Q

What is the overall charge of Tyrosine at pH 7?

A

It is neutral

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30
Q

What is the charge of the Tyrosine R group at high pH’s?

A

It will have a negative charge because the OH group can be deprotonated

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31
Q

What charge will the amino acid Tyrosine have at pH 14?

A

Because the amine group will be deprotonated and the hydroxyl group will also be deprotonated it will carry a -2 charge because the O- and the COO-

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32
Q

What would be the charge on Tyrosine at pH 1?

A

It will have a +1 charge because the amine group will be NH3+ and the carboxyl group will be COOH (neutral) and the OH will also be neutral

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33
Q

What is the pKa of carboxyl groups?

A

2.0

34
Q

What is the pKa of an amino group?

A

9.5 - 11

35
Q

Which amino acids have an ionizable R group?

A
  • Tyrosine
  • Histidine
  • Cysteine
36
Q

What is the formal charge of Tyrosine, Histidine and Cysteine at pH 7?

A

They carry no formal charge

37
Q

What are the Polar charged amino acids?

A
  • Aspartate
  • Glutamate
  • Arginine
  • Glycine
38
Q

What is the polarity and charge of Cysteine at pH 7?

A

Cysteine is Polar and uncharged

39
Q

what is the difference between the side chain of Cysteine and the side chain of Serine?

A

Cysteines side chain has a thiol group Serines side chain has a hydroxyl group

40
Q

Is Cysteine capable of forming H-bonds?

A

Cysteine can form H-bonds with the thiol group

41
Q

How happens to the side chain of Cysteine at high pH’s?

A

The Thiol group can be deprotonated

42
Q

What is the pKa for the Thiol group of Cysteine?

A

pka is 8.5

43
Q

What is the charge of Cysteine at pH 14?

A

-2 because the amine group is deprotonated to become neutral, the COO- group remains negative and the thiol group (SH) becomes deprotonated to become S-

44
Q

What is unique about Cysteine?

A

It can form covalent bonds with other Cysteine residues through disulphide bonds

45
Q

What are Disulphide bonds?

A

Sulphur Sulfur bonds that connect two Cysteine side chains together

46
Q

What is Cystine?

A

The dimer of two Cysteine residues after they have been joined by disulphide bonds

47
Q

What kind of environment is the cytosol within cells?

A

It is a reducing environment

48
Q

Where does Cystine formation occur?

A

Not in the cytosol because it requires a reducing environment. It occurs in extracellular proteins

49
Q

What is the polarity of cysteine disulfides and what is their acidity?

A

They are non-polar and they do not have a pKa so they are no acidic

50
Q

What aspect does Asparagine have in its side chain?

A

It has an amide aspect (NH2 group)

51
Q

What is the Polarity and charge of Asparagine?

A

It is polar and uncharged

52
Q

What is the functional group in the Asparagine side chain?

A

Carboxamide functional group

53
Q

Can Asparagine form H-bonds?

A

Yes with the carbonyl and NH2 group

54
Q

What can be H-bonds acceptors and H-bond donors in Asparagine side chain?

A

The NH2 can donate two H bonds and the carbonyl can accept two H bonds

55
Q

What functional group does Glutamine contain?

A

It contain a carboxamide functional group with one NH2 and one carbonyl the same as Asparagine

56
Q

What is the Polarity and charge of Glutamine?

A

It is polar uncharged

57
Q

What H bonds can the Glutamine side chain form?

A

It can be an H bond donor at NH2 and an H bond acceptor at the carbonyl

58
Q

What is the three letter code for Asparagine and Glutamine?

A
  • Asn

* Gln

59
Q

Describe the side chain of Histidine?

A

Heterocyclic and Aromatic

60
Q

What happens to the Histidine functional group at low and high pH values?

A

It’s positively charged at low pH’s by gaining a proton (acting as a base) and uncharged a high pH’s by losing the proton it gained

61
Q

What is the ring of Histidine known as?

A

Imidazole

62
Q

What is the charge of the side chain of Histidine at pH 7?

A

It is mostly neutral but some of the side chain is protonated because the pKa is 6

63
Q

What is the pKa of the histidine side chain and what does this mean?

A
  1. At <6 pH the side chain will begin to accept H+
64
Q

Why is histidine very frequently involved in enzymatic reactions?

A

Because it can act as either an acid or base

65
Q

What does the ionization state of Histidine depend on?

A

It chemical environment

66
Q

When can Histidine exclusively act as an H-bond donor?

A

When it is protonates

67
Q

When can histidine act as donor and acceptor?

A

When it is in the base form

68
Q

What are the charged amino acids?

A
  • Aspartate
  • Glutamate
  • Lysine
  • Arginine
69
Q

What is the rule surround pH and pKa?

A

If the pH is lower than the pKa the side chain will get protonated

70
Q

What functional group does Aspartate have in its side chain?

A

It has a carboxyl group

71
Q

What is the charge of aspartate at pH 7?

A

It is negatively charged due to the COO- in the side chain

72
Q

What is the pKa of the side chain of the carboxyl group in Aspartate?

A

4.0

73
Q

What kind of H bonds can Aspartate form?

A

It can be an H bond acceptor with its carbonyl groups

74
Q

Why are Aspartate and Glutamate described as neutral amino acids?

A

Because their root NEUTRAL structure can be deprotonated but their structure in a solution of pH 7 only has COO- groups which are bases

75
Q

Why is Aspartic Acid known as Aspartic acid at pH 1?

A

Because the carboxylate will gain H+ and become an acid

76
Q

What is the charge of Glutamate at pH 7?

A

It is negatively charged because of the COO- in the side chain

77
Q

What is the polarity of Glutamate?

A

It is very polar

78
Q

What kind of H bond interactions can Glutamate form?

A

They can be H bond acceptors

79
Q

What is Glutamate called at pH 1 and why?

A

It is called Glutamic acid because it has H’s on its carboxyl groups that can act as acids

80
Q

What is the pKa for the Glutamate and aspartate side chain?

A

Around 4

Biocheem (38 decks)

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