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Biomolecules > Amino acid nomenclature and stereochemistry > Flashcards

Amino acid nomenclature and stereochemistry Flashcards

1
Q

What is the basic structure of all amino acids?

A

A central carbon bonded to a hydrogen atom, a carboxyl group, an amino group and an R group/side chain.

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2
Q

What is the R group on glycine?

A

A hydrogen atom.

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3
Q

What is the side chain of proline?

A

The nitrogen of the amino group attached to the alpha carbon.

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4
Q

What is the relationship between the the two versions of each amino acid?

A

They are enantiomers.

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5
Q

What are the names of the two versions of each amino acid?

A

D- form and L- form.

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6
Q

What form of amino acid is used in the formation of proteins?

A

L- form

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7
Q

How many ionisable groups does each amino acid have?

A

At least 2

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8
Q

What is ionisation?

A

The conversion of an atom to an ion.

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9
Q

What is a zwitterion?

A

A molecule with two ionised groups but no net charge.

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10
Q

What makes amino acids amphoteric?

A

Their ionisable carboxyl and amino groups.

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11
Q

What determines whether amino and carboxyl groups are ionised?

A

pH

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12
Q

Is glycine ionised at pH 4-8?

A

Yes but it is a zwitterion.

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13
Q

What happens to glycine at pH 0-4?

A

Some molecules are ionised.

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14
Q

What is the carboxyl Pka?

A

The point where there are an equal number of ionised and non- ionised carboxyl groups.

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15
Q

When do non-ionised carboxyl groups predominate?

A

At a lower pH.

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16
Q

What happens to amino groups at pH 8?

A

Some lose protons.

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17
Q

What is the Pka of amino groups?

A

The point when the number of molecules with and without ionised amino groups are the same.

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18
Q

When do the non-ionised amino groups predominate?

A

At pH values above the Pka.

19
Q

At what pH can the zwitterions of each amino acid operate?

A

pH 7.4

20
Q

Why do aspartic acid and glutamic acid act as proton acceptors in biochemical reactions?

A

As they are fully ionised at pH 7.4.

21
Q

Why do arganine and lysine act as bases at pH 7.4?

A

As they have a positively charged side chain.

22
Q

Are the side chains of cysteine and tyrosine ionised at pH 7.4?

A

No

23
Q

Why can histidine act as a proton donor or acceptor?

A

As it has ionisable side chains and at pH 7.4 some molecules are ionised and some are non - ionised.

24
Q

By what is the polarity of some side chains caused?

A

Uneven distribution of electrons on the R group.

25
Q

What are the two rare amino acids not usually found in living systems?

A

Selenocysteine and pyrrolysine.

26
Q

What is the simplest post-translational modification?

A

The addition of hydroxyl, methyl and phosphate groups to the side chain.

27
Q

What regulates protein activity?

A

Amino acid modification.

28
Q

Where does the peptide bond form in a polypeptide?

A

Between the carboxyl group of one amino acid and the amino group of another.

29
Q

How does the polypeptide terminate?

A

With either a free amino group (N terminus) or a free hydroxyl group (C terminus).

30
Q

What is chemical direction of polypeptides?

A

Either N->C or C->N.

31
Q

In what direction does protein synthesis occur?

A

N->C, every amino acid is added to a free carboxyl.

32
Q

What is the structure of a peptide group?

A

2 alpha carbons with a carbon, nitrogen, oxygen and hydrogen between them.

33
Q

What are the characteristics of peptide groups?

A

The have a flat structure and are rigid; there is no rotation.

34
Q

What is the angle rotation around the alpha carbon - carbon bond called?

A

Psi

35
Q

What is the rotation angle around the nitrogen - alpha carbon bond called?

A

Phi

36
Q

What is the angle of psi and phi when two adjacent peptide groups are orientated on the same plane?

A

180 degrees.

37
Q

What happens to phi and psi when the bond is rotated clockwise?

A

They increase

38
Q

What happens to phi and psi when the bond is rotated counterclockwise?

A

They decrease

39
Q

Why do 77% of possible psi and phi combinations never occur?

A

Because of steric effects.

40
Q

What does the Ramachandran plot demonstrate?

A

the phi and psi combos that occur.

41
Q

What is primary structure?

A

The sequence of amino acids in the polypeptide.

42
Q

What is secondary structure?

A

The series of conformations i.e. helices, sheets and turns.

43
Q

What is tertiary structure?

A

The 3D configuration of a protein.

44
Q

What is quaternary structure?

A

Association between different subunits to form a subunit protein.

Biomolecules (4 decks)

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