Amino acid nomenclature and stereochemistry

Question 1

What is the basic structure of all amino acids?

Answer 1

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

Question 2

What is the R group on glycine?

Answer 2

A hydrogen atom.

Question 3

What is the side chain of proline?

Answer 3

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

Question 4

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

Answer 4

They are enantiomers.

Question 5

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

Answer 5

D- form and L- form.

Question 6

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

Answer 6

L- form

Question 7

How many ionisable groups does each amino acid have?

Answer 7

At least 2

Question 8

What is ionisation?

Answer 8

The conversion of an atom to an ion.

Question 9

What is a zwitterion?

Answer 9

A molecule with two ionised groups but no net charge.

Question 10

What makes amino acids amphoteric?

Answer 10

Their ionisable carboxyl and amino groups.

Question 11

What determines whether amino and carboxyl groups are ionised?

Answer 11

pH

Question 12

Is glycine ionised at pH 4-8?

Answer 12

Yes but it is a zwitterion.

Question 13

What happens to glycine at pH 0-4?

Answer 13

Some molecules are ionised.

Question 14

What is the carboxyl Pka?

Answer 14

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

Question 15

When do non-ionised carboxyl groups predominate?

Answer 15

At a lower pH.

Question 16

What happens to amino groups at pH 8?

Answer 16

Some lose protons.

Question 17

What is the Pka of amino groups?

Answer 17

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

Question 18

When do the non-ionised amino groups predominate?

Answer 18

At pH values above the Pka.

Question 19

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

Answer 19

pH 7.4

Question 20

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

Answer 20

As they are fully ionised at pH 7.4.

Question 21

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

Answer 21

As they have a positively charged side chain.

Question 22

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

Answer 22

No

Question 23

Why can histidine act as a proton donor or acceptor?

Answer 23

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

Question 24

By what is the polarity of some side chains caused?

Answer 24

Uneven distribution of electrons on the R group.

Question 25

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

Answer 25

Selenocysteine and pyrrolysine.

Question 26

What is the simplest post-translational modification?

Answer 26

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

Question 27

What regulates protein activity?

Answer 27

Amino acid modification.

Question 28

Where does the peptide bond form in a polypeptide?

Answer 28

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

Question 29

How does the polypeptide terminate?

Answer 29

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

Question 30

What is chemical direction of polypeptides?

Answer 30

Either N->C or C->N.

Question 31

In what direction does protein synthesis occur?

Answer 31

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

Question 32

What is the structure of a peptide group?

Answer 32

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

Question 33

What are the characteristics of peptide groups?

Answer 33

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

Question 34

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

Answer 34

Psi

Question 35

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

Answer 35

Phi

Question 36

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

Answer 36

180 degrees.

Question 37

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

Answer 37

They increase

Question 38

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

Answer 38

They decrease

Question 39

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

Answer 39

Because of steric effects.

Question 40

What does the Ramachandran plot demonstrate?

Answer 40

the phi and psi combos that occur.

Question 41

What is primary structure?

Answer 41

The sequence of amino acids in the polypeptide.

Question 42

What is secondary structure?

Answer 42

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

Question 43

What is tertiary structure?

Answer 43

The 3D configuration of a protein.

Question 44

What is quaternary structure?

Answer 44

Association between different subunits to form a subunit protein.