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Biokjemi > Amino acids > Flashcards

Amino acids Flashcards

1
Q

How many amino acids are commonly found in proteins

A

20 amino acids

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2
Q

What is the general structure of an amino acid

A

The alpha carbon with the amino group, carboxyl group, hydrogen and the radical

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3
Q

Which amino acid is the only amino acid not to have the general structure and how does it differ?

A

Proline -it is cyclic amino acid

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4
Q

Which amino acid is the only amino acid that doesn’t have stereoisomers?

A

The carbon in glycine isn’t a chiral center because the radical is a carbon atom

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5
Q

What is the name of the class of stereoisomers that almost all amino acids are?

A

Enantiomers -nonsuperposable mirror images of each other

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6
Q

Describe the D, L system

A

L isomers have the hydroxy group attached to the left side of the asymmetric carbon furthest from the carbonyl, while D isomers have the hydroxy group on the right side.

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7
Q

What form does almost all amino acid residues in protein molecules have

A

L-configuration -only 1% is D

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8
Q

What are the nonpolar amino acids called and what are their abbreviations?

A

Glycine (Gly, G), Alanine (Ala, A), Proline (Pro, P), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I) and Methionine (Met, M)

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9
Q

What is Glycines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: H
Abbreviation: Gly and G
Group: nonpolar

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10
Q

What is Alanines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: CH_3 (methyl)
Abbreviation: Ala and A
Group: nonpolar

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11
Q

What is Prolines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-CH_2-CH_2- (forming a pyrrolidine loop)
Abbreviation: Pro and P
Group: nonpolar

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12
Q

What is Valines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH-(CH_3)_2 (isopropyl)
Abbreviation: Val and V
Group: nonpolar

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13
Q

What is Leucines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-CH-(CH_3)_2 (isobutyl group)
Abbreviation: Leu and L
Group: nonpolar

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14
Q

What is Isoleucine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -C-CH_3
-CH_2-CH_3
Abbreviation: Ile and I
Group: nonpolar

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15
Q

What is Methionines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-CH_2-S-CH_3 (S-methyl thioether)
Abbreviation: Gly and G
Group: nonpolar

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16
Q

What are the aromatic amino acids called and what are their abbreviations?

A

Phenylalanine (Phe, F), Tyrosine (Tyr, Y), Tryptophan (Trp, W)

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17
Q

What is Phenylalanines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-C_6H_5 (benzyl)
Abbreviation: Phe and F
Group: aromatic

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18
Q

What is Tyrosines side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-C_6H_4-OH (hydroxyl group)
Abbreviation: Tyr and Y
Group: aromatic

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19
Q

What is Tryptophans side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-C=CH-NH ​(indole)
| |
C = C
/ \
CH=CH-CH=CH Abbreviation: Gly and G
Group: aromatic

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20
Q

What are the polar uncharged amino acids called and what are their abbreviations?

A

Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), Glutamine (Gln, Q)

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21
Q

What is Serine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-OH (hydroxymethyl group)
Abbreviation: Ser and S
Group: polar and uncharged

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22
Q

What is Threonine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH-OH
- CH_3
Abbreviation: Thr and T
Group: polar and uncharged

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23
Q

What is Cysteine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-SH
Abbreviation: Cys and C
Group: polar and uncharged

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24
Q

What is Asparagine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH_2-C=O
-NH2
Abbreviation: Asn and N
Group: polar and uncharged

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25
Q

What is Glutamine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH2-CH2-C=O
-NH2
Abbreviation: Gln and Q
Group: polar and uncharged

26
Q

What are the positively charged amino acids called and what are their abbreviations?

A

Lysine (Lys, K), Histidine (His, H) and Arginine (Arg, R)

27
Q

What is Lysine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH2-CH2-CH2-CH2-+NH3
Abbreviation: Lys and K
Group: positively charged

28
Q

What is Arginine side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH2-CH2-CH2-NH-C=+NH2
-NH2
Abbreviation: His, J
Group: positively charged

29
Q

What is Histidine side chain, abbreviations and which group of amino acids does it belong to?

A 
Radical: -CH2-C-NH
                       //     \
                    HC-N=CH
Abbreviation: His and H
Group: positively charged
30
Q

What are the negatively charged amino acids called and what are their abbreviations?

A

Aspartate (Asp, D) and Glutamate (Glu, E)

31
Q

What is Asparate side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH2-COO-
Abbreviation: Asp and D
Group: negatively charged

32
Q

What is Glutamate side chain, abbreviations and which group of amino acids does it belong to?

A

Radical: -CH2-CH2-COO-
Abbreviation: Glu and E
Group: negatively charged

33
Q

Which amino acids cluster together and thereby helps to stabilize the protein structure through the hydrophobic effect?

A

Alanine, Valine, Leucine and isoleucine (nonpolar)

34
Q

What is an ampholyte?

A

It is a substance that can work as an acid and as a base

35
Q

What is the primary structure of a protein?

A

The sequence of amino acid residues

36
Q

What is the secondary structure of a protein?

A

It refers to particularly stable arrangements of amino acids residues

37
Q

What is the tertiary structure of a protein?

A

It describes all aspects of the three-dimensional folding of a polypeptide

38
Q

What is the quaternary structure of a protein?

A

When a protein has two or more polypeptide subunits, their arrangement in space is referred to as quaternary structure

39
Q

The chirality of an amino acid results from the fact that its alpha carbon:

A

is bonded to four different chemical groups.

40
Q

Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side
chain ___________.

A

glycine; is a hydrogen atom

41
Q

Amino acids are ampholytes because they can function as either a(n):

A

acid or a base.

42
Q

Which of the following statements about aromatic amino acids is correct?
A) All are strongly hydrophilic.
B) Histidine’s ring structure results in its being categorized as aromatic or basic, depending on pH.
C) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.
D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the
phenylalanine R group.
E) The presence of a ring structure in its R group determines whether or not an amino acid is
aromatic.

A

C

43
Q

For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of
amino acids in solution will have:

A

a net positive charge

44
Q

The formation of a peptide bond between two amino acids is an example of a(n) ______________
reaction.

A

condensation

45
Q

What is the net charge for the isoelectric pH og a tetrapeptide

A

the total net charge is zero.

46
Q

Which of the following is correct with respect to the amino acid composition of proteins?
A) Larger proteins have a more uniform distribution of amino acids than smaller proteins.
B) Proteins contain at least one each of the 20 different standard amino acids.
C) Proteins with different functions usually differ significantly in their amino acid composition.
D) Proteins with the same molecular weight have the same amino acid composition.
E) The average molecular weight of an amino acid in a protein increases with the size of the protein.

A

C

47
Q

For the study of a protein in detail, an effort is usually made to first:

A

purify the protein.

48
Q 
In a mixture of the five proteins listed below, which should elute second in size-exclusion (gelfiltration) chromatography?
A) cytochrome c Mr = 13,000
B) immunoglobulin G Mr = 145,000
C) ribonuclease A Mr = 13,700
D) RNA polymerase Mr = 450,000
E) serum albumin Mr = 68,500
A

B

49
Q

The functional differences, as well as differences in three-dimensional structures, between two
different enzymes from E. coli result directly from their different:

A

amino acid sequences.

50
Q

Even when a gene is available and its sequence of nucleotides is known, chemical studies of the
protein are still required to determine:

A

the location of disulfide bonds.

51
Q

What are the structural characteristics common to all amino acids found in naturally occurring
proteins?

A

: All amino acids found in naturally occurring proteins have an alpha carbon to which are attached a
carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L
configuration.

52
Q

Briefly describe the five major groupings of amino acids.

A

Amino acids may be categorized by the chemistry of their R groups: (1) nonpolar aliphatics; (2)
polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged.

53
Q 
A: Tyr-Lys-Met
B: Gly-Pro-Arg
C: Asp-Trp-Tyr
D: Asp-His-Glu
E: Leu-Val-Phe

Which one of the above tripeptides:
a) is most negatively charged at pH 7?
b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and
hydrolyzed in acid?
c) contains the largest number of nonpolar R groups?
d) contains sulfur?
e) will have the greatest light absorbance at 280 nm?

A

a) D
b) A
c) E
d) A
e) C

54
Q

Draw the structures of the amino acids phenylalanine and aspartate in the ionization state you would
expect at pH 7.0. Why is aspartate very soluble in water, whereas phenylalanine is much less soluble?

A 
Phenylamaline:
              C(alpha)
               |
               C
       /               \
     C                C
     |         O       |
     C                C
       \               /
         C

aspartate’

Aspartate has a polar (hydrophilic) side chain, which forms hydrogen bonds with water. In
contrast, phenylalanine has a nonpolar (hydrophobic) side chain

55
Q

In the amino acid glycine, what effect does the positively charged —NH3
+
group have on the pKa of
an amino acid’s —COOH group?

A

The positively charged amino group stabilizes the negatively charged ionized form of the
carboxyl group, —COO–
, and repels the departing H+
thereby promoting deprotonation. The effect is
to lower the pKa of the carboxyl group

56
Q

How does the shape of a titration curve confirm the fact that the pH region of greatest buffering
power for an amino acid solution is around its pK’s?

A

In a certain range around the pKa’s of an amino acid, the titration curve levels off. This
indicates that for a solution with pH  pK, any given addition of base or acid equivalents will result in
the smallest change in pH—which is the definition of a buffer.

57
Q

The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the
histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work.

A

pH = pKa + log [conjugate base]/[acid]

pKa – pH = log [acid]/[conjugate base]

antilog (pKa – pH) =[acid]/[conjugate base]

antilog (6.0 – 5.4) =[acid]/ [conjugate base]

4 = [acid]/[conjugate base], or
4[conjugate base] = [acid]

Therefore, at pH 5.4, 4/5 (80%) of the histidine will be in the protonated form.

58
Q

What is the uniquely important acid-base characteristic of the histidine R group?

A

Only the imidazole ring of the histidine R group has a pKa near physiological pH (pKa = 6.0),
which suggests that histidine may provide buffering power in intercellular and intracellular fluids.

59
Q

Draw the structure of Gly–Ala–Glu in the ionic form that predominates at pH 7.

A

The peptide must have an amino-terminal Gly residue, a carboxyl-terminal Glu residue, and
ionized amino and carboxyl groups

60
Q

Lys residues make up 10.5% of the weight of ribonuclease. The ribonuclease molecule contains 10
Lys residues. Calculate the molecular weight of ribonuclease.

A

From the structure of lysine, we can calculate its molecular weight (146); when it condenses
(loses H2O, Mr = 18) to form a peptide bond, the resulting residue contributes 146 – 18 = 128 to the
protein’s molecular weight. If 10 Lys residues contribute 10.5% of the protein’s molecular weight,
each Lys residue is 1.05%. To calculate the total molecular weight, divide 128 by 1.05% (0.0105);
the result is 12,190. (The actual value is 13,700.)

Biokjemi (2 decks)

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