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biochemistry review > chapter 4: amino acids and buffers > Flashcards

chapter 4: amino acids and buffers Flashcards

1
Q

what form do alpha amino acids with a charged groups of opposite polarity take at physiological pH?

A

zwitterionic form.

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2
Q

pK1 refers to what

A

alpha-carboxylic acid group

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3
Q

pK2 refers to what?

A

alpha-amino group

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4
Q

pKR refers to what

A

side groups with acid-base properties

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5
Q

alpha carboxylic acid groups have pK around where? which means what?

A

2.2 so above pH 3.5 these groups almost entirely in carboxylate form

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6
Q

The alpha amino groups have pK around where? Which means what?

A

9.4 and therefore almost entirely in ammonium form below pH of 8.0

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7
Q

why are the 20 standard amino acids known as alpha amino acids?

A

because all except proline have a primary amino acid group and carboxylic acid group substituent on the same carbon atom

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8
Q

proline has what type of amino group?

A

cyclic secondary amino acid

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9
Q

In the physiological pH range, both the carboxylic acid and the amino groups of alpha amino acids are what? what does this mean?

A

completely ionized in physiological pH; therefore can act as an acid or base thus they are amphotric.

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10
Q

what does it mean to be amphoteric?

A

substances that can act as a base or acid

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11
Q

amphoteric substances are referred to as what?

A

ampholytes

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12
Q

Amino acids like ionic compounds are more soluble in what than what?

A

more soluble in polar solvents than nonpolar solvents

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13
Q

most amino acids have melting points of _____ while their nonionic derivatives usually have a melting point of _____.

A

300 degrees C and nonionic derivatives a melting point of 100 degrees C

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14
Q

how do alpha amino acids polymerize?

A

through the elimination of a water molecule. The resulting CO-NH linkage known a peptide bond.

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15
Q

polymers composed of two amino acids are what?

A

dipeptides

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16
Q

polymers composed of three amino acids are?

A

tripeptides

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17
Q

polymers composed of a few (3-10) amino acids are?

A

oligopeptides

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18
Q

polymers composed of any amino acids (>10) are?

A

polypeptides

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19
Q

Polypeptides are linear polymers liked how?

A

To neighbors in head-to-tail fashion rather than forming branched chains

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20
Q

nucleic acids that encode the amino acids sequences of polypeptides are what?

A

linear polymers

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21
Q

find number of protein molecules that can exist for a dipeptide? explain why

A

20^2 = 400 distinct dipeptides; This is because there is 20 different choices for the first amino acid and 20 choices for the second amino acids

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22
Q

find the number of protein molecules that can exist for a tripeptide

A

20^3 = 8000 different tripeptides; there are 20 possibilities for each of the 400 choices of dipeptides so (400 20 or 2020*20)

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23
Q

why is classifying amino acids by their side chains (R groups) according to their charge an polarity useful?

A

Proteins fold to native conformation largely in response to tendency to remove their hydrophobic side chains from contact with water and to solvate their hydrophilic side chains

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24
Q

Glycine has what?

A

smallest possible side chain, a H; thus nonpolar

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25
Q

Alanine, valine, Leucine, and isoleucine have what?

A

aliphatic hydrocarbon side chain

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26
Q

what does it mean to be aliphatic?

A

organic compound in which carbons form open chain

27
Q

Alanine has what on its carbon?

A

Methyl group (CH3)

28
Q

Methionine has what type of side chain?

A

nonpolar; thiol ether side chain

29
Q

Proline has what type of side chain?

A

nonpolar; conformational constraints of side chain due to being a secondary cyclic amino acid which is unique of the other amino acids

30
Q

Phenylalanine and tryptophan both contain what?

A

aromatic side chains characterized by being bulky as well as nonpolar

31
Q

How are phenyalanine and tryptonphan different in their side chain?

A

Phenylalanine has a phenyl moiety and tryptonphan has its idole group.

32
Q

how are Serine and Theronine alike?

A

uncharged polar amino acids with a hydroxylic R group of different sizes.

33
Q

How are Aspargine and Glutamine alike?

A

uncharged polar amino acids with amide-bearing side chains of different sizes

34
Q

what is the side chain Tyrosine like?

A

uncharged polar amino acid with a phenolic group

35
Q

What accounts for most of the absorbance and fluorescent exhibited by proteins?

A

Tyroseine’s phenolic (aromatic) group with the aromatic groups of phenylalanine and tryptophan.

36
Q

What is cysteine like?

A

uncharged polar amino acid with thiol group unique in that it forms disulfide bonds to another cysteine residue through the oxidation of their thiol group.

37
Q

how is the formation or a disulfide bond between cysteine important to protein structure?

A

it can join separate polypeptide chains or cross link two cysteines in the same chain

38
Q

which amino acids are positively charged polar amino acids

A

1) Lysine
2) Arginine
3) Histidine

39
Q

which amino acids are negatively charged polar amino acids?

A

1) Aspartic acid (Asparte)

2) Glutamic acid (Glutamate)

40
Q

Aspargine is what to Aspartic acid

A

the amide of aspartic acid

41
Q

Glutamine is what to Glutamic acid?

A

The amide of Glutamic acid

42
Q

The basic charged amino acids are what?

A

The amino acids that are positively charged at physiological pH which are

  • Lysine
  • Arginine
  • Histidine
43
Q

The acidic charged amino acids are what?

A

The amino acids that are negatively charged above pH 3

44
Q

Lysin is what

A

negative charged polar amino acid at physiological pH; butylammonium side chain

45
Q

Arginine is what

A

negative charged polar amino acid; bears a guanidino group on side chain

46
Q

Histidine is what?

A

negative charged polar amino acid; carries an imidazolium moiety on side chain

47
Q

Of the 20 amino acid what is the only amino acid that ionizes within a physical pH range?

A

histidine with pKR = 6.0

48
Q

What happens to Histidine at pH 6.0

A

Its Imizadole side group is only 50% charged so the histidine is neutral at basic end of the pysiological pH range.

49
Q

Histidine side chains often participate in what?

A

catalytic reactions of enzymes

50
Q

how many acid-base groups do alpha amino acids have?

A

two or for those with ionizable side groups, three

51
Q

what iscthe isoelectrical point, pI?

A

the pH at which a molecule carries no electrical charge

52
Q

what equation is used for alpha amino acids to determine the isoelectrical point?

A

Henderson-Hasselbalch equation

53
Q

in the Henderso-Hasselbalch equation what is the Ki amdvKj values for monoamine monocarboxylic acids such as glycine?

A

K1 and K2 respectively

54
Q

In the Henderson Hasselbalch equation what is the ki and kj for aspartic and glutamic acids?

A

K1 and KR, respectively

55
Q

In the Henderson Hasselbalch equation what is the Ki and Kj for arginine, histidine and lysine?

A

KR and K2 respectively

56
Q

what is the pKR of Lysine?

A

10.54

57
Q

What is the pKR of Arginine?

A

12.48

58
Q

What is the pKR of Histidine?

A

6.04

59
Q

what is the pKR of Aspartic acid?

A

3.9

60
Q

What is the pKR of Glutamic acid?

A

4.07

61
Q

what way do D isomers rotate?

A

clockwise

62
Q

what way do L isomers rotate?

A

counter clockwise

63
Q

All amino acids derived from proteins have what stereochemical configurstion

A

L

64
Q

what is an enantiomer

A

molecule that is mirror image of the other but different chiral centers

biochemistry review (13 decks)

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