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O Chem 2 > Amino Acids > Flashcards

Amino Acids Flashcards

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1
Q

What are amino acids?

A

Building blocks of proteins

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2
Q

How do amino acids differ?

A

-Differ in the nature of R groups

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3
Q

What do all amino acids contain?

A
  • Alpha amino group
  • alpha carboxylic group
  • H atom
  • R group
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4
Q

Why is glycine unique?

A

The simplest amino acid with an achiral carbon atom

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5
Q

Describe the structural components of amino acids

A
  • All amino acids have a chiral carbon except glycine
  • it is determined by the placement of the amino group
  • If the amino group is on the left it is an L-amino acid. If the amino group is in the right, D-amino acid
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6
Q

What are D-L based on?

A

Based on the structure of glyceraldehyde

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7
Q

What is the isoelectric point/pH?

A

The characteristic pH at which the net electric charge of an amino acid is zero (still charged but net charge is 0)

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8
Q

What is glycine’s pI?

A

5.97

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9
Q

How is charge affected by pH and pI?

A

The further the pH of an amino acid solution is from its pI, the greater the electric charge on that population of molecules

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10
Q

What is pka?

A

A measure of the tendency of a group to give up a proton

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11
Q

What happens at pH=pka?

A

A weak acid is half dissociated

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12
Q

Give the formula for pH

A

pH= pka + log ( [proton acceptor]\ [proton donor] )

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13
Q

What are essential amino acids?

A

Based on human nutrition, cannot be synthesized y humans and gained via diet

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14
Q

What are the essential amino acids that must be known?

A

A little humility in learning 10 tiny molecules pleases Vanessa

Arginine, leucine, histidine, isoleucine, lysine, tryptophan, threonine, methionine, phenylalanine and valine

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15
Q

List 3 non polar R groups amino acids

A

Alanine, valine and leucine

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16
Q

What are polar, uncharged R group amino acids?

A

Cysteine, serine

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17
Q

List aromatic R group amino acids

A

Phenylalanine and tyrosine

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18
Q

List the negatively charged(acidic ) R group amino acids

A

Aspartic acid, glutamic acid

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19
Q

List the positively charged (basic) R group amino acids

A

Histidine, lysine, arginine

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20
Q

What are characteristics of amino acids with non-polar side chains?

A
  • they do not bind nor give protons
  • they do not form hydrogen bonds
  • they take part in hydrophobic interactions
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21
Q

What are characteristics of amino acids that have acidic side chains?

A
  • They are proton donors
  • At neutral pH(physiological), side chains fully ionized or dissociated (COO-) and carry a net negative charge
  • they contribute a negative charge to proteins
  • typically have a pk lower than 7
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22
Q

What are the characteristics of amino acids with basic side chains?

A
  • side chains accept protons
  • They contribute a positive charge to proteins that contain them
  • have a pk above 7
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23
Q

Describe Lys and Arg side chains at physiological pH

A

Side chains are fully ionized, positively charged (NH3+) they are basic side chains

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24
Q

Describe the side chain of Histidine at physiological pH

A

Weakly basic and partially positively charged at physiological pH good buffering capacity

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25
Q

Compare and contrast UV absorbance between Try, Trp and phenylalanine

A

Try and Trp stringly absorb UV light at 280nm.

Absorbance at 280nm is approx, 4x higher for TRP than for Try

Phenylalanine does not show much absorbance

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26
Q

How are derive amino acids formed?

A

Amino acids formed by enzymatic modification of an amino acid after translation

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27
Q

Give examples of derived amino acids

A
  • hydroxylysine and hydroxyproline(collagen)
  • y(gamma)-Carboxyglutamic acid (blood clotting)
  • 3-methylhistidine, E-N- methyl lysine(muscle)
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28
Q

Describe the most important biological reaction of amino acids

A

Amino acids are combined in peptide linkages

Formed by linking alpha-COOH(C-terminal) of one amino acid to the alpha a-NH3 (N-terminal) group of another amino acid

Water is eliminated

29
Q

What is the charge of amino acids with uncharged polar side chains at neutral pH?

A

0 charge

30
Q

What amino acids can lose a proton at an alkaline pH but have uncharged polar side chains?

A

Cys and Tyr

31
Q

What amino acids with uncharged polar side chains can form hydrogen bonds via -OH group?

A

Ser, Thr and Tyr

32
Q

What amino acids with uncharged polar side chains, can form hydrogen bonds due to COOH and CONH groups?

A

Asn and Gln(glutamine) contain COOH/carboxy and CONH(Carboxyamine)

33
Q

What is a polypeptide?

A

Series of amino acids joined by pride bonds

34
Q

What is eliminated in the formation of peptide bonds?

A

Water

35
Q

What reaction forms a peptide bond?

A

Condensation redaction (dehydration) involving 2 reactions

36
Q

What is residue ?

A

Each amino acid unit in protein

37
Q

What must be done with amino acid samples before composition test?

A

Pure sample must be used, contamination results used in errors

38
Q

List the 3 methods of amino acid identification of a polypeptide

A
  1. Acid hydrolysis
  2. Chromatography
  3. Quantitative analysis
39
Q

Describe acid hydrolysis

A
  • Hydrolyzed by strong acid at 110 degrees Celsius for 24 Hours
  • Peptide bonds cleaved
  • Tryp mostly destroyed
  • Procedure gives composition but not sequence
40
Q

Describe chromatography of amino acid identification

A
  • Individual amino acids are separated by cation-exchange chromatography
  • Anion-exchanges resin used for positively charged amino acids
  • Eluted from column by buffers of increasing ionic strength and pH
  • amino acids separated at different ionic strength and pH
41
Q

How are individual amino acids separated by chromatography?

A
  • individual aa’s separated by cation-exchange chromatography
  • Anion-exchange resin for positively charged amino acids
  • Amino acids separated at different ionic strength and pH
42
Q

Describe the quantitative analysis in amino acid identification

A
  • Quantified with ninhydrin -> purple compound with amino acids, NH3 and amines(yellow color with imine group of Pro)
  • intensity of color is measured in spectrophotometer
  • if MW of protein known, number of residues can be known, otherwise, only ratio of number of molecules of each amino acid determined
43
Q

What is quantitative analysis done using?

A

Amino acid analyzer

44
Q

Ninhydrin is added to a chemical and a purple solution is present, what chemical group is indicated?

A

Imine group of Pro

45
Q

What is the abbreviation of arginine?

A

Arg

46
Q

What is the abbreviation of leucine?

A

Leu

47
Q

What is the abbreviation of histidine?

A

His

48
Q

What is the abbreviation of isoleucine

A

ILe

49
Q

What is the lysine abbreviation?

A

Lys

50
Q

What is the abbreviation of tryptophan?

A

Trp

51
Q

What is the abbreviation of threonine?

A

Thr

52
Q

What is the abbreviation of methionine?

A

Met

53
Q

What is the abbreviation of phenylalanine?

A

Phe

54
Q

What is the abbreviation of valine?

A

Val

55
Q

Describe a method of sequencing the peptide

A

Terminal residue analysis

Peptides can be sequenced either from the N terminal usually referred to as Edman degradation or from the C-terminal

56
Q

What is Edman reagent and what us it used to do?

A

Phenylisothiocyanate- used to label N-terminal residue under mildly alkaline conditions

57
Q

How does Edman reagent chemically do its job?

A

It makes N-terminal residue peptide bonds weak: break it without breaking others

58
Q

What chemical change does Edman reagent undergo when used for sequencing

A

Phenylisothiocyanate -> phenylthiohydanton

59
Q

What are requirements./ limitation of the Edman reagent?

A
  • Works under mildly alkaline conditions

- can be used for polypeptides of 100 amino acids or less

60
Q

Explain the actions of phenylisothiocyanate in N terminal labeling

A
  • labeling, Edman reagent binds to end terminal amino acid
  • release of amino acid derivative by acid hydrolysis.

Binding Edman reagent with the formin N terminal amino acid

61
Q

What methods can be used to sequence amino acids from the C-terminus?

A

No efficient method for sequencing peptones from the C-terminus

62
Q

What enzyme can be used to identify the C-terminal amino acid?

A

Carboxypeptidase

63
Q

Explain how carboxypeptidase is used to analyze C-terminal amino acids

A
  • Carboxypeptidase cleaves the C-terminal peptide bond, producing C-terminal a. acid and shortened peptide
  • further reaction cleaves the second amino acid that has now become the new C-terminal of the shortened peptide
  • eventually the entire peptide is hydrolyzed into its individual amino acid
64
Q

What kind f reactions are undergone by amino acids?

A
  • Many standard reactions of amines and carboxylic acids

- Conditions must be right, so that the amino group does not interfere with a carboxylic group reaction and vice versa

65
Q

List some typical reactions of amino acids

A
  • Esterification of amino group
  • Acylation of the amino group (formation of amides)
  • reaction with ninhydrin
66
Q

What is ninhydrin?

A

Common reagent for visualizing spots or bands of amino acids that have been separated by chromatography or electrophoresis

67
Q

What happens when ninhydrin reacts with amino acids?

A

One of the product is a deep violet, resonance stabilized anion called Ruhemann’s purple

68
Q

How does structure of amino acids affect reaction with ninhydrin?

A

Side Chain of amino acid is lost as an aldehyde.

Ninhydrin produces the same purple dye regardless of structure

69
Q

What is Ninhydrin used for?

A

To detect amino acids in a wide variety of substrates

O Chem 2 (22 decks)

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