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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
Compare and contrast UV absorbance between Try, Trp and phenylalanine
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
26
How are derive amino acids formed?
Amino acids formed by enzymatic modification of an amino acid after translation
27
Give examples of derived amino acids
- hydroxylysine and hydroxyproline(collagen) - y(gamma)-Carboxyglutamic acid (blood clotting) - 3-methylhistidine, E-N- methyl lysine(muscle)
28
Describe the most important biological reaction of amino acids
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
What is the charge of amino acids with uncharged polar side chains at neutral pH?
0 charge
30
What amino acids can lose a proton at an alkaline pH but have uncharged polar side chains?
Cys and Tyr
31
What amino acids with uncharged polar side chains can form hydrogen bonds via -OH group?
Ser, Thr and Tyr
32
What amino acids with uncharged polar side chains, can form hydrogen bonds due to COOH and CONH groups?
Asn and Gln(glutamine) contain COOH/carboxy and CONH(Carboxyamine)
33
What is a polypeptide?
Series of amino acids joined by pride bonds
34
What is eliminated in the formation of peptide bonds?
Water
35
What reaction forms a peptide bond?
Condensation redaction (dehydration) involving 2 reactions
36
What is residue ?
Each amino acid unit in protein
37
What must be done with amino acid samples before composition test?
Pure sample must be used, contamination results used in errors
38
List the 3 methods of amino acid identification of a polypeptide
1. Acid hydrolysis 2. Chromatography 3. Quantitative analysis
39
Describe acid hydrolysis
- Hydrolyzed by strong acid at 110 degrees Celsius for 24 Hours - Peptide bonds cleaved - Tryp mostly destroyed - Procedure gives composition but not sequence
40
Describe chromatography of amino acid identification
- 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
How are individual amino acids separated by chromatography?
- 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
Describe the quantitative analysis in amino acid identification
- 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
What is quantitative analysis done using?
Amino acid analyzer
44
Ninhydrin is added to a chemical and a purple solution is present, what chemical group is indicated?
Imine group of Pro
45
What is the abbreviation of arginine?
Arg
46
What is the abbreviation of leucine?
Leu
47
What is the abbreviation of histidine?
His
48
What is the abbreviation of isoleucine
ILe
49
What is the lysine abbreviation?
Lys
50
What is the abbreviation of tryptophan?
Trp
51
What is the abbreviation of threonine?
Thr
52
What is the abbreviation of methionine?
Met
53
What is the abbreviation of phenylalanine?
Phe
54
What is the abbreviation of valine?
Val
55
Describe a method of sequencing the peptide
Terminal residue analysis Peptides can be sequenced either from the N terminal usually referred to as Edman degradation or from the C-terminal
56
What is Edman reagent and what us it used to do?
Phenylisothiocyanate- used to label N-terminal residue under mildly alkaline conditions
57
How does Edman reagent chemically do its job?
It makes N-terminal residue peptide bonds weak: break it without breaking others
58
What chemical change does Edman reagent undergo when used for sequencing
Phenylisothiocyanate -> phenylthiohydanton
59
What are requirements./ limitation of the Edman reagent?
- Works under mildly alkaline conditions | - can be used for polypeptides of 100 amino acids or less
60
Explain the actions of phenylisothiocyanate in N terminal labeling
- 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
What methods can be used to sequence amino acids from the C-terminus?
No efficient method for sequencing peptones from the C-terminus
62
What enzyme can be used to identify the C-terminal amino acid?
Carboxypeptidase
63
Explain how carboxypeptidase is used to analyze C-terminal amino acids
- 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
What kind f reactions are undergone by amino acids?
- 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
List some typical reactions of amino acids
- Esterification of amino group - Acylation of the amino group (formation of amides) - reaction with ninhydrin
66
What is ninhydrin?
Common reagent for visualizing spots or bands of amino acids that have been separated by chromatography or electrophoresis
67
What happens when ninhydrin reacts with amino acids?
One of the product is a deep violet, resonance stabilized anion called Ruhemann’s purple
68
How does structure of amino acids affect reaction with ninhydrin?
Side Chain of amino acid is lost as an aldehyde. Ninhydrin produces the same purple dye regardless of structure
69
What is Ninhydrin used for?
To detect amino acids in a wide variety of substrates

O Chem 2 (22 decks)

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