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BIOCHEMISTRY > Amino Acid Chemistry > Flashcards

Amino Acid Chemistry Flashcards

1
Q

These are 💡complex, 💡organic nitrogenous substances with 💡very high molecular weights, found in all plant and animal cells and consisting largely or entirely of 💡alpha-amino acids united in 💡peptide linkage.

A

PROTEINS

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2
Q

It is one of the 20 alpha-amino acids normally found in proteins.

A

Standard amino acid

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3
Q

It is the 💡“building blocks of proteins”

It is an organic compound that contains both an 💡amino (-NH2) group and a 💡carboxyl (-COOH) group.

A

AMINO ACID

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4
Q

Functions of proteins:

A 
P – Proteins
R – Repair and build
O – Organs (Internal)
T – Tissues (Muscles)
E – Externally (Skin, Hair)
I – Internally (Blood, Bone) 
N – Nails
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5
Q

It is an amino acid in which the 💡amino group and the 💡carboxyl group are attached to the 💡alpha-carbon atom.

A

Alpha-amino acid

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6
Q

Functions of Amino Acids (BEDCAMP)

A

B - Building blocks of Proteins

E – Energy Source

D – Dephosphorylation and Phosphorylation

C – Components (Special Amino Acids) of certain Types of Proteins:

A – Acts as Chemical Messengers

M – Metabolic Intermediates

P - Precursor of Various Substances:

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7
Q

BASIC STRUCTURE OF AMINO ACIDS

A
  1. A basic amino group (-NH2)
  2. An Acidic carboxyl group (-COOH)
  3. A Hydrogen atom (-H)
  4. A distinctive side chain (-R)
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8
Q

Each amino acid has a central carbon, called the __, to which four different groups are attached:

A

Alpha carbon

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9
Q

It 💡dictates polarity, electrical charges, and properties of amino acids

A

R group

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10
Q

AA should always be in its __ (0 net charge): pH of blood = 7.4 (physiologic pH)

A

Neutral state

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11
Q

CLASSIFICATION OF AMINO ACIDS BASED ON POLARITY

A

I. AMINO ACIDS WITH NONPOLAR SIDE CHAIN OR R GROUP

II. AMINO ACIDS WITH UNCHARGED POLAR R GROUPS

III. AMINO ACIDS WITH POSITIVELY CHARGED R GROUPS

IV. AMINO ACIDS WITH NEGATIVELY CHARGED R GROUPS

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12
Q

AMINO ACIDS WITH NONPOLAR SIDE CHAIN OR R GROUP

  1. Glycine
  2. Alanine
  3. LEUCINE
  4. VALINE
  5. ISOLEUCINE
  6. PROLINE
  7. METHIONINE
  8. PHENYLALANINE
  9. TRYPTOPHAN
A

§ Do not bind nor give off protons

§ Do not participate in hydrogen or ionic bonds

§ Interact poorly with water

§ Side chains can be thought of as “oily” or lipid like, which promotes hydrophobic interactions

§ Play an important role in maintaining the conformation or 3D structure of proteins

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13
Q

Amino Acids with Aliphatic side chains

💡GA

A

Linear side chain

a. Glycine
b. Alanine

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14
Q

It is the 💡simplest/ smallest amino acid

It has 💡no chiral center

💡Do not exhibit optical activity

It would be 💡positively charged when the pH is at physiological state

Precursor for 💡heme abundant porphyrin ring in the human body

A

Glycine

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15
Q

Amino acid attached to the alpha carbon is 💡methyl group

It has an 💡aliphatic side chain but is 💡not branched

It exist in 💡dipolar form when the pH is at physiological state

AA with 💡zero net charge at physiological PH

A

Alanine

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16
Q

B. BRANCHED CHAIN AMINO ACIDS

💡 LIV PM

Bulky amino acids because of their R- groups

A
  1. LEUCINE
  2. VALINE
  3. ISOLEUCINE
  4. PROLINE
  5. METHIONINE
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17
Q
  • Has 💡sulfur and 💡methyl group
  • Methyl group can be transferred from methionine to another substance by means of 💡transmethylation reaction. You have to 💡activate the amino acid.
A

METHIONINE

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18
Q

It is the 💡activated form of methionine.

It is the 💡methyl group donor in methylation reactions

A

S-adenosylmethionine (SAM)

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19
Q

C. AMINO ACID WITH AROMATIC SIDE CHAINS

💡Tryp ni Phen

These are the only amino acids attributes to the 💡UV absorption properties of protein. (+Tyrosine)

A

PHENYLALANINE

TRYPTOPHAN

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20
Q

💡Benzene ring/phenyl ring

💡Precursor of tyrosine

A

PHENYLALANINE

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21
Q

💡Indole ring

Precursor of 💡niacin (pellagra), 💡melatonin, 💡indole 💡skatole and 💡serotonin.

A

TRYPTOPHAN

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22
Q
  • Having 💡zero net charge at neutral pH
  • Have functional groups capable of 💡hydrogen bonding with water
  • Important factor in 💡protein structure
  • The OH groups serve other function in proteins

💡TTSAG

A

II. AMINO ACIDS WITH UNCHARGED POLAR R GROUPS

  1. SERINE
  2. THREONINE
  3. TYROSINE
  4. Glutamine
  5. Asparagine
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23
Q

It is a 💡post-translational process in which the addition of 💡carbohydrates to proteins or lipids is catalyzed by enzymes.

A

Glycosylation

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24
Q

It is a 💡non-enzymatic reaction, 💡irreversible and 💡concentration- dependent, in which glucose or other carbohydrates are added onto proteins, lipids or DNA.

A

Glycation

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25
Q

HYDROXYL (POLAR) - CONTAINING AMINO ACIDS

💡TTS

  • Can participate in 💡hydrogen bond formation.
  • Can serve as a 💡site of attachment for phosphate groups
A
  1. SERINE
  2. THREONINE
  3. TYROSINE
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26
Q

Its side chain is the site of 💡glycosylation reaction.

When present in 💡active site of covalently modulated
💡regulatory enzymes, it can be 💡phosphorylated affecting enzyme activity:

A

Serine

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27
Q

💡Hydroxyphenyl ring
Derived from 💡phenylalanine
Precursor of 💡thyroid hormone, 💡phatycolanins, 💡epinephrine and 💡melanin.

A

Tyrosine

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28
Q
  • Site of 💡phosphorylation reaction
  • Important in 💡regulation of enzyme activity
  • Site of 💡glycosylation reaction important in formation of mucin
A

Hydroxyphenyl ring

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29
Q

AMIDE DERIVATIVES (with a carbonyl group)

*Can participate in hydrogen bonding

A
  1. Glutamine

2. Asparagine

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30
Q

It is the primary source of 💡Urinary Ammonia.

Important in 💡detoxification of Ammonia.

A

Glutamine

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31
Q
  • Contains 💡sulfhydryl (-SH) group
  • Contains the 💡thiol group in the side chain
  • When 2 adjacent cysteine residue combine a strong 💡disulfide bond is formed and 💡cystine is the resulting product
  • 💡Disulfide bond is also important in the 💡maintenance of protein structure both 💡tertiary and 💡quaternary structures of proteins.

It can be converted to 💡Taurine that conjugates with bile acid

It is a precursor of 💡thioethanolamine portion of COA:

A

CYSTEINE

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32
Q

It is formed when the –SH groups of two cysteines is oxidized to form a covalent cross-link.

A

Disulfide bond

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33
Q

It is formed when 💡two cysteine residues formed a 💡disulfide bond

A

Cystine

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34
Q

III. AMINO ACIDS WITH POSITIVELY CHARGED R GROUPS

Amino acids with 💡basic side chains

  • 💡Accepts protons

💡HAL

A

a. Lysine
b. Arginine
c. Histidine

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35
Q

It has 💡2 ionizable group
It has 💡epsilon amino group
Precursor of 💡L-carnitine
Carrier or shuttle of 💡beta oxidation of fats in the mitochondria

A

Lysine

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36
Q

It contains 💡guanido group

It is found in 💡urea cycle, intermediate

It forms the 💡putrescine 1,4 diaminobutane portion of 💡spermine and 💡spermidine.

Precursor to 💡Nitric Oxide

A

Arginine

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37
Q

Contains the 💡imidazole group

It is 💡weakly basic and largely 💡uncharged at physiologic pH

When it is incorporated into a protein, its 💡R group can be either positively charged (protonated) or neutral, depending on the ionic environment provided by the protein.

Responsible for 💡buffering capacity of hemoglobin

💡Best buffer at physiologic

It has 💡3 ionizable groupd

💡Proton acceptor and/or donor at physiological state

It carry a net charge of 💡+1 at the physiological PH

A

Histidine

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38
Q

IV. AMINO ACIDS WITH NEGATIVELY CHARGED R GROUPS

💡GluAs

(Amino acids with 💡acidic side chains)

  • 💡Proton donors
  • At physiologic pH, the side chains of these amino acids are 💡fully ionized, containing a 💡negatively charged carboxylate group (−COO−).
A

a. Glutamic acid

b. Aspartic acid

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39
Q

Interaction between acidic and basic amino acids results in the formation of?

A

Ionic bond (aka salt bond, electrostatic bond)

40
Q

Precursor of 💡GABA

It exist in 💡fully ionized form when the pH is at physiological state

A

Glutamic Acid

41
Q

It has 💡beta carboxylic acid in its side chain.

A.A. with 💡greatest negative charge

A

Aspartic Acid

42
Q

💡21st amino acid

  • Selenium
  • Containing 💡selenol group in place of sulfur containing thiol group
  • 💡No codon for selenocysteine
A

L-Selenocysteine

3-Selanyl-L-alanine

Selenium cysteine

43
Q

It replaces 💡sulfur analog of cysteine.

A

Selenium

44
Q

It is made up of 3 nucleotide residues.

It specifies kind of a.a. that will be incorporated to the protein during translation and synthesis

A

Codon

45
Q

💡22nd Amino acid

STOP codon: 💡UAG

💡METHANOGENIC Archaea

A

Pyrrolysine

46
Q

TYPES OF INTERACTIONS ENTERED INTO BY THE DIFFERENT R GROUPS OF AMINO ACIDS

A
  1. Hydrogen Bonding
  2. Ionic interaction
  3. Hydrophobic interaction of nonpolar R groups
  4. Disulfide bonds
47
Q

PHYSICAL PROPERTIES OF AMINO ACIDS

A
  1. Solubility
  2. Melting Points
  3. Optical Property
  4. UV absorption spectrum of aromatic amino acid
  5. Acid-base properties
48
Q

Most of the amino acids are soluble in water and insoluble in orgaic solvents

A

-

49
Q

Amino acids generally melting point

A

-

50
Q

All of the standard amino acids have the asymmetric alpha carbon bonded to four different substituent groups except?

A

Glycine

51
Q

All molecules with a __ are optically active because then can rotate the plane-polarized light either to the right (dextrorotatory) or to the left (levorotatory)

A

Chiral center

52
Q

UV (240-290 nm) absorption spectrum of aromatic amino acid is determined solely by:

A

Phe, Tyr, and Trp

53
Q

The 💡concentration of protons ([H+]) in aqueous solution is expressed as __.

A

pH

54
Q

Term used to refer when an amino acid can 💡act as a base and an acid

💡Proton donor and acceptor

A

Amphoteric (ampholytes)

55
Q

AA ACID-BASE PROPERTIES:

A

Amino acids in an aqueous solution contain 💡weakly acidic α-carboxyl groups and 💡weakly basic α-amino groups.

Each of the acidic and basic amino acids contains an 💡ionizable group in its side chain.

Thus, both free amino acids and some amino acids combined in peptide linkages can act as 💡buffers.

56
Q

It happens due to the presence of 💡center chiral carbon.

💡Basis of classification is the similarity to glyceraldehyde standard.

A

Stereoisomerism

57
Q

It is an equation 💡describes the quantitative relation between the concentration of the weak acid (HA) and its conjugate base (A) (it is the ionized form of a weak acid.

This equation demonstrates the quantitative relationship between the pH of the solution and concentration of a weak acid (HA) and its conjugate base (A−).

A

Henderson-Hassebalch Equation

pH = pKa + log (A-)/(HA)

58
Q

The __ is the ionized form of a weak acid.

A

“salt” or conjugate base

59
Q

The salt or conjugate base, A−, is the ionized form of a weak acid.

Ka = [H+][A-]/[HA]

A

Dissociation Constant of Acid (Ka)

60
Q

The larger the Ka, __, because most of the HA has been converted into H+ and A-

A

The stronger the acid

61
Q

The smaller the Ka, the less acid has dissociated and therefore __.

A

The weaker the acid

62
Q

Inc. H Concentration

A

Dec. pH

63
Q

It is a solution that 💡resists change in pH following the addition of acid or base.

It and can be created by mixing a weak acid (HA) with its conjugate base (A−).

If an acid is added to a buffer, A− can neutralize it, being converted to HA in the process. If a base is added, HA can likewise neutralize it, being converted to A− in the process.

A

Buffer

64
Q

A buffer can be created by mixing equal concentrations of a (1) __ and its (2)__.

A

(1) weak acid (HA)

2) conjugate base (A-

65
Q

If HA and A- are equal, the pH is equal to the __.

A

pKa

66
Q

If acid is added to such a solution, It can neutralize it, in the process being converted to HA

A

-

67
Q

It forms when NH2 group is oriented to the right.

A

D isomer

68
Q

💡Electrically neutral: zero charge.

Number of positive charge 💡equal to number of negative charge.

It is a molecule that has a positive charge on one atom and a negative charge on another atom, but which has 💡no net charge.

A

Zwitterion (Dipolar ion)

69
Q

In an acidic solution, the zwitterion __ a proton (H) to form a positively charged ion.

A

Accepts

70
Q

In basic solution, the -NH3 of the zwitterion __ a proton, and a negatively charged species is formed.

A

Loses

71
Q

Because of the extra site that can be protonated or deprotonated, acidic and basic amino acids have four charged forms in solution.

A

-

72
Q

Non polar amino acids

Do not occur in nature

A

Fully protonated form (pH1)

-1

73
Q

Protonic equilibria is the step by step dissociation of the amino acid starting from the fully protonated or positive form up to the fully ionized or negative form.
Uses:
• To predict charge of Amino acid in a given solution with known pH
• As a procedure for separating amino acids based on their charge

A

Titration of Amino Acids (Protonic equilibria)

74
Q

It is the pH at which an amino acid is 💡electrically neutral, that is, when the sum of the positive charges equals the sum of the negative charges.

pH is at 💡midpoint between pK values on either side of zwitterion species

A

Isoelectric Point (pI, pHI or IpH)

75
Q

Isoelectric point:

pH of neutral Amino acid = ?

A

6.0

76
Q

Isoelectric point:

pH of acidic Amino acid = ?

A

<6

77
Q

Isoelectric point:

pH of basic Amino acid = ?

A

> 6

78
Q

Dissociation of mono amino, monocarboxylic amino acid (neutral amino acid).

**2 Buffer zone

A

Alanine (+1 net charge) - H is dissociated from COOH, to form its zwitterion form (0 net charge). Then H+ is dissociated from NH3+, forming its fully ionized form (-1 net charge).

79
Q

Titration curve of mono amino, monocarboxylic amino acid (Neutral Amino Acid)

A

Lowest pH – fully protonated form (more dominant)

• pH raised (pK1 =2.34) – zwitterion and fully protonated forms
• pH = 6.02 – zwitterion forms (more dominant)
• pH raised (pK2 = 9.69) – fully ionized and zwitterion forms
o pH12=fully ionized form (more dominant)

80
Q

Formula for computing pI of 💡neutral amino acid:

A

pI = pK1 + pK2/ 2

81
Q

pI = pK1 + pK2/ 2

A

pK1 = dissociation constant of COOH

pK2 = dissociation constant of & -NH2

pK1, which is the disassociation constant of the α (alpha) carboxylic group is the most acidic group.

pK2, which is the dissociation constant of the
protonated α (alpha) amino group.

82
Q

Dissociation of diamino, monocarboxylic amino acid (basic amino acids)

A

• +2 – fully protonated form
o releases H+ (from alpha carboxyl group
COOH)

• +1 – partial protonated form of Histidine
o R group releases H+ (side chain)

• Net charge 0 – zwitterion form
o Releases H+from alpha amino group

• -1 – fully ionized form

83
Q

It is the strongest acidic group among the three

A

Carboxylic group

84
Q

When the carboxylic group becomes dissociated, it will become __.

A

Negatively charged.

85
Q

Titration Curve of diamino, mono carboxyclic amino acid (Basic Amino Acid):

A
  • pK1 – 1.82 (fully protonated)
  • pK2 – 6.0 (partially protonated, partial zwitterion)
  • pI – zwitterion form (higher pH than neutral amino acids because of the addition of an extra positive charge)
  • pK3 – 9.2 (fully ionized, partial zwitterion form)
  • pH 12 – fully ionized forms
86
Q

Formula for computing pI of 💡basic amino acid:

A

pI = pK2+pKr/ 2

87
Q

pI = pK2+pKr/ 2

A

pKr = dissociation constant of R group

pK2 = dissociation constant of & -NH2

88
Q

Dissociation of monoamino, dicarboxylic amino acids (acidic amino acids)

A

• +1 - fully protonated form
o releases H+ ( from alpha carboxyl group COOH)

• net charge 0 – zwitterion form
o R group releases H+

  • -1 - Releases H+ from alpha amino group
  • -2 – fully ionized form
  • pI = lower pH because the acidic side chain introduced another negative charge
89
Q

Formula for computing pI of 💡acidic amino acid:

A

pI = pK1+pKr/ 2

90
Q

Bicarbonate as a buffer:

A
  • Increase in bicarbonate ion causes pH to rise

* Pulmonary obstruction causes an increase in carbon dioxide and the pH to fall

91
Q

Other applications of the Henderson-Hasselbalch Equation:

A

Bicarbonate as a buffer

DRUG ABSORPTION

92
Q

These functional groups of amino acids can readily ionized.

A

ALPHA CARBOXYL AND ALPHA AMINO GROUPS

93
Q

It is a special amino acid that is a 💡component of collagen

It is primarily serve as 💡building blocks of proteins.

It is unusual amino acids that have been modified during 💡post-translational process of protein synthesis.

A

Hydroxyproline

94
Q

It is a term used when amino acid is 💡electrically neutral.

A

Dipolar

95
Q

pI = pK1+pKr/ 2

A

pK1 = dissociation constant of COOH

pKr = dissociation constant of & -R group

96
Q

Conjugation of 💡glycine with 💡benzoic acid which is a food additive will form

A

Hippuric acid

97
Q

It is a reaction that convert 💡histidine to histamine

A

Decarboxylation

BIOCHEMISTRY (11 decks)

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