- 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

II. AMINO ACIDS WITH UNCHARGED POLAR R GROUPS 1. SERINE 2. THREONINE 3. TYROSINE 4. Glutamine 5. Asparagine

Amino Acid Chemistry Flashcards by Adrian Tiglao

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.

PROTEINS

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

Standard amino acid

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It is the 💡“building blocks of proteins”

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

AMINO ACID

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Functions of proteins:

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

Alpha-amino acid

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Functions of Amino Acids (BEDCAMP)

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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BASIC STRUCTURE OF AMINO ACIDS

A basic amino group (-NH2)
An Acidic carboxyl group (-COOH)
A Hydrogen atom (-H)
A distinctive side chain (-R)

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

Alpha carbon

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

R group

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

Neutral state

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CLASSIFICATION OF AMINO ACIDS BASED ON POLARITY

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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AMINO ACIDS WITH NONPOLAR SIDE CHAIN OR R GROUP

Glycine
Alanine
LEUCINE
VALINE
ISOLEUCINE
PROLINE
METHIONINE
PHENYLALANINE
TRYPTOPHAN

§ 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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Amino Acids with Aliphatic side chains

💡GA

Linear side chain

a. Glycine
b. Alanine

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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

Glycine

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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

Alanine

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B. BRANCHED CHAIN AMINO ACIDS

💡 LIV PM

Bulky amino acids because of their R- groups

LEUCINE
VALINE
ISOLEUCINE
PROLINE
METHIONINE

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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.

METHIONINE

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It is the 💡activated form of methionine.

It is the 💡methyl group donor in methylation reactions

S-adenosylmethionine (SAM)

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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)

PHENYLALANINE

TRYPTOPHAN

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💡Benzene ring/phenyl ring

💡Precursor of tyrosine

PHENYLALANINE

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💡Indole ring

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

TRYPTOPHAN

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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

II. AMINO ACIDS WITH UNCHARGED POLAR R GROUPS

SERINE
THREONINE
TYROSINE
Glutamine
Asparagine

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

Glycosylation

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

Glycation

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HYDROXYL (POLAR) - CONTAINING AMINO ACIDS 💡TTS - Can participate in 💡hydrogen bond formation. - Can serve as a 💡site of attachment for phosphate groups

1. SERINE 2. THREONINE 3. TYROSINE

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:

Serine

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

Tyrosine

- Site of 💡phosphorylation reaction - Important in 💡regulation of enzyme activity - Site of 💡glycosylation reaction important in formation of mucin

Hydroxyphenyl ring

AMIDE DERIVATIVES (with a carbonyl group) *Can participate in hydrogen bonding

1. Glutamine | 2. Asparagine

It is the primary source of 💡Urinary Ammonia. Important in 💡detoxification of Ammonia.

Glutamine

- 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:

CYSTEINE

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

Disulfide bond

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

Cystine

III. AMINO ACIDS WITH POSITIVELY CHARGED R GROUPS Amino acids with 💡basic side chains - 💡Accepts protons 💡HAL

a. Lysine b. Arginine c. Histidine

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

Lysine

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

Arginine

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

Histidine

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. Glutamic acid | b. Aspartic acid

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

Ionic bond (aka salt bond, electrostatic bond)

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

Glutamic Acid

It has 💡beta carboxylic acid in its side chain. A.A. with 💡greatest negative charge

Aspartic Acid

💡21st amino acid - Selenium - Containing 💡selenol group in place of sulfur containing thiol group - 💡No codon for selenocysteine

L-Selenocysteine 3-Selanyl-L-alanine Selenium cysteine

It replaces 💡sulfur analog of cysteine.

Selenium

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

Codon

💡22nd Amino acid STOP codon: 💡UAG 💡METHANOGENIC Archaea

Pyrrolysine

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

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

PHYSICAL PROPERTIES OF AMINO ACIDS

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

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

Amino acids generally melting point

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

Glycine

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)

Chiral center

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

Phe, Tyr, and Trp

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

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

Amphoteric (ampholytes)

AA ACID-BASE PROPERTIES:

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.

It happens due to the presence of 💡center chiral carbon. 💡Basis of classification is the similarity to glyceraldehyde standard.

Stereoisomerism

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−).

Henderson-Hassebalch Equation pH = pKa + log (A-)/(HA)

The __ is the ionized form of a weak acid.

“salt” or conjugate base

The salt or conjugate base, A−, is the ionized form of a weak acid. Ka = [H+][A-]/[HA]

Dissociation Constant of Acid (Ka)

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

The stronger the acid

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

The weaker the acid

Inc. H Concentration

Dec. pH

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.

Buffer

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

(1) weak acid (HA) | 2) conjugate base (A-

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

pKa

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

It forms when NH2 group is oriented to the right.

D isomer

💡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.

Zwitterion (Dipolar ion)

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

Accepts

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

Loses

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

Non polar amino acids | Do not occur in nature

Fully protonated form (pH1) | -1

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

Titration of Amino Acids (Protonic equilibria)

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

Isoelectric Point (pI, pHI or IpH)

Isoelectric point: pH of neutral Amino acid = ?

6.0

Isoelectric point: pH of acidic Amino acid = ?

Isoelectric point: pH of basic Amino acid = ?

Dissociation of mono amino, monocarboxylic amino acid (neutral amino acid). **2 Buffer zone

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).

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

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)

Formula for computing pI of 💡neutral amino acid:

pI = pK1 + pK2/ 2

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.

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

• +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

It is the strongest acidic group among the three

Carboxylic group

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

Negatively charged.

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

* 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

Formula for computing pI of 💡basic amino acid:

pI = pK2+pKr/ 2

pKr = dissociation constant of R group pK2 = dissociation constant of & -NH2

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

• +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

Formula for computing pI of 💡acidic amino acid:

pI = pK1+pKr/ 2

Bicarbonate as a buffer:

* Increase in bicarbonate ion causes pH to rise | * Pulmonary obstruction causes an increase in carbon dioxide and the pH to fall

Other applications of the Henderson-Hasselbalch Equation:

Bicarbonate as a buffer DRUG ABSORPTION

These functional groups of amino acids can readily ionized.

ALPHA CARBOXYL AND ALPHA AMINO GROUPS

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.

Hydroxyproline

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

Dipolar

pI = pK1+pKr/ 2

pK1 = dissociation constant of COOH pKr = dissociation constant of & -R group

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

Hippuric acid

It is a reaction that convert 💡histidine to histamine

Decarboxylation

Amino Acid Chemistry Flashcards

(97 cards)