Biochemistry: Structure and Functions of Amino Acids

A comprehensive set of vocabulary flashcards covering the structure, classification, functions, and clinical correlations of amino acids based on medical biochemistry lecture notes.

α-amino acids

molecules containing the following groups attached to the α-carbon

• α-amino group

• α-carboxyl group

• hydrogen (H) atom

• side chain (R) → determines charge/polarity

amino acid function

components of

• peptides, proteins, phospholipids

precursors

• keto acids, biogenic amines, glucose, nucleotides, heme, creatine

neurotransmitter

• glutamate, aspartate, glycine

transport molecule

• NH₂ groups

nutritionally essential amino acids

arginine (R), histidine (H), isoleucine (I), lysine (K), methionine (M), phenylalanine (F), threonine (T), tryptophan (W), valine (V)

• PVT TIM HALL / MATT VIL PHLy

nutritionally nonessential amino acids

alanine (A), asparagine (N), aspartate (D), cysteine (C), glutamate (E), glutamine (Q), glycine (G), proline (P), serine (S), tyrosine (Y)

nutritionally semiessential

amino acids that are synthesized at rates inadequate to support the growth of children

• arginine → essential under conditions with positive nitrogen balance

• cysteine → produced from methionine → essential in methionine deficiency

• tyrosine → produced from phenylalanine → essential in phenylanaine deficiency / PKU

Proteinogenic amino acids

The group of $20$ different amino acids encoded by the genetic code for protein synthesis.

alanine (ala / A)

A nonpolar amino acid often used in the classification and study of amino acid structures.

arginine (arg / R)

A positively charged, basic amino acid that is considered nutritionally semiessential.

asparagine (asn / N)

A polar, uncharged amino acid that is a derivative of aspartate.

aspartic acid (asp / D)

A polar, negatively charged (acidic) amino acid also known as aspartate.

cysteine (cys / C)

A sulfur-containing, polar uncharged amino acid capable of forming disulfide bonds.

glutamine (gln / Q)

A polar, uncharged amino acid that acts as a transport form of ammonia in the blood.

glutamic acid (glu / E)

A polar, negatively charged amino acid that serves as the highest concentration amino acid in the brain.

glycine (gly / G)

The smallest amino acid, which lacks a chiral center and acts as an inhibitory neurotransmitter.

histidine (his / H)

A basic amino acid with an ionizable side chain pKa of approximately $6.0$, giving it high buffering capacity.

isoleucine (ile / I)

One of the three branched-chain amino acids that is nutritionally essential and nonpolar.

leucine (leu / L)

A branched-chain amino acid that is strictly ketogenic and nutritionally essential.

lysine (lys / K)

A basic, positively charged amino acid that is strictly ketogenic and essential.

methionine (met / M)

An essential, nonpolar, sulfur-containing amino acid that serves as a precursor for cysteine.

phenylalanine (phe / F)

An essential, aromatic, nonpolar amino acid that is the precursor for tyrosine.

proline (pro / P)

An amino acid with a secondary amino group and a rigid ring structure that introduces bends into protein chains.

serine (ser / S)

A polar, uncharged amino acid containing a hydroxyl group that can be a site for phosphorylation.

threonine (thr / T)

An essential, polar, uncharged amino acid containing a hydroxyl group.

tryptophan (trp / W)

A large, essential aromatic amino acid that is a precursor for serotonin and niacin.

tyrosine (tyr / Y)

A non-essential aromatic amino acid produced from phenylalanine; it is a precursor for catecholamines.

valine (val / V)

An essential, nonpolar, branched-chain amino acid.

succotash

combination of corn & lima beans that together provide all essential amino acids required by humans used by Native American hunters & warriors

• corn → tryptophan & lysine deficient

• beans & legumes → contain small amount of methionine

nonpolar amino acids

hydrophobic amino acids found in the interior of globular proteins or surface of proteins interacting with lipid layers of cellular membranes

• 2 pKa vales (due to ionziable carboxyl & amino groups)

• pH 7 = 0 net charge

  • carboxyl group = depronated (-1)

  • amino group = fully protonated (+1)

Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), Methionine (Met), Phenylalanine (Phe), Tryptophan (Trp), Glycine (Gly)

non-polar amino acids

polar amino acids

hydrophilic (water-soluble side chains) amino acids found in regions that make contact with aqueous solutions such as the cytosol or extracellular environment

Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N), Glutamine (Gln, Q), and Cysteine (Cys, C), with Tyrosine (Tyr, Y)

polar uncharged (neutral) amino acids

Aspartate (Asp, D), Glutamate (Glu, E)

polar negatively charged (acidic) amino acids

Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

polar positively charged (basic) amino acids

pKa

acid dissociation constant (-log10Ka) ; measure of the strength of an acid in solution

• ~ 2 for all of the primary carboxylic acid groups

• ~ 9.5 (8.8 - 11.0) for all of the amino groups

physiologic pH (7.4)

• amino groups are generally positively charged

• carboxylic acid groups are negatively charged.

primary carboxylic acid pKa

~ 2 for all of the amino acids

• at pKa - 50% of the molecules dissociated into carxylate anions & protons

• pH pf 7.4 - > 99% of molucules are dissociated

$\alpha$-amino group pKa

~$9.5$ (ranging from $8.8$ to $11.0$) for all of the amino acids

• at pH 7.4 - most are fully protonated & carry a positive charge

Protonation rule

If the pH of a solution is $1$ or more units below the pKa of a group, the proton remains on the group.

Deprotonation rule

If the pH of a solution is $1$ or more units above the pKa of a group, the proton is removed from the group.

Aspartic acid side chain pKa

The ionizable side chain pKa for aspartic acid is $3.9$.

Glutamic acid side chain pKa

The ionizable side chain pKa for glutamic acid is $4.3$.

Arginine side chain pka

The ionizable side chain pKa for arginine is $12.5$.

Lysine side chain pKa

The ionizable side chain pKa for lysine is $10.5$.

glucogenic amino acids

18 amino acids that can be converted into glucose during fasting or starvation

• produces glucose precursosrs as products of their degradation

Ketogenic Amino Acids

Leucine and Lysine; amino acids converted into ketone bodies that do not affect blood glucose levels.

Collagen and Proline

Collagen is rich in proline residues, which help form specific shapes and bends due to the amino acid's rigid ring.

Glycine as a neurotransmitter

Glycine acts as an inhibitory neurotransmitter specifically in the brainstem and spinal cord.

Heme synthesis

Glycine is a required component for the synthesis of heme, as well as bile salts, purines, and creatine.

Clostridium tetani toxin

A toxin that causes muscle spasms by preventing the release of the inhibitory amino acids glycine and GABA.

Branched-chain amino acids (BCAAs)

Valine, Leucine, and Isoleucine, which make up $25\%$ of amino acids in proteins and are primarily metabolized in muscle.

Maple syrup urine disease (MSUD)

A metabolic disorder caused by a deficiency in branched-chain keto-acid dehydrogenase, leading to elevated Val, Leu, and Ile.

Phenylketonuria (PKU)

A condition caused by phenylalanine hydroxylase deficiency, requiring tyrosine supplementation and avoidance of aspartame.

Aspartame

An artificial sweetener that is a methyl ester of aspartic acid and phenylalanine; contraindicated in PKU.

Catecholamines

Biological substances including Dopamine, Norepinephrine, and Epinephrine synthesized from Tyrosine.

TKR (Tyrosine Kinase Receptor)

A type of cell surface receptor where tyrosine residues are found and utilized for signaling.

Melatonin and Serotonin precursor

Tryptophan is the precursor molecule used to produce both melatonin and serotonin.

Hartnup disease

An autosomal recessive disorder involving a defect in the neutral amino acid transporter (NAAT), leading to tryptophan deficiency.

3D symptoms

The clinical presentation of niacin/tryptophan deficiency (Pellagra) seen in Hartnup disease: dermatitis, diarrhea, and dementia.

Cystine

A molecule formed when two cysteine molecules are oxidized and linked by a disulfide bond.

Glutathione (GSH)

A tripeptide containing cysteine that acts as a detoxifying agent and reactive oxygen species (ROS) scavenger.

S-adenosyl methionine (SAM)

A modified form of methionine that acts as the universal methyl group donor in anabolic reactions.

Surfactant component

Phosphatidylcholine, synthesized using methyl groups from methionine, is a key component of lung surfactant.

Cystinuria

An autosomal recessive defect in the COLA transporter affecting the reabsorption of Cystine, Ornithine, Lysine, and Arginine.

Urinary cyanide-nitroprusside test

The diagnostic test used to detect excess cystine in the urine, indicating cystinuria.

Ammonia transport

Glutamine serves as the transport form of ammonia in the blood from the CNS to the liver.

GABA precursor

Glutamate is the immediate precursor in the synthesis of $\gamma$-aminobutyric acid (GABA), an inhibitory neurotransmitter.

MSG symptom complex

A set of symptoms caused by the excitogenic effects of excess monosodium glutamate.

Histones and Lysine

Histone proteins are rich in lysine, using its positive charge to interact with DNA.

Histamine

A major inflammatory mediator synthesized from the amino acid Histidine.