Amino Acids and Their Classification

Amino Acids

• Amino acids have a carboxyl group, an amino group, and a side chain, all bonded to an alpha-carbon atom.
• At a physiological pH, amino acids have a positive charge on their amino group and a negative charge on their carboxy group.
• Peptide bonds link adjacent amino acid residues in a protein chain.
• Proteins usually have 20 amino acids.
• The L-amino acid configuration exists in proteins.

Amino Acid Classes

• Only L-amino acids are in proteins.
• The essential amino acids PVT TIM HaLL are: Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Leucine, Lysine.
• Glucogenic amino acids are: Methionine, histidine, valine.
• Glucogenic/ketogenic amino acids: Isoleucine, phenylalanine, threonine, tryptophan.
• Leucine and lysine are the only purely ketogenic amino acids.
• Aspartic acid and glutamic acid are acidic amino acids.
• Acidic amino acids are negatively charged at body pH.
• Arginine, histidine, and lysine are basic.
• Arginine is most basic.
• Histidine has no charge at body pH.
• Arginine and histidine are required during growth periods.
• Arginine and lysine are found in histones, which bind negatively charged DNA.

Catabolism of Amino Acids

• Amino acid catabolism generates common metabolites (eg, pyruvate, acetyl-CoA) that serve as metabolic fuels.
• Excess nitrogen is converted to urea and excreted by the kidneys.

Urea Cycle

• The urea cycle converts excess nitrogen from amino acid catabolism into urea for excretion.
• Key intermediates in the urea cycle: Ornithine, Citrulline, Arginine, Aspartate.

Ornithine Transcarbamylase Deficiency

• Most common urea cycle disorder.
• It is X-linked recessive, while other urea cycle enzyme deficiencies are autosomal recessive.
• It interferes with the body's ability to eliminate ammonia and is often evident in the first few days of life, but may appear later.
• Excess carbamoyl phosphate is converted to orotic acid, part of the pyrimidine synthesis pathway.
• Findings include elevated orotic acid in blood and urine, decreased BUN, and symptoms of hyperammonemia, but no megaloblastic anemia (vs orotic aciduria).

Clinical Features of Urea Cycle Defects

• Increased ammonia levels ([NH4+]) lead to hyperammonemia.
• Blood glutamine levels are increased.
• BUN levels are decreased.
• Cerebral edema often occurs.
• Symptoms include lethargy, convulsions, coma, and potentially death.
• Carbamoyl phosphate synthetase deficiency: No orotic aciduria, autosomal recessive.
• Ornithine transcarbamoylase deficiency: Orotic aciduria, X-linked recessive, Carbamoyl-P leaks out of the mitochondria, and affects pyrimidine pathway.

De Novo Pyrimidine & Purine Synthesis

• Several immunosuppressive, antineoplastic, and antibiotic drugs function by interfering with nucleotide synthesis.
• Leflunomide inhibits dihydroorotate dehydrogenase in pyrimidine synthesis.
• 5-fluorouracil (5-FU) and its prodrug capecitabine form 5-F-dUMP, inhibiting thymidylate synthase (↓ dTMP).
• 6-mercaptopurine (6-MP) and its prodrug azathioprine inhibit de novo purine synthesis.
• Azathioprine is metabolized via a purine degradation pathway and can cause immunosuppression when administered with a xanthine oxidase inhibitor.
• Mycophenolate and ribavirin inhibit inosine monophosphate dehydrogenase.
• Hydroxyurea inhibits ribonucleotide reductase, affecting both purine and pyrimidine synthesis.
• Methotrexate (MTX), trimethoprim (TMP), and pyrimethamine inhibit dihydrofolate reductase and lower deoxythymidine monophosphate [dTMP] levels.
• Methotrexate affects humans, trimethoprim affects bacteria, and pyrimethamine affects protozoa.
• CPS1 is found in the mitochondria in the liver for the urea cycle.
• CPS2 is found in the cytosol and is responsible for pyrimidine synthesis found in most cells.

Transport of Ammonia by Alanine

• Alanine transports ammonia from muscle to the liver.
• In the muscle, amino acids are converted to α-ketoacids while α-ketoglutarate is converted to glutamate. Glutamate is converted to alanine.
• Glucose is converted to pyruvate, then Lactate, the lactate goes through the Cori Cycle
• In the liver, alanine is converted back to pyruvate and then to glucose, α-ketoglutarate is formed, and urea is produced.

Hyperammonemia

• Hyperammonemia can be acquired (e.g., liver disease) or hereditary (e.g., urea cycle enzyme deficiencies).
• Symptoms include flapping tremor (asterixis), slurring of speech, somnolence, vomiting, cerebral edema, and blurred vision.
• Elevated NH3 alters the amounts of α-ketoglutarate, glutamate, GABA, and glutamine, leading to CNS toxicity through increased GABAergic tone, TCA cycle inhibition, and cerebral edema.
• Treatment involves limiting protein in the diet.
• Lactulose can acidify the GI tract to trap NH4+ for excretion.
• Antibiotics (e.g., rifaximin) can reduce ammoniagenic bacteria.
• Benzoate, phenylacetate, or phenylbutyrate can react with glycine or glutamine, forming products that the kidneys excrete.

Amino Acid Derivatitives

• Phenylalanine becomes Tyrosine via BH4, Tyrosine becomes Dopa via BH4, Dopa becomes Dopamine via B6, Dopamine becomes NE via Vitamin C, and NE becomes Epi via SAM.
• Tyrosine also becomes thyroxine and melanin.
• Tryptophan becomes Niacin via B2 & B6 and Serotonin via BH4, Serotonin can become Melatonin via B.
• Histidine becomes Histamine via B6.
• Glycine becomes Porphyrin via B6 and then Heme.
• Glutamate becomes GABA via B6 and Glutathione.
• Arginine becomes Creatine, Urea, and Nitric oxide via BH4.

Catecholamine Synthesis/Tyrosine Catabolism

• Phenylalanine becomes Tyrosine via Phenylalanine hydroxylase & BH4.
• Tyrosine becomes DOPA via Tyrosine hydroxylase & BH4.
• DOPA becomes Dopamine via DOPA decarboxylase & B6.
• Dopamine becomes Norepinephrine via Dopamine B-hydroxylase & Vitamin C.
• Norepinephrine becomes Epinephrine via Phenylethanolamine-N-methyltransferase & SAM.
• Carbidopa inhibits DOPA decarboxylase.
• Albinism is a result of a deficiency of Tyrosinase
• PKU is a result of a deficiency of Phenylalanine hydroxylase (PAH)

Phenylketonuria (PKU)

• PKU is caused by a deficiency of phenylalanine hydroxylase (PAH); as a result, tyrosine becomes essential, and phenylalanine levels increase, leading to increased phenyl ketones in the urine.
• Autosomal recessive.
• Screening occurs 2-3 days after birth (normal at birth because of the maternal enzyme during fetal life).
• Findings include intellectual disability, microcephaly, seizures, hypopigmented skin, eczema, and a musty body odor.
• Treatment includes decreasing phenylalanine and increasing tyrosine in the diet and tetrahydrobiopterin supplementation.
• Phenyl ketones include phenylacetate, phenyllactate, and phenylpyruvate.
• The disorder of aromatic amino acid metabolism leads to a musty body odor.
• Patients with PKU must avoid the artificial sweetener aspartame because it contains phenylalanine.

Alkaptonuria

• Congenital homogentisate oxidase deficiency in tyrosine to fumarate degradative pathway.
• Leads to pigment-forming homogentisic acid buildup in tissue. Autosomal recessive.
• Findings include bluish-black connective tissue, ear cartilage, and sclerae (ochronosis); urine turns black on prolonged exposure to air.
• May have debilitating arthralgias (homogentisic acid toxic to cartilage).

Albinism

• Deficiency in tyrosinase.
• Autosomal recessive.
• No DOPA converted to melanin.
• The two types of albinism are occulocutaneous and ocular.
• Absence of melanin in hair (white), eye (photophobia, nystagmus), and skin (pink) results in hypopigmentation with an increased risk of UV light-related skin cancer.

Branched Chain Amino Acids

• The branched chain amino acids are Leucine, Valine, and Isoleucine.
• They go through branch chain aminotransferase but not in the liver to create keto acid.
• Then TPP, Lipoate, FAD, and NAD+ convert the keto acid to Keto acyl CoA via branch chain α-Keto acid dehydrogenase Complex, a deficiency here results in Maple Syrup Disease in which urine has the odor of maple syrup.

Propionate Connection

• Propionate is converted to Propionyl-CoA through the use of CoA-SH, Mg2+, and Acyl-CoA synthetase.
• Propionyl-CoA is then converted to D-Methyl-malonyl-CoA through the use of Biotin, ATP, and Propionyl-CoA Carboxylase.
• D-Methyl-malonyl-CoA is converted to L-Methyl-malonyl-CoA through the use of METHYLMALONYL-CoA RACEMASE.
• L-Methyl-malonyl-CoA is converted to Succinyl-CoA through the use of B12 coenzyme and METHYLMALONYL-CoA ISOMERASE.

Clinical Correlations for Branched Chain Deficiencies

• Deficiency in Branched chain α-keto dehydrogenase-Maple syrup causes the urine to have the odor of maple syrup.
• Symptoms: include feeding difficulties, lethargy, vomiting, encephalopathy-mental retardation, seizure, hypoglycemia, protein intolerance, ketosis, coma, and ultimately death.
• Deficiency in Propionic carboxylase- Propionic Acidemia results in No conversion of Propionic acid to methyl malonyl CoA then to succinyl CoA.
• Symptoms: Neurologic and developmental complications.
• Treatment: with a low-protein diet; L-Carnitine improves (β-oxidation of fatty acids) and the intake of methionine, valine, isoleucine and odd-chain fatty acids is increased.
• Deficiency in methyl malonyl CoA mutase(isomerase) in this pathway lead to methyl malonyl acidemia.
• The patient will experience Neurologic Arid developmental complications.
• Rule out vitamin B12 deficiency as a cause.

Maple Syrup Urine Disease

• Maple Syrup Urine Disease is caused by the Blocked degradation of branched amino acids (Isoleucine, leucine, valine) due to branched-chain α-ketoacid dehydrogenase (B₁).
• This leads to an increase of α-ketoacids in the blood, especially those of leucine.
• Treatment includes restriction of isoleucine, leucine, valine in diet, and thiamine supplementation
• Autosomal recessive.
• Presentation in infants vomiting and poor feeding will produce urine that smells like maple syrup/bunt sugar. It causes progressive neurological decline.

Organic Acidemias

• Protein metabolism of Valine, Odd-chain fatty acids, Methionine, Isoleucine, and Threonine can result in Methylmalonic Acidemia and Propionic Acidemia
• Commonly present in infancy with poor feeding, vomiting, hypotonia, high anion gap metabolic acidosis, hepatomegaly, and seizures. Results in Organic acid accumulation.
• Results in inhibition of gluconeogenesis, leading to fasting blood glucose levels, ↑ ketoacidosis → resulting in high anion gap metabolic acidosis
• Leads to urea cycle inhibition, resulting in hyperammonemia.
• Treatment: low-protein diet limited in substances that metabolize into propionyl-CoA: Valine, Odd-chain fatty acids, Methionine, Isoleucine, and Threonine (VOMIT).

Methionine-Methyl Trap

• Methionine is synthesized from Homocysteine, and the enzyme Methionine synthase requires THF4 and Cobalamin.
• Methionine is then converted to S-adenosyl methionine using ATP
• S-adenosyl methionine is converted to S-adenosyl homocysteine using a Methyl transferase.
• S-adenosyl homocysteine is then converted back to Homocysteine.
• Serine is converted to Cystathionine using the Cystathionine synthase and requires Vitamin B6.
• Cystathionine is converted to Cysteine using Cystathionase and requires Vitamin B6.

Recall of Methionine

• α1-antitrypsin-increases the oxidized form of Methionine when there is Lung- smoking, resulting in increased lung damage.
• Cardiac situations are linked to decreased homocysteine, thus there are fewer cardiac diseases
• Alcoholism (cirrhosis) is linked to decreased B9 and increased homocysteine.
• Megaloblastic anemia can be result of Deficient Vit B9

Abormal Cystathionine Function

• Deficiency of Cystathionine β-Synthase can lead to Homocystinuria which can be caused by autosomal recessive. and results marked increase in homocysteine and metabolism.
• Clinical Features: Homocysteine damages endothelial cells which causes thrombosis resulting in thrombotic vascular diseases, there is a 50% chance of developing a myocardial infarction, stroke, or serious blood clot before the age of 30 years, osteoporosis(skeletal deformities), ectopia lentis- abnormalities of the ocular lens (dislocation(similar to Marfan syndrome), arachnodactyly ("spider fingers"), and mental retardation.
• Treatment: Requires High doses of vitamin B6, restriction of methionine, addition of cysteine

Homocystinuria

• There are 4 Causes (all autosomal recessive):
• Cystathionine synthase deficiency (treatment: ↑ methionine, ↓ cysteine, ↑ B6, B12, and folate in diet
• ↑ affinity of cystathionine synthase for pyridoxal phosphate (treatment: ↑↑ B6 and ↓ cysteine in diet)
• Methionine synthase (homocysteine methyltransferase) deficiency (treatment: ↑ methionine in diet)
• Methylenetetrahydrofolate reductase (MTHFR) deficiency (treatment: ↑ folate in diet)
• In all forms there is an excess homocysteine.
• HOMOCYstinuria: ↑↑ Homocysteine in urine, Osteoporosis, Marfanoid habitus, Ocular changes (downward and inward lens subluxation), Cardiovascular effects (thrombosis and atherosclerosis → stroke and MI), kyphosis, intellectual disability, hypopigmented skin. In homocystinuria, lens subluxes "down and in" (vs Marfan, "up and fans out").

Cystinuria

• Hereditary Defect is the renal PCT and intestinal amino acid transporter prevents reabsorption of Cystine, Ornithine, Lysine, and Arginine (COLA).
• Cystine is made of 2 cysteines connected by a disulfide bond.
• Excess cystine in the urine can lead to recurrent precipitation of hexagonal cystine stones A
• Treatment: requires urinary alkalinization (eg, potassium citrate, acetazolamide) and chelating agents (eg, penicillamine) ↑ solubility of cystine stones; good hydration; diet low in methionine.
• Autosomal recessive. Common (1:7000).
• Cystinuria detected with urinary sodium- cyanide nitroprusside test and proton nuclear magnetic resonance spectroscopy of urine.

Homocysteine vs Methylmalonic

• Folate and B12 both become homocysteine
• B12 becomes methylmalonic acid

Deficiencies of Folate and B12

• Hematocrit goes down in both Folate Deficiency and B12 Deficiency
• MCV goes up in both Folate Deficiency and B12 Deficiency
• Homocysteine goes up in both Folate Deficiency and B12 Deficiency
• Methylmalonic Acid stays normal in Folate Deficiency and goes up in B12 Deficiency
• Neuro Symptoms stays None in Folate Deficiency and appears in B12 Deficiency

Summary On Genetic Disorders

• Tyrosinosis (AR) leads Liver damage (hepatitis progressing to cirrhosis and hepatocellular carcinoma) and kidneys (aminoaciduria and renal tubular acidosis).
• Maple syrup urine disease (AR) presents with Feeding difficulties vomiting and urine smells of maple syrup Treat by restricting Isoleucine Leucine and Valine
• Homocystinuria Defective homocysteine metabolism. High homocysteine with downward lens dislocation.
• Propionic acidemia: Neurologic and developmental complications; Treatment: low-protein diet;
• Methylmalonic acidemia :Defective methylmalonic acid metabolism. Neurologic and developmental complications: Treatment: low-protein diet;

More Genetic Disorders

• Classic PKU (autosomal recessive, AR): Leads Mental retardation, fair skin and urine smells like mousy odor
• Albinism (AR) can not covert tyrosine which results Absence of melanin in hair
• Alkaptonuria (AR) Homogentiside 1 urine (turns black when oxidized by light) Articular cartilage and sclera darken (ochronosis) 

Structure and Properties of Proteins

• The sequence of the amino acids in a polypeptide chain denotes its primary structure.
• The primary structure is linear, ordered, and 1-dimensional.
• By convention, the primary structure is written from the amino end to the carboxyl end.
• A perfectly linear amino acid polymer is neither functional nor energetically favorable due to the need for folding.

Primary Structure of Insulin

• The primary structure of human insulin has two chains:
  • CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
  • CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT

Insulin

• Preproinsulin is synthesized in the RER of pancreatic β cells.
• The "presignal" is cleaved, resulting in proinsulin formation.
• Proinsulin is stored in secretory granules.
• Proinsulin is cleaved, resulting in the exocytosis of insulin and C-peptide equally.
• Elevated levels of both insulin and C-peptide are seen in endogenous insulin secretion (e.g., type 2 DM, insulin secretagogues, insulinoma), whereas exogenous insulin lacks C-peptide.
• Insulin is synthesized in the pancreas and cleared by both the liver and kidneys.

Protein Secondary Structure

• Secondary structure defines the configurational relationships between residues about 3-4 amino acids apart in linear structure.
• It is stabilized by non-covalent bonding.
• Secondary structures are non-linear and 3-dimensional.
• Secondary structures are localized to regions of an amino acid chain.
• They form and are stabilized by hydrogen bonding, electrostatic interactions, and van der Waals interactions.

Alpha Helix

• It is a spiral structure composed of polypeptides that forms the backbone and side chains of amino acids extending between NH and C=O groups.
• It's the most common and stable conformation of a polypeptide chain.
• Abundant in hemoglobin and myoglobin and absent in chymotrypsin.
• Proline and hydroxyproline will not allow the alpha -helix.

Beta Pleated Sheet

• The polypeptide is almost fully extended.
• Hydrogen bonds between NH and C=O groups of neighboring polypeptide segments stabilize it.
• Adjacent strands can run in the same direction (parallel) or opposite direction (anti-parallel) with regard to the amino and carboxy terminal.

Collagen Triple Helix

• Its amino acid sequence is Gly-X-Y repeating structure
• And has 2º structure stabilized by interchain hydrogen

Tertiary Structure

• Non-linear and 3 DIMENSIONAL
• It is global but restricted to the amino acid polymer
• Formed and stabilized by hydrogen bonding and non-covalent interactions toward hydrophobic packing towards solvents.

Quaternary Structure

• Certain polypeptides aggregate to form one functional unit.
• The structure is non-linear.
• It is global and across distinct amino acid polymers
• Formed by hydrogen bonding, covalent bonding, hydrophobic packing, and hydrophilic exposure.

Hemoglobin Structure

• Hemoglobin structure is stabilized by H-bonding, electrostatic bonds, hydrophobic interactions, and Van Der Walls forces.
• Each polypeptide chain is termed a subunit or monomer.
• Hemoglobin is made of 2 α subunits and 2 β subunits.

Extracelluar Pro-Collagen

• Hydroxylation of proline and lysine in collagen requires a di-oxygenase with Fe and requires Vitamin C keeps the iron reduced.
• Glycosylation – hydroxylysine with glucose is needed
• Spontaneous disulfide bond formation at the C-terminal peptides and the Golgi for assembly

Crosslinks in Collagen

• Cross links are formed by lysyl/prolyl oxidase requires copper as a co enzyme
• Oxidative deamination of lysines and hydroxylysines forms Allysine (aldehyde) This reacts with amino group of a nearby lysine or hydroxylysine to form interchain cross-link Which is important for collagen tensil strength

Cross Linking

• Excessive cross links cause problems in OLD AGE and result in the Hardening of ligaments (STIFF) and Prone to tear
• Whereas less cross-linking leads to Weak collagen and Menke's disease

Synthesis of Collagen

• Collagen is synthesized with translation of Gly-X-Y Usually pro, lys, or hydro
• It needs hydroxylization which needs vitamin C - deficiency is scurvy
• needs Glycosulation problems is it needs to osteogenesis imperfecto triple helix problems
• Exocytosis , alignment and crosslinked
• problems with cross will leads Menkes disease - lysyl oxidate

Scab - Collagen Types

• Type 1 bone and tendons Type 2 Cartlidge Type 3 arteries (eee = 3e's) Type 4 bm basement membranes floors.

Osteogenesis Imperfecta

• Genetic bone disorder (brittle bone caused by a variety of gene defects (most commonly COLIAI and COLIA2). Most common form is autosomal dominant
• Patients can't BITE: Bones = multiple fractures, (eye) = blue sclerae, Teeth = dental imperfections, Ear = hearing loss

Elhers -Danilo Syndrome

• Genetic Collaged is faulty
• can be caused to be hyper extinsible for a mutation in Collagen v

Elastin

• 3D chains that are linked
• lysyl oxidase is needed
• desmoes account for elastic

Elastin Structure Function

• Elastin inter converts number or de conformation ( dis disordered)
• Crosslinking is less Stable returns to deconsformatn

Elasin Criss-linking

• Lysinonoreudine and Desmozine - some lysed oxidized requires