Amino Acid Structure Quiz

Amino Acid Structure

• Isoleucine side chain contains a branched hydrocarbon chain
• Phenylalanine side chain contains an aromatic ring
• Methionine side chain contains a sulfomethyl group
• Histidine has basic properties
• Glycine is the only amino acid that does not have stereo-isomers
• Lysine, arginine, and histidine have no charge in a weakly alkaline medium
• All hydrophobic amino acids except lysine have no charge

Protein Structure

• Primary structure: linear sequence of amino acids joined by peptide bonds
• Primary structure is stabilized by peptide bonds
• Basis of the protein primary structure is the polypeptide chain
• Tertiary structure: arrangement of the entire polypeptide chain in space
• Factors that form the protein tertiary structure: water environment, hydrophobic interactions, and ionic bonds
• Quaternary structure: location of protomers and the character of bonds between them in an oligomeric protein

Protein-Ligand Interactions

• Western blot analysis involves antigen-antibody interactions
• Protein-ligand interactions are complementary in shape and charge
• Myoglobin has a non-protein part (heme) that binds to globin via a coordination bond
• In lipoproteins, hydrophobic bonds are formed between lipid and protein parts
• In nucleoproteins, ionic bonds are formed between nucleic acid and protein parts

Protein Stability and Denaturation

• Factors affecting protein stability: charge of the protein molecule, hydration shell, and molecular weight
• Denaturation involves the destruction of non-covalent bonds, including hydrogen, ionic, and disulfide bonds
• Denaturation leads to changes in protein solubility, loss of function, and changes in non-covalent bonds

Enzymes

• Characteristics of enzymes: high specificity, high efficiency, and optimal pH and temperature
• Factors affecting enzyme activity: substrate concentration, enzyme concentration, pH, temperature, and inhibitors
• Competitive inhibitors bind to the active site, while non-competitive inhibitors bind to an allosteric site
• Allosteric effectors can be activators or inhibitors, and their action can be reversed by increasing substrate concentration
• Coenzymes: NAD+, NADP+, FMN, and FAD are coenzymes of oxidoreductases
• Enzyme regulation: feedback inhibition, allosteric regulation, and covalent modification

Enzyme Kinetics

• Michaelis-Menten constant (Km) is the substrate concentration at which the reaction rate is half-maximal
• Km value indicates the enzyme's affinity for the substrate
• Lineweaver-Burk graph: built in the double reciprocals of enzymatic reaction rate and substrate concentration
• Types of enzyme inhibitors: competitive, non-competitive, and uncompetitive

Enzyme Classification

• Oxidoreductases: catalyze oxidation-reduction reactions
• Transferases: catalyze the transfer of a functional group
• Hydrolases: catalyze the hydrolysis of a covalent bond
• Ligases: catalyze the formation of a covalent bond
• Lyases: catalyze the cleavage of a covalent bond without hydrolysis
• Isomerases: catalyze the rearrangement of a molecule### Enzymes
• A quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) in an enzyme
• Enzymes have 4 isoenzyme forms
• Lactate dehydrogenase catalyzes the reaction of reversible conversion of pyruvate to lactate
• Oxidoreductases, like lactate dehydrogenase, catalyze oxidation and reduction reactions
• Enzymes can be used as drugs, but their use is limited by their short duration of action, high specificity, low stability, and difficulty in obtaining highly purified preparations

Enzyme Leaks

• Enzyme leakage from the cell into the blood is influenced by:
  • Size of enzyme molecules
  • Presence of enzyme activators
  • Intracellular localization of enzymes
  • Enzyme life-time

Immobilized Enzymes

• Advantages of immobilized enzymes over non-immobilized enzymes:
  • Reusability
  • Increased stability
  • Directional transport (targeted delivery)

Urine Diastase

• Urine diastase is:
  • A diagnostic test for pancreatic diseases
  • Measures amylase activity in urine
  • Not a measure of starch or its cleavage products in urine

Treatment of Septic Wounds

• Enzymes used in treatment of septic wounds:
  • Trypsin
  • Deoxyribonuclease
  • Not alkaline phosphatase or amylase

Pancreatic Autolysis

• Activation of trypsin and other enzymes can lead to pancreatic autolysis

Indicator Enzymes

• Indicator enzymes are:
  • Enzymes whose increased activity in plasma indicates pathology in internal organs and tissues
  • Examples: aminotransferases, lactate dehydrogenase, creatine kinase

Aerobic Glycolysis

• Reaction of aerobic glycolysis associated with oxidative phosphorylation:
  • Glyceraldehyde 3-phosphate + NAD+ + H3PO4 → 1,3-Diphosphoglycerate + NADH

Gluconeogenesis

• Gluconeogenesis is the synthesis of glucose from non-carbohydrate sources
• Gluconeogenesis involves the reversal of glycolysis, with some modifications
• Phosphofructokinase is not a gluconeogenic enzyme

Glycogenolysis

• Glycogenolysis is the breakdown of glycogen to glucose
• Glycogen phosphorylase cleaves α-1,4-glycosidic bonds in glycogen

Glycogen Synthesis

• Glycogen synthase catalyzes the formation of α-1,4-glycosidic bonds in glycogen
• The inclusion of 1 mole of glucose into glycogen requires 6 moles of high-energy compounds

Phosphofructokinase

• Phosphofructokinase catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-diphosphate

Glycolysis

• Pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to pyruvate
• During anaerobic glycolysis, NADH is oxidized to NAD+ while reducing pyruvate to lactate
• During aerobic glycolysis, NADH is oxidized to NAD+ in the electron transport chain

Glucose Transport

• Insulin-dependent glucose transporters are present in:
  • Adipose tissue
  • Skeletal muscles

Indigestible Polysaccharides

• Indigestible polysaccharides include:
  • Cellulose
  • Pectins
  • Not glycogen or lactulose

Carbohydrate Metabolism

• Stages of aerobic glucose oxidation to end products (CO2 and H2O):
  • Glycolysis
  • Oxidative decarboxylation of pyruvate
  • Tricarboxylic acid cycle

Pentose Phosphate Pathway

• The pentose phosphate pathway:
  • Generates NADPH in the cytosol
  • Provides ribose-5-phosphate for nucleic acid synthesis
  • Involves the reduction of NADP+

Uronic Acid Pathway

• The uronic acid pathway:
  • Provides UDP-glucuronic acid for detoxification of xenobiotics and biosynthesis of glycosaminoglycans
  • Involves the oxidation of glucose to glucuronic acid

Glucose-6-Phosphatase Deficiency

• Glucose-6-phosphatase deficiency leads to:
  • Von Gierke's disease
  • Impaired glycogenolysis and glucose release from the liver

Blood Glucose Regulation

• Insulin decreases blood glucose by:
  • Stimulating glycolysis
  • Inhibiting gluconeogenesis and glycogenolysis
• Glucagon and epinephrine increase blood glucose by:
  • Stimulating glycogenolysis and gluconeogenesis
  • Inhibiting glycolysisHere are the study notes:
• Lipid Metabolism*

Fatty Acid Oxidation

• Electron Transport Chain: Uncoupling of tissue respiration and phosphorylation occurs due to increasing the permeability of the inner mitochondrial membrane to protons.
• Inhibitors of Cytochrome c Oxidoreductase: Cyanides bind to the iron atoms of cytochromes a and a3, inhibiting tissue respiration.

Regulation of Lipid Metabolism

• Regulatory Enzymes of Citric Acid Cycle: Isocitrate dehydrogenase is the regulatory enzyme of the citric acid cycle.
• Inhibitor of Regulatory Enzymes: ATP is an inhibitor of regulatory enzymes of the citric acid cycle.

Lipid Structure and Classification

• Triacylglycerols: Consist of a glycerol backbone and three fatty acid chains.
• Phospholipids: Amphipathic molecules composed of a glycerol backbone, two fatty acid chains, and a phosphate group.
• Lecithin: A type of phospholipid with a choline head group.
• Sphingomyelin: A type of phospholipid with a sphingosine backbone and a choline head group.
• Styrene: A type of simple lipid.
• Cholesterol: A type of unsaponifiable lipid.

Lipid Digestion and Absorption

• Lipases: Pancreatic lipase hydrolyzes triacylglycerols into fatty acids and glycerol.
• Micelle Formation: Bile salts facilitate the formation of micelles, which are absorbed into enterocytes.

Fatty Acid Synthesis

• Acetyl-CoA Carboxylase: The key enzyme in fatty acid synthesis, catalyzing the reaction of acetyl-CoA and CO2 to form malonyl-CoA.
• NADPH: The coenzyme required for fatty acid synthesis.

Cholesterol Synthesis

• Mevalonate: An intermediate in cholesterol synthesis.
• Farnesyl Pyrophosphate: An intermediate in cholesterol synthesis, with 15 carbon atoms.

Eicosanoids

• Arachidonic Acid: The precursor for eicosanoid synthesis.
• Thromboxanes: Involved in platelet aggregation.

Let me know if you'd like me to clarify or expand on any of these points!

Identify the structural features of various amino acids, including isoleucine and phenylalanine.