Biochemistry Honor - Advanced

Science & Health

Requirements

1. Have the Biochemistry Honor.

   Answer: The Pathfinder must have already earned the Basic Biochemistry honor (CS-021), proven by the badge on the uniform and the record in the SGC (Club Management System). Without the prerequisite, they cannot start the advanced version, which delves deeper into carbohydrate metabolism, gluconeogenesis, regulatory hormones, fasting, and metabolic diseases such as diabetes. — The prerequisite rule is universal in the 'advanced' honors of the SAD. Basic Biochemistry covers the fundamentals of macromolecules (carbohydrates, lipids, proteins, nucleic acids) and enzymes. The advanced version (CS-022), built on this base, details metabolic pathways (glycolysis, the Krebs cycle, the respiratory chain), hormonal regulation, and pathophysiology. The SGC is the SAD's online platform that records honors. The badge for the basic one is placed above the right pocket of the Pathfinders' standard uniform.

2. Define the following terms:
   • Synthesis
   • Anabolism
   • Catabolism
   • Reduction
   • Oxidation
   • Photosynthesis
   • Hormone

   Answer: 1) Synthesis: the process of producing a more complex molecule from simpler molecules. 2) Anabolism: the set of constructive metabolic pathways that build complex molecules and consume (spend) energy. 3) Catabolism: the set of degradative metabolic pathways that break complex molecules into simpler ones and release energy. 4) Reduction: a chemical reaction in which a substance gains electrons (decreases the oxidation number). 5) Oxidation: a chemical reaction in which a substance loses electrons (increases the oxidation number). 6) Photosynthesis: the process by which plants produce glucose using sunlight, carbon dioxide (CO2), and water, releasing oxygen. 7) Hormone: a chemical messenger produced by glands, which is transported by the blood and regulates the functions of target cells or organs. — Basic biochemistry is precise: anabolism + catabolism = metabolism. Redox reactions (reduction-oxidation) are coupled — whoever loses an electron is oxidized, whoever gains one is reduced. Mnemonic OIL RIG: Oxidation Is Loss, Reduction Is Gain. Photosynthesis (6CO2 + 6H2O + light → C6H12O6 + 6O2) occurs in chloroplasts. Hormones include insulin (pancreas), thyroxine (thyroid), adrenaline (adrenal), testosterone/estrogen (gonads). Each term is fundamental to the complex metabolic pathways studied in the advanced course.

3. Besides supplying energy, what other functions do carbohydrates have?

   Answer: Structural: cellulose forms the wall of plant cells; chitin makes up the exoskeleton of insects. Reserve: glycogen accumulates in the liver and muscles. Cellular recognition: glycoproteins and glycolipids in the membrane act in signaling. Component of DNA/RNA: ribose and deoxyribose are part of the nucleic acids. Lubrication: hyaluronic acid in the joints. — Carbohydrates go far beyond energy. Structural: cellulose (plants), chitin (arthropods/fungi), peptidoglycan (bacteria). Reserve: glycogen in liver/muscle (animals), starch (plants). Recognition: ABO blood groups are determined by glycoproteins; viral antigens use carbohydrates. Nucleic structure: ribose in RNA, deoxyribose in DNA. Joints: hyaluronic acid, glycosaminoglycans (proteoglycans of cartilage). Coagulation: heparin. These roles make carbohydrates essential to life in all biological domains.

4. How are carbohydrates classified?

   Answer: By the number of sugar units: monosaccharides (1 — glucose, fructose, galactose), disaccharides (2 — sucrose, lactose, maltose), oligosaccharides (3-10), and polysaccharides (many — starch, glycogen, cellulose). Also by function: energy, structural, or reserve. — The primary classification is by degree of polymerization. Monosaccharides are the monomers (3 to 7 carbons: trioses, tetroses, pentoses, hexoses); they are sweet and soluble. Disaccharides: joined by a glycosidic bond (common sucrose, lactose from milk). Oligosaccharides appear in glycoproteins. Polysaccharides are macromolecules: starch (plant), glycogen (animal), cellulose (structural plant), chitin (animal). By function: energy (glucose), reserve (starch, glycogen), structural (cellulose, chitin). Glucose is the main cellular fuel.

5. What are the consequences of a lack of glucose in the body?

   Answer: Hypoglycemia: trembling, cold sweat, hunger, tachycardia, weakness, irritability. In severe cases: confusion, seizures, loss of consciousness, coma, and death. The brain depends on glucose; the lack of it compromises neurons before other tissues. Treatment: simple sugar or IV glucose. — Glucose is the main energy substrate for the brain (it consumes 120 g/day, 20% of basal expenditure). The central nervous system has a minimal glycogen reserve, being the first affected by a drop. When blood glucose < 70 mg/dL, adrenergic symptoms appear (trembling, sweating — adrenaline); below 50 mg/dL, neurological symptoms emerge (confusion, coma). Common causes: prolonged fasting, insulin overdose (in diabetics), strenuous exercise. Acute treatment: ingest 15-20g of simple carbohydrate (juice, candy) or glucagon IM in an emergency.

6. To keep glucose levels constant during fasting, the body is capable of producing this carbohydrate. How does the gluconeogenesis (or neoglucogenesis) pathway occur?

   Answer: The synthesis of glucose from non-carbohydrate sources, in the liver and kidneys. Substrates: lactate, glycerol, and glucogenic amino acids. It occurs during prolonged fasting, expends energy, and is regulated by glucagon (activates) and insulin (inhibits). Essential for supplying the brain and red blood cells during prolonged fasting. — The pathway is essentially the reverse of glycolysis, but with 4 of its own enzymes (pyruvate carboxylase, PEPCK, fructose-1,6-bisphosphatase, glucose-6-phosphatase) that bypass the 3 irreversible reactions. It is located in the cytosol and mitochondria of the hepatocyte. During fasting: the pancreas releases glucagon → activates adenylate cyclase → cAMP → PKA → phosphorylates enzymes → activates gluconeogenesis and inhibits glycolysis. Substrates: the Cori cycle (muscle lactate), the glucose-alanine cycle, glycerol from lipolysis. It is important to maintain blood glucose at ~90 mg/dL for the brain during fasting.

7. What is the importance of the hormones insulin and glucagon in the human body? Where are they produced?

   Answer: The pancreas, in the islets of Langerhans: insulin (beta cells) and glucagon (alpha). Insulin lowers blood glucose after a meal by storing it as glycogen/fat. Glucagon raises blood glucose during fasting through gluconeogenesis and glycogenolysis. They act antagonistically to keep blood glucose at 70-100 mg/dL. — The pancreas has two functions: exocrine (pancreatic juice) and endocrine (islets of Langerhans, ~1% of the mass). α (alpha) cells produce glucagon; β (beta) produce insulin; δ (delta) somatostatin; PP pancreatic polypeptide. Insulin: its tyrosine-kinase receptor activates GLUT4 in muscle/adipose tissue, stimulates glycogen synthesis, lipogenesis, and protein synthesis. Glucagon: a G-protein-coupled receptor activates adenylate cyclase → cAMP → activates hepatic glycogenolysis and gluconeogenesis. Dysregulation causes diabetes (insulin deficit) or hypoglucagonemia.

8. What is the metabolism of a fasting individual like?

   Answer: During fasting, glucagon and cortisol rise and insulin falls. The liver releases glucose through glycogenolysis (12-24h) and then gluconeogenesis. Adipose tissue releases fatty acids; muscle yields amino acids. Ketogenesis increases in fasting >3 days, generating ketone bodies for the brain. It maintains blood glucose and energy. — Fasting is the classic test of metabolic control. Phases: post-absorptive (4-12h, glycogenolysis), early (12-72h, gluconeogenesis), prolonged (>72h, ketosis). In prolonged fasting, the brain adapts to use ketone bodies (acetoacetate, beta-hydroxybutyrate), replacing up to 70% of glucose. Hormones: glucagon (high), insulin (low), cortisol (high), GH (high). Adaptations: reduction of basal metabolism (-15% in 1 week), muscle protein sparing through ketosis. Reason for limits: ~30-40 days without food (with water), a crucial evolutionary regulation.

9. What is the metabolism of a well-fed individual like?

   Answer: In the fed state, insulin predominates and glucagon falls. Absorbed glucose is immediate energy, and the excess becomes glycogen and fat (lipogenesis). Amino acids go to protein synthesis, and fatty acids form triglycerides in adipose tissue. Anabolic pathways predominate, storing energy for fasting. — After a mixed meal (carbohydrate, protein, lipid), insulin is released, activating GLUT4 in muscle/adipose tissue. Liver: glucose → glycogen (up to 100g) and the excess → fatty acids → triglycerides exported in VLDL. Muscle: glucose → glycogen (up to 400g) and protein synthesis. Adipose tissue: triglycerides from the diet (via chylomicrons) or from hepatic synthesis (VLDL) are stored after hydrolysis by LPL. Glycemic peak ~1h, return to baseline in 2-3h. Anabolic rest in this period allows tissue repair and growth.

10. What disease results from the lack of insulin production by humans? What are the main characteristics of this disease?

    Answer: Type 1 Diabetes Mellitus (T1DM): autoimmune, which destroys the beta cells of the pancreas, with an absolute deficiency of insulin. Characteristics: hyperglycemia, glycosuria, polyuria, polydipsia, polyphagia, weight loss, ketosis. It arises in childhood. Treatment: insulin therapy, diet, and monitoring. — T1DM represents 5-10% of diabetes cases. Etiology: autoimmunity (anti-GAD, anti-IA2, anti-islet antibodies), with a genetic component (HLA-DR3/DR4) and environmental triggers. Without insulin: glucose does not enter the cells → hyperglycemia → glycosuria → osmotic polyuria → dehydration and thirst (polydipsia). Diabetic ketoacidosis is an acute emergency. Differentiation: T2DM has insulin resistance initially, with preserved production; T1DM has a total lack. Insulin therapy is vital — Frederick Banting discovered insulin in 1921, revolutionizing the treatment, which was previously lethal.

11. Excess carbohydrates and amino acids are stored in the body through their conversion into lipids. How are lipids synthesized in the body? Where are lipids stored?

    Answer: Lipogenesis occurs in the liver: glucose becomes pyruvate and acetyl-CoA, the base of fatty acids. They bind to glycerol forming triglycerides, exported in VLDL to adipose tissue. Ketogenic amino acids follow the same route. Main deposit: the body's subcutaneous and visceral adipose tissue. — De novo lipogenesis is predominant in the liver. Acetyl-CoA (from the carbohydrate/protein excess) is carboxylated to malonyl-CoA by acetyl-CoA carboxylase (the regulated step). Fatty acid synthase produces palmitate (C16). Triglycerides (3 fatty acids + glycerol) are packed into VLDL and exported. Adipocytes hydrolyze (LPL) and re-esterify for storage. A normal adult has 10-20 kg of fat, enough for 2-3 months without eating. The hormone insulin activates lipogenesis; glucagon and adrenaline activate lipolysis during fasting.

12. What are the types of lipids that exist in humans?

    Answer: Triglycerides (energy storage in adipose tissue). Phospholipids (cell membranes). Steroids such as cholesterol (membranes, hormones) and sex hormones. Sphingolipids (nervous system). Glycolipids (cellular recognition). Waxes (protection). Free fatty acids (fuel). Lipoproteins (transport: chylomicrons, VLDL, LDL, HDL). — Lipids are a diverse class united by solubility in organic solvents. Triglycerides are 95% of body fat. Phospholipids form the bilayer of membranes (phosphatidylcholine, phosphatidylserine). Cholesterol is the precursor of steroid hormones (cortisol, aldosterone, testosterone, estrogen) and vitamin D. Sphingolipids are abundant in the myelin sheath. Lipoproteins transport lipids in the blood (HDL 'good', LDL 'bad'). Each type has a specific physiological function essential to the human organism.

13. Amino acids are produced by living beings. The so-called producers are capable of synthesizing all 20 essential amino acids; mammals can synthesize only some. What are the precursors used for the synthesis of these amino acids? How do mammals obtain the amino acids they are not able to synthesize?

    Answer: Precursors: Krebs intermediates, pyruvate, 3-phosphoglycerate, PEP, and ribose-5-P. Mammals synthesize 11 non-essential ones via transamination. The 9 essential ones (Phe, Val, Thr, Trp, Ile, Met, His, Leu, Lys) come from the diet, in animal proteins or combined plant legumes. — In humans, there are 20 protein amino acids: 9 essential and 11 non-essential. The non-essential ones derive from metabolic intermediates via transamination (transfer of the amino group from glutamate). The essential ones are lost evolutionarily because they can come from the diet. Mnemonic PVT TIM HALL: Phe, Val, Thr, Trp, Ile, Met, His, Arg (in children), Leu, Lys. Food sources: complete protein in eggs, milk, meat, fish; in vegetables — a combination of beans+rice, soy, quinoa. Deficiency causes kwashiorkor and marasmus.

14. Make a table of the biosynthetic families of amino acids according to their metabolic precursors.

    Answer: Alpha-ketoglutarate family: Glu, Gln, Pro, Arg, Lys (in some pathways). Oxaloacetate family: Asp, Asn, Met, Thr, Lys, Ile. Pyruvate family: Ala, Val, Leu. 3-phosphoglycerate family: Ser, Gly, Cys. Phosphoenolpyruvate and erythrose-4-phosphate family: Phe, Tyr, Trp (aromatics). Ribose-5-phosphate family: His. — Classification by precursor groups amino acids by the metabolic origin of their carbon skeleton. Glutamate is the central amino acid (it receives NH3 from glutamate dehydrogenase, donates the amine via transamination). Aspartate and oxaloacetate originate the branched family with Met/Thr/Ile. Aromatics (Phe/Tyr/Trp) come from the shikimate pathway (in plants/microbes; humans only have Tyr from Phe). Histidine is unique, coming from ribose-5-phosphate + ATP. All involve transamination for the amino group and specific enzymes for the skeleton.

15. The amino group is very important for the synthesis of amino acids. How is this amino group obtained? Explain the nitrogen cycle.

    Answer: The amino group comes from ammonia (NH3), incorporated into glutamate by glutamate dehydrogenase, which can then transfer the group to other amino acids via transamination. Nitrogen cycle: bacteria fix atmospheric N2 into NH3; others nitrify (NH3→NO2→NO3); plants absorb nitrate; animals consume plants. Denitrification returns N2 to the air, closing the natural cycle. — Molecular nitrogen (N2) is 78% of the atmosphere but inert. Fixing bacteria (Rhizobium, Azotobacter) use nitrogenase to reduce N2 to NH3. NH3 enters amino acids via glutamate (the universal precursor). In organisms: amino acids → proteins. Decomposition: ammonification returns NH3 to the soil. Nitrification (Nitrosomonas, Nitrobacter) oxidizes NH3 to nitrite and nitrate. Anaerobic denitrification (Pseudomonas) reduces NO3 to N2, closing the cycle. Industrial fertilization via the Haber-Bosch process produces synthetic NH3, altering the earth's natural cycle.

16. Nitrogen fixation is very important; it is carried out by bacteria. Some bacteria live in symbiosis with legumes. Explain how the symbiosis between bacteria and legumes occurs. Relate legumes and nitrogen fixation to crop rotation.

    Answer: Bacteria-legume symbiosis: bacteria of the genus Rhizobium (and similar) present in the soil penetrate through the root hairs of legumes (beans, soy, peas, peanuts, clover) and induce the formation of nodules on the roots. Inside the nodules, the plant provides sugars (energy from photosynthesis) and an environment with low oxygen concentration (protected by leghemoglobin); in exchange, the bacteria use the enzyme nitrogenase to fix atmospheric nitrogen (N2), converting it into ammonia (NH3) that the plant assimilates to make amino acids and proteins. It is a mutualistic relationship. Relationship with crop rotation: since legumes enrich the soil with fixed nitrogen, their planting is alternated with crops that deplete nitrogen (corn, wheat, rice). Thus, rotation with legumes naturally replenishes the soil's nitrogen, reduces the need for chemical fertilizers, improves fertility for the next crop, breaks cycles of pests and diseases, and lowers agricultural production costs. — The symbiosis begins with the release of flavonoids by the legume's root, attracting specific Rhizobium (each legume has its partner bacteria). The bacteria produce Nod factors that induce the formation of nodules. Inside the nodule, the anaerobic environment allows the action of nitrogenase (sensitive to O2, protected by leghemoglobin). The legume fixes 50-300 kg of N/ha/year. Classic rotation: corn-soy-wheat-legume. It reduces fertilizer costs, prevents erosion, and breaks the pest cycle. An age-old sustainable agricultural practice.

17. How does photosynthesis occur and what is its importance for life on earth?

    Answer: In the chloroplasts, chlorophyll absorbs light and converts CO2 and H2O into glucose, releasing O2. It has a light phase (ATP/NADPH) and a dark phase (the Calvin cycle, which fixes CO2). The basis of the terrestrial food chain, it produces atmospheric O2 and removes CO2, regulating the climate of planet Earth. — Photosynthesis is the process that sustains life. Light phase (thylakoids): chlorophyll a/b absorbs photons, the photolysis of water releases O2, generates ATP (photophosphorylation) and NADPH. Dark phase (stroma): the Calvin cycle uses ATP/NADPH to fix CO2 into ribulose-1,5-bisphosphate via Rubisco (the most abundant enzyme on Earth), producing glyceraldehyde-3-phosphate and glucose. Importance: it produces ~330 billion tons of O2/year; removes ~120 Gt of atmospheric CO2; it is the autotrophic basis of almost all food chains.

18. What factors affect photosynthesis?

    Answer: Light (intensity, quality, duration). CO2 (saturation ~1000 ppm). Temperature (optimal 25-35°C). Water (stress closes the stomata). Mineral nutrients (N, P, K, Mg for chlorophyll). O2 concentration (high inhibits Rubisco). The age of the leaf and the genetics of the plant also affect it. — The photosynthetic rate is multifactorial. Light curve: it increases until saturation. CO2: limiting under current conditions (~415 ppm); commercial greenhouses raise it to 1000-1500 ppm. Temperature: enzymes follow Q10 (doubling every 10°C up to the optimum). Water: stress closes the stomata, reducing CO2. N and Mg are part of chlorophyll; P goes into ATP/NADPH. High O2 induces photorespiration via Rubisco. C4 plants (corn, sugarcane) and CAM (cacti) evolved for hot/dry climates, using CO2 pumping or nighttime opening of the stomata.

19. Which organisms are capable of carrying out photosynthesis?

    Answer: Plants (all terrestrial ones with chlorophyll), algae (green, red, brown, diatoms, dinoflagellates), cyanobacteria (oxygenic photosynthetic bacteria), and anoxygenic photosynthetic bacteria (green and purple sulfur, which use H2S instead of water). All have pigments such as chlorophyll, bacteriochlorophyll, carotenoids, and phycobilins to capture sunlight. — There are two large groups: oxygenic (which produce O2) — plants, algae, cyanobacteria; anoxygenic (which do not produce O2) — green/purple bacteria. Cyanobacteria emerged ~3.5 billion years ago and were responsible for the Great Oxygenation Event on Earth (~2.4 billion years ago). Endosymbiosis (Lynn Margulis) postulates that chloroplasts descend from cyanobacteria engulfed by eukaryotic cells. Marine diatoms produce ~50% of current atmospheric O2. Carotenoids protect chlorophyll against excess light.

20. Carbon is a very important atom for all forms of life. Explain the carbon cycle.

    Answer: Plants and algae absorb CO2 via photosynthesis, turning it into biomass. Animals consume plants and return CO2 through respiration. Decomposers recycle dead matter releasing CO2. The combustion of fossil fuels releases accumulated CO2. The oceans absorb CO2 in equilibrium with the global atmosphere. — The carbon cycle is central to life and the climate. Reservoirs: atmosphere (~870 Gt C), ocean (~38,000 Gt), biosphere (~2,000 Gt), soil (~1,500 Gt), fossil fuels (~5,000 Gt). Natural flows: photosynthesis (~120 Gt/year absorbed), respiration (~120 Gt/year emitted). Human activity: burning of fossil fuels (~10 Gt/year), deforestation (~1-2 Gt/year). Atmospheric CO2 rose from 280 ppm (pre-industrial) to 420 ppm today, causing warming. Reforestation and clean energy are key responses.

21. What is the relationship between DNA, RNA, and proteins?

    Answer: DNA stores genetic information in a sequence of nucleotides. RNA is transcribed from the DNA and functions as an intermediate messenger. Proteins are translated by the ribosome from messenger RNA, assembling amino acids in the dictated order. Summary: DNA → RNA → protein (Crick's central dogma, 1958), with reverse transcription in viruses as an exception. — Francis Crick formalized the central dogma in 1958. Replication: DNA → DNA (maintains the information). Transcription: DNA → mRNA (nucleus, RNA polymerase). Translation: mRNA → protein (ribosome, cytoplasm; tRNA brings the amino acid). Each codon (3 nucleotides) corresponds to 1 amino acid by the universal genetic code. Exceptions: retroviruses (HIV) use reverse transcriptase (RNA → DNA); catalytic RNAs (ribozymes). Modern molecular biology (PCR, CRISPR, sequencing) is built on this dogma.

22. What are the applications of the study of DNA?

    Answer: Genetic diagnosis, forensics (paternity, criminal), gene therapy, engineering (insulin, GMOs), mRNA vaccines, sequencing (Human Genome), personalized medicine (oncology), anthropology (ancestry), and conservation of endangered species. Vast and current applications. — The study of DNA revolutionized science. Diagnosis: PCR detects specific mutations. Forensics: STR profiling identifies individuals with 1 in billions. CRISPR-Cas9 (2012, Doudna/Charpentier) corrects mutations. Engineering: modified bacteria produce insulin (1982), Humulin was the first recombinant drug. mRNA vaccines (Pfizer, Moderna): the code for the viral spike protein. The Human Genome (2003) sequenced ~3 billion pairs. Personalized medicine uses NGS to choose oncological treatment based on tumor DNA.