Biochemistry Video Flashcards: Protein Structure, Metabolism, Glycogen, and Related Topics

A comprehensive set of quiz-style questions (Q&A) drawn from the video notes, covering protein structure, metabolism, glycogen biology, enzymes, and related pathologies.

What mutation causes Sickle Cell Anemia and why does this single mutation have wide-ranging effects?

Glu6Val (E6V) mutation in beta-globin. It causes HbS to polymerize when deoxygenated, distorting red cells, occluding vessels, causing pain crises, autosplenectomy, and increased infection risk (e.g., Salmonella osteomyelitis). Sickle cell patients also have a susceptibility to osteomyelitis (bone infection) by salmonella, which is an unusual pathogen for this infection

Name several methods for amino acid identification.

Ninhydrin (color change), chromatography, and mass spectrometry.

Peptide bonds connect which groups during protein linking?

The amino group (NH3) of one amino acid to the carboxyl group (COOH) of the adjacent amino acid.

List the levels of protein structure and which are affected by denaturation.

Primary, Secondary, Tertiary, and Quaternary structures. Denaturation disrupts secondary, tertiary, and quaternary structures but does not break peptide bonds (primary).

Name diseases associated with protein misfolding (including infections).

Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyloidoses, and prion diseases.

Which amino acids are essential and what is unique about the essential AAs listed as PVT TIM HALL and ARG/His?

Essential AAs: Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine (PVT TIM HALL). Arginine and Histidine are truly essential in children; others are essential in adults.

Which two amino acids are not essential but are made from essential AAs, and which are they?

Tyrosine (from phenylalanine) and Cysteine (from methionine/serine pathway).

Compare Kwashiorkor and Marasmus and explain the edema in relation to proteins.

Kwashiorkor = protein deficiency with edema, muscle wasting, fatty liver; edema due to low serum albumin. Marasmus = caloric and protein deficiency with severe wasting; edema is not prominent; overall energy deficiency.

Describe the structural and functional differences between myoglobin and hemoglobin and how 2,3-BPG affects their oxygen-binding curves.

Myoglobin: single subunit, high O2 affinity, stores/releases O2 in muscle; Hemoglobin: 4 subunits, cooperative O2 binding, delivers O2 from lungs to tissues. 2,3-BPG shifts Hb curve to the right (decreases O2 affinity) without affecting myoglobin.

What is the composition of hemoglobin and which component does lead poisoning affect?

Hemoglobin consists of heme (iron, protoporphyrin) and globin chains (alpha/beta; HbA, HbA2, HbF). Lead poisoning inhibits enzymes in heme synthesis (protoporphyrin ring formation) causing anemia.

What substance in blood indicates recycled hemoglobin, and which globin chain types change between Hb types?

Bilirubin indicates heme turnover and recycling. Globin chain composition changes between Hb types: HbA (α2β2), HbA2 (α2δ2), HbF (α2γ2).

Which components of the myoglobin/globin interact with heme and porphyrin?

Distal histidine interacts with bound oxygen; proximal histidine coordinates the iron in the heme prosthetic group.

What is ferric (Fe3+) vs ferrous (Fe2+) iron in heme and what pathology involves nonfunctional iron?

Fe2+ (ferrous) binds O2; Fe3+ (ferric) cannot bind O2. Methemoglobin is the ferric form; Methemoglobinemia is due to Fe3+ accumulation or defective reduction to Fe2+.

What is the condition characterized by oxidation of Fe2+ to Fe3+ and how is it treated?

Methemoglobinemia; treated with methylene blue which helps reduce Fe3+ back to Fe2+.

How does methemoglobin relate to cyanide poisoning treatment?

Methemoglobinemia can be used therapeutically to bind cyanide, pulling it away from cytochrome oxidase and restoring cellular respiration; nitrite therapy increases methemoglobin formation for cyanide poisoning.

Explain positive and negative cooperative binding in hemoglobin and whether myoglobin shows cooperativity.

Positive cooperativity: binding of O2 to one subunit increases affinity of others (Hb). Negative cooperativity is a decrease in affinity upon binding elsewhere (less common here). Myoglobin has a single subunit and shows no cooperativity.

What is thalassemia and how is it classified?

Genetic loss or mutation of globin genes. Alpha-thalassemia (loss of one to four alpha genes) and beta-thalassemia (loss of beta gene). Severity increases with more alleles mutated.

What is HbA1c and why is it clinically useful?

HbA1c is glycosylated hemoglobin; reflects average blood glucose over ~120 days; used for diagnosis and monitoring of diabetes.

Outline the steps of collagen synthesis and where disease can interrupt each step.

1) Translation of preprocollagen; 2) hydroxylation of proline/lysine (requires vitamin C); 3) glycosylation; 4) triple-helix formation (procollagen); 5) exocytosis to extracellular space; 6) cleavage of N/C terminals to form tropocollagen; 7) self-assembly and cross-linking (copper-dependent lysyl oxidase). Defects can cause scurvy (vitamin C deficiency) and osteogenesis imperfecta, EDS, Menkes disease (copper transport) and other connective tissue disorders.

What are the main types of collagen and where are they located?

Type I: bone, skin, tendon, dentin; Type II: cartilage; Type III: arteries, reticulin; Type IV: basement membranes.

Describe the formation of elastin.

Elastin contains glycine, proline, and lysine; lysine residues can be cross-linked to form elastic fibers. Proline can be hydroxylated; lysine is not hydroxylated in elastin formation.

What is M358 in AAT and why is it clinically relevant?

Methionine at position 358 (M358) in alpha-1 antitrypsin; smoking oxidizes M358, reducing AAT’s protease inhibition and increasing risk of emphysema.

Differentiate competitive vs noncompetitive inhibition.

Competitive inhibition: inhibitor binds active site; increases Km, Vmax unchanged. Noncompetitive inhibition: inhibitor binds allosteric site; decreases Vmax, Km unchanged.

What are isozymes (isoenzymes)?

Different molecular forms of the same enzyme produced in different tissues; catalyze the same reaction but have different kinetics and subunit compositions.

Compare a kinase to a phosphorylase.

Kinase adds a phosphate group; phosphorylase removes a phosphate group (dephosphorylation may activate or deactivate enzymes depending on context).

Define holoenzyme, apoenzyme, and cofactors.

Apoenzyme is the protein part; holoenzyme is the apoenzyme bound to its cofactor (cofactor may be organic coenzyme or inorganic ion). Prothetic groups are tightly bound cofactors (e.g., heme in hemoglobin).

Which liver and muscle serum enzymes are commonly used to assess organ damage?

ALT and AST for liver; Alkaline phosphatase for bone or biliary obstruction; CK (and CK-MB) for muscle/heart; LDH isozymes; Troponin I/T and CK-MB for myocardial infarction.

When do cardiac troponin and CK-MB rise after a myocardial infarction and what are their peak times?

Troponin begins rising ~2 hours, peaks at 24–48 hours, returns to baseline in 7–11 days. CK-MB rises ~4–6 hours, peaks around 24 hours, returns to baseline ~72 hours.

What is the difference between ETC decoupling and direct complex inhibition?

Decoupling uncouples oxidative phosphorylation from electron transport (no ATP production despite ongoing electron transport). Direct complex inhibitors block specific ETC complexes (e.g., rotenone blocks complex I) reducing ATP production.

Glycerol-3-phosphate shuttle vs malate-aspartate shuttle: ATP yield per NADH?

Glycerol-3-phosphate shuttle yields ~1.5 ATP per cytosolic NADH. Malate-aspartate shuttle yields ~2.5 ATP per cytosolic NADH.

List common ETC inhibitors and uncouplers.

Uncouplers: valinomycin, 2,4-DNP. Inhibitors: Rotenone (complex I), Amytal (complex I), Antimycin A (complex III), Cyanide/Azide (cytochrome oxidase), Oligomycin (ATP synthase).

Describe how cyanide poisoning affects the ETC and how nitrite/thiosulfate can reverse it.

Cyanide inhibits cytochrome c oxidase (complex IV), halting electron transport. Nitrite induces methemoglobinemia, which binds cyanide, freeing cytochrome oxidase; thiosulfate enhances cyanide detoxification.

Define anabolic vs catabolic pathways.

Anabolic pathways build complex molecules using energy; catabolic pathways break down molecules to release energy.

Why is acetyl-CoA a convergence point and why can it’t be reversibly converted back to pyruvate?

Acetyl-CoA sits at the junction of many pathways but cannot be converted directly back to pyruvate in humans due to regulatory and energetic constraints; gluconeogenesis does not convert acetyl-CoA to pyruvate.

Describe lactic acidosis.

A buildup of lactate due to insufficient oxygen (hypoxia) or impaired oxidative metabolism, leading to increased anaerobic glycolysis and a high anion gap metabolic acidosis.

Explain ketosis vs ketoacidosis.

Ketosis is a normal rise in ketone bodies during fasting or low carbohydrate intake. Ketoacidosis is a dangerous accumulation of ketone bodies and acidification of blood (e.g., DKA, alcoholic ketoacidosis).

How are energy stores and brain energy usage described during fasting?

Glycogen stores last ~18 hours; after depletion, gluconeogenesis supplies glucose; the brain requires blood glucose; muscles can use BCAAs when fasting; liver supplies glucose via gluconeogenesis.

What is the significance of the PPP and what enzyme deficiency is notable?

The PPP (pentose phosphate pathway) generates NADPH and ribose-5-phosphate. G6PD deficiency reduces NADPH production, impairing red cell antioxidant defenses.

How do insulin and glucagon regulate carbohydrate metabolism?

Insulin promotes glycolysis and glycogen synthesis; glucagon promotes gluconeogenesis and glycogenolysis via cAMP/PKA signaling in liver and adipose tissue.

Differentiate isomers, epimers, and enantiomers; D vs L sugars.

Isomers share formula but differ in structure; epimers are isomers differing at one stereocenter; enantiomers are non-superimposable mirror images. D- and L- refer to configuration around the highest-numbered chiral carbon; most sugars in nature are D.

What bonds form glycosidic linkages and what is the difference between N-glycosidic and O-glycosidic bonds?

Glycosidic bonds join sugars. N-glycosidic bonds link sugars to nitrogen (e.g., nucleotides: base-sugar linkage). O-glycosidic bonds link sugars via oxygen (typical in glycoproteins and glycolipids).

Describe glycosaminoglycans (GAGs) and their role.

GAGs are heteropolysaccharides rich in acidic sugars and amino sugars with sulfates; highly negatively charged; provide structural ECM and are abundant in basement membranes.

Differentiate glycoproteins from proteoglycans.

Glycoproteins have carbohydrate by weight relatively low and serve signaling/functional roles; proteoglycans are heavily glycosylated with GAG chains, mainly structural ECM components.

What is I-cell disease and its underlying defect?

I-cell disease is due to failure to phosphorylate mannose on lysosomal enzymes, leading to inclusion bodies and widespread lysosomal storage.”

Describe normal digestion enzymes and what H2 gas indicates.

Salivary and pancreatic enzymes (e.g., amylase) initiate carbohydrate digestion; H2 gas in breath indicates carbohydrate malabsorption or fermentation by colonic bacteria (e.g., lactose/fructose intolerance).

Which GLUT transporter responds to insulin and which transports fructose?

GLUT4 is insulin-responsive (muscle, adipose). GLUT5 transports fructose; it is not insulin-dependent.

Name the irreversible steps of glycolysis and the kinases involved.

Irreversible steps: hexokinase/glucokinase (glucose to G6P), phosphofructokinase-1 (F6P to F1,6BP), pyruvate kinase (PEP to pyruvate).

What is the effect of arsenate poisoning and fluoride on glycolysis?

Arsenate substitutes for phosphate in glyceraldehyde-3-phosphate formation, creating no net ATP gain; fluoride inhibits enolase, preventing ATP generation in glycolysis.

Describe pyruvate kinase (PK) deficiency and how it differs from G6PD deficiency.

PK deficiency causes hemolytic anemia due to impaired glycolytic ATP production in RBCs; G6PD deficiency causes oxidative damage to hemoglobin ( Heinz bodies ) due to reduced NADPH and weakened red cell antioxidant capacity.

How is PK regulated and what does that imply about glucagon’s effect?

PK is inhibited by phosphorylation; glucagon signaling promotes phosphorylation, reducing glycolysis. Dephosphorylation activates PK in insulin-rich states.

Explain the Pasteur effect.

Under aerobic conditions, glycolysis is slower and more ATP is produced per glucose; under anaerobic conditions, glycolysis accelerates to compensate for lack of oxidative phosphorylation.

What is the Tandem enzyme concept in regulation?

In tissues, a tandem enzyme module is regulated by phosphorylation state: insulin promotes dephosphorylation, activating the kinase activity of the tandem enzyme and shifting metabolism toward glycolysis or other pathways.

Describe the PDH complex and its key coenzymes.

PDH converts pyruvate to acetyl-CoA; E1 requires thiamine (TPP), E2 uses lipoic acid, E3 uses FAD and NAD+. PDH links glycolysis to the TCA cycle.

Where do irreversible steps of the TCA cycle occur and which enzymes are involved?

Irreversible steps are catalyzed by citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase; these are regulated by energy state and substrate availability.

Where does the TCA cycle take place and which enzyme links it to the ETC?

TCA occurs in the mitochondria. Succinate dehydrogenase is a TCA enzyme that also functions as Complex II in the ETC, linking the cycles.

How many ATP are produced per acetyl-CoA in the TCA plus shuttles, and what does this depend on?

Approximately 10–12 ATP per acetyl-CoA, depending on the shuttle used (malate–aspartate vs glycerol phosphate) that transfers NADH equivalents into the mitochondria.

Which steps can be reversed in gluconeogenesis and what enzymes catalyze them?

Four irreversible glycolysis steps are reversed by: 1) Pyruvate carboxylase; 2) PEP carboxykinase (PEPCK); 3) Fructose-1,6-bisphosphatase; 4) Glucose-6-phosphatase.

Where do gluconeogenesis enzymes localize and what cofactor does Pyruvate Carboxylase require?

PYC is mitochondrial; PEPCK is split between mitochondria and cytosol; G6Pase in the endoplasmic reticulum. Pyruvate Carboxylase requires biotin and CO2.

List gluconeogenic precursors other than glucose.

Lactate (Cori cycle), alanine, glycerol (from fat breakdown) which feed into gluconeogenesis or TCA intermediates.

What is the purpose of the PPP and what happens in G6PD deficiency?

PPP generates NADPH and ribose-5-phosphate for biosynthesis. G6PD deficiency impairs NADPH production, reducing RBC capacity to handle oxidative stress.

How does excess alcohol affect metabolism?

Increased NADH/NAD+ ratio disrupts multiple pathways; inhibits fatty acid oxidation and gluconeogenesis, promotes fatty liver; can lead to hypoglycemia and lactic acidosis.

Summarize glycogen degradation steps and diseases that result from defects.

Glycogenolysis: glycogen phosphorylase cleaves glucose-1-phosphate from non-reducing ends; debranching enzyme handles limit dextrins. Defects cause glycogen storage diseases (e.g., Type I von Gierke with G6Pase deficiency affecting gluconeogenesis).

Outline glycogen synthesis steps.

Glycogen synthase extends glycogen chains by adding glucose from UDP-glucose; branching enzyme creates α(1→6) branches; coordinated by glycogenin as primer.

How is glycogen metabolism regulated by hormones?

Epinephrine and glucagon activate Gs signaling, increasing cAMP, activating PKA, which phosphorylates and activates glycogen phosphorylase and inhibits glycogen synthase; PPI (protein phosphatase) reverses this to promote synthesis.