Study sheet: Biochemistry Master Exam Review

📋 Course Outline

1. Enzyme Structure and Catalysis
2. Enzyme Regulation and Clinical Use
3. Glycolysis and Its Regulation
4. Gluconeogenesis and Glucose Cycles
5. Glycogen Synthesis and Breakdown
6. TCA Cycle and Energy Products
7. Pyruvate Dehydrogenase Complex
8. Pentose Phosphate Pathway
9. Fatty Acid Oxidation and Ketones
10. Amino Acid Nitrogen Disposal
11. Protein Digestion and Ammonia Transport
12. Vitamin Functions and Deficiencies
13. DNA Replication and Telomeres
14. DNA Repair and Packaging
15. Transcription RNA Processing and Translation

📖 1. Enzyme Structure and Catalysis

🔑 Key Concepts & Definitions

• Enzyme : a biological catalyst that increases the rate of a reaction without being consumed

★ Must-know

📌 The substrate is the substance acted on by an enzyme, and it binds at the enzyme’s active site.

Further detail

📌 In the lock-and-key model, the active site is already complementary to the substrate, whereas in the induced-fit model, substrate binding changes the enzyme’s conformation.

• The six enzyme classes are:
  • oxidoreductases
  • transferases
  • hydrolases
  • lyases
  • isomerases
  • ligases

💡 Memory Hook

Enzyme + substrate → enzyme–substrate complex → product

📖 2. Enzyme Regulation and Clinical Use

🔑 Key Concepts & Definitions

• Holoenzyme : an active enzyme composed of an apoenzyme and its required cofactor or coenzyme

★ Must-know

📌 Competitive inhibition occurs when an inhibitor competes for the active site and can be overcome by increasing substrate concentration, whereas noncompetitive inhibition involves another site and reduces catalytic activity.

Further detail

• For human enzymes, the optimum temperature is generally around 37°C, whereas excessive temperature can denature enzymes.

💡 Memory Hook

Competitive inhibition uses the active site; noncompetitive inhibition uses another site

📖 3. Glycolysis and Its Regulation

🔑 Key Concepts & Definitions

• Glycolysis : a cytosolic pathway of 10 reactions that converts one six-carbon glucose into two three-carbon pyruvate molecules

★ Must-know

• The net yield of glycolysis per glucose is 2 ATP, 2 NADH, and 2 pyruvate.

• PFK-1 is the major regulatory and rate-limiting enzyme of glycolysis; ATP inhibits it and ADP stimulates it according to the lecture.

• Red blood cells depend on anaerobic glycolysis because they lack mitochondria, producing lactate from pyruvate.

Further detail

• 🔄 The ten glycolytic reactions proceed through:
  1. glucose to G6P
  2. G6P to F6P
  3. F6P to F1,6-BP
  4. F1,6-BP to DHAP plus G3P
  5. DHAP to G3P
  6. G3P to 1,3-BPG
  7. 1,3-BPG to 3-PG
  8. 3-PG to 2-PG
  9. 2-PG to PEP
  10. PEP to pyruvate

💡 Memory Hook

Investment → cleavage → payoff: 2 ATP used, then 4 ATP and 2 NADH produced

📖 4. Gluconeogenesis and Glucose Cycles

🔑 Key Concepts & Definitions

• Gluconeogenesis : the formation of glucose from non-carbohydrate precursors, occurring mainly in the liver and approximately 10% in the kidney

★ Must-know

• The three gluconeogenic bypasses are:

  • pyruvate to PEP
  • fructose-1,6-bisphosphate to fructose-6-phosphate
  • glucose-6-phosphate to glucose

• Pyruvate carboxylase requires biotin, occurs in mitochondria, uses ATP, and is activated by acetyl-CoA, while PEP carboxykinase uses GTP.

• Increased fructose-2,6-bisphosphate stimulates glycolysis, whereas decreased fructose-2,6-bisphosphate stimulates gluconeogenesis.

Further detail

📐 Formula — The energy cost of producing one glucose is $2\ pyruvate + 4\ ATP + 2\ GTP + 2\ NADH \rightarrow glucose$, requiring 6 high-energy phosphate bonds.

💡 Memory Hook

Insulin favors glycolysis, whereas glucagon favors gluconeogenesis

📖 5. Glycogen Synthesis and Breakdown

🔑 Key Concepts & Definitions

• Glycogen : the highly branched storage form of glucose in animals, with α(1→4) bonds in linear chains and α(1→6) bonds at branches

★ Must-know

• 🔄 Glycogenesis proceeds through:
  1. G6P to G1P by phosphoglucomutase
  2. G1P to UDP-glucose by UDP-glucose pyrophosphorylase
  3. UDP-glucose to glycogen by glycogen synthase

📌 Liver glycogen maintains blood glucose and can release glucose, whereas muscle glycogen supplies energy only to muscle because muscle lacks glucose-6-phosphatase.

Further detail

• Von Gierke disease is caused by glucose-6-phosphatase deficiency, whereas McArdle disease is caused by muscle glycogen phosphorylase deficiency.

💡 Memory Hook

Glycogen synthase builds glycogen; glycogen phosphorylase breaks it down

📖 6. TCA Cycle and Energy Products

★ Must-know

• The TCA cycle occurs in the mitochondrial matrix and is a central pathway for carbohydrate, fat, and amino-acid oxidation.

• The eight TCA intermediates are:

  • citrate
  • isocitrate
  • α-ketoglutarate
  • succinyl-CoA
  • succinate
  • fumarate
  • malate
  • oxaloacetate

• Succinate dehydrogenase is the only TCA enzyme that produces FADH₂.

Further detail

• Succinyl-CoA to succinate produces GTP by substrate-level phosphorylation.

💡 Memory Hook

Citrate → isocitrate → α-ketoglutarate → succinyl-CoA → succinate → fumarate → malate → oxaloacetate

📖 7. Pyruvate Dehydrogenase Complex

🔑 Key Concepts & Definitions

• PDH complex : irreversibly converts pyruvate into acetyl-CoA, CO₂, and NADH in the mitochondrial matrix

★ Must-know

• The five PDH cofactors are:

  • TPP
  • lipoic acid
  • CoA
  • FAD
  • NAD⁺

• PDH kinase is activated by ATP, NADH, and acetyl-CoA, causing PDH phosphorylation and inhibition when energy is abundant.

Further detail

• Vitamin B1 deficiency can impair PDH and α-ketoglutarate dehydrogenase and causes beriberi and Wernicke-Korsakoff syndrome.

💡 Memory Hook

Tender Loving Care For Nancy: TPP, lipoate, CoA, FAD, NAD⁺

📖 8. Pentose Phosphate Pathway

🔑 Key Concepts & Definitions

• Pentose phosphate pathway : a cytosolic pathway that produces NADPH and ribose-5-phosphate

★ Must-know

• The oxidative phase is irreversible and produces 2 NADPH per glucose-6-phosphate.

• G6PD deficiency lowers NADPH and reduced glutathione, causing oxidative damage and hemolysis, especially after oxidant drugs, severe infection, or fava beans.

Further detail

• NADPH supports:
  • fatty-acid synthesis
  • steroid synthesis
  • glutathione regeneration
  • drug detoxification
  • phagocytosis
  • protection of red blood cells

💡 Memory Hook

G6PD deficiency → low NADPH → low reduced glutathione → oxidative hemolysis

📖 9. Fatty Acid Oxidation and Ketones

★ Must-know

• 🔄 Each β-oxidation cycle consists of:

  1. dehydrogenation producing FADH₂
  2. hydration
  3. a second oxidation producing NADH
  4. thiolysis producing acetyl-CoA

• Long-chain fatty acids enter the mitochondrial matrix through the carnitine shuttle, and malonyl-CoA inhibits CPT-I.

• Every β-oxidation cycle produces $1\ acetyl-CoA + 1\ NADH + 1\ FADH_2$.

Further detail

• According to the lecture, palmitate yields 8 acetyl-CoA, 7 NADH, 7 FADH₂, and a net 129 ATP after activation cost.

• MCAD deficiency impairs medium-chain fatty-acid oxidation and causes hypoglycemia and hypoketonemia, so fasting should be avoided.

💡 Memory Hook

Dehydrogenation → hydration → oxidation → thiolysis

📖 10. Amino Acid Nitrogen Disposal

📝 Essential Points

• The three ketone bodies are:

  • acetoacetate
  • β-hydroxybutyrate
  • acetone

• Ketogenesis occurs in the liver during fasting, prolonged exercise, or low-carbohydrate conditions when fatty-acid oxidation raises acetyl-CoA and oxaloacetate is diverted to gluconeogenesis.

• Mitochondrial HMG-CoA synthase is the rate-limiting enzyme of ketogenesis.

📌 The liver cannot use ketone bodies because it lacks thiophorase, and red blood cells cannot use them because they lack mitochondria.

• In uncontrolled type 1 diabetes, increased ketone bodies cause ketonemia, ketonuria, and metabolic acidosis, while acetone produces fruity breath.

💡 Memory Hook

Toxic ammonia → urea formation in the liver → urinary nitrogen excretion

📖 11. Protein Digestion and Ammonia Transport

🔑 Key Concepts & Definitions

• Urea cycle : converts toxic ammonia into urea mainly in the liver, after which urea travels through blood to the kidney and urine

★ Must-know

• One urea nitrogen comes from ammonia, the second comes from aspartate, and its carbon comes from CO₂ or HCO₃⁻.

• The five urea-cycle enzymes are:

  • CPS-I
  • ornithine transcarbamoylase
  • argininosuccinate synthetase
  • argininosuccinate lyase
  • arginase

• CPS-I uses 2 ATP and is activated by N-acetylglutamate, while OTC deficiency is the most common inherited urea-cycle disorder and is X-linked.

Further detail

• The first two urea-cycle reactions occur in the mitochondrial matrix and the remaining reactions occur in the cytosol.

💡 Memory Hook

Stomach pepsinogen → pepsin; intestine enteropeptidase → trypsin; trypsin activates pancreatic zymogens

📖 12. Vitamin Functions and Deficiencies

★ Must-know

📌 Fat-soluble vitamins A, D, E, and K are stored in liver or adipose tissue and carry a greater risk of toxicity, whereas water-soluble vitamins include the B-complex and vitamin C.

• Vitamin A supports vision, reproduction, growth, epithelial maintenance, and immunity, and its early deficiency sign is night blindness.

• 🔄 Vitamin D activation proceeds from:

  1. skin D3
  2. liver 25-hydroxy-D
  3. kidney 1,25-dihydroxy-D or calcitriol

• Vitamin K is required for carboxylation of clotting factors, and deficiency causes bleeding and hypoprothrombinemia.

• The active forms of vitamins B1, B2, B3, B5, B6, and B7 are respectively TPP, FMN/FAD, NAD⁺/NADP⁺, CoA, PLP, and a carboxylation cofactor.

• Folate supports one-carbon metabolism, DNA synthesis, and red blood cell production, while vitamin B12 supports homocysteine to methionine and methylmalonyl-CoA to succinyl-CoA.

Further detail

• Vitamin C is required for collagen hydroxylation, wound healing, and increased iron absorption, and its deficiency causes scurvy.

💡 Memory Hook

ADEK are fat-soluble; B vitamins support cofactors and C supports collagen

📖 13. DNA Replication and Telomeres

🔑 Key Concepts & Definitions

• DNA replication : bidirectional synthesis of DNA in the 5′→3′ direction, using complementary antiparallel strands

★ Must-know

• A pairs with T through 2 hydrogen bonds, G pairs with C through 3 hydrogen bonds, and DNA strands are joined by phosphodiester bonds.

• Helicase unwinds DNA, SSB proteins prevent reannealing, topoisomerase relieves supercoiling, and primase makes the RNA primer.

📌 The leading strand is synthesized continuously, whereas the lagging strand is synthesized discontinuously as Okazaki fragments.

• In bacteria, DNA polymerase III performs main DNA synthesis and proofreading through 3′→5′ exonuclease activity, while DNA polymerase I removes RNA primers and fills the gaps.

Further detail

• Eukaryotes have multiple replication origins; Pol α initiates, Pol ε synthesizes the leading strand, Pol δ synthesizes the lagging strand, Pol β repairs DNA, and Pol γ replicates mitochondrial DNA.

• Telomerase maintains telomere length using an RNA template and is especially active in gametes, stem cells, and tumor cells.

💡 Memory Hook

Unwind → prime → extend 5′→3′ → remove primers → ligate fragments

📖 14. DNA Repair and Packaging

🔑 Key Concepts & Definitions

• Nucleosome : DNA wrapped around histone proteins and is a structural unit of chromatin

★ Must-know

📌 Mismatch repair corrects replication mismatches, nucleotide excision repair removes bulky lesions such as UV-induced thymine dimers, and base excision repair removes individual abnormal bases.

• Base excision repair removes an abnormal base with DNA glycosylase, cuts the AP site with AP endonuclease, and completes repair with DNA polymerase and ligase.

• Xeroderma pigmentosum results from defective nucleotide-excision repair and causes increased UV sensitivity and skin-cancer risk.

Further detail

📌 Double-strand breaks are repaired mainly by nonhomologous end joining or homologous recombination.

💡 Memory Hook

NER repairs bulky lesions; BER repairs individual abnormal bases

📖 15. Transcription RNA Processing and Translation

🔑 Key Concepts & Definitions

• Transcription : the synthesis of RNA from DNA, producing RNA in the 5′→3′ direction without requiring a primer

★ Must-know

• Bacterial transcription uses one major RNA polymerase whose sigma-containing holoenzyme recognizes promoters at the -35 TTGACA sequence and the -10 Pribnow box TATAAT.

• RNA polymerase I produces 28S, 18S, and 5.8S rRNA, RNA polymerase II produces the mRNA precursor, and RNA polymerase III produces tRNA and 5S rRNA.

• The 5′ cap contains 7-methylguanosine, the poly-A tail is added to the 3′ end after an AAUAAA signal, and splicing removes introns while retaining exons.

• The genetic code has 64 codons, including 61 amino-acid codons and three stop codons: UAA, UAG, and UGA; AUG is the start codon for methionine.

📌 A silent mutation does not change the amino acid, a missense mutation changes one amino acid, a nonsense mutation creates a premature stop codon, and a frameshift mutation changes the reading frame through an insertion or deletion not in multiples of three.

• The ribosomal A site accepts incoming aminoacyl-tRNA, the P site holds peptidyl-tRNA, and the E site releases empty tRNA.

• 🔄 Translation proceeds through:

  1. initiation
  2. elongation
  3. termination

Further detail

• Rho-independent termination uses a GC-rich hairpin followed by a U-rich sequence, whereas rho-dependent termination uses the ATPase/helicase activity of rho protein.

💡 Memory Hook

Transcription → capping/polyadenylation/splicing → translation: A site → P site → E site

📊 Synthesis Tables

Core metabolic pathway comparison

Pathway	Location	Main output or role
Glycolysis	Cytosol	Pyruvate, ATP, and NADH
Gluconeogenesis	Mainly liver	Glucose formation
TCA cycle	Mitochondrial matrix	NADH, FADH₂, GTP, and regenerated oxaloacetate
Pentose phosphate pathway	Cytosol	NADPH and ribose-5-phosphate