Source: APK2105C Final Exam Review, University of Florida
Tags: transcription, translation, DNA replication, mRNA, tRNA, rRNA, enzymes, catalysis, cofactors, coenzymes, ATP, glycolysis, Krebs cycle, oxidative phosphorylation, electron transport chain, APK2105C
Difficulty: Intermediate Prerequisites: Parts 1 and 2 of these notes. You should be comfortable with nucleotides, DNA structure, protein structure, functional groups and the basics of chemical bonds.
This section covers two big themes. First, how the cell turns genetic information into functional proteins (transcription, translation, DNA replication). Second, how the cell fuels itself: chemical reactions, enzymes, and the three pathways that regenerate ATP (creatine phosphate, glycolysis, and the Krebs cycle paired with oxidative phosphorylation). These topics are the mechanistic heart of cell physiology. If you understand them, nearly every downstream topic (muscle contraction, nerve signalling, hormonal regulation) becomes easier.
DNA is transcribed into mRNA in the nucleus, then mRNA is translated into protein at the ribosomes. Enzymes are protein catalysts that lower activation energy without changing reaction direction or energy yield. ATP is the cell's energy currency, resynthesised by creatine phosphate transfer, glycolysis (in the cytosol) and the Krebs cycle plus oxidative phosphorylation (in the mitochondria). One molecule of glucose yields approximately 38 ATP.
Gene
The portion of DNA that codes for a particular protein.
Sense strand (template strand)
Only one side of the DNA ladder holds the genetic code. A DNA triplet (three bases) codes for one amino acid.
mRNA (messenger RNA)
A strand that carries information from DNA to the ribosome.
tRNA (transfer RNA)
Depicted as a clover shape. Its job is to transfer amino acids to the ribosome for protein assembly.
rRNA (ribosomal RNA)
A globular molecule that makes up part of the ribosome itself.
Transcription
The process of copying DNA into a complementary mRNA strand. It occurs in the nucleus.
Initiation (transcription)
Transcription begins when the enzyme RNA polymerase attaches to the promoter region next to the start of the gene and pries the DNA strands apart. The binding of RNA polymerase to the promoter causes DNA to uncoil.
Elongation
RNA polymerase moves along the sense strand, linking nucleotides together to form pre-mRNA.
Terminator sequence
Once RNA polymerase passes this sequence, the enzyme releases the complete mRNA and detaches from the DNA.
Introns and exons
Introns are non-coding regions of excess bases within the mRNA. They are removed before the mRNA leaves the nucleus. Exons are the remaining correct coding sequences, which are spliced together.
5' cap and polyA tail
A chemical cap is added to the 5' end (necessary for initiating translation). A polyA tail (several adenine nucleotides) is added to the 3' end to protect the mRNA from degradation in the cytosol.
Translation
The process by which mRNA information is converted into an actual protein. It occurs at the ribosomes with the help of tRNA. During translation, protein is synthesised in the cytoplasm.
AUG (initiator codon)
The initiator codon composed of the sequence AUG. It codes for the amino acid methionine. Termination codons do not code for amino acids.
DNA replication
The process of precisely copying DNA before cell division. The two complementary strands separate, and each strand serves as a template for a new complementary strand, producing two identical DNA molecules. Each nucleotide pairs with its complement (A with T; C with G).
Binding of a small ribosomal subunit to mRNA
Binding of initiator tRNA to mRNA
Binding of large ribosomal subunit to mRNA
Binding of a 2nd tRNA with its amino acid to the A site
Formation of covalent bond between methionine and the second amino acid
(Exam answer order: 3, 1, 2, 4, 5)
Metabolism
The sum of the thousands of chemical reactions that occur within the body.
Reactants (remnants) and products
A chemical reaction changes entering substances (reactants) into different substances (products).
Catabolic reaction
The breakdown of larger molecules into smaller ones. Energy is liberated.
Anabolic reaction
The synthesis of larger molecules from smaller ones. Energy is added. Making or synthesising a protein is an anabolic reaction.
Metabolic pathway
A series of reactions linked for a common purpose. The final product is the end product; substances in the middle are intermediates.
Hydrolysis
The breaking of bonds within a molecule by the addition of water, forming new products.
Condensation
The reverse of hydrolysis: smaller molecules join to form a larger one, releasing water. Peptide bond formation and the addition of phosphate to ADP to form ATP are both condensation reactions.
Phosphorylation
The addition of a phosphate group to a molecule. The bond formed is a phosphate bond.
Dephosphorylation
The removal of a phosphate group. The best example is removing one of the three phosphate groups from ATP. These are called dephosphorylation reactions.
Oxidation
The removal of electrons (or hydrogen atoms) from a molecule.
Reduction
The addition of electrons to a molecule. Oxidation and reduction are usually coupled: one molecule is reduced, resulting in the oxidation of another.
Potential energy
The energy stored in chemical bonds.
Transition state
A high-energy intermediate form that reactant molecules pass through before becoming products.
Activation energy
The extra energy molecules must acquire to surmount the energy barrier and enter the transition state.
Enzymes
Specific proteins that overcome activation energy for specific reactants. They act as catalysts to increase the reaction rate. They are classified as proteins.
Substrate
The molecule that fits and binds to the enzyme's active site. A substrate is the same as a reactant.
Active site
The specific region on the enzyme where the substrate binds.
Lock-and-key model
The substrate fits the active site precisely, like a key in a lock.
Induced fit model
The substrate fits the active site more like a foot fits a sock: the substrate alters the conformation of the active site upon binding.
Cofactor
An additional molecule required for some enzymes to function. Without it, the enzyme loses its shape and activity. One important group of cofactors are trace metals (iron, copper, magnesium, zinc), obtained through diet.
Magnesium
A cofactor that helps liberate energy from ATP in skeletal muscles.
Coenzymes
Larger organic molecules (derived from vitamins) that form part of the enzyme's active site and function in the transfer of chemical groups.
Vitamin C
A coenzyme needed to make collagen, important for anchoring skin, bones and teeth.
FAD (flavin adenine dinucleotide) and NAD (nicotinamide adenine dinucleotide)
Coenzymes important in oxidation-reduction reactions in the mitochondria for energy liberation.
Pepsin
An enzyme secreted by cells in the stomach lining. It breaks food proteins into smaller fragments and functions optimally at a pH around 2.
Affinity
A measure of how tightly substrate molecules bind to an enzyme's active site. High affinity translates into higher rates of catalysed reaction.
Van der Waals forces
Weak forces that occur when electrons end up on one side of an atom, causing polarisation without covalent or ionic bonding.
Ligands
Molecules that interact with proteins. Substrates act as ligands. Binding between a ligand and a protein is specific.
Modulators
Molecules that bind to an enzyme's regulatory site and alter the shape of the active site, changing the enzyme's catalytic rate. An activator increases activity; an inhibitor decreases it.
Covalent regulation
Changes in enzyme activity brought about by covalent bonding of a chemical group at a special site, catalysed by another enzyme (Enzyme A). Removal of the group requires yet another enzyme (Enzyme B).
Protein kinase
An enzyme that covalently modulates another enzyme, typically by phosphorylation, for the purpose of cell signalling.
Rate-limiting step
The slowest reaction in a metabolic pathway. The enzyme catalysing it is the rate-limiting enzyme. Increasing or decreasing the activity of this enzyme changes the rate of the entire pathway.
Feedback inhibition
A product (often the end product) of a pathway allosterically inhibits an enzyme earlier in the pathway.
End-product inhibition
A specific form of feedback inhibition where the end product inhibits an upstream enzyme.
Feed-forward activation
An intermediate product in a pathway increases the activity of a downstream enzyme, speeding up the pathway.
Law of mass action
An enzymatic reaction rate is directly proportional to the concentrations of the reacting substances.
Enzyme activity increases as temperature rises, up to roughly 37 °C.
Around 40 °C a short plateau is reached, then the rate drops abruptly to zero as the enzyme denatures.
At low temperatures, enzyme activity can fall below the level needed to support cell function.
Most enzymes function best at pH 7. Stomach enzymes (e.g. pepsin) function at about pH 2.
ATP (adenosine triphosphate)
The most important energy-transferring compound in cells. When one phosphate bond is broken, energy is liberated to power the cell's work. The body contains about 85 grams of ATP at any given time.
ATP hydrolysis
The reaction splitting ATP into ADP and inorganic phosphate (Pi). Water is technically a reactant, though it is usually omitted from the equation. When cells need energy, they hydrolyse previously synthesised ATP.
Adenosine diphosphate (ADP)
The nucleotide from which ATP is resynthesised by adding an inorganic phosphate via substrate-level phosphorylation.
Heat
When ATP is broken down, heat is produced. This can maintain body temperature, but excess heat (e.g. during exercise) must be eliminated.
Sun
The initial source of all cellular energy. Plants convert solar energy into carbohydrates, fats and protein; humans eat those plants (or animals that ate those plants).
Three pathways to resynthesise ATP:
Substrate-level phosphorylation using creatine phosphate.
Glycolysis (breakdown of glucose).
Krebs cycle + oxidative phosphorylation (in mitochondria).
Creatine phosphate
A high-energy compound in cells (especially brain and skeletal muscle). The enzyme creatine kinase transfers a phosphate group from creatine phosphate to ADP, producing ATP. When energy demand decreases, excess ATP rephosphorylates creatine for future use. Think of creatine phosphate as a buffer for ATP, keeping levels normal during brief bursts of high demand.
Glycolysis
The breakdown of glucose in the cytosol to produce ATP and pyruvate. It yields a net gain of 2 ATP directly. Its true importance is supplying pyruvate to the mitochondria and producing H⁺ (via NADH+H⁺) to prime oxidative phosphorylation.
Pyruvate
The product of glycolysis under aerobic conditions. It enters the mitochondrial matrix to be further metabolised. Under aerobic conditions, pyruvate is converted to acetyl-CoA.
NAD (nicotinamide adenine dinucleotide)
A co-enzyme acting as a hydrogen ion carrier. It extracts hydrogen ions during glycolysis and transports them to the electron transport chain. Any drop in NAD levels threatens all ATP production because NAD is necessary for both glycolysis and the Krebs cycle.
Lactic acid (lactate)
If oxygen becomes limited, pyruvate is converted to lactic acid in the cytosol. Lactic acid produces H⁺ ions and interferes with cellular functioning. The enzyme lactate dehydrogenase (LDH) catalyses this conversion.
Isoform
Any of two or more functionally similar proteins with slightly different amino acid sequences. The H-type isoform of LDH (heart) preferentially converts lactate back to pyruvate. The M-type (muscle) preferentially converts pyruvate to lactate.
Linking step
The conversion of pyruvate into acetyl-CoA, linking glycolysis to the Krebs cycle. For each pyruvate, one NAD⁺ is reduced to NADH+H⁺ and one CO₂ is released.
Krebs cycle (citric acid cycle)
Takes place in the mitochondrial matrix. Its primary substrate is acetyl-CoA. Its true significance is not direct ATP production (2 ATP per glucose) but the reduction of the coenzymes NAD and FAD, which carry energy to the electron transport chain. By the end of each turn, 3 CO₂ molecules are generated as end products. CoA serves to transfer hydrogen ions and electrons.
FAD (flavin adenine dinucleotide)
Another carrier in the Krebs cycle that, like NAD, transports H⁺ to the inner membrane to power the electron transport chain.
Electron transport chain (ETC) / respiratory chain
Located on the inner mitochondrial membrane. It consists of five complexes plus ATP synthase. The three proton pumps are NADH dehydrogenase (complex 1), cytochrome b-c1 (complex 2) and cytochrome oxidase (complex 3). NADH+H⁺ dumps electrons at complex 1. Coenzyme Q shuttles electrons from complex 1 to complex 2. Cytochrome c shuttles electrons one at a time from complex 2 to cytochrome oxidase. Oxygen is the final electron acceptor, forming water.
Protons
H⁺ ions pumped across the inner mitochondrial membrane from the matrix into the intermembrane space, creating a hydrogen ion gradient.
ATP synthase
A molecular machine that converts the energy stored in the hydrogen ion gradient into chemical energy in ATP. It works like a turbine. The F1 ATPase head is where Pi is bonded to ADP to form ATP.
Chemiosmotic theory
The three-part process: (1) electrons power the ETC pumps, (2) H⁺ ions are pumped into the intermembrane space, (3) ATP synthase uses the resulting gradient to make ATP. This is the theory of oxidative phosphorylation.
Chemiosmotic coupling
The harnessing of energy from ETC reactions to drive ATP synthesis. Ideally, each NADH+H⁺ yields 3 ATP and each FADH₂ yields 2 ATP. If protons bypass ATP synthase, the gradient converts to heat instead.
ATP yield from one glucose molecule
34 ATP from the electron transport chain and oxidative phosphorylation. 38 ATP total from one molecule of glucose (including glycolysis and the Krebs cycle).
Oxygen free radicals
Reactive molecules that damage cells, including DNA. Oxidative stress contributes to inflammatory diseases and can cause cell death.
Antioxidants
Enzymes and dietary molecules (vitamin E, vitamin C) that counter the effects of free radicals.
Gluconeogenesis
Formation of new glucose from non-carbohydrate sources, mainly in the liver from amino acids.
Glycogenolysis
Breakdown of glycogen into individual glucose molecules.
Glycogenesis
Synthesis of glycogen from glucose, stored in liver and muscle.
Lipogenesis
Synthesis of fats (triglycerides) from fatty acids.
Lipolysis
Breakdown of fats into individual fatty acids for metabolism.
Proteolysis
Breakdown of protein into amino acids. These can be used for gluconeogenesis or can enter the Krebs cycle directly.
Transcription (DNA → mRNA, in the nucleus):
RNA polymerase binds the promoter and uncoils DNA.
It reads the sense strand, linking RNA nucleotides into pre-mRNA (elongation).
At the terminator sequence, the enzyme detaches.
Introns are removed; exons are spliced together.
A 5' cap and 3' polyA tail are added to protect and prepare the mRNA.
Translation (mRNA → protein, at the ribosome in the cytoplasm):
The small ribosomal subunit binds mRNA, followed by initiator tRNA (carrying methionine), then the large subunit.
Each codon on mRNA is read, and tRNA delivers the matching amino acid.
Peptide bonds form between successive amino acids.
The process continues until a termination codon is reached.
DNA replication:
The two strands of DNA separate.
Each strand serves as a template; nucleotides pair with their complements (A–T, C–G).
Two identical double-stranded DNA molecules result.
Enzymes accelerate metabolic reactions by lowering the activation energy barrier.
They do not change the direction of the reaction or the amount of energy released or required. They only affect the rate.
The rate increases as enzyme concentration increases.
Enzyme–substrate binding can follow the lock-and-key model (precise fit) or the induced fit model (substrate alters active site shape).
Cofactors (trace metals) and coenzymes (organic molecules from vitamins, e.g. NAD, FAD, vitamin C) assist enzymes.
Enzyme activity is regulated by modulators (activators and inhibitors), covalent regulation (phosphorylation by protein kinase), feedback inhibition and feed-forward activation.
Creatine phosphate pathway: fastest, used for very short bursts. Creatine kinase transfers a phosphate from creatine phosphate to ADP.
Glycolysis: occurs in the cytosol. Glucose → 2 pyruvate, net 2 ATP, 2 NADH+H⁺. The real value is providing substrates for mitochondrial ATP production.
Krebs cycle + oxidative phosphorylation: occurs in the mitochondria. Pyruvate → acetyl-CoA (linking step) → Krebs cycle (matrix) → ETC and ATP synthase (inner membrane). This pathway harvests the remaining energy, yielding 34 ATP via oxidative phosphorylation. Total per glucose: approximately 38 ATP.
Without O₂, the ETC stalls, NADH+H⁺ cannot be oxidised, NAD⁺ is depleted, and both glycolysis and the Krebs cycle slow or stop.
Pyruvate is converted to lactate by LDH in the cytosol, generating some NAD⁺ to keep glycolysis running at a reduced rate.
This is not sustainable long-term because ATP supply dwindles and lactic acid accumulation interferes with cellular function.
Glycolysis summary: Glucose → 2 Pyruvate + 2 ATP (net) + 2 NADH+H⁺
Linking step: Pyruvate + CoA + NAD⁺ → Acetyl-CoA + CO₂ + NADH+H⁺
Krebs cycle (per acetyl-CoA): produces 3 NADH+H⁺, 1 FADH₂, 1 ATP (via GTP), 2 CO₂
ETC yield: each NADH+H⁺ → ~3 ATP; each FADH₂ → ~2 ATP
Total ATP per glucose: ~38 (2 from glycolysis + 2 from Krebs + 34 from oxidative phosphorylation)
Coenzyme Q accepts electrons from FADH₂ (first ETC component for FADH₂)
Creatine supplements used by athletes work by increasing the creatine phosphate pool in muscle cells, extending the period of rapid ATP resynthesis during short, intense exercise (sprinting, weightlifting). Glycolysis and lactic acid production explain the "burn" you feel during high-intensity effort when oxygen delivery cannot keep pace with demand.
Students often think enzymes provide energy for reactions. They do not. Enzymes lower the activation energy barrier; the energy for the reaction comes from the reactants themselves.
Glycolysis is sometimes described as "anaerobic" in a way that implies it only occurs without oxygen. Glycolysis occurs in the cytosol regardless of oxygen availability. What changes without oxygen is what happens to pyruvate afterwards.
The Krebs cycle does not directly use oxygen. Oxygen is the final electron acceptor in the ETC, not in the Krebs cycle itself. However, the Krebs cycle slows without oxygen because NAD⁺ cannot be regenerated.
"38 ATP per glucose" is an ideal maximum. Actual yield in living cells is somewhat lower due to proton leak and transport costs.
⚠️ Know the correct order of translation initiation steps (3, 1, 2, 4, 5 from the source material).
⚠️ Be able to distinguish transcription (DNA → mRNA, nucleus) from translation (mRNA → protein, cytoplasm/ribosomes).
⚠️ Understand that enzymes affect rate only, not direction or energy yield.
⚠️ Know the three ATP resynthesis pathways and where each occurs (cytosol vs. mitochondria).
⚠️ Be ready to trace the fate of pyruvate under aerobic (→ acetyl-CoA → Krebs) vs. anaerobic (→ lactate in the cytosol) conditions.
⚠️ ATP yield numbers: 2 (glycolysis), 2 (Krebs), 34 (oxidative phosphorylation), 38 (total per glucose).
⚠️ The first ETC component that accepts electrons from FADH₂ is coenzyme Q.
⚠️ ATP synthase uses the hydrogen ion gradient across the inner mitochondrial membrane to produce ATP.
Fill in the blank: The enzyme that binds to the promoter to begin transcription is _______ _______. (RNA polymerase.)
True or false: Introns are the coding sequences of mRNA. (False, introns are non-coding. Exons are the coding sequences.)
Fill in the blank: The total ATP yield from one molecule of glucose is approximately _______. (38.)
True or false: Enzymes change the direction of a reaction. (False, they only change the rate.)
Fill in the blank: Under anaerobic conditions, pyruvate is converted to _______ in the _______. (Lactate, cytosol.)
Q: Outline the main steps of transcription.
A: RNA polymerase binds the promoter and uncoils DNA. It reads the sense strand and links RNA nucleotides together (elongation). When it reaches the terminator sequence, the enzyme releases the mRNA. Introns are removed, exons are spliced, a 5' cap and 3' polyA tail are added, and the mature mRNA moves to the cytoplasm.
Q: What is the difference between the lock-and-key model and the induced fit model of enzyme action?
A: In the lock-and-key model, the substrate fits the active site precisely. In the induced fit model, the active site changes shape when the substrate binds, like a sock conforming to the shape of a foot.
Q: Describe the three pathways cells use to resynthesise ATP.
A: (1) Creatine phosphate: creatine kinase transfers a phosphate from creatine phosphate to ADP, very rapid but short-lived. (2) Glycolysis: glucose is broken down in the cytosol to pyruvate, yielding 2 net ATP and NADH+H⁺. (3) Krebs cycle + oxidative phosphorylation: in the mitochondria, acetyl-CoA enters the Krebs cycle, and the resulting NADH+H⁺ and FADH₂ feed the electron transport chain, which drives ATP synthase to produce the bulk of ATP (34 from oxidative phosphorylation).
Q: Why is oxygen important for ATP production even though the Krebs cycle does not directly use it?
A: Oxygen is the final electron acceptor in the electron transport chain. Without it, the ETC stalls, NADH+H⁺ cannot be re-oxidised to NAD⁺, and the resulting NAD⁺ shortage slows both glycolysis and the Krebs cycle, drastically reducing total ATP output.
Q: What is feedback inhibition?
A: A product (often the end product) of a metabolic pathway allosterically inhibits an enzyme earlier in the same pathway, slowing the pathway when enough product has accumulated.
Q: ATP is synthesised by substrate-level phosphorylation during which two processes?
A: Glycolysis and the Krebs cycle.
The metabolic pathways here connect directly to membrane transport (Part 4): the Na⁺/K⁺ pump alone can use up to 40% of a cell's ATP. Understanding ATP hydrolysis and resynthesis is also essential for muscle physiology later in the course, because muscle contraction depends on a continuous supply of ATP from these same pathways. Enzyme regulation (feedback inhibition, covalent regulation) reappears in hormonal signalling, where protein kinases are central players.
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