Biochemistry: Midterm 2 Review

Comprehensive review flashcards covering metabolic pathways including glycolysis, gluconeogenesis, glycogen metabolism, pentose phosphate pathway, pyruvate dehydrogenase complex, citric acid cycle, mitochondrial electron transport, oxidative phosphorylation, and photosynthesis.

How do catabolism and anabolism differ in terms of molecule size, electron transfer, and energy exchange?

Catabolism breaks down larger molecules into smaller ones, is an oxidative process where electrons are lost, and releases energy used to synthesize $ATP$. Anabolism combines smaller molecules to make larger ones, is a reductive process that gains electrons, and consumes energy stored in $ATP$.

What is the complete stoichiometric equation for anaerobic glycolysis (fermentation)?

$$\text{glucose} + 2\text{ADP} + 2\text{P}_i \rightarrow 2\text{lactate} + 2\text{ATP} + 2\text{H}_2\text{O}$$

What is the complete stoichiometric equation for the aerobic metabolism of glucose?

$$\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 + 32\text{ADP} + 32\text{P}_i \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + 32\text{ATP}$$

How do the roles of NADH and NADPH differ in metabolism?

$NADH$ is generated in catabolic pathways and is used to produce $ATP$, whereas $NADPH$ is used in anabolic pathways as a reducing agent.

Which coenzymes are derived from vitamins B2, B3, and B5?

$FAD$ and $FMN$ are derived from vitamin B2 (riboflavin); $NAD$ and $NAD^+$ are derived from vitamin B3; Coenzyme A ($\text{CoA}$) is derived from vitamin B5.

What is proteolytic activation of an enzyme?

The irreversible, permanent conversion of an inactive protein precursor (proenzyme or zymogen) to its active form through the cleavage of one or more peptide bonds, commonly found in digestion.

What are the three irreversible steps of glycolysis and the enzymes that catalyze them?

Step 1 catalyzed by hexokinase ($\text{glucose} \rightarrow \text{G6P}$), Step 3 catalyzed by phosphofructokinase-1 or PFK-1 ($\text{F6P} \rightarrow \text{F-1,6-BP}$), and Step 10 catalyzed by pyruvate kinase ($\text{PEP} \rightarrow \text{pyruvate}$).

What is the first committed and rate-limiting step of glycolysis?

Step 3: the conversion of fructose-6-phosphate ($\text{F6P}$) to fructose-1,6-bisphosphate ($\text{F-1,6-BP}$) catalyzed by phosphofructokinase-1 ($\text{PFK-1}$).

What is the net summary equation for glycolysis per molecule of glucose?

$$\text{Glucose} + 2\text{NAD}^+ + 2\text{ADP} + 2\text{P}_i \rightarrow 2\text{pyruvate} + 2\text{NADH} + 2\text{H}^+ + 2\text{ATP}$$

How is phosphofructokinase-1 (PFK-1) allosterically regulated?

$\text{PFK-1}$ is inhibited by high levels of $ATP$ (negative allosteric inhibitor) and $\text{H}^+$, and is activated by $AMP$ and fructose-2,6-bisphosphate ($\text{F-2,6-BP}$).

What two sequential reactions make up alcoholic fermentation in yeast?

First, pyruvate is converted to acetaldehyde by pyruvate decarboxylase, releasing $\text{CO}_2$. Second, acetaldehyde is reduced to ethanol by alcohol dehydrogenase, regenerating $\text{NAD}^+$.

What is the pathway and net energy cost of the Cori cycle?

Lactate produced in active muscle enters the blood and travels to the liver, where it is converted to pyruvate and then to glucose via gluconeogenesis. Glucose travels back to muscle for energy. Muscle glycolysis produces $2\,\text{ATP}$ per glucose, while the liver consumes $6\,\text{ATP}$ equivalents to convert $2$ lactate molecules back into glucose.

What are the four enzymes that bypass the three irreversible steps of glycolysis in gluconeogenesis?

Pyruvate carboxylase and phosphoenolpyruvate carboxykinase (PEPCK) bypass pyruvate kinase; Fructose-1,6-bisphosphatase (FBPase-1) bypasses PFK-1; Glucose-6-phosphatase (G6Pase) bypasses hexokinase.

What are the cellular location, required cofactor, and energy source for pyruvate carboxylase?

It is located in the mitochondria, requires the cofactor biotin (vitamin B7), and consumes $ATP$.

How does oxaloacetate leave the mitochondria during gluconeogenesis?

Oxaloacetate cannot directly cross the mitochondrial membrane; it is converted to malate, exported to the cytoplasm, and re-oxidized back to oxaloacetate.

How does fructose-2,6-bisphosphate (F-2,6-BP) reciprocally regulate glycolysis and gluconeogenesis?

$\text{F-2,6-BP}$ activates $\text{PFK-1}$ to increase glycolysis and inhibits $\text{FBPase-1}$ to decrease gluconeogenesis.

What two catalytic activities are carried out by the glycogen debranching enzyme?

Transferase activity (shifts three glucose residues from a branch to an adjacent linear chain) and $\alpha\text{-1,6}$-glucosidase activity (hydrolyzes the remaining $\alpha\text{-1,6}$ branch-point glucose to release free glucose).

How does phosphorylation reciprocally regulate glycogen phosphorylase and glycogen synthase?

Phosphorylation activates glycogen phosphorylase (favoring glycogen breakdown) and inactivates glycogen synthase. Dephosphorylation (via protein phosphatase 1) inactivates glycogen phosphorylase and activates glycogen synthase.

What are the physiological triggers and actions of glucagon and epinephrine on glycogen metabolism?

Glucagon is released when blood glucose is low to increase liver glycogen breakdown and release glucose into the blood. Epinephrine is released during exercise or stress to increase muscle glycogen breakdown for energy.

What are the two major physiological products of the pentose phosphate pathway (PPP)?

$NADPH$ (used for biosynthesis and defense against reactive oxygen species) and Ribose-5-phosphate ($\text{R5P}$, used for nucleotide, DNA, RNA, and coenzyme synthesis).

What is the net reaction of the oxidative phase of the pentose phosphate pathway?

$\text{G6P} + 2\text{NADP}^+ + \text{H}_2\text{O} \rightarrow \text{Ru5P} + \text{CO}_2 + 2\text{NADPH} + \text{H}^+$ catalyzed by glucose-6-phosphate dehydrogenase (G6PD).

How many carbons do Xu5P, Su7P, and E4P contain, and is each an aldose or a ketose?

Xylulose-5-phosphate ($\text{Xu5P}$) has $5$ carbons and is a ketose; Sedoheptulose-7-phosphate ($\text{Su7P}$) has $7$ carbons and is a ketose; Erythrose-4-phosphate ($\text{E4P}$) has $4$ carbons and is an aldose.

How many carbons are transferred by transketolase versus transaldolase in the nonoxidative phase of PPP?

Transketolase transfers $2$-carbon units, whereas transaldolase transfers $3$-carbon units.

Which pathway combination is utilized when a cell requires only NADPH?

PPP phase I + PPP phase II + gluconeogenesis (re-converting the recycled fructose-6-phosphate and glyceraldehyde-3-phosphate back into glucose-6-phosphate to produce more $NADPH$).

How does NADPH maintain cellular defense against reactive oxygen species (ROS) via glutathione?

Reduced glutathione ($\text{GSH}$) reduces ROS and becomes oxidized to $\text{GSSG}$. $NADPH$ provides reducing equivalents to reduce $\text{GSSG}$ back into active $\text{GSH}$.

What overall reaction is catalyzed by the pyruvate dehydrogenase complex (PDC)?

$\text{Pyruvate} + \text{CoA} + \text{NAD}^+ \rightarrow \text{Acetyl-CoA} + \text{CO}_2 + \text{NADH} + \text{H}^+$ in the mitochondrial matrix.

What are the three enzyme components of the pyruvate dehydrogenase complex and their prosthetic groups?

E1: pyruvate dehydrogenase (uses thiamine pyrophosphate, TPP); E2: dihydrolipoyl transacetylase (uses lipoamide / lipoic acid); E3: dihydrolipoyl dehydrogenase (uses FAD and NAD+).

Which allosteric molecules inhibit and activate the pyruvate dehydrogenase complex (PDC)?

Inhibited by high $ATP$, high $NADH$, and high acetyl-CoA. Activated by pyruvate and $ADP$.

How does the cell balance the availability of acetyl-CoA and oxaloacetate (OAA) using pyruvate?

When acetyl-CoA is low, the pyruvate dehydrogenase complex (PDC) is activated to produce acetyl-CoA. When acetyl-CoA is high, pyruvate carboxylase is activated to convert pyruvate into oxaloacetate.

Which citric acid cycle enzyme is embedded in the inner mitochondrial membrane rather than the matrix?

Succinate dehydrogenase (which also functions as Complex II of the electron transport chain).

What are the high-energy yields and carbon loss per single turn of the citric acid cycle from one acetyl-CoA?

$3\,\text{NADH}$, $1\,\text{FADH}_2$, $1\,\text{GTP}$ (or $ATP$), and $2\,\text{CO}_2$.

What are the three irreversible, regulated enzymatic steps of the citric acid cycle?

Step 1: Citrate synthase ($\text{acetyl-CoA} + \text{OAA} \rightarrow \text{citrate}$); Step 3: Isocitrate dehydrogenase ($\text{isocitrate} \rightarrow \alpha\text{-ketoglutarate}$); Step 4: Alpha-ketoglutarate dehydrogenase complex ($\alpha\text{-ketoglutarate} \rightarrow \text{succinyl-CoA}$).

What determines the direction of electron flow along the mitochondrial electron transport chain?

Electrons flow spontaneously from carriers with a lower (more negative) redox potential to carriers with a higher (more positive) redox potential, terminating at oxygen ($\text{O}_2$).

How many protons are pumped into the intermembrane space per electron pair by Complexes I, II, III, and IV?

Complex I pumps $4\,\text{H}^+$, Complex II pumps $0\,\text{H}^+$, Complex III transfers/contributes $4\,\text{H}^+$, and Complex IV pumps $2\,\text{H}^+$.

How do ubiquinone (Q) and cytochrome c differ in location and electron-carrying capacity?

Ubiquinone is a hydrophobic electron carrier located within the inner mitochondrial membrane that carries $2$ electrons and $2$ protons. Cytochrome c is a hydrophilic carrier in the intermembrane space that carries only $1$ electron.

Why does the oxidation of one NADH yield approximately 2.5 ATP while one FADH2 yields only 1.5 ATP?

Electrons from $NADH$ enter at Complex I, resulting in a total of $10\,\text{H}^+$ pumped. Electrons from $FADH_2$ enter at Complex II (which pumps zero protons), bypassing Complex I and transferring only $6\,\text{H}^+$. Since approximately $4\,\text{H}^+$ are required per $ATP$, $NADH$ yields $\approx 2.5\,\text{ATP}$ and $FADH_2$ yields $\approx 1.5\,\text{ATP}$.

What are the three conformational states of the catalytic beta (β) subunits in the F1 component of ATP synthase?

L (Loose) state where $ADP$ and $\text{P}_i$ bind; T (Tight) state where $ATP$ is synthesized from $ADP$ and $\text{P}_i$; O (Open) state where synthesized $ATP$ is released and new substrates can enter.

What balanced reaction describes the photolysis of water by the water-oxidizing complex (WOC)?

$$2\text{H}_2\text{O} + 4\text{ photons} \rightarrow 4e^- + 4\text{H}^+ + \text{O}_2$$

What is the overall stoichiometry of the noncyclic light reactions of photosynthesis?

$$2\text{NADP}^+ + 3\text{ADP} + 3\text{P}_i + 2\text{H}_2\text{O} + 8\text{ photons} \rightarrow 2\text{NADPH} + 3\text{ATP} + \text{O}_2 + 2\text{H}^+$$

What are the products and stoichiometry of cyclic photophosphorylation?

$2\text{ADP} + 2\text{P}_i + 4\text{ photons} \rightarrow 2\text{ATP}$. It does not produce $NADPH$ and does not produce $\text{O}_2$.

What reaction is catalyzed by Rubisco in carbon fixation?

Rubisco combines one molecule of $\text{CO}_2$ with the $5$-carbon substrate ribulose-1,5-bisphosphate ($\text{RuBP}$) to form an unstable $6$-carbon intermediate that splits into two molecules of $3$-phosphoglycerate ($\text{3-PGA}$).

How much ATP and NADPH are consumed by the Calvin cycle per molecule of CO2 fixed?

$3\,\text{ATP}$ and $2\,\text{NADPH}$ per single $\text{CO}_2$ molecule fixed ($9\,\text{ATP}$ and $6\,\text{NADPH}$ per $3\,\text{CO}_2$).

What is the initial four-carbon CO2 acceptor in C4 photosynthesis, and what problem does it mitigate?

Oxaloacetate ($\text{OAA}$) is the initial $4$-carbon carrier formed by PEP carboxylase. It concentrates $\text{CO}_2$ around Rubisco, thereby reducing photorespiration caused by Rubisco's oxygenase activity.

What three conditions in the chloroplast stroma stimulate the carbamation and activation of Rubisco?

High $\text{CO}_2$, high stromal $\text{pH}$ (alkaline), and high stromal $\text{Mg}^{2+}$ concentration.

How does light trigger enzyme activation via the thioredoxin regulatory system in chloroplasts?

Light excitation of Photosystem I (PSI) produces reduced ferredoxin ($\text{Fd}$). Reduced ferredoxin reduces thioredoxin via ferredoxin-thioredoxin reductase. Reduced thioredoxin then reduces disulfide bonds on target metabolic enzymes, activating them.