Comprehensive BioChem 2 Final Study Guide

A set of 55 Question-and-Answer flashcards covering key definitions, metabolic pathways (glycolysis, TCA cycle, glycogen metabolism, gluconeogenesis, PPP, lipid metabolism, β-oxidation), and nitrogen disposal (urea cycle) from the BioChem 2 study guide.

What is metabolism?

The totality of an organism’s chemical reactions, organized into pathways.

What does enthalpy (ΔH) represent in thermodynamics?

The heat content or change in total energy of a system.

What does entropy (ΔS) measure?

The degree of disorder in a system; it increases with energy dispersal.

Define free energy (ΔG).

Energy available to do work at constant temperature and pressure, calculated as ΔG = ΔH − TΔS.

What sign of ΔG indicates a spontaneous (exergonic) reaction?

ΔG < 0.

What is an exergonic reaction?

A reaction that releases free energy and is spontaneous.

What is an endergonic reaction?

A reaction that absorbs free energy and is non-spontaneous (ΔG > 0).

Differentiate between a cofactor and a coenzyme.

A cofactor is an inorganic ion (e.g., Mg²⁺); a coenzyme is an organic molecule (e.g., NAD⁺, TPP).

How do anabolism and catabolism differ?

Anabolism builds complex molecules and consumes energy; catabolism breaks down molecules and releases energy.

What is bioenergetics?

The study of energy flow and transformation in living systems.

Write the reaction catalyzed by hexokinase.

Glucose + ATP → Glucose-6-phosphate + ADP (Mg²⁺ required).

Which glycolytic step is rate-limiting and regulated allosterically by ATP, AMP, and citrate?

Phosphofructokinase-1 converting Fru-6-P + ATP → Fru-1,6-bisP + ADP.

What products does aldolase generate from fructose-1,6-bisphosphate?

Dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP).

Which enzyme converts DHAP to GAP in glycolysis?

Triose phosphate isomerase.

What is the energy yield of glyceraldehyde-3-P dehydrogenase?

It forms 1,3-bisphosphoglycerate and reduces NAD⁺ to NADH.

What reaction does pyruvate kinase catalyze and what activates it?

PEP + ADP → Pyruvate + ATP; it is activated by fructose-1,6-bisphosphate (feed-forward).

Which ions are cofactors for pyruvate kinase?

K⁺ and Mg²⁺.

Where does glycolysis occur within the cell?

In the cytosol.

What is the first step of the TCA cycle and its enzyme?

Acetyl-CoA + oxaloacetate → citrate via citrate synthase.

Which TCA enzyme contains a [4Fe–4S] cluster?

Aconitase.

What is the rate-limiting enzyme of the TCA cycle?

Isocitrate dehydrogenase.

List the five cofactors required by α-ketoglutarate dehydrogenase.

TPP, lipoic acid, FAD, NAD⁺, and CoA.

Which TCA enzyme directly generates GTP?

Succinyl-CoA synthetase (also called succinate thiokinase).

Which TCA enzyme is also Complex II of the electron-transport chain?

Succinate dehydrogenase.

What is the overall location of the TCA cycle in eukaryotic cells?

The mitochondrial matrix.

Describe the branching pattern of glycogen.

Linear α(1→4) glucose chains with α(1→6) branches every 8–12 residues.

What enzyme primes glycogen synthesis by self-glucosylation?

Glycogenin.

Which enzyme adds glucose units from UDP-glucose to a growing glycogen chain?

Glycogen synthase.

What two activities does the debranching enzyme possess?

Transferase that moves a three-residue limit branch and α(1→6) glucosidase that releases free glucose.

What cofactor does glycogen phosphorylase require?

Pyridoxal phosphate (PLP).

Which mitochondrial enzyme converts pyruvate to oxaloacetate in gluconeogenesis?

Pyruvate carboxylase (biotin-dependent).

What reaction does PEP carboxykinase catalyze?

Oxaloacetate + GTP → phosphoenolpyruvate + CO₂.

Which enzyme hydrolyzes fructose-1,6-bisphosphate in gluconeogenesis?

Fructose-1,6-bisphosphatase.

Where is glucose-6-phosphatase located within the cell?

In the lumen of the endoplasmic reticulum (mainly in liver).

Name two key negative regulators of gluconeogenesis.

Fructose-2,6-bisphosphate and AMP.

What is produced during the oxidative phase of the pentose phosphate pathway?

NADPH and ribulose-5-phosphate (plus CO₂).

Which PPP enzyme is TPP-dependent and transfers two-carbon units?

Transketolase.

Why is NADPH important?

It provides reducing power for biosynthetic reactions and antioxidant defense.

Differentiate saturated and unsaturated fatty acids.

Saturated FAs have no double bonds (e.g., palmitate 16:0); unsaturated FAs contain cis double bonds that introduce kinks (e.g., oleate 18:1Δ9).

Outline the final step in triacylglycerol synthesis.

DGAT (diacylglycerol acyltransferase) acylates diacylglycerol to form triacylglycerol.

Which enzyme mobilizes stored triacylglycerol during lipolysis?

Hormone-sensitive lipase.

What activates fatty acids for β-oxidation?

Acyl-CoA synthetase uses ATP and CoA to form acyl-CoA.

How are long-chain acyl-CoAs transported into mitochondria?

They are converted to acyl-carnitine by carnitine palmitoyltransferase I, translocated, and reconverted by CPT II.

List the four recurring reactions of the β-oxidation cycle.

(1) Acyl-CoA dehydrogenase (oxidation, FADH₂), (2) enoyl-CoA hydratase (hydration), (3) β-hydroxyacyl-CoA dehydrogenase (oxidation, NADH), (4) thiolase (cleavage by CoA).

What is the main product of each round of β-oxidation?

One acetyl-CoA and an acyl-CoA shortened by two carbons.

In amino-acid catabolism, what molecule first receives the amino group?

α-Ketoglutarate, forming glutamate via aminotransferases.

Which enzyme oxidatively deaminates glutamate to release NH₄⁺?

Glutamate dehydrogenase.

What is the committed, ATP-using first step of the urea cycle?

Carbamoyl phosphate synthetase I converting NH₄⁺ + HCO₃⁻ + 2 ATP → carbamoyl phosphate.

Which urea-cycle intermediate exits the mitochondrion to the cytosol?

Citrulline.

Which enzyme of the urea cycle produces fumarate?

Argininosuccinase (cleaving argininosuccinate).

What final reaction releases urea?

Arginase converts arginine to urea and ornithine.