ATP and Metabolism
What molecule is the cell’s main immediate source of usable energy?
ATP (Adenosine triphosphate)
What is anaerobic respiration? Which step of cellular respiration occurs during anaerobic respiration? Why?
Metabolic process where cells break down glucose to produce energy without using molecular oxygen.
Glycolysis
During which phase of the cell cycle does a cell grow and perform its normal functions?
G1
What enzyme prevents DNA supercoiling?
Topoisomerase
What enzyme synthesizes RNA from a DNA template during transcription?
RNA polymerase.
What is the difference between anabolic and catabolic reactions?
Anabolic reactions build larger molecules and require energy. Catabolic reactions break down molecules and often release energy.
What are the main products of the Krebs cycle from one acetyl-CoA molecule?
3 NADH, 1 FADH₂, 1 ATP, and 2 CO₂.
What are the purposes of the G2 checkpoint and the spindle checkpoint?
The G2 checkpoint checks whether DNA replication is complete and whether DNA damage needs to be addressed. The spindle checkpoint ensures chromosomes are properly attached to the spindle before separation.
What are the functions of DNA polymerase 1, 2, and 3?
DNA polymerase 1: RNA primer removal and DNA repair (filling gaps)
DNA polymerase 2:DNA repair and backup for Pol III (UV damage)
DNA polymerase 3: Main enzyme for DNA synthesis (leading/lagging strands)
Where do transcription and translation occur in eukaryotic cells?
Transcription occurs in the nucleus. Translation occurs at ribosomes in the cytoplasm or on the rough endoplasmic reticulum.
What is the difference between endergonic and exergonic (what is their delta G symbol)
Endergonic reaction: Requires an input of energy to occur. The products have more free energy than the reactants. ΔG > 0 (positive).
Exergonic reaction: Releases free energy. The products have less free energy than the reactants. ΔG < 0 (negative).
What is the difference in potential energy between NADH and FADH2? Explain in detail. Bonus: Give the exact amount of ATP produced per molecule
NADH has a higher potential energy than FADH2 and this can be seen in the Electron Transport Chain. NADH donates its electrons in complex I and its protons are pumped from mitochondrial matrix into the intermembrane space, creating a larger proton gradient. While FADH2 donates its electrons to Complex II, which does not pump protons, leading to a lower energy yield. As a result, NADH contributes to generating approximately 2.5 ATP per molecule, while FADH2 generates about 1.5 ATP.
A cell has damaged DNA but continues dividing because a checkpoint protein is nonfunctional. What could happen, and why?
Damaged DNA may be passed to daughter cells, increasing mutations and genomic instability and potentially contributing to cancer.
Why is one new DNA strand synthesized continuously while the other is made in fragments? What are the fragments called/what are they and which enzyme joins them together?
DNA strands are antiparallel, and DNA polymerase can synthesize only in the 5′ to 3′ direction. This creates a continuous leading strand and a discontinuous lagging strand.
Okazaki fragments are short DNA segments made on the lagging strand. DNA ligase joins them by sealing breaks in the sugar-phosphate backbone.
If the DNA template strand is 3′-TAC GGA CTT-5′
What is Coding strand:
What is RNA strand:
Amino acids:
coding 5′-ATG CCT GAA-3′
mRNA 5′-AUG CCU GAA-3′
met, Ile, Ser, Stop
A researcher adds a chemical that inhibits an enzyme responsible for breaking down glucose during cellular metabolism. The cell still has a sufficient supply of oxygen and ATP at the start of the experiment. Predict how this inhibition could affect the cell’s ability to produce ATP over time, and explain why oxygen availability alone cannot maintain ATP production.
ATP production will decrease over time because glucose breakdown provides the electrons and intermediate molecules needed to drive cellular respiration. Even though oxygen is available as the final electron acceptor, the cell cannot maintain normal ATP production if glucose metabolism is disrupted. Oxygen alone cannot generate ATP because electrons must be supplied to the electron transport chain to establish the proton gradient that drives ATP synthase.
Two cells have the same glucose supply. Cell A has functioning mitochondria, while Cell B has a defective ATP synthase that cannot allow protons to flow through it. Which cell will produce more ATP through oxidative phosphorylation, and why?
Cell A will produce more ATP because its ATP synthase can use the proton gradient to make ATP. Cell B cannot efficiently use the proton gradient to produce ATP through oxidative phosphorylation.
A cell has a mutation that causes cyclin levels to remain high even when they should normally decrease. Predict how this could affect cyclin-dependent kinase (CDK) activity and cell-cycle progression. Explain how this mutation could contribute to cancer.
Cyclins activate CDKs by binding to them. If cyclin levels remain abnormally high, CDKs may stay active when they should normally be turned off. This could cause the cell to progress through checkpoints at inappropriate times and divide when it should not. Over time, this loss of normal cell-cycle regulation could contribute to uncontrolled cell division and cancer development.
Why does DNA synthesis need a Primer made from RNA? What is responsible for this?
DNA polymerases can’t initiate DNA synthesis on their own. They can only add nucleotides to an existing strand and need the primer to provide the starting point for DNA Synthesis. There is no known DNA polymerase that can initiate DNA synthesis. This is important so that DNA replication can happen efficiently and accurately. Primase is responsible for synthesizing the primers.
A gene undergoes a single-nucleotide substitution that changes an mRNA codon from UGG to UGA. Another mutation deletes one nucleotide from the coding region of a different gene. Identify the type of mutation in each case and predict how each could affect the resulting protein.
The UGG → UGA substitution is a nonsense mutation because UGA is a stop codon. Translation will terminate prematurely, potentially producing a shortened, nonfunctional protein. The single-nucleotide deletion is a frameshift mutation because it shifts the reading frame, changing the downstream codons and potentially introducing a premature stop codon. Both mutations can disrupt protein function, but the frameshift may alter many amino acids downstream of the deletion.
A cell has a mutation that prevents an enzyme from transferring a phosphate group from ATP to a target protein. The target protein normally changes shape after phosphorylation, allowing it to transport a substance against its concentration gradient. Predict how this mutation affects ATP use, protein function, and active transport. Explain why having abundant ATP in the cell would not necessarily solve the problem.
ATP may still be present, but the enzyme cannot transfer its phosphate group to the target protein. Without phosphorylation, the protein may not undergo the conformational change needed to transport the substance against its concentration gradient. Active transport would therefore decrease or stop. Having abundant ATP would not solve the problem because the issue is not ATP availability; it is the inability to transfer the phosphate group needed to activate the transport protein.
A researcher adds a chemical that blocks the electron transport chain in a cell's mitochondria. Predict what will happen to oxygen consumption, NADH and FADH2 consumption, and ATP production through oxidative phosphorylation.
Oxygen consumption will decrease or stop because electrons can no longer reach oxygen through the electron transport chain. The oxygen remains available in the cell and can diffuse away if it is not consumed. It may also be used by other cellular processes that require oxygen, if those processes are occurring.
Blocking the electron transport chain causes NADH and FADH₂ to build up because they are not being oxidized efficiently; their levels increase, while NAD⁺ and FAD become less available; the cell has fewer available electron carriers in their oxidized forms.
As a result, proton pumping across the inner mitochondrial membrane decreases or stops, causing the proton gradient to weaken. ATP synthase relies on this gradient to produce ATP, so ATP production through oxidative phosphorylation decreases dramatically or stops. The cell may still produce some ATP through glycolysis, but it will lose a major source of energy.
A researcher discovers that cancer cells have a mutation that inactivates the p53 protein. What is p53's function? Predict how this mutation could affect cell division, DNA integrity in daughter cells, and the development of cancer.
Without functional p53, cells with damaged DNA may fail to stop at cell-cycle checkpoints, particularly before DNA replication or mitosis. These cells may continue dividing and pass mutations to daughter cells, leading to genomic instability. Over time, the accumulation of mutations can disrupt additional cell-cycle controls and contribute to uncontrolled cell division and tumor formation.
A researcher discovers that DNA ligase is not functioning in a cell. Which part of DNA replication will be most directly affected, and what will happen to the newly synthesized DNA?
The lagging strand will be most directly affected because its Okazaki fragments cannot be properly joined together. The DNA will contain unsealed breaks in its sugar-phosphate backbone.
Sickle cell disease results from a single nucleotide substitution in the beta-globin gene that changes the sixth amino acid from glutamic acid to valine. A researcher finds that a patient produces normal amounts of beta-globin mRNA, but the hemoglobin proteins form aggregates when oxygen levels decrease. Using your knowledge of transcription, translation, and protein structure, explain why mRNA production can remain normal even though hemoglobin function is impaired. Then explain how the amino acid substitution changes protein interactions and leads to sickle-shaped red blood cells.
Transcription can remain normal because RNA polymerase can still transcribe the altered gene into mRNA. However, the nucleotide substitution changes an mRNA codon, causing a different amino acid to be incorporated during translation. Valine is hydrophobic, whereas glutamic acid is negatively charged and hydrophilic. This substitution creates a hydrophobic region on hemoglobin that promotes interactions between deoxygenated hemoglobin molecules. These molecules polymerize into long fibers, which distort red blood cells into a sickle shape. The cells become less flexible and more fragile, contributing to blocked blood vessels and hemolytic anemia.