BIO - Study Guide ( Extra )

All the other stuff we should review lol

If an enzyme is catalyzing an exergonic reaction, what will the enzyme do to each of the following?

• a. the initial energy of the reactants = No change.

• b. the initial energy of the products = No change.

• c. the activation energy of the reaction = Decrease it.

• d. the energy difference between the reactants and products (Delta G) = No change.

Why does pepsin have a different pH optimum than chymotrypsin? What would happen to protein digestion rates in the stomach if someone took a LOT of antacids, and brought their stomach pH to 6?

• Pepsin works in the highly acidic stomach (optimum pH ~2); chymotrypsin works in the alkaline small intestine (optimum pH ~8).

• Effect of antacids: If stomach pH rose to 6, pepsin would denature and become inactive, significantly slowing down or stopping protein digestion in the stomach.

What is being screened for in newborn screening for PKU? Why is this done at the time of birth? Why not wait until the baby is a little older?

Screening looks for high levels of the amino acid phenylalanine. It is done at birth because brain damage from PKU begins immediately upon the ingestion of protein (milk) and is irreversible; early intervention prevents intellectual disability.

What is the treatment for PKU? Explain the rationale for this treatment.

• Treatment: A strict diet low in phenylalanine.

• Rationale: Since the body cannot break down Phe, limiting intake prevents it from reaching toxic levels that cause brain damage.

You have discovered an inhibitor of PAH. It has a structure that is very similar to a monosaccharide. Do you predict this to be a competitive or non-competitive inhibitor of PAH? Explain your answer.

Non-competitive. The natural substrate for PAH is the amino acid phenylalanine. A monosaccharide (sugar) does not resemble an amino acid, so it is unlikely to fit into the active site. It would likely bind elsewhere and change the enzyme's shape.

What is Alli?

It is an over-the-counter weight-loss drug that acts as a lipase inhibitor, preventing the digestion and absorption of fats.

What was the evidence that Alli is significantly better than placebo?

• Clinical trial data showed that patients taking Alli lost significantly more weight over time compared to those on a placebo, as unabsorbed fat was excreted rather than stored.

Why are Na+ ions hydrophilic?

• They are charged ($+$), allowing them to form favorable electrostatic interactions with the partial negative charges of water molecules.

Why is methane (CH_4) hydrophobic?

• It is non-polar and uncharged; it cannot form hydrogen bonds or electrostatic interactions with water.

Is olive oil hydrophilic or hydrophobic? Explain the basis for its interactions.

Hydrophobic. It consists of non-polar triglycerides that do not mix with water because they cannot form hydrogen bonds.

If a cell lacks channel proteins, can ions cross it down their gradient?

• Generally no, unless there is a specific carrier protein for that ion. Ions cannot use simple diffusion.

Describe what happens to a human cell and a plant cell in each solution:

• Hypertonic: Human cell shrivels (crenation); Plant cell becomes plasmolyzed (membrane pulls away from the wall).

• Isotonic: Human cell is normal; Plant cell is flaccid (limp).

• Hypotonic: Human cell lyses (bursts); Plant cell is turgid (firm/normal).

Identify the signal, receptor, transduction, and response in skeletal muscle contraction (ACh example).

• Signal: Acetylcholine (ACh).

• Receptor: ACh receptor on the muscle cell surface.

• Transduction: Intracellular events, including the increase in Ca2+ concentration.

• Response: Muscle contraction.

How can a cell turn off its response to a signal molecule?

By removing the signal molecule, dephosphorylating proteins (via phosphatases), or degrading second messengers.

Compare and contrast type 1 and type 2 diabetes

• Type 1: Autoimmune destruction of insulin-producing cells; no insulin is made.

• Type 2: Cells fail to respond to insulin (insulin resistance); often linked to obesity/lifestyle.

Identify parts of a RTK (Hydrophobic/Hydrophilic/Binding/Phosphorylated).

• Hydrophobic: Transmembrane alpha-helix.

• Hydrophilic: Extracellular binding domain and intracellular tail.

• Bind ligand: Extracellular domain.

• Become phosphorylated: Tyrosine residues on the intracellular tail.

Describe RTK mutations.

• Unable to respond: Mutation in the extracellular binding site or kinase domain.

• Response in absence of signal: Mutation causing the RTK to dimerize or stay phosphorylated without a ligand (oncogenic).

B-Raf mutant melanoma treated with Zelboraf (inhibitor). If a 2nd mutation occurs in Ras (permanently bound to GTP), will the cell divide?

Yes. Ras is "upstream" of Raf. If Ras is permanently active, it will continue to signal to the rest of the pathway (assuming the mutation bypasses the need for the specific part of Raf that Zelboraf inhibits, or if the cell finds an alternative kinase cascade). However, strictly speaking, if Zelboraf blocks Raf, a mutation in Ras (upstream) usually won't help unless it activates a different pathway, but in most exam scenarios, if the "brake" (inhibitor) is at Raf, an "on" switch at Ras remains blocked. Note: Check your specific lecture slides on Zelboraf resistance for the exact mechanism preferred by your professor.