Board Review Questions and Answers 2009

Related: Biochemistry Questions - BioenergeticsEnergyMetabolism - BiochemistryLearningModules

Transcription, DNA, Genetics

Subject: DNA polymerase

Question: Does DNA Poly III have 3-5 exonuclease activity?

Answer: Yes. - Joe Hacia (

Subject: DNA transcription

Question: When I get a transcription question, and a base sequence, how do I know if they are referring to the coding strand or template strand? what is the difference between these?

Answer: The CODING strand is the strand of DNA that the mRNA ends up looking like (except that the introns are removed and there are Us instead of Ts). The Template strand works like a template to allow the RNA to be made. It is the OTHER strand, opposite the coding strand. What is given in questions is usually the CODING strand. We use it because it looks like the mRNA and we can look at it and see what the protein will look like... kind of the way we look at pictures to order reprints, rather than the negatives (template strand) because they look very different from the final product. That being said, there might be questions when they specify they are giving you template strand sequence. It is hard to generalize. It really depends on what the question is about. Just remember: The CODING strand is the one that the RNA will look like. The TEMPLATE strand is the one the RNA will be built onto, so it will be complementary to the RNA (and go in the opposite direction (the pairing is anti-parallel). - Ite Laird-Offringa (

Carbohydrates, Glycogen

Subject: Location of Glucose-6-Phosphatase

Question: Is G-6-Phosphatase in the RER or SER membrane?

Answer: Lipids are in SER. G-6-Pase in RER - Vijay Kalra (

Subject: AMP and PFK-1

Question: My book mentions that AMP allosterically activates PFK-1, where does it come from?

Answer: ATP hydrolosis leads to ADP, which in turn is converted to AMP. - Vijay Kalra (

Answer; ATP, ADP and AMP are all normal metabolites in the cell involved in various reactions. For example, AMP and PPi (inorganic pyrophosphate) are generated from ATP during the formation of aminoacyl-tRNA and fatty acyl-CoA (see reactions below). The level of intracellular AMP is an general indicator of the energy level in the cell and is used to regulate the AMP-activated Protein Kinase (AMPK) which is involved in controlling lipid metabolism and other metabolic processes. - RayMosteller (

Reaction: Alanine + tRNA + ATP ==> Alanyl-tRNA + AMP + PPi

Reaction: palmitic acid + CoA + ATP ==> palmitoyl-CoA + AMP + PPi

Reaction: PPi + H2O ==> 2 Pi (Enzyme: pyrophosphatase)

Phosphofructokinase 1 (PFK-1) on Wikipedia

AMP-activated Protein Kinase (AMPK) on Wikipedia

Adenosine monophosphate (AMP) on Wikipedia

Adenosine Monophosphate (AMP) from Wikipedia

Bioenergetics and Energy Metabolism

Question: How does pyruvate get into the mitochondria from the cytoplasm?

Answer: Pyruvate enters the mitochondria in exchange for OH- - Vijay Kalra (

Answer: All metabolites enter or leave the mitochondria through reciprocal exchange mechanisms involving transport carriers (proteins) in the inner mitochondrial membrane. This is a form of "facilitated diffusion" or "passive mediated transport" not "active transport". For example, the Malate-Aspartate shuttle (see diagram below) involves the reciprocal exchange of Malate for α-ketoglutarate and Aspartate for Glutamate. Only very small molecules such as oxygen, carbon dioxide, ammonia, and water can diffuse through the inner mitochondrial membrane without a transport carrier. - RayMosteller (

Malate-Aspartate Shuttle from Malate-Aspartate Shuttle on Wikipedia

Subject: Gluconeogenesis from Acetyl CoA?

Question: If malate can leave the TCA cycle (malate shuttle) for gluconeogenesis, then isn’t that the same as "making" glucose from acetyl-coA?

Answer:Pyruvate in the mitochondria is converted to OAA by Pyruvate Carboxylase. OAA in mitochondria is converted to malate, which is transported out of mitochondria into the cytoplasm. Malate in the cytosol is converted to OAA by malate dehdrogenase. OAA is converted to PEP , which then is converted to glucose in the liver. Gluconeogenesis proceeeds.

AcetylCoA cannot be converted to Glucose. Acetyl CoA provides energy via TCA cycle , necessary for gluconeogenesis. - Vijay Kalra (

Subject: Cytochrome c location in mitochondria

Question: Where exactly is cytochrome c, i remember there being a discrepancy about this (inner or outer part of the inner mitochondrial membrane)?

Answer: Cytochrome c is loosely bound to the outer surface of the inner mitochondrial membrane (see image below). Cytochrome c is mobile in the inner membrane transporting reducing equivalents (electrons) between Complex III (Cytochrome bc1) and Complex IV (Cytochrome aa3). Cytochrome c is released from mitochondria during programmed cell death (apoptosis) after formation of the mitochondrial apoptosis-induced channel (MAC) in the outer mitochondrial membrane. Cytochrome c is a small, highly conserved protein (~100 amino acids) found in all aerobic organisms. The fact that Cytochrome c is small and serves multiple, essential roles in the cell explains the fact that it must be structurally conserved in nature (see structure below). - RayMosteller (

Cytochrome c on Wikipedia

Electron transport chain on Wikipedia

Apoptosis on Wikipedia - Good article with great images

Mitochondrial apoptosis-induced channel (MAC) on Wikipedia

Apoptosis on YouTube - Clever animation

Apoptosis on Google video - Time-lapse electron microscopy

Mitochondrial Electron Transport Chain (from Wikipedia)

Structure of Cytochrome c (from Wikipedia)

Mitochondrial Electron Transport Chain

Cytochrome c

Subject: Mitochondrial GTP

Question: Can GTP be converted to ATP (i.e. GTP made in the TCA cycle)

Answer: The high energy phosphate group of GTP can be transferred (from the guanine nucleotide to the adenine nucleotide) but not the purine base, ribose and other 2 phosphates (see reaction below). The GTP is probably used directly as a substrate or modulator in other mitochondrial reactions. - RayMosteller (

Reaction: GTP + ADP ==> GDP + ATP

Contact: RayMosteller (

None: QuestionsAndAnswers/BiochemQuestions/BoardReview2009 (last edited 2009-05-08 19:50:47 by RayMosteller)