Biochemistry : Anabolic Pathways and Synthesis

Study concepts, example questions & explanations for Biochemistry

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Example Questions

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Example Question #1 : Anabolic Pathways And Synthesis

Which of the following statements is false about the human genome?

Possible Answers:

The sequences which code for proteins make up about 2% of the genome

Repeated sequences make up about 5% of the genome

Paralogs are homologous gene sequences caused by duplication events within the genome

None of the other answers are false

There are about 20,000 proteins that are coded for by the genome

Correct answer:

Repeated sequences make up about 5% of the genome

Explanation:

Scientists have indeed counted about 20,000 proteins coded for by the genome. Coding sequences are only about 2% or less of the genome. The definition of paralogs is genes related by duplication within a genome. Within the genome, not about 5%, but rather about 50%, of DNA sequences are repeated.

Example Question #1 : Protein Synthesis

Where does the pentose phosphate pathway primarily take place? 

Possible Answers:

The brush border of the small intestine

The cytosol of the liver

The mitochondria of the liver

The mitochondria of the kidney

Correct answer:

The cytosol of the liver

Explanation:

The pentose phosphate pathway (also known as the hexose monophosphate shunt or HMS), which mainly serves to produce  for anabolic reduction reactions and ribose-5-phosphate for nucleic acid production, takes place in the cytosol of hepatic cells.

Example Question #1 : Protein Synthesis

Which of the following amino acids can be created from the carbon skeleton of oxaloacetate?

Possible Answers:

Valine

Glutamine

Leucine

Histidine

Methionine

Correct answer:

Methionine

Explanation:

From the carbon skeleton of oxaloacetate, methionine can be created.  However, glutamine comes from alpha ketoglutarate, valine and leucine come from pyruvate, and histidine comes from ribose-5-phosphate.

Example Question #1 : Anabolic Pathways And Synthesis

Which of the following molecules is not necessary to create glutamate from alpha-ketoglutarate?

Possible Answers:

ATP

Carbon dioxide

NADPH

Alpha-ketoglutarate

Correct answer:

Carbon dioxide

Explanation:

The reaction for the conversion of glutamine into glutamate is:

As seen in the reaction above, carbon dioxide is uninvolved.

Example Question #1 : Anabolic Pathways And Synthesis

Which of the following correctly lists the severity of damage done by mutations in DNA from most severe to least?

Possible Answers:

Silent, missense, nonsense

Nonsense, silent, missense 

Nonsense, missense, silent

Missense, nonsense, silent

Correct answer:

Nonsense, missense, silent

Explanation:

When a change results in an early stop codon, nonsense mutation occurs and the protein is done being read early, often resulting in a nonfunctional protein. When a base change results into a different amino acid, this is a missense mutation. When a base change occurs but results in the same amino acid being read, this is considered a silent mutation. 

Example Question #6 : Anabolic Pathways And Synthesis

Which of the following correctly describes the function of a signal sequence with respect to proteins?

Possible Answers:

Serves as a signal for chaperone proteins to help fold the protein into the correct conformation

Marks the protein to be destined inside the nucleus

Allows the protein to be recognized by the ubiquitination pathway for degradation

Transports proteins that are destined for the secretory pathway within cells

Allows the protein or peptide to act as a signaling molecule by recognizing its associated receptor

Correct answer:

Transports proteins that are destined for the secretory pathway within cells

Explanation:

To answer this question, it's essential to have an understanding of what a signal sequence is.

A signal sequence (also sometimes called a signal peptide) is a specific sequence of amino acids on a polypeptide that appears near the beginning of translation. When this signal sequence is present, it causes a temporary halt in the translation process. Meanwhile, another protein called a signal recognition particle (SRP) comes along and binds to the ribosome that is translating the polypeptide. Together, this polypeptide-ribosome-SRP complex is transferred from the cytosol to the surface of the endoplasmic reticulum (ER). Once there, the complex allows the polypeptide to resume synthesis, but in doing so, causes it to be synthesized into the inner lumen of the endoplasmic reticulum. Consequently, this polypeptide will go on to be modified within the ER and also the Golgi apparatus. Afterwards, it will be sent off within a vesicle, where is will either be A) secreted outside of the cell or B) incorporated into the endomembrane system of the cell (in other words, the peptide will be inserted into a membrane such as the plasma membrane, ER membrane, Golgi membrane, etc.). Lastly, it is the nuclear localization sequence (NLS) that, when added to a protein, allows it to enter the nucleus through the nuclear membrane.

Example Question #3 : Anabolic Pathways And Synthesis

Which of of the following are the termination signals for translation?

Possible Answers:

UAG, UAA, UTA

GUA, UAA, UAG

GUA, GAU, UAA

UAA, UGA, UAG

TUA, UAG, GAU

Correct answer:

UAA, UGA, UAG

Explanation:

Just as there is an initiation codon regulating translation, there are termination codons that code for the end of translation. The three termination codons are UAA, UAG, and UGA. 

A helpful mnemonic for these are the phrases:

You are annoying (UAA)

You are gross (UAG)

You go away (UGA)

Example Question #1 : Protein Synthesis

What are some post-translational modifications collagen goes thru before attaining its final structure?

I. The precursor collagen molecule undergoes hydroxylation of selected proline and lysine amino acids.

II. The procollagen precursor is glycosylated by the addition of galactose and glucose.

III. Procollagen has amino and carboxy procollagen extension propeptides that make it soluble.

IV. Procollagen proteinases remove extension peptides from the ends of the molecule to form collagen.

Possible Answers:

I, II, and III

I and II

I, III, and IV

I, II, III, and IV

I and IV

Correct answer:

I, II, III, and IV

Explanation:

Procollagen has amino and carboxy procollagen extension propeptides that make it soluble. The preprocollagen undergoes both hydroxylation and glycosylation at specific aminoacid residues to form procollagen. Once secreted extracellularly, proteinases remove the extension peptides from procollagen to form the final collagen molecule.

Example Question #4 : Anabolic Pathways And Synthesis

Which of the following enzyme cofactors transfer methyl groups?

Possible Answers:

S-adenylosyl methionine, tetrahydrofolate

B12 cobalamin, S-adenylosyl methionine, tetrahydrofolate

B12 cobalamin, S-adenylosyl methionine, tetrahydrofolate, biotin

Tetrahydrofolate, biotin

Correct answer:

B12 cobalamin, S-adenylosyl methionine, tetrahydrofolate

Explanation:

Biotin moves carboxyl groups in the enzyme acetyl-CoA carboxylase. Tetrahydrofolate and S-adenylosyl methionine move methyl groups in amino acid synthesis and post-translational modifications such as DNA methylation. B12 cobalamin is a cofactor in the reactions producing succinyl-CoA and methionine, where it transfers methyl groups to complete the products.

Example Question #1 : Translation

Which of the following is a true statement regarding translation in eukaryotes?

Possible Answers:

All translation begins on bound ribosomes attaches to the rough endoplasmic reticulum

During translation, the polypeptide is synthesized beginning from its carboxy terminus and ending with its amino terminus

The Shine-Delgarno sequence is a stretch of nucleotides on the RNA to be translated, which helps to initiate polypeptide synthesis by allowing the ribosomes to bind to the RNA

All translation begins in the cytoplasm on free ribosomes

tRNA acts as the template for polypeptide synthesis during translation

Correct answer:

All translation begins in the cytoplasm on free ribosomes

Explanation:

Translation is a process by which polypeptides are synthesized from a mRNA transcript, which was previously synthesized from the process of transcription. During this process, tRNA acts as a carrier by bringing with it specific amino acids to the ribosome, which are then incorporated into a growing polypeptide chain.

Eukaryotic translation differs in quite a few ways from prokaryotic translation. For one thing, prokaryotic mRNA contains a Shine-Delgarno sequence, which serves as a binding site for prokaryotic ribosomes to assemble on the mRNA. This binding, in turn, helps to initiate translation in prokaryotic cells. Eukaryotic cells do not contain a Shine-Delgarno sequence.

Furthermore, in eukaryotes, translation always begins with the assembly of ribosomal subunits on mRNA in the cytosol. Therefore, translation always begins on free ribosomes in the cytosol! Sometimes, translation will also finish on free ribosomes if the resulting protein is destined to stay within the cytosol where it will serve its function. Alternatively, if the first few amino acids of the polypeptide consists of a specific "signal sequence," translation will be temporarily paused. During this time, the entire ribosome-mRNA-polypeptide complex will be translocated to the rough endoplasmic reticulum. Once attached, polypeptide synthesis will resume and the polypeptide will thread its way into the endoplasmic reticulum. As it does so, additional folding and post-translational modifications are usually done to the polypeptide for it to carry out its proper function. Generally, polypeptides that make their way through the endoplasmic reticulum are destined either to be secreted out of the cell, or to become incorporated into the endomembrane system of the cell. And finally, as polypeptides are synthesized on a ribosome, whether it is free or bound, the amino terminus (aka N-terminus) side of the polypeptide is synthesized first and the carboxy terminus (aka C-terminus) is synthesized last.

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