All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources
Example Questions
Example Question #4 : Gene Regulation
What regulatory element promotes RNA polymerase II binding as well as binding of factors that facilitate the unwinding of DNA prior to translation?
TATA box
5' untranslated region
None of the other answers
3' untranslated region
Translation start site
TATA box
The correct answer is TATA box. Found in about 24% of human gene promoters, this regulatory element is mostly found in genes transcribed by RNA polymerase II, and as such, recruits this enzyme to the promoter. Additionally, the TATA binding protein aids in unwinding DNA.
Example Question #401 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology
In a hypothetical situation, the enhancer region of gene X, which controls tail length in mice, is mutated such that transcription factors bind to the enhancer region at a much higher efficiency than if the region were wild-type. What is a reasonable phenotypic outcome possible from this mutation in gene X's enhancer region?
Tail length is increased due to increased activity of the gene's promoter.
There will be no phenotype because enhancers are not coding regions.
Tail length is not changed because the enhancer region does not dictate gene expression.
The mouse will be globally larger because increased transcription at the enhancer will impact any gene behind the enhancer.
Tail length is decreased because any mutation will cause a loss-of-function of these regulatory regions.
Tail length is increased due to increased activity of the gene's promoter.
This question is inspired by a real life example, in which if you put a bat enhancer region in front of the gene that controls limb development in mice, the limbs are longer due to changes in the enhancer activity, which increases the activity of the promoter. By permitting more transcription factor interaction with the regulatory region, one might expect that this type of mutation may increase the tail length of the mouse because more "pro-tail length" protein is being made.
Example Question #1 : Help With Gene Regulation Proteins
Histone acetyltransferases (HATs) transfer acetyl groups from acetyl CoA to lysine residues on histones. What is the purpose of this transfer?
Promote formation of euchromatin and increase gene expression
Prevent DNA degredation by endonucleases
Prevent transcription factors from binding to DNA
Facilitate phosphorylation of these lysines by kinases
Signal for ubiquitin-mediated degredation of histones
Promote formation of euchromatin and increase gene expression
The correct answer is to promote formation of euchromatin and increase gene expression. Acetylation of histones "relaxes" DNA coiling around histones by reducing the affinity between histones and DNA. This allows transcription factors to bind promoter regions and promote increased gene expression via transcription.
Example Question #2 : Help With Gene Regulation Proteins
What is the role of mediator in gene expression?
Mediator facilitates alternative splicing of newly synthesized mRNA transcripts
Mediator is not involved in gene expression
Mediator suppresses transcription by methylating histone lysines
Mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II
Mediator is a thermostable DNA polymerase that replicates DNA in extreme temperatures
Mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II
The correct answer is that mediator is a coactivator of transcription and serves to recruit transcription factors and RNA polymerase II. Mediator does not directly initiate transcription; however, by protein-protein interactions, it recruits the necessary proteins to sites of transcription.
Example Question #3 : Help With Gene Regulation Proteins
NFkB is a transcription factor that is held inactive in the cytoplasm when bound by its inhibitor, IkB. Upstream signaling that activates NFkB causes what effect?
Ubiquitin-mediated degradation of NFkB, allowing IkB to translocate to the nucleus and initiate transcription
Recruitment of transcription factors and coactivators of transcription to the cytoplasmically sequestered NFkB
Ubiquitin-mediated degradation of NFkB
Ubiquitin-mediated degradation of IkB, causing a conformational shift in NFkB that renders its DNA-binding domain inaccessible
Ubiquitin-mediated degradation of IkB, allowing NFkB to translocate to the nucleus and initiate transcription
Ubiquitin-mediated degradation of IkB, allowing NFkB to translocate to the nucleus and initiate transcription
Upstream signaling, such as from a toll-like receptor, causes IKK to phosphorylate IkB, signaling for its ubiquitin-mediated degradation. Since NFkB is no longer bound by its inhibitor, IkB, it translocates to the nucleus where it binds specific motifs in the genome to recruit other transcriptional machinery and initiate transcription.
Example Question #4 : Help With Gene Regulation Proteins
Which of the following is not a way in which transcription factors influence gene-specific transcription?
Recruiting other transcription factors
Recruiting DNA polymerase
Promoting euchromatin formation
Recruiting RNA polymerase holoenzyme
Binding transcription factor-specific DNA motifs
Recruiting DNA polymerase
The correct answer is recruiting DNA polymerase. DNA polymerase is involved in DNA replication, not transcription. Pioneer transcription factors can bind specific DNA motifs and promote euchromatin formation, allowing other transcription factors to bind the less organized DNA. Transcription factors can recruit other transcription factors and the RNA polymerase holoenzyme to promoters to promote gene-specific transcription.
Example Question #1 : Help With Rna In Gene Regulation
Which of the following types of RNA have been shown to regulate protein synthesis?
I. lncRNA
II. miRNA
III. tRNA
I and II
I, II, and III
I and III
II only
I, II, and III
Protein synthesis can be directly affected by molecules involved in translation, or indirectly by molecules involved in the transcription of mRNA templates.
Transfer RNA (tRNA) is involved in translation and serves the function of bringing amino acids to ribosomes. Due to its important function in translation tRNA, is capable of globally controlling translation and, therefore, is involved in protein regulation.
Long non-coding RNA (lncRNA) has been shown to regulate transcription in a number of ways. One of the most prominent is the existence of a lncRNA (Xist) that inactivates the majority of the extra X-chromosome in human females.
Micro RNA (miRNA) is involved in a process known as RNAi and is capable of controlling the translation of targeted molecules of mRNA.
Example Question #2 : Help With Rna In Gene Regulation
X-chromosome inactivation occurs in females in which one X-chromosome is silenced and transcriptionally inactivated. The X-inactive specific transcript (Xist) gene is responsible for mediating this inactivation.
What does Xist encode?
Ribosomal RNA
MicroRNA
Protein
Long non-coding RNA
Piwi-interacting RNA
Long non-coding RNA
The correct answer is long non-coding (lnc) RNA. Xist lncRNA coats the X-chromosome from which it is transcribed, effectively silencing that X-chromosome. MicroRNAs are small RNAs (~20 base pairs (bp)) and play a role in RNA silencing and post-transcriptional regulation of gene expression. Short interfering RNAs are double-stranded (20-25 bp) and play a role in post-transcriptional gene silencing. Piwi-interacting RNAs are small non-coding RNAs that interact with piwi proteins in epigenetic and post-transcriptional silencing of genetic elements such as retroposons. While MicroRNAs, siRNAs and Piwi-interacting RNAs all silence genes, the mechanism of X-chromosome inactivation requires Xist lncRNA.
Example Question #51 : Molecular Biology And Genetics
Mutations in two or more genes cause cell death, however, a mutation in only one of the genes is not lethal.
Which of the following best describes this phenomenon?
Oncogene addiction
Apoptosis
Synthetic lethality
Secondary mutations
Oncogenic shock
Synthetic lethality
Synthetic lethality is the correct answer. The combinatorial effect of multiple mutated genes disrupts homeostasis in cells, inducing cell death. A mutation in only one gene can be compensated for in cells by altering the expression of other genes, such as turning on anti-apoptotic signaling pathways.
Oncogene addiction occurs when a tumor cell relies on the expression of a particular oncogene (mutated gene) for survival.
Oncogenic shock refers to an increase in pro-apoptotic signaling and a decrease in anti-apoptotic signaling upon removal of an oncoprotein.
Apoptosis refers to the process of programmed cell death.
Secondary mutations occur in a cancer cell that is treated with a therapeutic agent to promote resistance to that specific agent.
Example Question #52 : Molecular Biology And Genetics
When modifiying histones with either activating or repressing marks, such as with acetyl and methyl groups, histone acetyltransferases and histone methyltransferases normally modify which amino acid?
Aspartic acid
Phenylalanine
Lysine
Alanine
Guanine
Lysine
Histones are almost always modified on lysines. Acetylation normally is an activating mark, and methylation is normally a repressing mark of chromatin structure.
Note that guanine is not an amino acid, but a nucleotide.
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