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Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

Is RNA polymerase affected by proteins bound to the coding sequence of a gene?


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I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like:

-Ptet-(Gene1)-PLacO-(Gene2)-

I want to express each gene using either aTc or IPTG, but I want to make sure that the transcription of each gene can be controlled independently.

Let say I only add aTc and transcription is initiated at the Ptet location, would RNA polymerase bump into LacI bound to the PLacO promoter and stop transcribing? Or would it knock-off LacI transcribe (Gene 2)? I am not sure whether or not need to include terminator sequence to make sure the expression of each gene is decoupled.


Nice question! First of all make sure that you have multiple transcription stop / terminator sequences at the end of your first gene . This is quite standard procedure. Also in your case the phenomenon called transcription interference (TI) comes handy. Here's a review on TI. In short:

the term TI usually refers to the direct negative impact of one transcriptional activity on a second transcriptional activity in cis.

Although TI is mostly defined as two transcription events affecting each other, at the low level the basis of it is that two proteins bound to the DNA affect each other's activity. Now since LacI's function is to inhibit transcription, thus it is strongly bound to the DNA and I'd say even if a polymerase somehow slips through the polyA signals at the end of the first gene it is likely to be stopped by the LacI already bound at the second promoter.

Alternatively you could put a weak promoter opposing the first gene and drive its expression, so it would collide with the oncoming polymerase from the first gene thus stopping it before reaching the second gene. Also here is another article on TI, that proposes a gene regulation network based on TI.


RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

Transcriptional gene silencing controls transposons and other repetitive elements through RNA-directed DNA methylation (RdDM) and heterochromatin formation. A key component of the Arabidopsis RdDM pathway is ARGONAUTE4 (AGO4), which associates with siRNAs to mediate DNA methylation. Here, we show that AGO4 preferentially targets transposable elements embedded within promoters of protein-coding genes. This pattern of AGO4 binding cannot be simply explained by the sequences of AGO4-bound siRNAs instead, AGO4 binding to specific gene promoters is also mediated by long non-coding RNAs (lncRNAs) produced by RNA polymerase V. lncRNA-mediated AGO4 binding to gene promoters directs asymmetric DNA methylation to these genomic regions and is involved in regulating the expression of targeted genes. Finally, AGO4 binding overlaps sites of DNA methylation affected by the biotic stress response. Based on these findings, we propose that the targets of AGO4-directed RdDM are regulatory units responsible for controlling gene expression under specific environmental conditions.


Is RNA polymerase affected by proteins bound to the coding sequence of a gene? - Biology

Exam 3: Ch. 17: From Gene to Protein

Nearly every mRNA gene that codes for a protein begins with the start codon, AUG, and thus begins with a methionine.

Nearly every protein-coding sequence ends with one of the three stop codons (UAA, UAG, and UGA), which do not code for amino acids but signal the end of translation.

During translation, nucleotide base triplets (codons) in mRNA are read in sequence in the 5’ → 3’ direction along the mRNA. Amino acids are specified by the string of codons. What amino acid sequence does the following mRNA nucleotide sequence specify?

Express the sequence of amino acids using the three-letter abbreviations, separated by hyphens (e.g., Met-Ser-Thr-Lys-Gly).

An amino acid sequence is determined by strings of three-letter codons on the mRNA, each of which codes for a specific amino acid or a stop signal. The mRNA is translated in a 5’ → 3’ direction.

Which amino acid does the codon GCA code for?

To identify the amino acids specified by the mRNA sequence, you first need to subdivide the sequence into codons of three nucleotides each. This can be done by placing a space between each codon. Which of the following is the correct division of the codons for the sequence given? Look for the correct placement of spaces.

The role of DNA in determining amino acid sequences

Before a molecule of mRNA can be translated into a protein on the ribosome, the mRNA must first be transcribed from a sequence of DNA.

What amino acid sequence does the following DNA nucleotide sequence specify?

Express the sequence of amino acids using the three-letter abbreviations, separated by hyphens (e.g., Met-Ser-His-Lys-Gly).

Before mRNA can be translated into an amino acid sequence, the mRNA must first be synthesized from DNA through transcription. Base pairing in mRNA synthesis follows slightly different rules than in DNA synthesis: uracil (U) replaces thymine (T) in pairing with adenine (A). The codons specified by the mRNA are then translated into a string of amino acids.

Steps to convert a DNA sequence into an amino acid sequence.

  1. First, transcribe the DNA sequence to determine the mRNA sequence. Be sure to remember the following:
    • The mRNA strand is complementary to the DNA strand.
    • Uracil (U) takes the place of thymine (T) in RNA to pair with A on the DNA.
    • The RNA is assembled in an antiparallel direction to the template strand of DNA. A 3’→ 5’ direction in DNA is transcribed in a 5’ → 3’ direction in RNA.
  2. Next, subdivide the mRNA sequence into the individual three-letter codons in the 5’ to 3’ direction.
  3. Then, refer to the table of codons to identify the three-letter abbreviation for the amino acid that corresponds to each codon.

This chart shows how to decode an example DNA sequence. Remember to first determine the mRNA sequence that is complementary to the DNA template strand’s sequence. Be sure to write the mRNA sequence in a 5’ to 3’ direction, and to use U to pair with A.

The flow of information in a cell proceeds in what sequence?

A. from DNA to RNA to protein

B. from RNA to DNA to protein

C. from RNA to protein to DNA

D. from DNA to protein to RNA

E. from protein to RNA to DNA

A. from DNA to RNA to protein

This is known as the central dogma of biology.

A codon consists of _____ bases and specifies which _____ will be inserted into the polypeptide chain.

Three nucleotide bases make up a codon and specify which amino acid comes next in the sequence.

A particular triplet of bases in the template strand of DNA is 5' AGT 3'. The corresponding codon for the mRNA transcribed is _____.

The figure above shows a simple metabolic pathway. According to Beadle and Tatum's hypothesis, how many genes are necessary for this pathway?

D. It cannot be determined from the pathway.

Refer to the metabolic pathway illustrated above. If A, B, and C are all required for growth, a strain that is mutant for the gene-encoding enzyme A would be able to grow on medium supplemented with _____.

In the process of transcription, _____.

B. mRNA attaches to ribosomes

D. proteins are synthesized

Which of the following specifies a single amino acid in a polypeptide chain?

A. the three-base sequence of mRNA

B. the complementarity of DNA and RNA

C. the aminoacyl-tRNA synthetase

D. the base sequence of the tRNA

A. the three-base sequence of mRNA

In the diagram, the gray unit represents _____.

RNA polymerase untwists a portion of the DNA double helix.

In the diagram, the green unit represents _____.

The promoter is the region of DNA at which the process of transcription begins.

In the diagram below, the two blue strands represent _____.

RNA is not a double helix. DNA is a double helix.

Which of these correctly illustrates the pairing of DNA and RNA nucleotides?

In RNA, uracil takes the place of thymine.

The direction of synthesis of an RNA transcript is _____.

Nucleotides are added to the 3' end of RNA.

Where does RNA polymerase begin transcribing a gene into mRNA?

A. It starts at one end of the chromosome.

B. The ribosome directs it to the correct portion of the DNA molecule.

C. Transfer RNA acts to translate the message to RNA polymerase.

D. It starts after a certain nucleotide sequence called a promoter.

E. It looks for the AUG start codon.

D. It starts after a certain nucleotide sequence called a promoter.

Remember that RNA polymerase is an enzyme.

In both eukaryotes and prokaryotes, RNA polymerase binds to the gene's promoter and begins transcription at a nucleotide known as the start point, although in eukaryotes the binding of RNA polymerase to the promoter requires transcription factors.

Transcription in eukaryotes requires which of the following in addition to RNA polymerase?

A. aminoacyl-tRNA synthetase

B. several transcription factors

B. several transcription factors

During RNA processing a(n) _____ is added to the 5' end of the RNA.

B. a long string of adenine nucleotides

E. modified guanine nucleotide

E. modified guanine nucleotide

The 5' cap consists of a modified guanine nucleotide.

During RNA processing a(n) _____ is added to the 3' end of the RNA.

B. a long string of adenine nucleotides

E. modified guanine nucleotide

B. a long string of adenine nucleotides

A poly-A tail is added to the 3' end of the RNA.

Spliceosomes are composed of _____.

A. snRNPs and other proteins

B. polymerases and ligases

D. the RNA transcript and protein

A. snRNPs and other proteins

These are the component of spliceosomes.

The RNA segments joined to one another by spliceosomes are _____.

Exons are expressed regions.

Translation occurs in the _____.

Ribosomes, the sites of translation, are found in the cytoplasm.

After an RNA molecule is transcribed from a eukaryotic gene, what are removed and what are spliced together to produce an mRNA molecule with a continuous coding sequence?

This RNA processing does not occur in bacterial cells.

Introns, intervening sequences, are removed and the exons, expressed sequences, are spliced together.

Alternative RNA splicing _____.

A. increases the rate of transcription

B. can allow the production of proteins of different sizes and functions from a single gene

C. can allow the production of similar proteins from different RNAs

D. is a mechanism for increasing the rate of translation

B. can allow the production of proteins of different sizes and functions from a single gene

Use this model of a eukaryotic transcript to answer the following question. E = exon and I = intron

Which components of the previous molecule will also be found in mRNA in the cytosol?

Locations of the processes involved in protein synthesis

In eukaryotic cells, the processes of protein synthesis occur in different cellular locations.

Drag the labels to the appropriate targets to identify where in the cell each process associated with protein synthesis takes place.

What occurs during some key processes of protein synthesis?

Match these key processes involved in protein synthesis to descriptions of what occurs at each step.

Where are cytoplasmic and secreted proteins made?

Both cytoplasmic and secreted proteins can only be synthesized in the presence of a ribosome. This diagram shows the two kinds of ribosomes:

  • free ribosomes, which are found in the cytoplasm
  • bound ribosomes, which are found on the membrane of the rough endoplasmic reticulum (ER)

Which statement correctly describes where cytoplasmic and secreted proteins are synthesized?

A. Both cytoplasmic and secreted proteins are synthesized on free ribosomes.

B. Cytoplasmic proteins are synthesized on free ribosomes, whereas secreted proteins are synthesized on ribosomes bound to the rough ER.

C. Cytoplasmic proteins are synthesized on ribosomes bound to the rough ER, whereas secreted proteins are synthesized on free ribosomes.

D. Both cytoplasmic and secreted proteins are synthesized on ribosomes bound to the rough ER.

B. Cytoplasmic proteins are synthesized on free ribosomes, whereas secreted proteins are synthesized on ribosomes bound to the rough ER.

Roles of RNA in protein synthesis in eukaryotes

RNA plays important roles in many cellular processes, particularly those associated with protein synthesis: transcription, RNA processing, and translation.

Drag the labels to the appropriate bins to identify the step in protein synthesis where each type of RNA first plays a role. If an RNA does not play a role in protein synthesis, drag it to the “not used in protein synthesis” bin.

In eukaryotes, pre-mRNA is produced by the direct transcription of the DNA sequence of a gene into a sequence of RNA nucleotides. Before this RNA transcript can be used as a template for protein synthesis, it is processed by modification of both the 5' and 3' ends. In addition, introns are removed from the pre-mRNA by a splicing process that is catalyzed by snRNAs (small nuclear RNAs) complexed with proteins.

The product of RNA processing, mRNA (messenger RNA), exits the nucleus. Outside the nucleus, the mRNA serves as a template for protein synthesis on the ribosomes, which consist of catalytic rRNA (ribosomal RNA) molecules bound to ribosomal proteins. During translation, tRNA (transfer RNA) molecules match a sequence of three nucleotides in the mRNA to a specific amino acid, which is added to the growing polypeptide chain.

RNA primers are not used in protein synthesis. RNA primers are only needed to initiate a new strand of DNA during DNA replication.

The role of RNA primers

DNA synthesis (replication) and RNA synthesis differ in their needs for primer molecules.

  • In DNA replication, DNA polymerase cannot initiate the formation of a new strand of DNA directly from DNA nucleotides alone. Instead, the process requires an RNA primer to which the nucleotides of the new DNA strand attach.
  • In RNA synthesis, in contrast, RNA polymerase can initiate the formation of a new strand of RNA without any primers.

How do tRNA and rRNA function in protein synthesis?

Both tRNA (transfer RNA) and rRNA (ribosomal RNA) play essential roles in protein synthesis.

Which two statements correctly describe the roles of tRNA and rRNA in protein synthesis?

A. rRNA is the major structural component of ribosomes and is involved in binding both mRNA and tRNAs.

B. tRNAs implement the genetic code, translating information from a sequence of nucleotides to the sequence of amino acids that make up a protein.

C. tRNA transfers a nucleotide sequence from the DNA in the nucleus to the site of protein synthesis in the cytoplasm.

D. rRNA has many variations, each of which binds a specific amino acid.

What is the role of mRNA in protein synthesis?

mRNA (messenger RNA) plays a key role in protein synthesis as the intermediate between the information encoded by a sequence of bases in DNA (a gene) and the sequence of amino acids that make up the protein product.

Which three statements correctly describe the role that mRNA plays in protein synthesis in eukaryotes?

A. mRNA is produced only after the steps of RNA processing.

B. mRNA is the template for protein synthesis in translation.

C. mRNA links together amino acids, forming a polypeptide chain.

D. mRNA carries genetic information from the nucleus to the cytoplasm.

E. mRNA is the immediate product of transcription.

snRNAs and RNA processing

One stage of RNA processing in eukaryotes involves the removal of introns--non-coding regions interspersed within the coding regions of the pre-mRNA. In this RNA splicing process, the machinery that catalyzes the removal of introns (called the spliceosome) is composed of proteins and snRNAs (small nuclear RNAs).

The snRNAs (and associated proteins) have two functions in the splicing process:

  • to bind to specific sequences of RNA that specify the location of the intron in the pre-mRNA, and
  • to catalyze the splicing process itself.

Martian Part 1

Life as we know it depends on the genetic code: a set of codons, each made up of three bases in a DNA sequence and corresponding mRNA sequence, that specifies which of the 20 amino acids will be added to the protein during translation.

Imagine that a prokaryote-like organism has been discovered in the polar ice on Mars. Interestingly, these Martian organisms use the same DNA → RNA → protein system as life on Earth, except that

  • there are only 2 bases (A and T) in the Martian DNA, and
  • there are only 17 amino acids found in Martian proteins.

Based on this information, what is the minimum size of a codon for these hypothetical Martian life-forms?

F. The answer cannot be determined from the information provided.

In the most general case of x bases and y bases per codon, the total number of possible codons is equal to x y .

In the case of the hypothetical Martian life-forms, is the minimum codon length needed to specify 17 amino acids is 5 (2 5 = 32), with some redundancy (meaning that more than one codon could code for the same amino acid).

For life on Earth, x = 4 and y = 3 thus the number of codons is 4 3 , or 64. Because there are only 20 amino acids, there is a lot of redundancy in the code (there are several codons for each amino acid).

Martian Part 2

A simple mathematical equation can correctly express the maximum number of codons that can be constructed from x different bases, with a codon length ofy bases. Recall that for life on Earth,

  • there are 4 different bases (A, T, G, and C),
  • a codon is 3 bases long, and
  • there are a total of 64 possible codons that specify the 20 different amino acids (some amino acids are specified by more than one amino acid). This chart shows this redundancy in the genetic code for life on Earth.

Which of the following equations can be used to calculate the maximum number of codons (N) that can be constructed from x different bases when there are y bases per codon?


16.2 Prokaryotic Gene Regulation

In this section, you will explore the following question:

  • What are operons and what are the roles of activators, inducers, and repressors in regulating operons and gene expression?

Connection for AP ® Courses

The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. Simply stated, if a cell does not transcribe the DNA’s message into mRNA, translation (protein synthesis), does not occur. Bacterial genes are often organized into common pathways or processes called operons for more coordinated regulation of expression. For example, in E. coli, genes responsible for lactose metabolism are located together on the bacterial chromosome. (The operon model includes several components, so when studying how the operon works, it is helpful to refer to a diagram of the model. See Figure 16.3 and Figure 16.4.) The operon includes a regulatory gene that codes for a repressor protein that binds to the operator, which prevents RNA polymerase from transcribing the gene(s) of interest. An example of this is seen in the structural genes for lactose metabolism. However, if the repressor is inactivated, RNA polymerase binds to the promoter, and transcription of the structural genes occurs.

There are three ways to control the transcription of an operon: inducible control, repressible control, and activator control. The lac operon is an example of inducible control because the presence of lactose “turns on” transcription of the genes for its own metabolism. The trp operon is an example of repressible control because it uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase. If tryptophan is not needed by the cell, the genes necessary to produce it are turned off. Activator control (typified by the action of Catabolite Activator Protein) increases the binding ability of RNA polymerase to the promoter. Certain genes are continually expressed via this regulatory mechanism.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP ® Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.B Expression of genetic information involves cellular and molecular mechanisms.
Essential Knowledge 3.B.1 Gene regulation results in differential gene expression, leading to cell specialization
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively
Learning Objective 3.21 The student can use representations to describe how gene regulation influences cell products and function.
Essential Knowledge 3.B.2 A variety of intercellular and intracellular signal transmissions mediate gene expression.
Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively.
Learning Objective 3.23 The student can use representations to describe mechanisms of the regulation of gene expression.

Teacher Support

When discussing the operons with students, challenge them to think about what would happen if there were a gene mutation that disrupted the function of one of the proteins that controls transcription of the operon. For example, if the repressor protein in the lac operon has a mutation that prevents it from binding to lactose, then the repressor will remain bound to the operator and will prevent transcription of the operon even in the presence of lactose. This video describes two other examples of mutations in the lac operon.

Introduce the regulation of transcription in the lac operon using visuals such as this video.

The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons . For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac) operon.

In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers. Repressors are proteins that suppress transcription of a gene in response to an external stimulus, whereas activators are proteins that increase the transcription of a gene in response to an external stimulus. Finally, inducers are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate.

The trp Operon: A Repressor Operon

Bacteria such as E. coli need amino acids to survive. Tryptophan is one such amino acid that E. coli can ingest from the environment. E. coli can also synthesize tryptophan using enzymes that are encoded by five genes. These five genes are next to each other in what is called the tryptophan (trp) operon (Figure 16.3). If tryptophan is present in the environment, then E. coli does not need to synthesize it and the switch controlling the activation of the genes in the trp operon is switched off. However, when tryptophan availability is low, the switch controlling the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized.

A DNA sequence that codes for proteins is referred to as the coding region. The five coding regions for the tryptophan biosynthesis enzymes are arranged sequentially on the chromosome in the operon. Just before the coding region is the transcriptional start site . This is the region of DNA to which RNA polymerase binds to initiate transcription. The promoter sequence is upstream of the transcriptional start site each operon has a sequence within or near the promoter to which proteins (activators or repressors) can bind and regulate transcription.

A DNA sequence called the operator sequence is encoded between the promoter region and the first trp coding gene. This operator contains the DNA code to which the repressor protein can bind. When tryptophan is present in the cell, two tryptophan molecules bind to the trp repressor, which changes shape to bind to the trp operator. Binding of the tryptophan–repressor complex at the operator physically prevents the RNA polymerase from binding, and transcribing the downstream genes.

When tryptophan is not present in the cell, the repressor by itself does not bind to the operator therefore, the operon is active and tryptophan is synthesized. Because the repressor protein actively binds to the operator to keep the genes turned off, the trp operon is negatively regulated and the proteins that bind to the operator to silence trp expression are negative regulators .


Mitochondrial Machineries for Protein Import and Assembly

Nils Wiedemann and Nikolaus Pfanner
Vol. 86, 2017

Abstract

Mitochondria are essential organelles with numerous functions in cellular metabolism and homeostasis. Most of the >1,000 different mitochondrial proteins are synthesized as precursors in the cytosol and are imported into mitochondria by five transport . Read More

Figure 1: Overview of the five major protein import pathways of mitochondria. Presequence-carrying preproteins are imported by the translocase of the outer mitochondrial membrane (TOM) and the presequ.

Figure 2: The presequence pathway into the mitochondrial inner membrane (IM) and matrix. The translocase of the outer membrane (TOM) consists of three receptor proteins, the channel-forming protein To.

Figure 3: Role of the oxidase assembly (OXA) translocase in protein sorting. Proteins synthesized by mitochondrial ribosomes are exported into the inner membrane (IM) by the OXA translocase the ribos.

Figure 4: Carrier pathway into the inner membrane. The precursors of the hydrophobic metabolite carriers are synthesized without a cleavable presequence. The precursors are bound to cytosolic chaperon.

Figure 5: Mitochondrial intermembrane space import and assembly (MIA) machinery. Many intermembrane space (IMS) proteins contain characteristic cysteine motifs. The precursors are kept in a reduced an.

Figure 6: Biogenesis of β-barrel proteins of the outer mitochondrial membrane. The precursors of β-barrel proteins are initially imported by the translocase of the outer membrane (TOM), bind to small .

Figure 7: The dual role of mitochondrial distribution and morphology protein 10 (Mdm10) in protein assembly and organelle contact sites. Mdm10 associates with the sorting and assembly machinery (SAM) .

Figure 8: Multiple import pathways for integral α-helical proteins of the mitochondrial outer membrane. The precursors of proteins with an N-terminal signal anchor sequence are typically inserted into.

Figure 9: The mitochondrial contact site and cristae organizing system (MICOS) interacts with protein translocases. MICOS consists of two core subunits, Mic10 and Mic60. Mic10 forms large oligomers th.


Translation Assembles a Specific Protein According to the mRNA Code

Floating in the cell cytosol are amino acids and small RNA molecules called transfer RNA or tRNA. There is a tRNA molecule for each type of amino acid used for protein synthesis.

When the ribosome reads the mRNA code, it selects a tRNA molecule to transfer the corresponding amino acid to the ribosome. The tRNA brings a molecule of the specified amino acid to the ribosome, which attaches the molecule in the correct sequence to the amino acid chain.

The sequence of events is as follows:

  1. Initiation. One end of the mRNA molecule binds to the ribosome.
  2. Translation. The ribosome reads the first codon of the mRNA code and selects the corresponding amino acid from the tRNA. The ribosome then reads the second codon and attaches the second amino acid to the first one.
  3. Completion. The ribosome works its way down the mRNA chain and produces a corresponding protein chain at the same time. The protein chain is a sequence of amino acids with peptide bonds forming a polypeptide chain.

Some proteins are produced in batches while others are synthesized continuously to meet the ongoing needs of the cell. When the ribosome produces the protein, the information flow of the central dogma from DNA to protein is complete.


Question: 1. Which Of The Following Is The Definition Of A Gene? The RNA Component Of Ribosomes RNA That Carries A Protein-building Message A Unit Of Information Encoded In The Sequence Of Nucleotide Bases In DNA RNA That Delivers Amino Acids To A Ribosome During Translation 2. In Gene Expression, A Gene Is Select Answer Into MRNA, Which Is Then Select Answer .

RNA polymerase assembles a strand of mRNA complementary to the noncoding strand of DNA.

RNA polymerase assembles a strand of mRNA complementary to the coding strand of DNA.

RNA polymerase binds to a gene's promoter.

RNA polymerase moves over the gene and unzips the double helix to form a "transcription bubble."

5. Before mRNA exits the nucleus, it is modified to remove select answer and keep select answer select answer are three nucleotide units of information in mRNA that specifies a particular amino acid. They correspond to complementary sets of three nucleotides on tRNA called select answer

Which of the following codons is called the "start" codon?

Where does the transcription of DNA into mRNA occur in eukaryotes?

Where does translation of mRNA into polypeptides occur?

Which of the following amino acids is carried by the tRNA that initiates translation?

Which of the following are stages of translation? Select all that apply.

A tRNA binds to the second codon and its carried amino acid forms a peptide bond with methionine.

Ribosomal subunits and a tRNA-carrying methionine converge on the start codon of an mRNA.

As the ribosome moves from codon to codon, amino acids brought by successive tRNAs to the ribosome form a growing polypeptide.

When the ribosome reaches a stop codon, its subunits detach, and the mRNA and new polypeptide are released.

The binding of a tRNA to the third codon causes the ribosome to release the first tRNA and move to the next codon.

Which of the following mutations can cause a single amino acid difference during the translation of mRNA into protein?

Mutations in regulatory sites

How can transcription factors influence the transcription of DNA? Select all that apply.

Enhance transcription by helping RNA polymerase bind to promoters

Inhibit transcription by blocking the progress of RNA polymerase along a DNA molecule

Inhibit translation by preventing the binding of mRNA to ribosomes

Inhibit transcription by preventing RNA polymerase from binding to promoters

Which of the following defines a master regulator?

A gene whose expression triggers a gene expression cascade that ultimately changes cells in a lineage to more differentiated types

A condensed, inactivated X chromosome in the body cell of a female mammal

A technique of introducing a mutation that disables expression of a gene in an organism

A regulatory protein that influences transcription by binding directly to DNA

Which of the following causes epigenetic modifications to DNA that affect gene expression without changing the DNA sequence?


CircRNA biology

CircRNAs are single-stranded covalently closed circular RNA molecules generated from a broad array of genomic regions, ranging from intergenic, intronic and coding sequences to 5′- or 3′-untranslational sequences (Chen & Yang, 2015 Memczak et al., 2013). Two models of circRNA biosynthesis have been proposed, both involving back-splicing catalyzed by the spliceosomal machinery. The first of the two, the “exon skipping” model, begins with classical splicing to generate linear RNA. The downstream exon links to the upstream exon, with one or more exons being skipped the skipped exons then further back-splice to form precursor circRNAs, which undergo further processing to become mature circRNAs. (B) The second of the two models, the “direct back-splicing” circularization model, is related mostly to complementary motifs in this, the complementary pairing RNA back-splices to produce a precursor circRNA together with an exon-intron(s)-exon intermediate, and the latter is further processed to produce a linear RNA with skipped exons or which is targeted for degradation (Ashwal-Fluss et al., 2014 Jeck & Sharpless, 2014 Lasda & Parker, 2014) (Fig. 1).

Figure 1: Proposed circRNA formation models.

To date, four functions have been defined for the circRNAs. First, circRNAs harbor miRNA complementary sequences, facilitating their combination with and ability to adjust the biological function of a large number of miRNAs by functioning as molecular sponges. A specific example of this is the circMTO1, which acts as the sponge of miR-9 to suppress hepatocellular carcinoma progression (Han et al., 2017). Furthermore, one circRNA may combine with several kinds of miRNAs for instance, circHIPK3 has been reported to combine with 9 miRNAs (miR-29a, miR-29b, miR-124, miR-152, miR-193a, miR-338, miR-379, miR-584 and miR-654) to synergistically inhibit cell proliferation (Zheng et al., 2016). Second, circRNAs can directly regulate transcription, splicing and expression of a parental gene. The exon-intron circRNAs (EIciRNAs) are examples of this regulation, interacting with RNA polymerase II and enhancing transcription of their parental genes (Li et al., 2015). Third, circRNAs directly interact with proteins, such as the ternary complex circ-Foxo3-p21-CDK2, which serves to arrest the function of CDK2 and interrupt cell cycle progression (Du et al., 2016). However, studies indicate that one circRNA might simultaneously harbor more than one of the above functions, which is evidenced by the finding that circ-Amotl1 can act both as a sponge for miR-17 to promote cell proliferation, migration and wound healing and as a target for protein binding (c-Myc, Akt1 and PDK1) to promote the proliferation of tumor cells and enhancing cardiac repair (Yang et al., 2017a Yang et al., 2017c Zeng et al., 2017). Fourth, Dong et al. developed a computational pipeline (CIRCpseudo), and indicated that stabilized circRNAs could form circRNA pseudogenes by retrotranscribing and integrating into the genome (Dong et al., 2016). However, there is only one paper on circRNA’s formation of pseudogenes, which does not explain the specific mechanism of it. We need more evidence to prove this idea. More interestingly, the latest research is hinting at a potential fourth function of circRNAs: translation (Fig. 2), which opens a new field for researchers to explore the biological functions of circRNA-derived proteins. For detailed information on the biology of circRNA, please see the review written by Li X et al. (Barrett & Salzman, 2016 Chen, Chen & Chuang, 2015 Li, Yang & Chen, 2018).

Figure 2: Functions of circRNAs.


Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Additional file 1: Supplementary Figures.

Fig. S1 fRIP-Seq optimization. Fig. S2 The effect of transcript localization on reassociation and fRIP-Seq enrichment. Fig. S3 Validation of fRIP-Seq antibodies by western blot. Fig. S4 ADAR preferentially binds to Alu elements and adjacent regions. Fig. S5 fRIP-Seq broadly agrees with CLIP-Seq. Fig. S6 fRIP-Seq targeted transcripts are affected by protein depletion. Fig. S7 fRIP-Seq coverage displays light positional biases. Fig. S8 Nuclear fRIP-Seq matches whole cell fRIP-Seq. Fig. S9 The cohesin subunit STAG2 specifically binds a small cohort of transcripts encoding centrosome-localized proteins. Fig. S10 lncRNA association with CAPs is more specific than CAP association with mRNAs. Fig. S11 DNMT1 binds a GC-rich motif in lncRNAs. Fig. S12 UUUUAAAA is a polarizing, conserved, 3’ motif. Fig. S13 K-mers predict RNA binding preferences. Fig. S14 Transposable elements correlate with RNA binding. Fig. S15 Proteins with both fRIP and ChIP suggest a weak relationship. Fig. S16 Chromatin marks correlate with gene abundance. Fig. S17 fRIP versus chromatin mark correlations are FPKM-driven. Fig. S18 Protein binding to RNA relates to local chromatin over the gene body. (PDF 22097 kb)


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