Cell Bio Exam 2 (Shannon MST)

Given the structure of the nitrogenous bases, it seems probable that DNA contains thymine instead of uracil beacuse

If cytosine is reanimated, altered bases can be detected and removed

A difference between initiation of translation in prokarytoes and eukaryotes is

In prokaryotes the ribosome recognizes the RBS, whereas in eukaryotes the ribosome recognizes the 5' cap

The size of the plasma membrane

Is about 6-10nm thick

In bacterial cells, the tryptophan operon encodes the genes needed to synthesize tryptophan. What happens when the concentration of tryptophan inside a cell is high?

It activates the tryptophan repressor, which shuts down expression of the tryptophan operon. The tryptophan repressor is always present in the bacterial cell and its conformation depends on the presence or absence of the amino acid tryptophan. If tryptophan is present, it will bind to the repressor and this conformation is able to bind to the operator sequence of the Trp operon to turn off transcription. If tryptophan is absent, the repressor protein is no longer able to bind to the operator, which allows transcription to proceed. In this way, the concentration of tryptophan provides feedback inhibition of the Trp operon, using the tryptophan repressor as the on/off switch. The figure provides an overview of this regulation.

The binding of a neutrophil (type of white blood cell) to the cells lining a blood vessel (endothelial cells) is mediated by interaction between

Recognition of a specific carbohydrate group on a cell surface by lectin

The sigma subunit of bacterial RNA polymerase ___________________.

Recognizes promoter sites in the DNA

c-Met is an oncogene that contributes to the development of certain cancers by triggering cell division and tumor growth. In a 2009 article, Yan and colleagues found regions in the 3' untranslated region of c-Met mRNA complementary to microRNA-1/206. In addition, higher levels of microRNA-1/206 were associated with slower cell proliferation. What is a likely explanation for the inverse correlation between microRNA-1/206 and cell proliferation?

MicroRNA-1/206 targets c-Met mRNA for destruction via RISC. In their 2009 article (MicroRNA-1/206 Targets c-Met and Inhibits Rhabdomyosarcoma Development), Yan and colleagues found an inverse correlation between microRNA-1/206 and c-Met protein levels. MicroRNAs are noncoding regulatory RNAs that down-regulate gene expression by binding complementary mRNAs and destroying them via the RNA-induced silencing complex (RISC). Researchers use double-stranded RNAs to prevent the expression of selected genes, a technique known as RNA interference.

In eukaryotes, multiple genes can be expressed simultaneously by

the binding of a specific transcriptional regulator to several genes. In eukaryotes, gene expression is often decided by a committee of transcriptional regulators. A single transcriptional regulator can act as the final voice in the committee to turn on expression by coordinated binding to several genes at once.

What is the main function of the TATA-binding protein?

to promote initiation of transcription The TATA-binding protein is a subunit of RNA polymerase II that helps initiate transcription. When the TATA-binding protein binds to the TATA sequence in DNA, the protein causes the DNA helix to bend. The kink that occurs is thought to signal assembly of the transcriptional complex and initiation of transcription.

A primary transcript (immature, non-processed) single-stranded RNA molecule has the following nucleotide composition: 30% A, 20% G, 24% C, and 26% U. What is the nucleotide composition of the double-stranded DNA molecule from which it was transcribed?

28% A, 22% G, 22% C, and 28% T DNA contains the bases adenine (A), thymine (T), guanine (G), and cytosine (C). On the other hand, RNA contains A, G, C, and uracil (U). Because the DNA molecule is double-stranded, the nucleotide composition of both strands must be taken into account when compared to the single-stranded nature of RNA. The template DNA strand that encodes this RNA molecule would contain: 30% T, 20% C, 24% G, and 26% A. The nontemplate strand, sometimes called the "sense strand" of the DNA, which is complementary to the template strand, would contain: 30% A, 20% G, 24% C, and 26% T. The double helix would thus contain an average of these values: 28% A, 22% G, 22% C, and 28% T.

The sequence of the coding strand of a DNA molecule (that is, the DNA strand that contains the codons specifying the protein sequence) is 5'-CGGATGCTTA-3'. What is the sequence of the RNA made from this DNA?

5'-CGGAUGCUUA-3' One of the major chemical differences between DNA and RNA is the presence of thymine (not uracil) in DNA and the presence of uracil (not thymine) in RNA. If the sequence of the coding strand of a DNA molecule (that is, the DNA strand that contains the codons specifying the protein sequence) is 5'-CGGATGCTTA-3', then the sequence of the RNA made from this DNA would be 5'-CGGAUGCUUA-3'. Transcription generates an antiparallel and complementary strand of nucleic acid. When a single-stranded nucleic acid sequence is written out, it is convention to write the sequence in the 5'-to-3' direction. Therefore, 5'-CGGAUGCUUA-3' RNA is complementary to 5'-CGGATGCTTA-3' DNA. Review the figure below to help you keep track of coding versus template strands of DNA and how RNA is related to each.

The CAP activator protein and the Lac repressor both control the Lac operon (see Figure below). Where does the CAP protein bind?

Activator binding site

TFIIH is required for transcription to begin because it

Acts as a helicase to open up the DNA template

Which of the following events occur when TATA-binding protein binds to the DNA?

An eight-stranded β-sheet domain of the TATA-binding protein lies on the DNA helix. The DNA backbone is kinked nearly 90 degrees.Binding leads to assembly of the rest of the transcription complex at the initiation site. The TATA-binding protein contains an eight-stranded β-sheet domain that lies on the DNA helix. Binding of the protein causes the DNA to bend nearly 90 degrees. This kink in the DNA is thought to lead to assembly of the transcription complex at the initiation site, leading to transcription at the gene. Other subunits separate the two strands of DNA.

Ribozymes

Are RNAs with catalytic activity

Porins

Are found in bacterial membranes. Have β-sheet structure. Function as channels

Carbohydrates associated with the plasma membrane

Are part of glycolipids Are covalently attached to the extracellular regions of transmembrane proteins. Are involved in cell-cell recognition

The terminator sequence is found where?

At the end of many prokaryotic genes

Choose the statement that is not true regarding the function of bacterial RNA polymerase.

Bacterial RNA polymerase can transcribe along the DNA in either direction. RNA polymerase can only transcribe DNA in the 3'-to-5' direction, resulting in an RNA molecule that always grows in a 5'-to-3' direction. This is the same directionality as DNA synthesis, as both polymers grow by forming new phosphodiester bonds that require a free 3' hydroxyl group to react with the 5' phosphate on the incoming nucleotide. Sometimes the directionality of transcription can be confusing because either DNA strand can serve as the template for transcription. This means that for two adjacent genes, one DNA strand may be the template for the first gene and proceed "left to right" whereas the other DNA strand is the template for the second gene and proceeds "right to left." However, in both cases, the DNA template is read 3' to 5', owing to the antiparallel arrangement of the DNA double helix.

If the lac operon has neither CAP nor repressor bound to it then the bacteria are in which media?

Both glucose and lactose are present in the media

The operator is

Bound by repressor

Which of the following describes the Lac operon in E. coli when lactose, but not glucose, is present in the culture medium?

CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lacoperon is expressed. The expression of the Lac operon is tightly regulated by the type of carbohydrate present in the environment. Glucose is the preferred carbohydrate source and only in its absence will the necessary small molecule, cAMP, be found. cAMP binding to the CAP activator is necessary but not sufficient for the expression of the Lac operon. In addition to low glucose levels, there must also be lactose present in the environment. If this is the case, allolactose, a derivative of lactose, can bind to the Lac repressor and cause it to release from the promoter. Therefore, as outlined in the figure below, the Lac operon is only expressed when glucose is absent and lactose is present because the CAP activator is bound to the promoter, but the Lac repressor is not. This ensures that the genes in the Lac operon are expressed only in the conditions where lactose is the only carbohydrate source available.

Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble?

CGU and CGA

Different cells make different mRNAs because

Cells produce different regulatory transcription factors

Which does not affect gene expression at the post-transcriptional level?

DNA methylation Regulation of gene expression can occur at many points and in many ways. Among the answer choices, only DNA methylation does not occur at the post-transcriptional level. DNA methylation modifies cytosine nucleotides within certain sequences of DNA and heavily methylated genes are not transcribed. Any regulation that occurs after a transcript has been synthesized is considered post-transcriptional.

Researchers often want to isolate a certain type of RNA. For some RNA species, this can be accomplished via affinity chromatography, using beads coated with chains of poly-deoxythymidine (poly-dT). The desired RNA will stick to the beads while unwanted RNAs will flow through the column. The retained RNA can then be eluted.What RNA species can be purified using this method?

Eukaryotic mRNA In eukaryotes (but not prokaryotes), mRNAs receive several modifications, such as a 5' methylguanosine cap and a 3' poly-A tail. These modifications increase mRNA stability and aid nuclear export. The poly-A tail allows researchers to isolate eukaryotic mRNAs away from noncoding RNAs, which lack this feature.

RNA polymerase, like DNA polymerase, requires a primer to provide a 3'OH before synthesis can begin.

False

The cell cortex is a region surrounding the nucleus that is rich in microtubules.

False

Transcriptional regulators usually interact with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix.

False

The 5' UTR of both prokaryotic and eukaryotic mRNAs can regulate translation by

Forming a hairpin loop structure

Termination of transcription of mRNA in eukaryotes

Happens after a conserved cleavage site is transcribed in the mRNA

During the process of transcription, where does the energy that drives phosphodiester bond formation come from?

Hydrolysis of NTPs to NMPs

Many antibiotics work by inhibiting bacterial protein synthesis. Investigators have isolated a promising new compound and wish to determine its mechanism of action. Using a cell-free translation system similar to the ones originally used to deduce the genetic code, the researchers incubate their drug with the synthetic polynucleotide 5'-AUGUUUUUUUUU.In the absence of the drug, this polynucleotide directs the synthesis of the peptide Met-Phe-Phe-Phe. When the drug is added, only the peptide Met-Phe is produced. Based on this observation, which is most likely the mechanism of action of this potential new antibiotic?

It blocks translocation of the large ribosomal subunit, preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome. This antibiotic likely blocks translocation of the large ribosomal subunit (step 3 in the figure below), preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome. The two-amino-acid peptide can form because the initiator tRNA that carries methionine will bind to the P site, and the A site can accomodate the tRNA that recognizes UUU (which codes for phenylalanine). Because the ribosome can't translocate, no additional amino acids can be added. Translocation inhibitors are a known mechanism of action for antibiotics. An example of an antibiotic that uses this mode of action is cycloheximide.

What is the function of a miRNA?

It regulates gene function

Which of the following statements concerning leucine zipper protein dimerization and DNA binding is correct?

Leucine zipper proteins function as a dimer with both subunits making contact with the sequence-specific DNA site. Leucine zipper proteins dimerize through interactions between the leucine zipper domain α helices on two subunits. The helices contain hydrophobic side chains, including many leucine side chains, which pack tightly together. The α helices extend around both sides of the DNA molecule. The polar side chains in these regions of the α helices make hydrogen bonds with specific bases in the DNA major groove, leading to sequence-specific binding.

MyoD is a transcriptional regulator involved in differentiation of muscle cells. Which of the following are true about the regulation of gene expression by MyoD?

MyoD is usually expressed only in muscle cells. MyoD requires other proteins to activate transcription. MyoD can cause some cells, such as fibroblasts, to express muscle specific genes when artificially expressed

The capping of eukaryotic mRNA

Occurs at the 5' end. Is the addition of a 7-methylguanosine. Helps the ribosome recognize the message for translation

Which of these is an evolutionarily ancient defense mechanism that protects a variety of organisms from viral infection?

RNA interference (RNAi) RNA interference (RNAi) is an evolutionarily ancient defense mechanism that protects a variety of organisms from viral infection. Recall that many viruses have RNA genomes; therefore, having a mechanism to selectively target foreign RNA is advantageous to cells. RNAi has been found to occur in a wide range of life-forms, including plants, worms, and even single-celled fungi, and can protect these organisms, which lack a true immune system, from infection.

The flow of information from DNA to protein....

Requires RNA. Is the central dogma. Requires translation

Formation of the translation initiation complex in eukaryotes

Requires proteins called eukaryotic initiation factors (eIFs)

What is false regarding codons in mRNA molecules?

Some codons code for more than one amino acid. The nucleotide sequence of an mRNA is translated into the amino acid sequence of a protein via the genetic code. This code is made up of three-nucleotide codons that are recognized in a complementary fashion by the anticodon on a tRNA molecule, which is responsible for bringing the appropriate amino acid into the growing polypeptide. None of the codons code for more than one amino acid, even though some amino acids are coded for by multiple codons.

Suppose the 3' splice site is mutated from AGG to ACG. Predict the consequence of this mutation.

Splicing would begin but not be properly completed if the 3' splice site is altered. The 3' splice site is not used in the first several steps of splicing, so the beginning of splicing could still occur. The U1 snRNP binds to the 5' splice site, and BBP and U2AF bind the branch-point site. The U2 snRNP then binds the branch-point site and the U4/U6 and U5 snRNPs bind to the 5' splice site. At this point, the adenine in the branch-point site attacks the 5' splice site and the 5' end of the intron binds the branch-point adenine to form a lariat. The 3' end of the first exon would now attack the 3' splice site, but this requires the conserved sequence. If this sequence is mutated, the exon is unable to attack this 3' splice site and it will not be used. This could either block splicing or the first exon will search for the next available 3' splice site. The mutated 3' splice site could be skipped over and the second exon and next intron could be removed.

You are studying a mRNA that is regulated by a specific miRNA. You hypothesize that the regulatory sequence is in the 3'UTR. If your hypothesis is correct, then which of the following would be true?

The RISC complex would be targeted to the 3'end of the mRNA

Which of the following is true of a hydropathy analysis of a transmembrane protein?

The alpha helices that are embedded in the lipid bilayer can be predicted

You are studying a set of mouse genes whose expression increases when cells are exposed to the steroid hormone cortisol, and you believe that the same cortisol-responsive receptor protein regulates all of these genes. Which of the following statements below should be true if your hypothesis is correct?

The cortisol-responsive genes share a DNA sequence in their regulatory regions that binds the cortisol-bound receptor protein.

Which of the following statements is supported by the information in this image and is consistent with your knowledge regarding genomic architecture in prokaryotes and eukaryotes?

The eukaryotic cell must have a nuclear spliceosome to remove introns from RNA. The eukaryotic cell must have a nuclear spliceosome to remove introns from RNA because eukaryotic protein-coding genes contain both exons and introns (noncoding sequences). By contrast, bacterial genes lack introns and hence do not need splicing. When eukaryotic mRNAs are spliced, this process occurs in the nucleus and, therefore, before ribosomal translation in the cytoplasm. Bacterial cells do not have a nucleus and since they also do not require splicing, they are able to undergo simultaneous transcription and translation of their genes.

Which of the following statements most accurately describes the expression of the repressor protein of the tryptophan operon?

The gene for the tryptophan repressor is expressed constitutively. The Trp operon contains the genes that code for the necessary enzymes to synthesize the amino acid tryptophan from precursors. If tryptophan is low in a cell, the operon is expressed so that the cell can synthesize the tryptophan it needs. If tryptophan in the cell is high, then the operon is turned off. The Trp repressor is a molecular "switch" that controls gene expression at the Trp operon. If tryptophan binds to the Trp repressor, then the repressor adopts a conformation that allows it to bind to the promoter region of the Trp operon and prevent transcription. In the absence of tryptophan, the Trp repressor is inactivated and it can no longer bind to the promoter, allowing transcription to take place. This mechanism of regulation is depicted in the figure below. For the Trp repressor to be able to function as the molecular switch, it must always be present in the cell so that it can quickly respond to changes in the concentration of tryptophan in the cell.

What would happen to the helix-3 interaction with DNA if a mutation occurred that altered this adenine (as shown) to guanine?

The integrity of the interaction would decrease because one of the two hydrogen bonds would not be able to form. If guanine replaced adenine, the integrity of the protein-DNA interaction would decrease because one of the two hydrogen bonds would not be able to form. This is because adenine contains an amino group hydrogen atom that interacts with an asparagine carbonyl oxygen atom; however, this interaction would not form if guanine were present in place of adenine. If guanine were present, there would actually be a repulsion between the partially negatively charged carbonyl group oxygen of the asparagine residue and the partially negatively charged carbonyl group oxygen of the guanine nitrogenous base. Hydrogen bonds form when there is a favorable interaction between a partial negative charge (from electronegative atoms such as O or N) and a partial positive charge, such as a hydrogen atom covalently bonded to a more electronegative atom.

Which of the following statements is true?

The lifetime of a eukaryotic mRNA is positively correlated with the length of the polyA tail. Many eukaryotic mRNAs have a longer lifetime than bacterial mRNAs. The longer the lifetime of an mRNA, the more protein it can produce. An important level of regulation of gene expression is determined by the lifespan of an RNA molecule because the longer it persists, the more protein it can produce. Many factors influence how long an individual mRNA persists in a cell, including what type of cell produced it. In bacteria, most mRNAs only last a few minutes. Conversely, in eukaryotes, the range of lifespans is much broader, with some mRNAs lasting for several hours. An important difference between bacteria and eukaryotes is the processing of the ends of eukaryotic mRNAs: the addition of a 5' cap and 3' poly-A tail promotes longer-term stability of these mRNAs. Finally, the sequence of the mRNA itself—primarily a stretch called the 3' untranslated region, which is situated between the 3' end of the protein-coding sequence and the poly-A tail—impacts its longevity.

What is the ultimate fate of an mRNA that is targeted by a microRNA (miRNA)?

The mRNA will be destroyed by nucleases. miRNAs are small RNA molecules that provide a mechanism for post-transcriptional regulation of gene expression by recognizing specific mRNAs through complementary base pairing and preventing their translation. When interacting with an miRNA, the mRNA will be destroyed by nucleases—either within the RISC or by other nucleases. The miRNA itself is not degraded in this process, allowing it to bind to other target mRNAs and trigger their destruction as well. Thus, miRNA-based mRNA destruction can potently inhibit expression of particular genes.

If a cell activates an enzyme to shorten fatty acid tails of membrane lipids from 18 C to 16 C, which would likely result?

The membrane would become more fluid

In bacteria, what would be the consequence of a protein binding to and blocking the ribosomal binding site on an mRNA?

The small ribosomal subunit will not be able to bind to the mRNA, and translation will be inhibited. Translation of bacterial mRNA requires the ribosome-binding site of the mRNA to be exposed so that the ribosome can attach. This site is located immediately upstream of the AUG start codon and the binding of a protein, such as a translation repressor protein shown in the figure below, will block the site and prevent the ribosome from binding to the mRNA. If the ribosome does not bind, translation cannot occur.

To crack the genetic code, researchers introduced synthetic messenger RNAs into in vitro translation systems and determined which proteins were produced from these synthetic mRNAs. mRNAs consisting of poly-UUC led to production of three different proteins: poly-Phe, poly-Ser, and poly-Leu. What best explains this result?

The synthetic mRNA was read in all three reading frames. The genetic code does not change in vitro as compared to in vivo. However, unlike when in vivo, in which translation begins at an initiating methionine start codon, when in vitro, the ribosome can be forced to translate any message in all three reading frames. Thus the UUCUUCUUCUUC message was read three different ways. Starting at the first U, UUC codes for Phe, as shown in the figure. If the ribosome started at the second U, the message was read as repeating UCU codons, so poly-Ser was produced. In the third reading frame, the ribosome read the message as repeating CUU codons, resulting in poly-Leu.

Which of the following statements is not true about the differences between liver cells and kidney cells in the same organism?

They contain different genes. Specialized cells, such as liver and kidney cells, do contain the same genes, but they just express them differently. This is referred to as differential gene expression. We know that all cells in a human are the descendants of an initial cell that was created at fertilization, and so they must be genetically identical to one another. Because most specialized cell types in a multicellular organism contain all the same genes that were present in the fertilized egg that gave rise to them, they retain the instructions necessary to form the whole organism. Thus, cell differentiation is instead achieved by changes in gene expression.

What happens to the miRNAs that are bound in a RISC?

They remain bound to the RISC, where they can target the elimination of multiple mRNAs. When an miRNA is bound to RISC, it remains bound to the RISC and can target the elimination of multiple mRNAs. This feature allows a single miRNA molecule to inactivate many mRNA molecules. The stable association of miRNA with RISC allows for persistent enforcement of translational silencing by binding to, and removing, the specific mRNA whenever it appears in the cytosol.

Which of the following statements about eukaryotic activator proteins is false?

They stimulate transcriptional initiation by opening up the double helix. Eukaryotic activator proteins do not help open up the double helix. However, they can help initiate gene transcription through other mechanisms, as shown in the figure. For example, activator proteins can recruit enzymes that will modify histones, thereby enabling them to bind other proteins necessary for transcription initiation. Also, chromatin-remodeling complexes can reconfigure chromatin to make it more accessible to transcription machinery. They do this by making the TATA box more accessible, for example.

What is true of eukaryotic mRNAs?

Transcription of the 3' end includes a conserved cleavage site.They are processed by enzymes that ride on the phosphorylated tail of RNA polymerase II.They are translated after they are exported from the nucleus. Unlike prokaryotes, where transcription and translation can occur simultaneously, these two events are separated in time and space in eukaryotes. In eukaryotes, transcription takes place in the nucleus and the transcript must also undergo processing here to become a mature mRNA. After this occurs, the mRNAs are exported to the cytosol where they interact with ribosomes to carry out translation.

A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule's synthesis is completed.

True

FRAP can be used to study either lipid or protein dynamics.

True

Operons are typically found in prokaryotic cells

True

Soap can disrupt the lipid bilayer.

True

Some membrane proteins function as transporters to move molecules across the membrane.

True

The repressor for the trp operon is active (will prevent transcription) when bound to tryptophan.

True

RNA polymerase

Uses single stranded DNA as a template. Can unwind the DNA helix during transcription. Binds NTPs at the active site.

The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made of the repeating dinucleotide CGCG...?

a peptide containing alternating arginines and alanines The sequence of nucleotides in an mRNA molecule is read consecutively in groups of three, termed codons. In this question, and depending on where translation begins along the repetitive polynucleotide CGCG..., two different codons are possible: CGC and GCG. These two codons specify arginine and alanine, respectively. The peptide produced would therefore contain alternating residues of these two amino acids.An mRNA sequence can be translated in any one of three different reading frames, depending on where the decoding process begins. However, in the cell, and unlike the synthetic example of this question, only one of the three possible reading frames in mRNA specifies the correct protein. A special signal at the beginning of each mRNA molecule sets the correct reading frame—the AUG start translation codon.

What is an operon?

a set of genes transcribed as a single mRNA from a single promoter Operons, a common feature of the prokaryotic genome, are defined by the coordinated expression of their resident genes under the control of a single promoter. Each operon produces a single mRNA that encodes multiple proteins, termed a polycistronic mRNA. This arrangement allows genes whose products function together in the cell, as in a metabolic pathway, to be regulated together. For example, the figure shows the Trp operon, which codes for the enzymes needed to synthesize the amino acid tryptophan.

Within the ribosome, the formation of peptide bonds is catalyzed by what component?

an RNA molecule in the large ribosomal subunit The eukaryotic ribosome is a large complex of four rRNAs and more than 80 small proteins, arranged into two subunits: the large and the small ribosomal subunits. The small ribosomal subunit matches the tRNAs to the codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that covalently link the amino acids together into a polypeptide chain. The peptidyl transferase activity of the ribosome is responsible for formation of the peptide bonds in the growing polypeptide.

The piece of RNA below includes the region that codes the binding site for the initiator tRNA needed in translation.5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′Using a codon chart, determine which amino acid will be on the tRNA that is the first to bind to the A-site of the ribosome?

arginine

To reinforce cell identity, vertebrate cells can methylate which nucleotide?

cytosine that falls next to guanine in the sequence CG DNA methylation occurs in vertebrates on particular cytosine nucleotides located next to a guanine nucleotide in the sequence 5'-CG-3.' This modification is one of the ways that differentiated cells maintain their differentiated identity through rounds of cell division, because heavily methylated genes will not be transcribed. Additionally, methylation patterns are preserved through rounds of DNA replication because the enzyme that carries out methylation uses the pattern found on the parental strand of a newly replicated DNA molecule to add methyl groups to the appropriate cytosine nucleotides on the daughter DNA strand. Maintaining cell memory through DNA methylation is an example of a epigenetic inheritance.

What type of molecule triggers RNA interference (RNAi)?

foreign, double-stranded RNA RNA interference is thought to have evolved as an ancient mechanism for cells to fight infections. Double-stranded RNAs are produced by many viruses and transposable elements, and are thus recognized as "foreign." Double-stranded, foreign RNAs are cut into short pieces, termed siRNAs by Dicer. The siRNAs then interact with RISC proteins, which remove one of the strands of RNA, leaving a single-stranded siRNA complexed to RISC that can then base-pair with complementary foreign RNA molecules, targeting them for destruction.

In eukaryotes, what must assemble at a promoter before RNA polymerase can transcribe a gene?

general transcription factors Unlike prokaryotes, eukaryotic RNA polymerase cannot start transcription by itself. For transcription to begin in eukaryotes, an entire complex of proteins, termed transcription factors, must assemble on the promoter before RNA polymerase can bind and initiate transcription. Transcription factors "tell" RNA polymerase where the start of a gene is and also open the double helix to reveal the template strand so that transcription can initiate. In this way, transcription factors can be thought of as performing a similar role as sigma factor in prokaryotic transcription.

Using a codon chart, determine which amino acid a tRNA with the anticodon 5′-UAG-3′ will carry.

leucine (Leu)

How many different aminoacyl-tRNA synthetases do most organisms have?

one for each amino acid Most organisms have a unique aminoacyl-tRNA synthetase for each amino acid. Because there are 20 common amino acids found in proteins, there are 20 different aminoacyl-tRNA synthetase enzymes. Each aminoacyl-tRNA synthetase must recognize the appropriate amino acid along with the appropriate tRNA molecule. For example, in a tRNA that is specific for the amino acid glutamine, nucleotides in both the anticodon loop and the amino-acid-accepting arm are recognized by the synthetase enzyme.

The figure depicts which of the following mechanisms that cells use to maintain their identity through cell divisions?

positive feedback A master transcription regulator that controls its own expression, as well as the expression of other cell type specific genes, can create a positive feedback loop. Because the regulator is present in the precursor cell before division, the protein will be present in the progeny cells, and thus will drive further expression of the regulator.

Eukaryotic repressor proteins can decrease transcription using which of the following mechanisms?

preventing the assembly of the transcription initiation complex Eukaryotic repressor proteins can act to reduce transcription by inhibiting assembly of the transcriptional initiation complex, or they can recruit histone-modifying complexes like deacetylases, which remove the activating acetyl groups from nearby histones.

Which of the following mechanisms describes how eukaryotic activator proteins can regulate chromatin packaging to enhance transcription?

recruiting chromatin-remodeling complexes to eject or slide nearby nucleosomes Activator proteins in eukaryotes can act to enhance transcription in a variety of ways, but the regulation transcription through chromatin is typically via (1) attraction of histone-modifying complexes that place activating marks (like acetyl groups) on histones, or (2) the recruitment of chromatin-remodeling complexes.

Which macromolecule(s) is/are critical in the active site of the ribosome for catalysis of peptide bond formation?

ribosomal RNA The ribosomal RNA is the critical component in the active site as this site is made of only ribosomal RNA. The protein helps support the RNA but does not participate in the catalysis of peptide bond formation. The ribosomal RNA base-pairs with the tRNA holding the growing polypeptide, helping to position it in the correct orientation. Other RNA nucleotides base-pair with the incoming tRNA to position the amino acids. Further hydrogen-bonding positions the amino acids, facilitating new peptide bond formation.

What is the name of the subunit of bacterial RNA polymerase that recognizes the promoter of a gene?

sigma factor In bacteria, the sigma (σ) factor of RNA polymerase is primarily responsible for recognizing the promoter sequence on the DNA. It is able to "see" the sequence of the promoter, even though the DNA remains a double helix. Upon recognizing the promoter sequence, sigma factor begins to separate the strands of DNA and prevents them from reforming their double-stranded arrangement. As soon as RNA polymerase begins synthesizing the RNA transcript, sigma factor is then released.

What is the source of energy that drives transcription elongation forward?

the hydrolysis of high-energy bonds of ribonucleoside triphosphates The source of energy that drives transcription elongation forward is the hydrolysis of high-energy phosphate bonds of ribonucleoside triphosphates that are being incorporated into the growing RNA molecule. The nucleoside triphosphate is hydrolyzed to yield a nucleoside monophosphate, which forms a phosphodiester bond with the free 3' hydroxyl end of the RNA polymer, and a pyrophosphate molecule, which is subsequently hydrolyzed into two molecules of inorganic phosphate. The breakdown of pyrophosphate into inorganic phosphate renders the polymerization reaction essentially irreversible. Because the energy to drive polymerization is delivered by the nucleoside triphosphates themselves, no additional energy is needed for the catalytic activity of RNA polymerase.

Which is not an example of epigenetic inheritance?

the inheritance of a single point mutation in a gene The inheritance of a single nucleotide point mutation in a gene is not an example of epigenetic inheritance. Epigenetic inheritance involves transmission of gene expression patterns that do not involve a change in nucleotide sequence, for example, DNA methylation. These types of modification allow cell memory to be established from even a short-lived environmental signal.

Several organisms have a homologous protein (inherited from a common ancestor) that is highly similar at the amino acid level. You are comparing the genes that code for these proteins in the different organisms when you note that one of the codon nucleotide positions shows more nucleotide variation than the other nucleotide positions. In which codon nucleotide position do you expect to see the most variability among species?

third nucleotide position The genetic code is redundant, with most amino acids being coded for by several codons. In particular, the third nucleotide position in a codon often differs among codons that code for the same amino acid. Due to some tRNAs tolerating a mismatch at the third position (wobble), these codons may all bind to the same tRNA. Since mutations at this wobble position do not change the amino acid coded for, they are unlikely to change protein structure and hence tend to accumulate over time. In contrast, mutations at the first or second nucleotide position are more likely to change the codon to one that codes for a different amino acid. Mutations that change amino acid sequences will likely change protein structure and may negatively impact protein function. These mutations will be selected against and will not accumulate at the same rate as third-position neutral mutations.