Reading Quiz Ch 7 - 13 Flashcards
The process of gene expression always involves which process(es) described in the central dogma? Why?
a) transcription
b) translation
c) replication
d) transcription and translation
a) transcription
some genes that are expressed are functional RNA genes. The RNAs don’t undergo translation to protein because they do their job in the cell as an RNA
At which step of gene expression can cells amplify the number of copies a protein made from a single gene? Why?
a) both transcription and translation
b) transcription
c) translation
d) neither transcription nor translation
a) both transcription and translation
proteins can be made in large quantities by transcribing many mRNAs from the gene, and then each mRNA can be translated into many copies of the protein. In contrast, if just a few mRNAs are made, only a few copies of the protein are made.
Which nucleic acid often base pairs with itself to fold into complex three-dimensional shapes in the cell? Why?
a) RNA
b) neither RNA nor DNA
c) both RNA and DNA
d) DNA
a) RNA
RNA is often single-stranded and complementary regions will base pair with each other to form secondary and tertiary structures.
What is the difference between the mechanisms of DNA polymerase and RNA polymerase?
DNA polymerase needs a primer to provide a base-paired 3’ –OH to catalyze the polymerization reaction. RNA polymerase does not need a base-paired 3’ –OH, it can join two nucleotides together without a primer.
Why does RNA polymerase make more mistakes than DNA polymerase?
RNA polymerase lacks the ability to proofread its work. If an incorrectly base-paired nucleotide is added, it cannot excise the nucleotide and add the correct one.
Which characteristic of a replicating RNA polymerase allows multiple transcripts to be made simultaneously from the same region of DNA?
The RNA transcript dissociates from the DNA template immediately once they are made. This allows many RNA polymerases to form a “caravan” on the gene, producing many transcripts.
Which RNAs are never translated into protein? What are they collectively called?
tRNA, rRNA, and miRNA
noncoding RNAs
Shown below is a gene with the direction of transcription noted. How does the RNA polymerase know which strand to use as a template for the RNA, and which strand would it choose in this case?
It would use the bottom strand.
RNA polymerase binds to promoter sequences in a specific orientation. The RNA polymerase will then move away from the promoter using the promoter-dictated directionality and uses the 3’ to 5’ strand as a template to make a new RNA in the 5’ to 3’ direction.
What performs the function of bacterial sigma factor in eukaryotes?
General transcription factors
Sigma factor is an accessory protein to RNA polymerase in bacteria that helps the polymerase bind to the promoter region. In eukaryotes, this function is performed by a set of proteins called the general transcription factors.
The splicing of introns out of an mRNA molecule is catalyzed by
RNA molecules in the snRNPs that base pair with splice sites. This base-pairing helps promote the rearrangement of bonds to remove the intron.
Export of RNA from the nucleus requires the RNA to have which characteristic(s)?
RNAs must have the features of a processed mRNA. This includes being properly spliced (no introns), having a 5’ cap and a poly-A tail.
The reading frame to use for translating an mRNA into functional protein is determined by the…
location of an AUG.
The translation of an mRNA in eukaryotes begins when the initiator tRNA encounters the first AUG in an mRNA. The complex containing the initiator tRNA starts scanning the mRNA from the 5’ end to find the AUG.
Show below is a tRNA for tryptophan. Which of the locations on the tRNA accommodates looser base-pairing rules?
a) site 3
b) all of the sites maintain strict base-pairing rules
c) site 2
d) site 1
The third base in a codon can base-pair loosely with the corresponding base in an anticodon in a tRNA. This allows specific tRNAs to recognize more than one codon (called wobble base pairing) for a redundant genetic code.
How do tRNAs become attached to the correct amino acid?
Enzymes called aminoacyl-tRNA synthetases recognize tRNAs with a specific anticodon as well as the amino acid for the tRNA and catalyze a reaction to join them together. This is called “charging” a tRNA.
Using the genetic code below, determine the amino acids that a polynucleotide of UC would code for
Leu, Ser
The catalytic sites for peptide bond formation during translation are found in which part of the ribosome?
large subunit RNAs
The catalysis of the peptide bonds in the growing polypeptide chain during translation is performed by the rRNA of the large subunit. The ribosome is a ribozyme; proteins play a largely structural role.
What recognizes the stop codons in an mRNA?
release factor
When the ribosome encounters a stop codon, instead of a tRNA binding, a protein called release factor binds and catalyzes the addition of a water molecules to the carboxyl end of the polypeptide and releases it
What is the benefit of protein synthesis in polyribisomes?
More protein can be produced from a single RNA.
What is the name of the complex that degrades proteins that have reached the end of their lifespan, are damaged or are misfolded?
proteasome
The structure of the proteasome is shown below. What group is recognized by region A to indicate that the protein is marked to be eliminated? What are the functions of B and D?
Proteins marked for elimination have a chain of ubiquitin groups added to them.
This is recognized by region A and the protein is then threaded into the central cylindaer (B) to be degraded by the protease active sites (D).
Protein concentration can be regulated by all of the steps listed EXCEPT
a) DNA replication
b) RNA processing
c) mRNA stability
d) nuclear export
DNA replication
Why do we think RNA may have been a primitive autocatalytic system on early Earth?
RNA carries/stores information and through base-pairing rules, can act as a template for self-replication. It also had the ability to catalyze reactions.
Why is RNA thought to predate DNA in evolution?
a) RNA is less stable than DNA
b) RNA forms many different types of functional molecules, like snRNA, rRNA, and tRNA
c) The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth.
d) rRNA genes are more conserved through evolution
c) The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth.
Although the other selections are true, the sugar in RNA, ribose, is more easily produced from formaldehyde, which was abundant in the early environment of Earth.
DNA is a better molecule for long-term storage of genetic information than RNA because…
The deoxyribose sugar stabilizes the DNA chains; it allows the nucleotide chains to grow to longer lengths. In addition, the presence of thymine (rather than uracil) facilitates the detection and repair of damage.
Transplanting the nucleus of an epithelial cell into an egg cell lacking genetic information leads to the formation of
a) a hybrid cell that has characteristics of both embryonic cells and epithelial cells
b) another epithelial cell
c) a normally developing embryo
d) a dead cell
c) a normally developing embryo
Nuclear transplantation experiments took different types of adult body cells and placed them in egg cells without any DNA and these cells developed into normal embryos and then into a normal animal. This showed that differentiated cells contain all the genetic information for many any other type of cell.
A housekeeping gene is a gene whose cellular function is
a) involved in the removal of waste products from cells
b) turned off periodically for maintenance
c) important for processes found in all cell types
d) critical for specialized activities in a specific cell type
Housekeeping genes code proteins that play critical roles in basic cellular processes that are found in all cell types. They include the genes that encode the enzymes of glycolysis, gene expression, metabolism, and basic cell structure.
Which of the following is the main point of control for regulating gene expression levels?
a) transcription
b) protein degradation
c) mRNA degradation
d) translation
a) transcription
Inhibiting the transcription of genes that are not currently needed help keep unnecessary intermediates from being synthesized.
Mutations in which of the following elements would abrogate RNA polymerase’s ability to activate gene expression?
a) transcription termination site
b) regulatory DNA sequence region
c) promoter
d) major groove
RNA polymerase binds to the promoter, a specialized sequence that orients the enzyme in the direction of transcription.
Transcription will then start further downstream of the promoter at the transcription initiation site.
Excess amounts of the amino acid tryptophan result in the downregulation of the expression of the enzymes required for its synthesis due to …
the amino acid binding to the repressor protein, which activates it and enables it to bind to the operator sequence near the promoter. The binding of the repressor in the proximity of the promoter inhibits the binding of RNA polymerase, and thus the expression of the trp genes.
Generally, bacterial promoters that are regulated by transcriptional activators bind _____ to RNA polymerase, but promoters that are regulated with transcriptional repressors bind _____ to RNA polymerase.
weakly; strongly
Transcriptional activators in bacteria bind to an activator binding site to help the RNA polymerase bind to the promoter. Without this aid, the binding of the polymerase to the promoter is weak and does not activate transcription at high frequency.
Genes controlled by transcriptional repressors bind polymerase, and this binding can be blocked by the binding of the repressor in the region.
If lactose and glucose are both available to a bacterial cell, which carbon source(s) will be used?
Glucose
Bacteria prefer to use glucose whenever it is present. When glucose is present, it will be the only sugar used and expression of the Lac operon genes will be reduced. When only lactose is present, the production of lactose-breakdown enzymes will increase to enable the usage of this alternative carbon source.
Eukaryotic repressor proteins can decrease transcription using which of the following mechanisms?
Eukaryotic repressor proteins can act to reduce transcription by inhibiting the assembly of the transcriptional initiation complex, or they can recruit histone-modifying complexes like deacetylases, which remove the activating acetyl groups from nearby histones
How do eukaryotic activator proteins regulate chromatin packaging to enhance transcription?
1) attraction of histone-modifying complexes that place activating marks (like acetyl groups) on histones
2) the recruitment of chromatin-remodeling complexes to eject or slide nearby nucleosomes
What is the purpose of chromosome loops?
Enhancer sequences act at a distance from their target gene. They are prevent from inappropriately activating the transcription of other nearby genes by the formation of chromosome loops that restrict the engagement of enhancers to just the genes within the same loop
What is combinatorial control and how does it differ from operons?
In combinatorial control, transcriptional regulators function together to determine the level of expression of a particular gene.
Operons, on the other hand, are a set of genes under the control of a specific transcriptional regulator, a typical control mechanism in prokaryotes.
In eukaryotes, multiple genes can be expressed simultaneously by
a) the binding of a mediator complex to several genes at once
b) the binding of a specific transcriptional regulator to several genes
b) 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 combinatorial control to turn on expression by coordinated binding to several genes at once.
What is a reporter gene? What is its use case?
A reporter gene is an experimentally engineered regulatory DNA sequence that has been fused to a gene that encodes a protein that is easily observed.
It provides information into where and when a gene is expressed. The regulatory sequences drive the expression of a gene product that is easily monitored.
What is a master transcription regulator?
Master transcription regulators drive the development of a particular cell type and even whole organs by turning on specific genes. The master regulator turns on the expression of other transcriptional regulators that regulate other genes. Results in a cascade of expression, coordinating the formation of an organized group of cells.
How do cells maintain their identity through cell divisions?
A master transcription regulator that controls its own expression, as well as the expression of other cell-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.
collectively, the processes that alter the levels or activity of a gene product are called…
post-transcriptional control
MicroRNAs block the expression of a specific gene product by binding to the _____ and inhibiting _____
mRNA; translation
MicroRNAs form a complex with RISC proteins. Once the miRNA forms a complementary base-paired duplex with target RNA, it either targets the mRNA for destruction or reduces the efficiency of translation.
Which protein complex mediates the RNA interference (RNAi) process by inhibiting RNA polymerase via histone methylation and heterochromatin formation?
RITS
small interfering RNAs (siRNAs) can form a complex with different protein complexes to lead to different effects on gene expression.
siRNAs that form a complex with RITS (RNA-induced transcriptional silencing0 will bind to the RNA coming from RNA polymerase and will lead to the formation of repressive chromatin structures at that gene region.
What are the functions of long noncoding RNAs (lncRNA)?
Long noncoding RNAs (lncRNAs) are known to have functions in regulating gene activity but can also act as a scaffold for protein complex assembly. A prominent example is a lncRNA that helps the telomerase complex assemble.
What is a horizontal transfer?
The acquisition of DNA from another organism, which results in genetic change.
Which cells contribute to evolutionary changes in an organism? Why?
Mutations in germ-line cells contribute to evolutionary change because they are the cells that go on to form the progeny of the organism.
How do point mutations typically arise?
Replication errors
DNA polymerase has a low error rate but mistakes still occur and can be propagated into progeny cells. Other mutagenic phenomena are less common.
A mutation in the _____ of the gene encoding the enzyme lactase enables the expression of this gene in adults.
regulatory sequence
Normally, lactase is expressed only in infancy to help digest milk sugars. A mutation in the regulatory DNA sequences arose about 10,000 years ago that caused the expression of this enzyme in adults, allowing them to consume and digest milk for nutrition.
Shown here are regions of two homologous chromosomes. If homologous recombination occurred between the short repetitive sequence after the gene in Chromosome 1 and the short repetitive sequence before the gene in Chromosome 2, what would be the result?
The duplication of the gene would occur on Chromosome 1 and deletion would occur on Chromosome 2.
What are mobile genetic elements? How do they promote gene duplication and exon shuffling?
Mobile genetic elements have similar sequences to each other and are found throughout the genome. They serve as targets for unequal homologous recombination.
What percentage of human genes have clearly recognizable homologs in the fruit fly?
50%
These genes likely have common ancestry and have been more resistant to change over the years due to the need to preserve an important function.
Germ-line mutations that are deleterious are likely to be…
a) preserved or lost depending on chance
b) lost from a population
c) preserved in a population
b) lost in a population
Deleterious mutations in the germ-line have negative consequences on the organism, decreasing the likelihood of that organism to successfully reproduce and pass on the mutation. These types of mutations are likely to be lost in the population over time.
Which of the following DNA sequences is the LEAST likely to accommodate mutations? Why?
a) regulatory DNA sequences
b) ribosomal RNA sequence
c) DNA sequences found between genes
d) the coding sequence of a duplicated gene
b) ribosomal RNA sequence
genes that encode products with a specific and unique function cannot accommodate mutations easily. Many mutations will alter their function and lead to deleterious consequences.
What is conserved synteny? What does it suggest?
conserved synteny refers to the conservation of the order of genes on a region of a chromosome between species. This suggests that despite all the shuffling that genomes are subject to, these regions were resistant to change.
What is replicative transposition?
DNA-only transposition that involves the replication of the transposon DNA before mobilization and insertion at another location. Thus, the original copy remains in place.
Shown here is an expression vector.
For the gene of interest to be expressed in the cells, the gene of interest must be cloned where in this vector?
Expression vectors contain a promoter that drives transcription of the gene of interest.
Promoters have directionality so for the gene to be expressed the gene must be placed in the proper location relative to the promoter.
What kind of lipid molecules is represented in this figure?
phospholipid
Which type of movement is the least common for lipids in a bilayer? When does this movement occur?
Flip-flop
This only happens when catalyzed by transporter proteins.
Refer to the diagram below. If cells that cannot carry out fermentation were grown in anaerobic conditions, at which step would glycolysis halt?
step 6: where NAD+ is converted to NADH
