Cell Bio Exam II, problem set questions
T/F: DNA replication is a bidirectional process that is initiate at multiple locations along chromosomes in eukaryotic cells.
True.
T/F: Meselson and Stahl ruled out the dispersive model for DNA replication.
True.
Total nucleic acids are extracted from a culture of yeast cells and then mixed with resin beads to which the polynucleotide 5'-TTTTTTTTTTTTTTT-3' has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which type of nucleic acid is most abundant?
You would see an abundance of A. and a poly A tail.
What would happen if a DNA polymerase that operated in the 3' --> 5' direction were to remove an incorrect nucleotide from a growing DNA strand?
DNA synthesis from 3' --> 5' does not allow proofreading. If the last nucleotide added is mispaired and is removed, the last nucleotide on the growing strand is a nucleoside monophosphate and the nucleotide coming in only has a hydroxyl group on the 3' end. Thus, there is no favorable hydrolysis reaction to drive the addition of new nucleotides.
Why is DNA considered semiconservative?
Each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand,
Which of the following statements about DNA methylation in eukaryotes is false? a.) Appropriate inheritance of DNA methylation patterns involves maintenance methyltransferase. b.) DNA methylation involves a covalent modification of cytosine bases. c.) Methylation of DNA attracts proteins that block gene expression. d.) Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand.
d.) Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand. In truth, the methylated DNA strand corresponds to the old, parent strand.
snRNAs ________. a.) are translated into snRNPs b.) are important for producing mature mRNA transcripts in bacteria. c.) are removed by the spliceosome during RNA splicing d.) can bind to specific sequences at intron-exon boundaries through complementary base-pairing.
d.) can bind to specific sequences at intron-exon boundaries through complementary base pairing.
What would you expect to happen to the regulation of the enzymes that synthesize glutamine in cells expressing a mutant form of the glutamine repressor that cannot bind to DNA?
it would always make enzymes for glutamine synthesis
It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link the distantly bound transcription regulators the RNA polymerase and the general transcription factors include the large complex of proteins called the _____.
mediator
We discussed a paper in class that showed that rat pups of low licking and grooming mothers exhibit increased stress. Why is this?
The low groomed rats had increased stress due to increased methylation on the gene involved in shutting down stress.
What cause prion diseases?
The misfolded protein aggregating and misfolding other proteins it comes in contact with.
The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). How do these proteins cause disease?
These misfolded proteins (prions) that cause these diseases aggregate the other healthy proteins in the body, mutating them and misfolding them as well.
A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals while a white blood cell defends the body against infection. This is because:
They make some cell type specific mRNAs
What experimental result eliminated the dispersive model of DNA replication?
This was ruled out by using heat to denature the DNA duplexes and then comparing the densities of the single-stranded DNA. Had the dispersive model been correct, individual strands should have had an intermediate density, but only fully heavy and fully light strands were observed after being centrifuged.
Which of the following statements about transcriptional regulators is false? a.) 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. b.) transcriptional regulators will form hydrogen bonds, ionic bonds, and hydrophobic interactions with DNA. c.) the DNA binding motifs of transcriptional regulators usually bind in the major groove of the DNA helix. d.) the binding of transcriptional regulators generally does not disrupt the hydrogen bonds that hold the double helix together.
a.) transcriptional regulators usually interact with the sugar-phosphate backbone on the outside of the double helix to determine where to bind to the DNA helix. In truth, the transcriptional regulators interact with the nucleotide bases, not the sugar-phosphate backbone
The packing of DNA into chromatin also affects transcriptional initiation, and histone _____ is an enzyme that can render the DNA less accessible to the general transcription factors.
deacetylase
List three ways in which the process of eukaryotic transcription differs from the process of bacterial transcription.
1.) Bacteria only have one RNA Polymerase, Eukaryotic cells have RNA Polymerase I, II, and III. 2.) Bacterial RNA Polymerase only needs the sigma factor for initiation of transcription, Eukaryotic RNA Polymerase needs the general transcription factors (GTFs) 3.) Bacterial DNA has no nucleosomes, Eukaryotic DNA has nucleosomes, so it needs to unpack chromatin 4.) Bacteria mRNA has no capping, polydenylation, or splicing. Eukaryotic mRNA is capped, polydenylated, and spliced.
Describe the three existing models for DNA replication when these studies (Meselson/Stahl) were begun, and explain how one of them was ruled out definitively
1.) Conservative model: suggested a mechanism by which the original parental strands stayed together after replication and the daughter duplex was made entirely of newly synthesized DNA. 2.) Semiconservative model: proposed that the two DNA duplexes produced during replication were hybrid models, each having one of the parental strands and one of the newly synthesized strands. 3.) Dispersive model: predicted that the new DNA each contained segments of parental and daughter strands all throughout the molecule. This was ruled out by the density-gradient experiments.
What are good examples of housekeeping proteins? housekeeping proteins are proteins all cells have in common
1.) DNA repair enzymes 2.) histones 3.) RNA Polymerase 4.) Metabolism genes - GAPDH 5.) ATP synthase
During the chain elongation process of translating an mRNA into a protein, the growing polypeptide chain attached to a tRNA is bound to the __1__ site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the __2__ site by forming base pairs with the exposed codon in the mRNA.
1.) P 2.) A
MicroRNAs are noncoding RNAs that are incorporated into a protein complex called __1__, which searches the __2__ in the cytoplasm for sequence complementary to that of the miRNA. When such a molecule is found, it is then targeted for __3__. RNAi is triggered by the presence of foreign __4__ molecules, which are digested by the __5__ enzyme into shorter fragments approximately 23 nucleotide pairs in length.
1.) RISC 2.) mRNA 3.) destruction 4.) double stranded RNA 5.) Dicer
Once an mRNA is produced, its message can be decoded on ribosomes. The ribosome is composed of two subunits: the __1__ subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the __2__ subunit, which matches the tRNAs to the codons of the mRNA.
1.) large 2.) small
The __1__ enzyme catalyzes the formation of a new peptide bond between the growing polypeptide chain and the newly arriving amino acid. The end of a protein-coding message is signaled by the presence of a stop codon, which binds the __2__ called release factor. Eventually, most proteins will be degrades by a large complex of proteolytic enzymes called the __3__.
1.) peptidyl transferase 2.) protein 3.) proteasome
Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied. What contributes to the relative ease of strand separation by initiator proteins?
1.) replication origins are rich in A-T base pairs 2.) they only separate a few base pairs at a time 3.) once opened, other proteins of the DNA replication machinery bind to the origin.
Adenine is a purine with a:
2-ring structure
The human genome encodes about 21,000 protein coding genes. Approximately how many such genes does the typical differentiated human cell express at any one time?
5,000 to 15,000 proteins
Besides the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired?
A knick in the new strand.
The structure of Uracil is:
A single ring with 4 C and 2 N, bonded to 2 O.
How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter?
By looping out the intervening DNA between the regulatory DNA sequences and the promoter.
T/F: DNA replication origins are typically rich in G-C base pairs.
False. DNA replication origins are typically rich in A-T base pairs, since they are only held together by 2 H bonds, rather than the 3 H bonds that hold G-C together.
Unlike DNA, which typically forms a helical structure, different molecules of RNA can fol into a variety of three-dimensional shapes. This is largely because:
RNA is single stranded.
This factor (TFIID) binds at the DNA sequence called the _____ box, which is typically located 25 nucleotides upstream from the transcription start site.
TATA
In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor _____ to DNA, causing a marked local distortion in the DNA.
TFIID
in eukaryotic cells, once the RNA Polymerase II has been brought to the promoter DNA, it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor _____.
TFIIH
Explain how "light" DNA was separated from "heavy" DNA in the Meselson and Stahl experiments.
The DNA samples collected were placed into centrifuge tubes containing cesium chloride. After high-speed centrifugation for 2 days, the heavy and light DNA products were separated by density. (heavy at the bottom of the tube and light at the top)
The part of a ribose sugar where a new ribonucleotide will attach in an RNA molecule is:
The OH group on the front left Carbon.
The part of a ribose sugar that is different from the deoxyribose sugar used in DNA is:
The OH group on the front right Carbon, ribose has this OH group, while deoxyribose does not.
Researchers have isolated a mutant strain of E. coli that carries a temperature sensitive variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just as well as the wild-type cells. At the nonpermissive temperature, all of the cells in the culture tube die within 2 hours. DNA from mutant cells grown at the nonpermissive temp for 30 mins is compared with the DNA isolated from cells grown at the permissive temp. Explain the appearance of a distinct band with a size of 200 base pairs in the sample collected at the nonpermissive temp.
At the nonpermissable temperature, DNA ligase is unable to occur. So the Okazaki fragments are not covalently connected to each other into one continuous strand. SO the notable band at 200 bp is the typical size of an individual Okazaki fragment.
What is the epigenome?
DNA methylation histone modifications, they change transcription read out of genome without changing the DNA sequence.
The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in _____.
Degradation
If the genome of bacterium E. coli requires about 20 mins to replicate itself, how can the genome of the fruit fly (Drosophila) be replicated in only 3 mins?
Drosophila DNA contains more origins of replication than E. coli DNA, due to E. Coli being circular and Drosophila being linear.
T/F: When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate.
False. The two strands do need to separate for replication to occur, but this is accomplished by the binding of initiator proteins at the origin of replication.
DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction?
Hydrolysis of pyrophosphate (PP_i) to inorganic phosphate (P_i) + P_i
Most cells in the body of an adult human lack the telomerase enzyme because its gene is turned off and is therefore not expressed. An important step in the conversion of a normal cell into a cancer cell, which circumvents normal growth control, is the resumption of telomerase expression. Explain why telomerase might be necessary for the ability of cancer cells to divide over and over again.
In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each round of DNA replication, the length of telomeric DNA will shrink, until finally all the telomeric DNA has disappeared. Without telomeres capping the chromosome ends, the ends might be treated like breaks arising from DNA damage, or crucial genetic information might be lost. Cells whose DNA lacks telomeres will stop dividing or die. However, if telomerase is provided to cells, they may be able to divide indefinitely because their telomeres will remain a constant length despite repeated rounds of DNA replication.
What would expect to happen to the regulation of the enzymes that synthesize glutamine in cells expressing a mutant form of the glutamine repressor that binds to DNA even when no glutamine is bound to it?
The glutamine operon and enzymes for glutamine synthesis will always be off, and you need glutamine in the media.
A mismatched base pair causes a distortion in the DNA backbone. If this were the only indication of an error in replication, the overall rate of mutation would be much higher. Explain why.
Without additional marks that identify the difference between the newly synthesized strand and the template strand, the repair would be corrected only 50% of the time by random chance. There needs to be a mechanism to detect the newly replicated strand from the template strand. This way, the repair enzymes know which specific base-pair to replace.
Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. What is a protein domain?
a segment of polypeptide chain that folds independently into a stable structure.
What are operons?
a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.
The modular nature of the Eve gene;s regulatory region means that _____. a.) There are seven regulatory elements and each element is sufficient for driving expression in a single stripe. b.) All the laboratory elements for each stripe use the same transcriptional activators. c.) The E. Coli LacZ gene is normally only expressed in a single stripe--unlike Eve, which is expressed in seven stripes. d.) Transcription regulators only bind to the stripe 2 regulatory DNA segment in stripe 2.
a.) There are seven regulatory elements and each element is sufficient for driving expression in a single stripe.
Which of the following statements is true? a.) the two genes must be transcribed into RNA using the same strand of DNA. b.) if gene A is transcribed in a cell, gene B cannot be transcribed. c.) gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell. d.) if gene A is transcribed in a cell, gene B must be transcribed.
c.) gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell.
You have a segment of DNA that contain the following sequence: 5'-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3' 3'-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5' you know that the RNA transcribed from this segment contains the following sequence: 5'-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3' Which of the following choices best describes how transcription occurs? a.) the top strand is the template strand; RNA polymerase moves along this strand from 5' to 3' b.) the top strand is the template strand; RNA polymerase moves along this strand from 3'-5' c.) the bottom strand is the template strand; RNA polymerase moves along this strand from 5'-3' d.) the bottom strand is the template strand; RNA polymerase moves along this strand from 3'-5'
d.) the bottom strand is the template strand; RNA polymerase moves along this strand from 3'-5'.