MCB DNA Elements

Human females have 23 different chromosomes, whereas human males have 24

True

In the secondary structure of a DNA double helix, a purine (A or G) always base pairs with a pyrimidine (T or C). Why is this base-pair alignment critical to the structure of DNA?

Parining a purine with a pyrimidine ensures that the distance between the backbone strands is constant.

Which feature of DNA underlies its simple replication procedure?

The complementary relationship in the double helix

Which of the following correlates the best with biological complexity in eukaryotes?

Number of genes

What property of genome diversity accounts for a majority of the variation in genome size, even among related species?

The amount of noncoding DNA

The eukaryotic chromosomes are organized inside the nucleus with a huge compaction ratio of several thousand-fold and is further accentuated during the mitotic cycle. What interaction is responsible for such a tight packaging?

The various histone proteins that wrap and fold the DNA

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. The ability of these complexes to remodel the chromatin structure is dependent on which enzymatic function?

They have ATPase activity.

Which statement regarding heterchromatin in a typical mammalian cell is true?

The different types of heterochromatin share an especially high degree of compaction.

What is a characteristic of the acetylation of lysines on the histone tails?

It can be performed on methylated lysine only after they are first demethylated.

What is a characteristic of a chromatin “reader complex?”

It binds tightly to the chromatin only when a specific set of histone marks is present.

Variations in the structure of DNA, such as loops, or the chromatin organization such as euchromatin or heterochromatin, can influence gene expression and can be inherited by subsequent generations even though these changes do not result in alterations to the sequence of nucleotides. What is this type of inheritance called?

Epigenetic inheritance

Why are polytene chromosomes useful for studying chromatin?

They have distinct visible banding patterns.

What would most reliably suggest that a genomic sequence is functionally important?

Multispecies conservation of the sequence

Transposable elements occupy almost 10% of our genome

False

What is true about lampbrush chromosomes?

They are thought to have a structure that is relevant to mammalian chromosomes in interphase.

Conservation of genomic sequences between humans and chickens is mainly due to a specific type of selection, whereas the conservation observed between humans and chimpanzees is mostly due to the short time available for mutations to accumulate. What type of selection is responsible and what position on the DNA sequences of synonymous codons are nearly identical between humans and chimpanzees?

Purifying; third

Imagine a chromosome translocation event that brings a gene encoding a histone acetyl transferase enzyme from its original chromosomal location to a new one near heterochromatin. Which scenario is definitely NOT going to happen?

The level of gene product decreases due to a position effect, leading to an imbalance in the chromatin state of the cell that results in the activation of programmed cell death.

Most histone modifications are covalent modifications to already synthesized histones. Why do you think this characteristic is necessary for proper chromatin regulation?

Histone modifications need to be dynamic in order to effectively influence chromatin function. Covalent modifications can be easily added or replaced by enzymes.

Why are barrier DNA and the proteins that are able to associate with barrier DNA regions of the genome essential for proper chromatin structure?

The barrier DNA is a region that is unable to be incorporated into nucleosomes and therefore blocks the formation of heterochromatin.

What would you expect to observe when an SMC protein complex is loaded onto a prokaryotic chromosome at the origin of replication?

The formation of a DNA loop and the subsequent segregation of the two daughter DNA molecules away from each other

The molecular clock for molecular evolution suggests that the rate of change for DNA sequences is nearly constant, yet different categories of DNA accumulate changes at different rates. Which category would you predict has the lowest rate of DNA alterations?

Exons of essential genes

What is NOT an advantage of monoclonal antibodies over antisera?

They can bind to multiple antigenic sites on a macromolecule.

How are antibody- producing hybridoma cell lines immortalized to provide an unlimited source of monoclonal antibodies?

By cell fusion

Choose the correct order of the following cellular components. The order should illustrate the centrifugal force required to sediment the components by preparative ultracentrifugation, from low to high force required.

Nuclei, lysosomes, microsomes, ribosomes (free cytosolic).

Which of the following is NOT true of SDS-PAGE of proteins?

It requires the use of antibodies for visualization.

Hydrodynamic measurements can be used to calculate the approximate size and shape of a large protein complex using what method?

The velocity of the complex as it moves under centrifugal force and the migration of the complex as it moves through a gel-filtration column

What is a benefit of using NMR to determine protein structure rather -ray crystallography?

NMR can solve protein structures in aqueous solutions, while X-ray crystallography requires the protein to form a solid crystal.

You have carried out a genetic screen in a species of fish and have identified a new gene in this organism. You have cloned and sequenced the gene, but do not know anything about the biochemical function of the gene product. Which of the following is the most sensible next step in order to get clues about the function?

Using the BLAST algorithm to scan sequence databases for similar sequences

Which of these describes bacterial artificial chromosomes (BACs)?

They can maintain DNA sequences of hundreds of thousands of nucleotide pairs.

Which of the following allows many smaller strands of synthetic DNA with complementary ends to be joined together into one long strand of DNA?

Gibson assembly

For a complementation test to work, the mutations under study must be of what type?

Recessive

Which statement applies to single nucleotide polymorphisms?

They are common sequence variants that are passed down from one generation to the next.

What is one difference between polymorphisms and rare DNA variants?

Polymorphisms arose early in human history, while rare DNA variants are more recent.

Which of the following descriptions better applies to forward rather than reverse genetics?

It involves new gene discovery by genetic screens.

Which technique generates a complete list of all major mRNAs expressed in every cell type in an organism?

Ribosome profiling

Below are the steps in the common procedure to create transgenic plants. Which order reflects the correct sequence of events?

Removal of leaf tissue from a plant, Agrobacterium infection, callus growth, shoot/root induction

Susceptibility to drug and alcohol addiction is partially genetic. For example, the human dopamine receptor DRD2 is associated with cocaine and alcohol abuse; individuals carrying an A nucleotide, instead of the more common C nucleotide, at a certain position within the sixth intron of the DRD2 gene are at a significantly increased risk of abuse. This variation in sequence is an example of what?

SNP

Which of the following descriptions applies to velocity sedimentation rather than equilibrium sedimentation?

It uses a shallow sucrose gradient to stabilize the sedimentation bands against convection.

There are six possible reading frames for any double-stranded DNA. In the following schematic drawing of a genomic region in Escherichia coli, stop codons in each of these frames are indicated by black bars. Choose the reading frame in which the open reading frame (ORF) is translated in this region. [Diagram required: original document, Exam 2 Q39]

-1

The p53 gene is an important tumor suppressor gene in our genome. It codes for a transcription regulatory protein that can assemble into tetramers. A number of mutations in p53 render the protein inactive. These mutant protein molecules form mixed tetramers with wild-type p53 proteins and, in this case, the tetramer is inactive. The mutations can therefore be categorized as

Dominant- negative

In a bacterium that is normally cylindrical in shape, loss of either of two genes A and B results in round cells. Additionally, gain-of-function mutations in gene A can rescue the phenotype of gene B loss-of-function mutants. What phenomenon best describes this observation? The product of which gene is more likely to function upstream of the other one in determining cell shape in this bacterium?

Suppression; gene B

Histone proteins are among the most highly conserved proteins in eukaryotes. Histone H4 proteins from a pea and a cow, for example, differ in only 2 of 102 amino acids. However, comparison of the two gene sequences shows many more differences. These observations indicate that mutations that change amino acids must be selected against. Why do you suppose that most amino acid-altering mutations in histone genes are deleterious?

Most amino acid–altering mutations in histone genes are deleterious because histones perform an extremely constrained and essential structural role in packaging DNA. Histone H4 must interact precisely with other histones, with DNA, and within the tightly packed nucleosome, so even small changes can disrupt nucleosome stability or chromatin organization. Such disruptions can impair DNA replication, transcription, and repair, causing severe defects in cell viability. As a result, only silent mutations—or those that do not change the amino acid sequence—tend to persist, while mutations that alter amino acids are strongly selected against.

The body uses insulin, a small protein, as a hormone to control blood sugar levels. Originally, insulin was harvested from pig pancreas, and a small amount of insulin was produced during the process, creating great expense. However, for pharmaceutical use we now have a cheaper insulin that is produced by bacteria. Name two modern techniques that contributed to this important medical advancement, and explain how these techniques enable bacterial expression of a gene as well as the purification of the gene product. (Ignore any need for post-translational modifications for the activation of insulin.)

Two key modern techniques that enabled inexpensive bacterial production of insulin are recombinant DNA technology and affinity chromatography using engineered tags. Recombinant DNA methods allow scientists to insert the human insulin gene into a bacterial plasmid using restriction enzymes and DNA ligase; once transformed, the bacteria transcribe and translate this gene just like one of their own, producing large quantities of insulin. To purify the protein, the insulin gene can be engineered to include a short affinity tag (such as a His-tag), allowing the expressed protein to be captured on a specific resin—such as a nickel column—while other bacterial proteins wash away. Together, these technologies make it possible to express human insulin cheaply and purify it efficiently from bacterial cultures.

In contrast to histone acetylation, which always correlates with gene activation, histone methylation can lead to either transcriptional activation or repression. How do you suppose that the same modification—methylation—can mediate different biological outcomes?

Histone methylation can produce different outcomes because its effect depends on which amino acid residue is methylated and how many methyl groups are added. Different lysines or arginines on histone tails recruit different sets of regulatory proteins: some methyl marks attract factors that open chromatin and promote transcription, while others recruit proteins that compact chromatin and silence genes. In addition, mono-, di-, and trimethylation on the same residue can each signal distinct chromatin states. Thus, “methylation” is not a single uniform signal but a family of context-dependent marks interpreted by specific binding proteins.

Indicate which numbered feature (1 to 5) in the schematic drawing of the DNA double helix corresponds to each of the following in the order given below: Hydrogen-bonding Covalent linkage Phosphate group Nitrogen-containing base Deoxyribose sugar Your answer would be a five-digit number composed of digits 1 to 5 only, for example, 52431. [Diagram required: original document, Exam 2 Q45]

42351

For the Human Genome Project, cloning of large segments of our genome was first made possible by the development of yeast artificial chromosomes, which are capable of propagating in the yeast Saccharomyces cerevisiae just like any of the organism’s 16 natural chromosomes. In addition to the cloned human DNA, these artificial vectors were made to contain three elements that are necessary for them to function as a chromosome. What are these elements?

Origin of replication (ARS); centromere (CEN); telomeres (TEL).

Indicate which feature in the schematic drawing of a chromatin fiber corresponds to each of the following in the order given below: Nucleosome core particle; Linker DNA; Histone octamer; Non-histone protein; Your answer would be a four-digit number composed of digits 1 to 4 only, for example, 2431. [Diagram required: original document, Exam 2 Q47]

2134

What are the two mechanisms through which the ATP-dependent chromatin remodeling complexes are able to reorganize nucleosome structure?

Nucleosome sliding (repositioning); changes in nucleosome structure or composition (e.g., histone eviction or exchange).

Explain the difference between a gain-of-function mutation and a dominant- negative mutation. Why are both these types of mutation usually dominant?

A gain-of-function mutation produces a protein with increased activity or a new, abnormal function, whereas a dominant-negative mutation produces a protein that interferes with the function of the normal protein, often by forming defective complexes. Gain-of-function mutations are usually dominant because a single mutant copy is enough to produce the abnormal activity. Dominant-negative mutations are dominant because even one mutant protein can “poison” the normal protein’s function. In both cases, the presence of one altered allele is sufficient to affect the phenotype, so the mutations override the normal copy rather than being masked by it.

After treatment with mutation-inducing chemicals, a mutant melanogaster fruit fly has been identified that displays neuromuscular abnormalities that are similar to those seen in Parkinson’s disease. How can a researcher go about discovering which gene or genes have been affected to produce these effects?

A researcher can identify the affected gene in the mutant fruit fly by first performing genetic mapping to narrow down the chromosome region linked to the neuromuscular abnormalities. They can then use complementation tests with flies carrying known mutations to see if the mutant fails to complement any existing gene mutations, helping pinpoint the candidate gene. Once candidates are identified, DNA sequencing can reveal specific mutations responsible for the phenotype. RNA analysis can also be used to detect changes in gene expression or splicing that might contribute to the defects. Finally, introducing a normal copy of the candidate gene into the mutant fly can rescue the phenotype, confirming that the mutation in that gene causes the Parkinson’s-like symptoms. This combination of genetic and molecular approaches allows researchers to determine which gene or genes are responsible.