Question 1

Which of the following features of DNA underlies its simple replication procedure?

Accepted Answer

A)  The fact that it is composed of only four different types of bases 
B)  The antiparallel arrangement of the double helix 
C)  The complementary relationship in the double helix 
D)  The fact that there is a major groove and a minor groove in the double helix 
A)  The fact that it is composed of only four different types of bases 
B)  The antiparallel arrangement of the double helix 
C)  The complementary relationship in the double helix 
D)  The fact that there is a major groove and a minor groove in the double helix

Question 2

What features do Cajal bodies, interchromatin granule clusters, and nucleoli have in common?

Accepted Answer

A)  High permeability to the surrounding nucleoplasm 
B)  A network of macromolecules bound together by covalent linkages 
C)  A lipid bilayer membrane 
D)  The same set of RNA and protein molecules 
E)  The same size 
A)  High permeability to the surrounding nucleoplasm 
B)  A network of macromolecules bound together by covalent linkages 
C)  A lipid bilayer membrane 
D)  The same set of RNA and protein molecules 
E)  The same size

Question 3

For each of the following classifications, indicate whether you would expect to find an actively transcribed gene in the first category (1) or the second (2). Your answer would be a six-digit number composed of digits 1 and 2 only, e.g. 222121.
( )	1: Heterochromatin, or 2: euchromatin
( )	1: Chromosome puffs, or 2: condensed chromosome bands
( )	1: Nuclear periphery, or 2: the center of the nucleus
( )	1: Within the chromosome territory, or 2: extended out of the territory
( )	1: Apart from, or 2: close to actively transcribed genes within the nucleus
( )	1: 11-nm "beads-on-a-string" fibers, or 2: 30-nm fibers

Accepted Answer

More open chromatin is usually associa

Question 4

Indicate true (T) and false (F) statements below about the human genome. Your answer would be a six-letter string composed of letters T and F only, e.g. FTFFFT.
( )	Only about 1.5% of the human genome is highly conserved.
( )	Almost half of our genome is composed of repetitive sequences.
( )	Genes occupy almost a quarter of the genome.
( )	There are roughly as many pseudogenes in the human genome as functional genes.
( )	Transposable elements occupy almost 10% of our genome.
( )	On average, exons comprise 1.5% of our genes.

Accepted Answer

Only about 5% of our genome is highly

Question 5

In a double-stranded DNA molecule, one of the chains has the sequence CCCATTCTA when read from the 5? to the 3? end. Indicate true (T) and false (F) statements below regarding this chain. Your answer would be a four-letter string composed of letters T and F only, e.g. TTFT.
( )	The other chain is heavier, i.e. it has a greater mass.
( )	There are no C residues in the other chain.
( )	The 5?-terminal residue of the other chain is G.
( ) The other chain is pyrimidine-rich.

Accepted Answer

The sequence of the other ch

Question 6

Which of the following would most reliably suggest that a genomic sequence is functionally important?

Accepted Answer

A)  The presence of a long open reading frame in the sequence 
B)  Multispecies conservation of the sequence 
C)  Low copy number variation of the sequence 
D)  The presence of active chromatin marks over the sequence 
A)  The presence of a long open reading frame in the sequence 
B)  Multispecies conservation of the sequence 
C)  Low copy number variation of the sequence 
D)  The presence of active chromatin marks over the sequence

Question 7

Most fish genomes are at least 1 billion nucleotide pairs long. However, the genome of the puffer fish Fugu rubripes is quite small at only about 0.4 billion nucleotide pairs, even though the number of Fugu genes is estimated to be comparable to that of its relatives which have larger genomes. What do you think mainly accounts for the Fugu genome being this small?

Accepted Answer

A)  Evolutionary advantage of extremely small exon sizes in the Fugu lineage 
B)  Unusual disappearance of all intronic sequences from the Fugu genome 
C)  Increased abundance of transposable elements in the Fugu genome 
D)  Increased occurrence of mitotic whole-chromosome loss in the Fugu lineage 
E)  Low relative rate of DNA addition compared to DNA loss in the Fugu lineage 
A)  Evolutionary advantage of extremely small exon sizes in the Fugu lineage 
B)  Unusual disappearance of all intronic sequences from the Fugu genome 
C)  Increased abundance of transposable elements in the Fugu genome 
D)  Increased occurrence of mitotic whole-chromosome loss in the Fugu lineage 
E)  Low relative rate of DNA addition compared to DNA loss in the Fugu lineage

Question 8

As each cell in our body prepares for mitosis, its chromosomes start to look different. What are the changes in chromosome appearance that accompany the entry into M phase? Indicate true (T) and false (F) descriptions below. Your answer would be a five-letter string composed of letters T and F only, e.g. TTFFT.
( )	The chromosomes become readily visible by the naked eye.
( )	The chromosomes coil up further to become about 10 times shorter.
( )	Each chromosome is condensed and then replicated to form two sister chromatids.
( )	The typical diameter of a mitotic chromosome arm is about 70 nm.
( )	The two sister chromatids are disentangled from each other by the time chromosome condensation is complete.

Accepted Answer

The cells achieve an extra 10-fold com

Question 9

Polytene chromosomes are useful for studying chromatin because they …

Accepted Answer

A)  are smaller than regular chromosomes and easier to manipulate. 
B)  lack heterochromatin. 
C)  have distinct visible banding patterns. 
D)  can make polyploid cells. 
E)  All of the above. 
A)  are smaller than regular chromosomes and easier to manipulate. 
B)  lack heterochromatin. 
C)  have distinct visible banding patterns. 
D)  can make polyploid cells. 
E)  All of the above.

Question 10

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 of the following scenarios is definitely NOT going to happen?

Accepted Answer

A)  The gene gets silenced due to heterochromatin expansion, leading to the misregulation of gene expression for a number of critical genes. 
B)  The translocation event also brings along a chromatin barrier that can prevent heterochromatin expansion into the gene, and there is no phenotypic anomaly. 
C)  Since the gene encodes a histone acetyl transferase, it resists heterochromatin expansion by acetylating its own histones. 
D)  The level of the 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. 
A)  The gene gets silenced due to heterochromatin expansion, leading to the misregulation of gene expression for a number of critical genes. 
B)  The translocation event also brings along a chromatin barrier that can prevent heterochromatin expansion into the gene, and there is no phenotypic anomaly. 
C)  Since the gene encodes a histone acetyl transferase, it resists heterochromatin expansion by acetylating its own histones. 
D)  The level of the 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.

Question 11

Phylogenetic trees based on nucleotide or amino acid sequences can be constructed using various algorithms. One simple algorithm is based on a matrix of pairwise genetic distances (divergences) calculated after multiple alignment of the sequences. Imagine you have aligned a particular gene from different hominids (humans and the great apes), and have estimated the normalized number of nucleotide substitutions that have occurred in this gene in each pair of organisms since their divergence from their last common ancestor. You have obtained the following distance matrix.

Answer the following question(s) based on this matrix.
-If species A in the distance matrix represents human, indicate which of the other species (B to D) represents chimpanzee, gorilla, and orangutan, respectively. Your answer would be a three-letter string composed of letters B, C, and D only, e.g. DCB.

Accepted Answer

The lowest pairwise distance in the mat

Question 12

Which of the following is true regarding heterochromatin in a typical mammalian cell?

Accepted Answer

A)  About 1% of the nuclear genome is packaged in heterochromatin. 
B)  The DNA in heterochromatin contains all of the inactive genes in a cell. 
C)  Genes that are packaged in heterochromatin are permanently turned off. 
D)  The different types of heterochromatin share an especially high degree of compaction. 
E)  Heterochromatin is highly concentrated in the centromeres but not the telomeres. 
A)  About 1% of the nuclear genome is packaged in heterochromatin. 
B)  The DNA in heterochromatin contains all of the inactive genes in a cell. 
C)  Genes that are packaged in heterochromatin are permanently turned off. 
D)  The different types of heterochromatin share an especially high degree of compaction. 
E)  Heterochromatin is highly concentrated in the centromeres but not the telomeres.

Question 13

Five major types of chromatin were identified in studies performed on Drosophila melanogaster cells, although much more remains to be learned about chromatin diversity and dynamics. Which of the following is correct regarding these findings in Drosophila?

Accepted Answer

A)  These results were obtained using the 3C technique, which determines the positions of loops in the chromatin. 
B)  According to these results, there are four types of heterochromatin and only one type of euchromatin. 
C)  The Polycomb form of chromatin belongs to the euchromatin type. 
D)  In addition to these five major types of chromatin, there seem to be additional minor types as well. 
E)  The pattern of chromatin types in the chromosomes is constant across the different cell types in a multicellular organism. 
A)  These results were obtained using the 3C technique, which determines the positions of loops in the chromatin. 
B)  According to these results, there are four types of heterochromatin and only one type of euchromatin. 
C)  The Polycomb form of chromatin belongs to the euchromatin type. 
D)  In addition to these five major types of chromatin, there seem to be additional minor types as well. 
E)  The pattern of chromatin types in the chromosomes is constant across the different cell types in a multicellular organism.

Question 14

The genetic information carried by a cell is passed on, generation after generation, with astonishing fidelity. However, genomes are still altered over evolutionary time scales, and even their overall size can change significantly. Which of the following genome-altering events has increased the size of the mammalian genome the most?

Accepted Answer

A)  Transposition 
B)  Point mutation 
C)  Chromosomal deletion 
D)  Chromosomal inversion 
E)  Chromosomal translocation 
A)  Transposition 
B)  Point mutation 
C)  Chromosomal deletion 
D)  Chromosomal inversion 
E)  Chromosomal translocation

Question 15

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They …

Accepted Answer

A)  can slide nucleosomes on DNA. 
B)  have ATPase activity. 
C)  interact with histone chaperones. 
D)  can remove or exchange core histone subunits. 
E)  All of the above. 
A)  can slide nucleosomes on DNA. 
B)  have ATPase activity. 
C)  interact with histone chaperones. 
D)  can remove or exchange core histone subunits. 
E)  All of the above.

Question 16

Lampbrush chromosomes …

Accepted Answer

A)  are transcriptionally inactive. 
B)  are readily observed in the oocytes of humans and insects. 
C)  have thousands of duplicated DNA molecules arranged side by side. 
D)  are mitotic chromosomes with two sister chromatids attached together only at the centromere. 
E)  are thought to have a structure that is relevant to mammalian chromosomes in interphase. 
A)  are transcriptionally inactive. 
B)  are readily observed in the oocytes of humans and insects. 
C)  have thousands of duplicated DNA molecules arranged side by side. 
D)  are mitotic chromosomes with two sister chromatids attached together only at the centromere. 
E)  are thought to have a structure that is relevant to mammalian chromosomes in interphase.

Question 17

The globin gene family in mammals, birds, and reptiles is organized into ?- and ?-globin gene clusters that are located on two different chromosomes. In most fish and amphibians, however, the globin genes are close to each other on one chromosome. At which point (A to E) in the following simplified phylogenetic tree is a chromosomal translocation likely to have happened that placed the ?- and ?-globin genes on two separate chromosomes?

Accepted Answer

It appears that a chromosome

Question 18

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

Accepted Answer

A)  Number of genes per chromosome 
B)  Number of chromosomes 
C)  Number of genes 
D)  Genome size (number of nucleotide pairs) 
A)  Number of genes per chromosome 
B)  Number of chromosomes 
C)  Number of genes 
D)  Genome size (number of nucleotide pairs)

Question 19

The position effect variegation (PEV) phenotype described in this chapter can be used to identify new genes that regulate heterochromatin formation. For instance, strains of Drosophila melanogaster with the White variegation phenotype have been subjected to mutagenesis to screen for dominant mutations (in other genes) that either enhance or suppress PEV, meaning the mutations result in either lower or higher red pigment production, respectively. Which of the following mutations is expected to be an enhancer of variegation?

Accepted Answer

A)  A mutation that results in the loss of function of the fly's HP1 (heterochromatin protein 1) gene. 
B)  A loss-of-function mutation in a gene encoding a histone deacetylase that deacetylates lysine 9 on histone H3. 
C)  A gain-of-function mutation in a gene encoding a histone methyl transferase that trimethylates lysine 9 on histone H3, resulting in a hyperactive form of the enzyme. 
D)  A gain-of-function mutation in a gene encoding a histone acetyl transferase that normally acetylates lysine 9 on histone H3, resulting in higher expression of the protein. 
A)  A mutation that results in the loss of function of the fly's HP1 (heterochromatin protein 1) gene. 
B)  A loss-of-function mutation in a gene encoding a histone deacetylase that deacetylates lysine 9 on histone H3. 
C)  A gain-of-function mutation in a gene encoding a histone methyl transferase that trimethylates lysine 9 on histone H3, resulting in a hyperactive form of the enzyme. 
D)  A gain-of-function mutation in a gene encoding a histone acetyl transferase that normally acetylates lysine 9 on histone H3, resulting in higher expression of the protein.

Question 20

Indicate true (T) and false (F) statements below regarding human genetic variations. Your answer would be a four-letter string composed of letters T and F only, e.g. TFTF.
( )	The genomes of two randomly chosen humans are expected to be identical with respect to at least 99.99% of the nucleotides.
( ) 	Copy number variations can contain genes.
( )	If the frequency of a point mutation in a population is only 0.1%, with no mutation at this site in the rest of the population, then the variation is NOT considered to constitute a single-nucleotide polymorphism.
( )	Most of the common genetic variants in the current human population could have been present in a human ancestral population of only about 10,000 individuals.

Accepted Answer

A number of variations-such as scatter

Which of the following features of DNA underlies its simple replication procedure?

What features do Cajal bodies, interchromatin granule clusters, and nucleoli have in common?

Which of the following would most reliably suggest that a genomic sequence is functionally important?

Polytene chromosomes are useful for studying chromatin because they …

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 of the following scenarios is definitely NOT going to happen?

Which of the following is true regarding heterochromatin in a typical mammalian cell?

Five major types of chromatin were identified in studies performed on Drosophila melanogaster cells, although much more remains to be learned about chromatin diversity and dynamics. Which of the following is correct regarding these findings in Drosophila?

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They …

Lampbrush chromosomes …

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

Cells and Genomes

Cell Chemistry and Bioenergetics

Proteins

DNA Replication, Repair, and Recombination

How Cells Read the Genome: From DNA to Protein

Control of Gene Expression

Analyzing Cells, Molecules, and Systems

Visualizing Cells

Membrane Structure

Membrane Transport of Small Molecules and the Electrical Properties of Membranes

Intracellular Compartments and Protein Sorting

Intracellular Membrane Traffic

Energy Conversion: Mitochondria and Chloroplasts

Cell Signaling

The Cytoskeleton

The Cell Cycle

Cell Death

Cell Junctions and the Extracellular Matrix

Cancer

Development of Multicellular Organisms

Stem Cells and Tissue Renewal

Pathogens and Infection

The Innate and Adaptive Immune Systems

Filters

Exam 4: DNA, Chromosomes, and Genomes

Which of the following features of DNA underlies its simple replication procedure?

What features do Cajal bodies, interchromatin granule clusters, and nucleoli have in common?

Which of the following would most reliably suggest that a genomic sequence is functionally important?

Polytene chromosomes are useful for studying chromatin because they …

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 of the following scenarios is definitely NOT going to happen?

Which of the following is true regarding heterochromatin in a typical mammalian cell?

Five major types of chromatin were identified in studies performed on Drosophila melanogaster cells, although much more remains to be learned about chromatin diversity and dynamics. Which of the following is correct regarding these findings in Drosophila?

The chromatin remodeling complexes play an important role in chromatin regulation in the nucleus. They …

Lampbrush chromosomes …

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

Cells and Genomes

Cell Chemistry and Bioenergetics

Proteins

DNA Replication, Repair, and Recombination

How Cells Read the Genome: From DNA to Protein

Control of Gene Expression

Analyzing Cells, Molecules, and Systems

Visualizing Cells

Membrane Structure

Membrane Transport of Small Molecules and the Electrical Properties of Membranes

Intracellular Compartments and Protein Sorting

Intracellular Membrane Traffic

Energy Conversion: Mitochondria and Chloroplasts

Cell Signaling

The Cytoskeleton

The Cell Cycle

Cell Death

Cell Junctions and the Extracellular Matrix

Cancer

Development of Multicellular Organisms

Stem Cells and Tissue Renewal

Pathogens and Infection

The Innate and Adaptive Immune Systems

Filters