Download problem set

Chap. 6 Problem 2
Protein coding genes are grouped into the classes known as solitary (single)
genes, and duplicated or diverged genes in gene families (Table 6.1). In humans,
roughly equal numbers of protein-coding genes fall into these two categories.
Examples of gene and protein families are the ß-globin and tubulin families.
Gene families consist of duplicated genes that encode proteins with similar but
non-identical sequences. Pseudogenes are rare non-functional DNA sequences
derived from gene duplication or reverse transcription and integration of cDNA
sequences made from mRNA. Through sequence drift, they have become
nonfunctional. Tandemly repeated genes (e.g., rRNAs) were derived by gene
duplication but show minimal sequence drift. They commonly are present in
head-to-tail arrays in the genome.
Chap. 6 Problem 3
Satellite DNA is classified into 3 categories based on
length. Satellite DNA consists of 14-500 bp sequence
units that tandemly repeat over 20-100 kb lengths of
genomic DNA. Minisatellite DNA consists of 15-100
bp sequence units that tandemly repeat over 1-5 kb
stretches of DNA. Microsatellite DNA consists of 113 bp units that can repeat up to 150 times.
Although the sequences of satellite DNA are highly
conserved, the number of tandem copies at each locus
is highly variable between individuals. This originates
due to unequal crossing over during formation of
gametes in meiosis (Upper figure). DNA fingerprinting
is a method for identifying individuals based on
variations in minisatellite DNA (Fig. 6.7). In the
method, minisatellite DNA is amplified by PCR using
unique primers flanking repeat regions, and the
collection of fragments is run on a gel. Due to the
variation in the number of repeats at different loci,
different individuals can be readily distinguished.
Chap. 6 Problem 6
Mobile DNA is grouped into two classes,
DNA transposons and retrotransposons
(see Fig. 6.8). DNA transposons move
directly as DNA via a "cut-and-paste"
mechanism. Retrotransposons move via an
RNA intermediate and a "copy-and-paste"
mechanism, wherein the original copy of
the transposon is preserved. Insertion of
mobile DNA can directly cause mutations
that influence genome evolution. In
addition, mobile DNA plays an important
role in gene evolution via promoting exon
shuffling. Exons can be shuffled by
unequal crossing over between mobile DNA
elements such as the Alu sequence (Fig.
6.18, top), DNA transposon transposition
(Fig. 6.19a, middle), or LINE element
transposition (Fig. 6.19b, bottom).
Chap. 6 Problem 8
Paralogous genes are derived from gene
duplications and have diverged to
perform different functions in a given
organism. Orthologous genes typically
perform the same function in different
organisms, and have diverged in
sequence due to mutations associated
with speciation (Fig. 6.26b).
The complexity of an organism is not simply related to the size of its genome.
Due to alternative splicing of mRNA transcripts, many more proteins can be
encoded than there are genes. A small increase in gene number results in a
much larger increase in protein number, and associated complexity.
Chap. 6 Problem 9
Nucleosomes consist of 147 bp of DNA
wrapped in almost two turns around the
outside of an octamer of histone proteins
(Fig. 6.29). The octamer has a stoichiometry
of H2A2H2B2H32H42. Histones have a large
number of basic amino acids and bind to DNA
mostly by salt-bridge interactions to
phosphates in the DNA backbone. Another
histone, H1, binds to the linker DNA between
nucleosomes. Linker DNA is 15-55 bp in
length depending upon the organism. In 30nm fibers, nucleosomes bind to one another in
a spiral arrangement wherein ~6 nucleosomes
occur per turn (Fig. 6.30). Histone H1
molecules help mediate interactions between
individual nucleosomes. Interactions between
nucleosomes in 30-nm fibers also are
modulated by post-translational modification
of the tails of histones in the octamers (H3
& H4 in particular).
Chap. 6 Problem 11
Eukaryotic chromosomes consist of long linear DNA molecules in which the
DNA is wrapped around histones to form chromatin. The DNA occurs in a
highly condensed state in metaphase chromosomes and in a less condensed
form in interphase chromosomes. In both types of chromosomes, loops
composed of chromatin fibers project out from a scaffold composed of nonhistone proteins (Fig. 6.35). In interphase chromosomes, regions of the loops
containing non-expressed genes are thought to retain a condensed 30-nm
chromatin fiber structure. Regions containing expressed genes adopt the more
extended beads-on-a-string packing. 30-nm fibers attach to the scaffold at
scaffold-associated regions (SARs) and matrix attachment regions (MARs).
Protein-coding genes are not located in regions with SARs and MARs because
the DNA in these areas is highly condensed.
Chap. 6 Problem 15
Replication origins are DNA sequences at which DNA
synthesis initiates in S phase of the cell cycle. In
M phase, condensed metaphase chromosomes formed
after DNA replication are observed. They contain
two sister chromatids joined at a structure called
the centromere (Fig. 6.39). Centromeres are
required for chromatid separation in mitosis and are
the sites where mitotic spindle fibers attach. The
ends of chromatids are called telomeres. Telomeres
are important in preventing chromosome shortening
during replication. A special mechanism is needed
for the replication of DNA within the 3' ends of
DNA strands at chromosome ends. Otherwise,
chromosomes become shortened with each round of
replication, resulting eventually in deletion of
essential genes. a) If a chromosome lacked
replication origins, it could not duplicate during S
phase of the cell cycle. b) If a chromosome lacked
a centromere, the chromosome could be replicated,
but the two sister chromatids of a metaphase
chromosome may not segregate equally to the two
daughter cells during cell division.