1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why was this finding surprising? Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences were by far the principal component of centromeric DNA. However, Arabidopsis centromeres also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big surprise because it was thought that these regions were genetically inactive. 2. What differences in gene distribution and repetitive DNA content are seen when yeast and human chromosomes are compared? Ans. A typical region of a human chromosome will have few genes (most of which will contain introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast chromosomes have higher gene densities, with very few genes containing introns, and have few repeated sequences and much less nongenic DNA. 3. The human genome contains about 50,000 fewer genes than was predicted by many researchers. Why were these initial predictions so high? Ans. These early estimates were high because they were based on the supposition that, in most cases, a single gene specifies a single mRNA and a single protein. According to this model, the number of genes in the human genome should be similar to the number of proteins in human cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is much lower than this indicates that alternative splicing, the process by which exons from a pre-mRNA are assembled in different combinations so that more than one protein can be coded by a single gene is more prevalent than was originally appreciated. 4. What are the different methods used to catalog genes? What are the advantages or disadvantages of these methods? Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are incomplete because in most genomes many genes have unknown functions. Gene catalogs that are based on the identities of protein domains coded by genes are more comprehensive as these include many genes whose specific functions are unknown. 5. What is the function of the different genes in the human globin gene families? Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are expressed at different developmental stages and each includes at least one pseudogene. Note that expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is inactive. None of the other p

1. 1 Introduction to Genomics Wednesday,April 29, 2015
Assignment #2 Zohaib HUSSAIN Sp13-bty-001 BTY05
1. What did researchers find when they sequenced the centromeres of Arabidopsis? Why
was this finding surprising?
Ans: Before the Arabidopsis sequences were obtained it was thought that these repeat sequences
were by far the principal component of centromeric DNA. However, Arabidopsis centromeres
also contain multiple copies of genome-wide repeats, along with a few genes, the latter at a
density of 7–9 per 100 kb compared with 25 genes per 100 kb for the noncentromeric regions of
Arabidopsis chromosomes. The discovery that centromeric DNA contains genes was a big
surprise because it was thought that these regions were genetically inactive.
2. What differences in gene distribution and repetitive DNA content are seen when yeast
and human chromosomes are compared?
Ans. A typical region of a human chromosome will have few genes (most of which will contain
introns), several repeated sequences, and a large amount of nonrepetitive, nongenic DNA. Yeast
chromosomes have higher gene densities, with very few genes containing introns, and have few
repeated sequences and much less nongenic DNA.
3. The human genome contains about 50,000 fewer genes than was predicted by many
researchers. Why were these initial predictions so high?
Ans. These early estimates were high because they were based on the supposition that, in most
cases, a single gene specifies a single mRNA and a single protein. According to this model, the
number of genes in the human genome should be similar to the number of proteins in human

2. 2 Introduction to Genomics Wednesday,April 29, 2015
cells, leading to the estimates of 80,000–100,000. The discovery that the number of genes is
much lower than this indicates that alternative splicing, the process by which exons from a pre-
mRNA are assembled in different combinations so that more than one protein can be coded by a
single gene is more prevalent than was originally appreciated.
4. What are the different methods used to catalog genes? What are the advantages or
disadvantages of these methods?
Ans. Gene catalogs can be based on the known functions of genes, but such catalogs are
incomplete because in most genomes many genes have unknown functions. Gene catalogs that
are based on the identities of protein domains coded by genes are more comprehensive as these
include many genes whose specific functions are unknown.
5. What is the function of the different genes in the human globin gene families?
Ans. The globins are the blood proteins that combine to make hemoglobin, each molecule of
hemoglobin being made up of two a-type and two b-type globins.The a-globin cluster is located
on chromosome 16 and the b-cluster on chromosome 11. Both clusters contain genes that are
expressed at different developmental stages and each includes at least one pseudogene. Note that
expression of the a-type gene x2 begins in the embryo and continues during the fetal stage; there
is no fetal-specific a-type globin. The q pseudogene is expressed but its protein product is
inactive. None of the other pseudogenes is expressed.

3. 3 Introduction to Genomics Wednesday,April 29, 2015
6. What is the difference between a conventional pseudogene and a processed
pseudogene?
Ans. A conventional pseudogene has become inactivated due to mutation, while a processed
pseudogene arose by reinsertion of a cDNA copy of an mRNA.
7. What types of repetitive DNA are present in the human genome?
Ans. These are sequences that recur at many places in the genome. There are four main types of
genome-wide repeat, called LINEs (long interspersed nuclear elements), SINEs (short
interspersed nuclear elements), LTR (long terminal repeat) elements, and DNA transposons.
Most of the genome-wide repeats are located in the intergenic regions but several lie within
introns and Microsatellites are sequences in which a short motif is repeated in tandem. E.g One
of the microsatellites seen here has the motif CA repeated 12 times, giving the sequence:
5’–CACACACACACACACACACACACA–3’
3’–GTGTGTGTGTGTGTGTGTGTGTGT–5¢’
8. What does this picture represent? How are the different chromosomes distinguished?
Ans. The figure shows part of the human karyogram. The chromosomes are distinguished by
their size, the location of the centromere, and the banding patterns present after staining.

4. 4 Introduction to Genomics Wednesday,April 29, 2015
9. What type of pseudogene is shown in this diagram? Why is the newly integrated copy of
the gene not functional?
Ans. The figure shows a processed pseudogene, which is not functional because it is derived
from an mRNA, and hence lacks the nucleotide sequences needed to switch on and regulate gene
expression.
10. Identify the three types of bacteriophage capsid structure.
Ans. From left to right: icosahedral, filamentous, head-and-tail.