Genome

 

It is common to observe that mango seeds germinate to become mango plants, and that dogs only give birth to puppies and not to the young of any other animal. Humans give birth to human beings. It is truly marvelous that life perpetuates itself so faithfully! The fact that mango seeds invariably produce mango trees, dogs always give birth to puppies, and elephants only produce elephant calves speaks to the power of their inherent genetic code, the DNA within their cells. This DNA acts as a precise instruction manual, uniquely dictating the development and characteristics of each species. The DNA in a mango seed contains the complete blueprint for a mango plant, ensuring that its young follow the same developmental path. Likewise, the DNA of dogs and elephants contains the specific instructions for their respective species.

Genome

The term "genome," composed of "gene" and "chromosome," was first coined in 1920 by German botanist Hans Winkler. Currently, the term genome is described as "the complete genetic set of a living organism." The genome of most eukaryotes comprises several protein-coding genes, non-protein-coding genes, and transcriptional regulatory elements such as enhancers, suppressors, promoters, and so on. In addition, there are sequences responsible for the regulation of chromosome structure and dynamics. Therefore, the genome can be defined as the complete set of genes and all other functional and non-functional DNA sequences of an organism on a haploid set of chromosomes. It comprises both nuclear and mitochondrial DNA.

Genome sequencing 

Genome sequencing is the process of determining the complete DNA sequence of an organism's genome, including all chromosomal DNA and, in plants, chloroplast DNA.   By meticulously mapping out the order of the billions of nucleotide bases (A, T, C, and G), genome sequencing empowers researchers to conduct in-depth analyses of genetic variations within and between populations. This capability is invaluable for pinpointing specific gene mutations associated with diseases, paving the way for improved diagnostics and potential therapies. Furthermore, by comparing the complete genomes of different species, scientists can reconstruct evolutionary histories, unraveling the genetic relationships and the processes that have shaped the diversity of life, perhaps even shedding light on the unique adaptations of flora and fauna. This detailed genetic information is a cornerstone of modern biology, driving advancements in fields ranging from personalized medicine to conservation efforts.

MCQs on Genome Sequencing

1. The _____ resolution genome map is the genomic DNA sequence that can be considered as a type of ______ map describing a genome at the single base-pair level.
a) highest, physical                                          b) lowest, physical
c) highest, cytological                                     d) lowest, cytological
Key: a
Explanation: Physical maps at the highest resolution describe the genome at the single base-pair level.

2. Which of the following is untrue about DNA sequencing?
a) It is now routinely carried out using the Sanger method
b) This doesn’t make use of DNA polymerases
c) This involves the synthesis of DNA chains of varying length
d) The DNA synthesis is stopped by adding dideoxynucleotides
Key: b
Explanation: DNA polymerases are essential for synthesizing DNA chains in sequencing.

3. What is the molarity of urea used in sequencing gels?
a) 1 M                          b) 3 M                        c) 5 M                          d) 7 M
Key: d
Explanation: Sequencing gels typically use 7 M urea to prevent secondary structure.

4. The shotgun approach _______ sequences clones from _____ of cloned DNA.
a) randomly, one end                                      b) randomly, both ends
c) specifically, both ends                                d) specifically, one end
Key: b
Explanation: Shotgun sequencing randomly sequences both ends of DNA fragments.

Explanation: Shotgun sequencing relies on computational assembly, not prior mapping.

5. A sequencing gel is a ________________ gel.
a) Toxic                       b) Highly-polymerized            c) High resolution       d) Low resolution
Key: c
Explanation: Sequencing gels are high-resolution to separate DNA fragments by single bases.

7. The hierarchical genome sequencing approach is ______
a) entirely dissimilar to the shotgun approach
b) dissimilar to the shotgun approach
c) similar to the shotgun approach, but on a larger scale
d) similar to the shotgun approach, but on a smaller scale
Key: c
Explanation: Hierarchical sequencing uses mapped large fragments, then shotgun sequencing within those.

8. In hierarchical genome sequencing approach, based on the results of _______ mapping _______of the BAC clones on a chromosome can be determined.
a) physical, the locations and orders               b) physical, only the locations
c) cytological, only the locations                    d) physical, only the orders
Key: a
Explanation: Physical mapping determines both the location and order of BAC clones.

9. The hierarchical approach is ____ and _____ than the shotgun approach because it involves an initial clone-based physical mapping step.
a) slower, less costly                                       b) faster, more costly 

c) faster, less costly                                         d) slower, more costly
Key: d
Explanation: It is slower and more costly due to the initial mapping step.

10. Prior to getting electrophoresed in the sequencing gel, DNA is ____________
a) Purified                   b) Denatured                           c) Synthesized             d) Fragmented
Key: b
Explanation: DNA is denatured before electrophoresis in sequencing gels.

11. Chain-termination is a type of ______________
a) Sequencing              b) Vector generation   c) Antibiotic production         d) Gene manipulation
Key: a
Explanation: Chain-termination refers to Sanger sequencing.

12. The first significant DNA sequence to be obtained was that of ________
a) Lambda                   b) Plasmid                   c) Lactose                    d) Mammals
Key: a
Explanation: The first significant sequence was of lambda phage cohesive ends.

13. Which of the following best describes the primary advantage of next-generation sequencing (NGS) over Sanger sequencing?
a) Higher accuracy per base
b) Lower cost per base and massively parallel sequencing
c) Ability to sequence entire chromosomes in a single reaction
d) No requirement for DNA amplification
Key: b
Explanation: NGS enables high-throughput, cost-effective sequencing by processing millions of fragments simultaneously, unlike Sanger's sequential approach.

14. Which type of DNA cleavage is done in the Maxam Gilbert method?
a) Edge                        b) Interstitial               c) Base-specific           d) Gene-specific
Key: c
Explanation: Maxam-Gilbert sequencing uses base-specific cleavage.

15. What is the main enzyme component of Sanger sequencing?
a) Helicase                   b) Polymerase              c) Nuclease                  d) Gyrase
Key: b
Explanation: DNA polymerase is the key enzyme in Sanger sequencing.

16. Which of the following is used by DNA polymerase as a substrate?
a) Sucrose                    b) Lactose                   c) Nucleotide              d) Nucleoside
Key: c
Explanation: DNA polymerase uses nucleotides as substrates.

17. Which of the following act as chain terminator?
a) Exogenous              b) DNA           c) Deoxynucleotides               d) Dideoxynucleotides
Key: d
Explanation: Dideoxynucleotides terminate DNA chain elongation in Sanger sequencing.

18. The Klenow fragment is basically a _______________
a) DNA hybrid            b) DNA polymerase                c) RNA polymerase    d) Promoter
Key: b
Explanation: The Klenow fragment is a DNA polymerase used in sequencing.

19. ____________ is a chemically synthesized oligonucleotide.
a) Klenow fragment    b) DNA                                   c) Primer                      d) RNA
Key: c
Explanation: Primers are chemically synthesized oligonucleotides.

20. How many types of deoxynucleoside triphosphates are used in Sanger sequencing?
a) 1                              b) 2                                          c) 3                              d) 4
Key: d
Explanation: Four types (A, T, G, C) are used in Sanger sequencing.