Question 1

Which domain(s) have densely packed genomes with little noncoding space?

Accepted Answer

Bacteria and Archaea typically have densely packed genomes with little noncoding space, in contrast to Eukarya, which often have significant amounts of noncoding DNA.

Question 2

What marks the 5 ' end of an ORF in a DNA sequence?

Accepted Answer

The 5' end of an open reading frame (ORF) in a DNA sequence is marked by the start codon, which is ATG in DNA.

Question 3

The chemical difference between dideoxyribonucleotides used in Sanger sequencing and the deoxyribonucleotides normally found in DNA is the presence of a(n) _____ in the deoxyribose sugar of dideoxyribonucleotides.

Accepted Answer

Dideoxyribonucleotides, used in Sanger sequencing, have a hydrogen atom (-H) at the 3' position of the deoxyribose sugar instead of a hydroxyl group (-OH) found in normal deoxyribonucleotides. This absence of a 3' -OH group prevents the addition of subsequent nucleotides, thus terminating DNA synthesis.

Question 4

In whole-genome shotgun sequencing, ____.

Accepted Answer

Whole-genome shotgun sequencing involves breaking DNA into many random, overlapping fragments. These fragments are then sequenced, and computer algorithms are used to assemble these sequences into a continuous sequence, taking advantage of the overlaps to put the fragments in the correct order.

Question 5

To study how genes have evolved, scientists compare the genome sequences of related organisms, a research approach known as _____.

Accepted Answer

Comparative genomics is the study of the relationship between the genome sequences of different species to understand their evolutionary relationships and how genes have evolved over time.

Question 6

How do scientists most often access genome sequences determined by research projects?

Accepted Answer

Scientists most often access genome sequences through online public databases like GenBank, where research projects typically deposit their sequencing data for public access. This allows for the widespread sharing of genetic information within the scientific community.

Question 7

Which study indicates that some mutations are inherited from our parents?

Accepted Answer

The study of mutations in germline cells indicates that some mutations are inherited from our parents because germline cells are involved in reproduction, passing genetic information from parents to offspring.

Question 8

In the whole-genome shotgun method, the genome is fragmented and individual fragments are sequenced. How is the order of the nucleotides determined for the original intact chromosome?

Accepted Answer

The random fragmentation in the whole-genome shotgun method results in overlapping sequences. These overlaps allow bioinformatic tools to align and assemble the fragments in the correct order, reconstructing the original intact DNA molecule.

Question 9

Which element of a dideoxy sequencing reaction allows for visualization of the DNA sequence?

Accepted Answer

The mixture of the four dideoxyribonucleotides, each with a different fluorescent label, allows for the visualization of the DNA sequence in dideoxy sequencing (also known as Sanger sequencing). These labeled nucleotides terminate DNA synthesis at different points, creating fragments of various lengths that can be visualized and used to determine the DNA sequence.

Question 10

The percentage of the human genome sequence that is protein-coding is less than _____.

Accepted Answer

The percentage of the human genome that is protein-coding is less than 2%. Most of the genome consists of non-coding DNA, which includes regulatory sequences, introns, and non-coding RNAs.

Question 11

The human genome is composed of approximately _____ billion base pairs.

Accepted Answer

The human genome contains approximately 3 billion base pairs of DNA.

Question 12

The Human Genome Project completed in 2003 focused on sequencing the genome(s) of _____.

Accepted Answer

The Human Genome Project, while primarily focused on sequencing the human genome, also included work on other model organisms such as mice, fruit flies, and yeast to help understand the function of genes and genetic elements in humans.

Question 13

During a DNA sequencing experiment, the researcher adds all the required components to the reaction, but accidentally adds only one of the four dideoxynucleotides, the ddC. What products will be observed after this reaction is complete?

Accepted Answer

When ddC (dideoxycytidine) is added to a DNA sequencing reaction, it gets incorporated into the growing DNA strand in place of the normal nucleotide (dC). Since ddC lacks the 3' hydroxyl group necessary for forming a phosphodiester bond with the next nucleotide, the DNA chain elongation stops whenever ddC is incorporated. Therefore, all DNA fragments produced in this reaction will end in C, as ddC terminates the extension of the DNA strand at every point where a cytosine (C) would normally be incorporated.

Question 14

What is a difference between human male and female genomes?

Accepted Answer

Males have one X and one Y chromosome (making 24 different types of chromosomes considering the autosomes), while females have two X chromosomes (making 23 different types because they have two of the same sex chromosome).

Question 15

A scientist obtains the DNA sequence data for a bacterial plasmid. The data include As, Ts, and Gs, but no Cs.  What is the most likely cause of this result?

Accepted Answer

Omitting ddCs (dideoxycytidines) from the sequencing reaction would prevent the incorporation of these chain-terminating nucleotides at cytosine positions, leading to a lack of sequencing stops at Cs and thus no Cs being detected in the sequence data.

Question 16

Deoxyribonucleotides are included in the Sanger sequencing reaction mix to _____.

Accepted Answer

Deoxyribonucleotides serve as the building blocks for DNA polymerase to synthesize new DNA strands during Sanger sequencing. By incorporating these nucleotides, the reaction enables the production of multiple DNA fragments of varying lengths, which are essential for determining the sequence of the target DNA.

Question 17

When the human genome was sequenced, we learned that there are fewer than expected protein-coding genes (approximately 20,000). Yet, the total number of proteins produced in humans approaches 100,000. What accounts for this discrepancy in numbers?

Accepted Answer

The discrepancy between the number of protein-coding genes and the total number of proteins produced in humans is accounted for by the processing mechanisms for mRNAs, which allow multiple proteins to be produced from a single DNA sequence through processes such as alternative splicing.

Question 18

What is an open reading frame (ORF)?

Accepted Answer

An open reading frame (ORF) is defined as the sequence between and including a start codon and a stop codon, which potentially encodes a protein. It does not specifically exclude introns or exons nor is it exclusive to prokaryotes.

Question 19

In humans, the majority of a transcription unit is composed of ____.

Accepted Answer

In humans, the majority of a transcription unit is often composed of introns, which are segments of a gene that are transcribed into RNA but are removed during RNA processing and therefore do not encode protein. Exons, which do encode protein, typically make up a smaller portion of the transcription unit.

Question 20

Which pre-mRNA processing mechanism allows different proteins to be produced from the same DNA sequence?

Accepted Answer

Alternative splicing allows for the production of different proteins from the same DNA sequence by varying the combination of exons included in the final mRNA transcript.

Quiz 19: Genomes and Proteomes