Question

The human genome contains approximately \(10^{6}\) copies of an \(A l u\) sequence, one of the best-studied classes of short interspersed elements (SINEs), per haploid genome. Individual Alu units share a 282-nucleotide consensus sequence followed by a 3 '-adenine-rich tail region ISchmid (1998)]. Given that there are approximately \(3 \times 10^{9}\) base pairs per human haploid genome, about how many base pairs are spaced between each Alu sequence?

Short answer

Answer: Approximately \(3 \times 10^3\) base pairs.

Step-by-step solution

Calculate total base pairs of the human genome

There are approximately \(3 \times 10^9\) base pairs per human haploid genome.

Determine the number of Alu sequences

The human genome has roughly \(10^6\) copies of an Alu sequence per haploid genome.

Calculate the average spacing between Alu sequences

To find the average spacing between each Alu sequence, divide the total base pairs by the number of Alu sequences: \(\frac{Total \, base \, pairs}{Number \, of \, Alu \, sequences} = \frac{3 \times 10^9}{10^6}\)

Simplify the expression

Simplify the expression to find the number of base pairs spaced between each Alu sequence: \(\frac{3 \times 10^9}{10^6} = 3 \times 10^{9-6} = 3 \times 10^3\)

Answer

On average, there are approximately \(3 \times 10^3\) base pairs spaced between each Alu sequence in the human haploid genome.

Key concepts

Short Interspersed Elements (SINEs)

Short interspersed nuclear elements (SINEs) are a type of repetitive DNA sequences that are widely dispersed throughout the eukaryotic genomes. In the human genome, one of the most common types of SINEs is known as the Alu element. Named for its recognition site by the restriction enzyme AluI, an individual Alu sequence is typically about 300 base pairs long and originates from 7SL RNA, a component of the signal recognition particle.

These Alu elements do not code for proteins, but they can impact genetic functions in several ways. They have been implicated in gene regulation, recombination, and even in the evolution of the genome structure. Despite their non-coding nature, Alu sequences have been conserved throughout evolution, suggesting that they may have some functional importance. Interestingly, their widespread presence allows them to serve as useful markers in the study of genetic diversity and population genetics.

Haploid Genome Base Pairs

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. When we refer to the human haploid genome, we are considering only one set of chromosomes, which contains roughly 3 billion base pairs. A haploid genome, being half the diploid genome which is found in most cells, is what is passed on from each parent to child.

Within these 3 billion base pairs lies the entire blueprint for building and maintaining a human being, encoding tens of thousands of genes interspersed with non-coding segments, such as Alu sequences mentioned previously. Understanding the scope and function of this vast collection of base pairs is central to fields like genetics, genomics, and personalized medicine.

Genomic Sequence Calculation

Genomic sequence calculation involves the quantitative analysis of the nucleotide sequences in a genome. In the context of Alu sequences in the human genome, a simple calculation can illustrate the ubiquity of these elements: If there are approximately 1 million Alu sequences in the human haploid genome, as suggested by the exercise, we can estimate the average distance between them. This is done by dividing the total number of base pairs in the haploid genome (approximately 3 billion) by the quantity of Alu sequences.

By carrying out this division, \( \frac{3 \times 10^9}{10^6} \), we determine that there is an average spacing of roughly 3,000 base pairs between each Alu sequence. This calculation does not consider variability in distribution or clustering of Alu sequences, but it provides a basic understanding of how frequently these elements occur within the genomic landscape.

Nucleotide Consensus Sequence

A nucleotide consensus sequence is a way of representing the sequence of nucleotides in DNA or RNA that is common to many different molecules or species. The consensus sequence is derived from alignment of multiple sequences that are thought to have a common ancestor and is representative of common motifs that may have functional or evolutionary significance.

In reference to Alu elements, the consensus sequence of 282 nucleotides is typical of this type of SINE and is indicative of a common ancestral sequence from which various copies have been derived. The consensus sequence is crucial for understanding genetic variation and function, as even a single nucleotide change can sometimes lead to significant changes in phenotype or disease. Furthermore, the consensus sequence of Alu elements can be used in genetic research and forensic studies, as these sequences can be highly specific to individuals or populations.