9.3

What is a genome?

The complete collection of DNA sequences in an organism.

What is genome sequencing?

Determining the order of DNA bases (A, T, G, C) in a genome.

About how many protein-coding genes do humans have?

About 20,000.

Why can humans be complex despite having relatively few genes?

Alternative splicing and gene regulation allow many protein products and functions.

What are exons?

Parts of a gene's RNA transcript retained after splicing; they can include coding and untranslated sequences.

What are introns?

Sequences removed from a precursor RNA during splicing.

What is RNA splicing?

Removing introns and joining exons to form a mature RNA.

What is alternative splicing?

Joining exons in different combinations so one gene can make different RNA and protein products.

How common are introns in bacterial genes?

Few bacterial genes contain introns.

What percentage of human DNA directly codes for proteins?

Less than 1.5%.

About how much human DNA is within protein-coding genes when introns are included?

About 30%.

What is a transposon?

A DNA sequence capable of moving or copying itself to another genomic location.

What is a retrotransposon?

A transposable element that moves through an RNA intermediate converted back to DNA.

Approximately how much of the human genome is derived from transposons?

Nearly half.

Why are transposons important in evolution?

They can insert, duplicate, or rearrange DNA and change gene regulation.

What did the ENCODE project investigate?

Biochemical activity and potential functional elements across the human genome, including noncoding DNA.

What did ENCODE report about much of the human genome?

More than 80% showed transcription or other biochemical activity; activity does not necessarily prove biological function.

What are simple-sequence repeats (SSRs)?

Short DNA sequences repeated many times in tandem.

What are short tandem repeats (STRs)?

Short repeated DNA motifs that often vary in repeat number among people.

Why are STRs useful in forensic DNA analysis?

Their repeat counts vary among individuals and help distinguish DNA samples.

Where are prominent simple-sequence repeats found?

At centromeres and telomeres.

What is a single nucleotide polymorphism (SNP)?

A common variation at one DNA-base position in a population.

On average, how often do human DNA sequences differ at single-base positions?

About 1 in every 1,000 bases, according to the chapter.

Do all SNPs change traits or cause disease?

No. Many have little or no noticeable effect.

What is a haplotype?

A group of nearby DNA variants that tend to be inherited together.

Why are nearby SNPs often inherited together?

They are less likely to be separated by recombination.

What is a tag SNP?

A representative SNP used to identify a particular haplotype without testing every SNP.

How can haplotypes help researchers?

They help study genetic variation, disease associations, and human migration.

Why are mitochondrial DNA and Y-chromosome haplotypes useful for ancestry studies?

They are passed through maternal or paternal lineages with little or no recombination across most of their sequences.

What is comparative genomics?

Comparing genome sequences from different organisms to study genes and evolution.

How many chromosome pairs do humans have?

23 pairs.

How many chromosome pairs do chimpanzees and other great apes typically have?

24 pairs.

How did human chromosome 2 arise?

Fusion of two ancestral chromosomes in the human lineage.

Why is human chromosome 2 evidence of common ancestry?

Its structure corresponds to two separate chromosomes found in other great apes.

About how different are aligned human and chimpanzee DNA sequences at the base-pair level?

About 1.23%, according to the chapter.

Why are total human-chimp genome differences larger than base substitutions alone?

Insertions, deletions, duplications, and other rearrangements also differ; the chapter estimates over 4% overall.

What is a phylogenetic tree?

A diagram showing inferred evolutionary relationships among organisms or lineages.

What is an outgroup in comparative genomics?

A more distantly related species used to infer the ancestral DNA sequence.

How does an outgroup help identify a human-specific mutation?

It helps determine whether the human or chimpanzee version differs from their likely ancestor.

What kinds of chromosome changes can occur during evolution?

Duplications, inversions, insertions, deletions, transpositions, and fusions.

How can gene regulation contribute to human-specific traits?

Changing when, where, or how strongly genes are expressed can alter development and function.

What is HAR1?

A rapidly evolved human genomic region that produces a noncoding RNA associated with brain development.

What gene family does the chapter mention as duplicated in the human lineage?

Glutamate dehydrogenase genes.

What is linkage analysis?

Using the co-inheritance of DNA markers and a trait or disease to locate a related gene.

Why do DNA markers close to a disease gene help locate it?

Nearby markers are more likely to be inherited together with the disease gene.

What is a typical first step in linkage analysis?

Compare genetic markers in affected and unaffected members of families with the disease.

Which chromosome was linked to the early-onset Alzheimer disease gene PS1?

Chromosome 14.

What does PS1 encode?

Presenilin-1, a protein associated with certain inherited early-onset Alzheimer disease cases when mutated.

Does a genetic marker linked to a disease necessarily cause it?

No. It may simply be located near the disease-causing variant.

Why can some inherited diseases be difficult to map?

They may involve multiple genes, different mutations, or interactions between genes.

How do genome databases help find disease genes?

They identify genes in candidate regions and provide sequence and functional clues.

Where did anatomically modern humans arise according to the chapter?

Africa, approximately 250,000–350,000 years ago.

What can ancient DNA reveal?

Relationships, interbreeding, migrations, and genetic changes in past human populations.

What did ancient DNA reveal about Neanderthals and modern humans?

Their ancestors interbred; some present-day non-African genomes contain Neanderthal-derived DNA.

What proportion of Neanderthal-derived DNA does the chapter report for some non-African people?

Up to about 5%.

What does the chapter report about Denisovan ancestry?

Some Melanesian and Australian populations have up to about 6% Denisovan-derived DNA.

How can DNA help reconstruct ancient human migrations?

Comparing haplotypes and genetic differences reveals relationships among populations over time.

How might personal genome sequencing help medicine?

It may identify disease-related variants and help guide diagnosis, risk assessment, or treatment research.

What is gene therapy?

An approach to treating disease by adding, replacing, or altering genetic material.