The Human Genome Project fostered development of faster, less expensive sequencing techniques
3 Top-level/Main Ideas
1. The Human Genome Project (HGP) aimed to map and sequence the DNA of the human genome.
2. The whole-genome shotgun approach uses powerful software to sequence shorter fragments of DNA into a continuous sequence.
3. Metagenomics is the term that describes sequencing DNA from a community of species from an environmental sample.
4 Medium-level Ideas
1. The amount of nucleotides that could be sequenced in a day in 1980 could be sequenced in just one second in 2000, and machines that can sequence even faster are on the rise.
2. The goal of sequencing a genome is to know the whole nucleotide sequence of each chromosome.
3. New techniques allow speed to increase and cost to decrease by sequencing very small fragments at a time before piecing them together to form one, long sequence.
4. Metagenomics allows sequencing of DNA from mixed microbial populations.
Bottom-level Bullet Points
• HGP completed in 2003, papers published in 2006
• HGP sequenced using dideoxy chain termination method
• Sequencing uses high-throughput methods = produces high amounts of data
21.2 Scientists use bioinformatics to analyze genomes and their functions
3 Top-level/Main Ideas
1. Researchers around the world have access to a number of bioinformatics resources that contain links to databases, software, and other genomics information.
2. Gene annotation describes the process of identifying protein coding genes in a sequence and discovering their functions.
3. Genomics and proteomics are part of systems biology, which aims to study biology as a group of systems interacting.
4 Medium-level Ideas
1. GenBank is the NCBI’s database of sequences, and BLAST is the software that allows users to compare a DNA sequence with every sequence in GenBank.
2. To identify a gene, gene annotation uses computers to search for indicative patterns and expressed sequence tags, software to compare the unknown sequence to a known sequence in another organism, and RNA-seq or another method to confirm its identity.
3. ENCODE was a research project that applied experimental methods of sequencing to work towards learning as much as possible about function elements of the human genome.
4. An important use of systems biology is defining networks of gene and protein interactions.
Bottom-level Bullet Points
• Protein Data Bank has 3D protein structure images
• WD40 Domains = functional part of proteins/signal transduction pathways of eukaryotic proteins
• Cancer Genome Atlas = how biosystem changes lead to cancer
• Sequencing whole genomes of tumors allows for comparison of common abnormalities
21.3 Genomes vary in size, number of genes, and gene density
3 Top-level/Main Ideas
1. Bacterium genome sizes are much smaller than eukaryotic genomes, which have a wide range of genome sizes.
2. On average, bacteria and archaea will have fewer genes than eukaryotes do.
3. Gene density depends on how many genes are in a given length of DNA, comparing size and quantity of genes.
4 Medium-level Ideas
1. There is a wide range of genome sizes within groups of unicellular eukaryotes, insects, and plants, and a smaller range between mammals and reptiles.
2. Vertebrate genomes are more complex due to extensive alternative splicing of RNA transcripts.
3. Post-transcriptional modifications and other small RNAs are also thought to increase organismal complexity.
4. Mammals and humans have the lowest gene density because they have less genes even though they have more base pairs.
Bottom-level Bullet Points
• Eukaryotic genome size =/= correlation to phenotype
• Genes have many alternatively-spliced forms in humans
• Unicellular eukaryote genes Mb < bacterial/archaea Mb
21.4 Multicellular eukaryotes have a lot of noncoding DNA and many multigene families
3 Top-level/Main Ideas
1. Only a small fraction of multicellular eukaryotic gene sequences are used to code for proteins.
2. Transposable genetic elements are found in prokaryotes and eukaryotes and contribute to genetic variation.
3. Multigene families can consist of either identical or non-identical DNA sequences.
4 Medium-level Concepts
1. Gene-related regulatory sequences and introns make up about a quarter of the human genome, while the rest includes noncoding DNA, like gene fragments or pseudogenes.
2. Almost half of the human genome is made of transposable elements, which come in two types in eukaryotes – transposons, and the more common retrotransposons.
3. The amount of STR units can vary from site to site of a given genome, producing more genetic diversity.
4. Multigene families with identical DNA sequences result in RNAs while non-identical DNA sequences result in globins.
Bottom-level Bullet Points
• Repetitive DNA = STR or long/dispersed
• Pseudogenes = similar to real gene but has no real functional product
• Transposable elements move within genome through DNA/RNA intermediates
21.5 Duplication, rearrangement, and mutation of DNA contribute to genome evolution
3 Top-level/Main Ideas
1. Comparisons of chromosomal organizations allows inferences to be made about speciation and evolution.
2. Errors during meiosis can result in extra sets of chromosomes, duplication of small chromosomal regions, and slippage.
3. Transposable elements contribute to genome evolution by promoting recombination, disrupting cellular genes, and carrying genes or exons to new locations.
4 Medium-level Ideas
1. Analysis of evolutionary history can show that globin genes evolved from one common ancestral gene that underwent duplication and divergence into alpha and beta globin ancestral genes.
2. Lysozymes are an example of a gene that was duplicated in one lineage (mammal) but not another (avian), so it codes for two completely different sets of proteins in the two lineages.
3. Errors in meiosis can contribute to exon shuffling within a gene or between two different genes.
4. Chromosomal arrangements are believed to contribute to the generation of a new species.
Bottom-level Bullet Points
• Polyploidy = failure of homologous chromosomes to separate
• Mutations: effects are dependent upon the organism and the role of the gene in that organism
o Some mutations may be lethal or they could provide an advantage
21.6 Comparing genome sequences provides clues to evolution and development
3 Top-level/Main Ideas
1. By comparing genomes from both distantly and closely related species, one can determine which genes are conserved or which diverged.
2. The study of evolutionary developmental biology aims to understand how developmental processes of different multicellular organisms has evolved to allow modifications or new feature creations.
3. A homeobox codes for a homeodomain in encoded proteins and is widely conserved in animals.
4 Medium-level Concepts
1. Longer stretches of DNA have larger insertions and deletions and are more different in analysis in comparison to a single nucleotide substitution.
2. The FOXP2 gene is an example of a gene that underwent rapid change in the human lineage, and its mutations and expression in humans and other animals was studied to show that it activates genes related to vocalization.
3. Copy-number variants, single-nucleotide polymorphism, and variations in repetitive DNA are used to study genomic evolution by looking at differences in chromosomal inversion, deletions, and duplications.
4. Hox-genes, or homeobox-containing genes, were the first genes to have the homeobox sequence and was valuable enough to be conserved in organisms, unchanged, for hundreds of millions of years.
Bottom-level Bullet Points
• SNPs = single base pair sites where genetic variation is found in at least 1% of the population
• evo-devo compares developmental processes in terms of evolution
15 Questions for Chapter 21
1. Explain the method used to sequence the human genome.
a. This process is called dideoxy chain termination sequencing. To do this, one strand of a DNA fragment is used as a template for synthesis of a nested set of complementary DNA fragments which are analyzed to create the final sequence of DNA.
2. How does the whole-genome shotgun approach work, and why is it effective?
a. The whole-genome shotgun approach first clones and sequences fragments from randomly cut DNA before using computer programs to assemble the shorter sequences into a single, continuous sequence.
3. How has the development of internet databases helped to advance genomics?
a. The large availability of bioinformatics resources has allowed researchers to speed up the process of sifting through large amounts of information and improves the efficiency of DNA sequence analysis. Scientists can use the databases in programs like GenBank to attempt gene annotation as well.
4. Describe the process of gene annotation and its use in genomics.
a. Gene annotation describes identifying protein-coding genes in a DNA sequence to eventually determine their functions. To do this, computers are used to search for patterns that indicate the presence of genes. Then, software is used to compare those sequences with known genes from other organisms to try and figure out their identities and functions. Finally, their identities are confirmed using RNA-seq or another method.
5. How can systems biology be applied to medicine? Can you think of another use?
a. Systems biology was applied in the Cancer Genome Atlas project to determine how changes in biological systems lead to cancer. Systems biology could also be applied by studying diseases; by looking at how different diseases interact with the human body, scientists can create preventative methods for these illnesses.
6. Why do humans have the lowest gene density?
a. Although they have many base pairs, not all of the base pairs will code for genes. Many of the base pairs in the human genome are noncoding, and because of this, humans will have less genes.
7. Explain how alternative splicing results in gene diversity.
a. Alternative splicing allows one gene to code for more than one protein after a spliceosome removes introns and uses the remaining exons to form mRNA. Multiple mRNAs are formed which will result in multiple types of proteins, and this results in gene diversity.
8. Why is there so much noncoding DNA in humans?
a. Only a small portion of DNA actual encodes functional proteins. The rest of the DNA, the noncoding DNA, can have several functions. For one, some of it is used to control gene activity and regulate transcription by determining when and where genes are activated. They provide sites for transcription factors to bind, which will promote transcription to form specific proteins.
9. Explain why simple sequence DNA plays a structural role for chromosomes.
a. Simple sequence DNA, which is a short piece of DNA that contains repeating base patterns, is concentrated mostly at the telomeres and centromeres of the chromosomes. Because they are most commonly found at these two locations, it can be assumed that the structure of a chromosome is built around the simple sequence DNA.
10. Describe Barbara McClintock’s experiments with Native American corn and what they show us about transposable elements.
a. Her experiment centered around studying the structure and function of chromosomes in cells, looking at how genes interacted and were regulated in the corn. Her observations of the corn she bred showed evidence that small portions of DNA (transposable elements) would naturally break off and move to other sections of the genome, causing the gene to have a completely different function. The experiments showed that these elements can contribute to genomic diversity.
11. Define multigene families. How do they differ depending on if they have identical or nonidentical DNA sequences?
a. Multigene families are a collection of genes that have either very similar or totally identical sequences and help us to classify organisms of similar origins. If they have identical DNA sequences, they will form result in either (the more common) a type of RNA or a histone protein. If they have nonidentical DNA, they will form globins, which are a group of proteins that include alpha and beta polypeptide subunits of hemoglobin.
12. Explain how errors in meiosis lead to genome variation.
a. If homologous chromosomes fail to separate after metaphase I, polyploidy can occur, leading to a duplicated set of chromosomes and resulting in a lethal mutation or, in some cases, provide genetic advantages that can be passed on if the organism survives. Another error can lead to the duplication of small chromosomal regions, changing the phenotype of the organism. It unequal crossing over occurs during prophase I, chromosomes can be affect by either a deletion or duplication of a particular gene. Transposable elements can also effect the outcome of crossing over during meiosis.
13. Describe how exons play a role in genome evolution.
a. Exons can be duplicated or shuffled around when rearranging a gene. A particular exon can be duplicated on one chromosome but deleted on another, altering the function of these chromosomes. Different exons can also be shuffled around, being mixed and matched within a gene or on two different genes, all due to errors in meiosis. These possibilities can lead to new proteins with new functions.
14. Why are animals with similar homeoboxes so different? (For example, humans and mice)
a. The homeoboxes in these animals control initial development, such as developmental genes, which can be found in vertebrates and invertebrates. Each animal lineage then developed their own vertebrate or invertebrate genes, amongst others, that allow them to have certain characteristics that differentiate them significantly from one another. However, they still all have the same, base homeobox for development.
15. Overall, describe some methods scientists use to study gene evolution.
a. For one, they can sequence entire genomes of organisms to find commonalities and differences to see where they diverged evolutionarily in terms of base pairings. Also, they can use these sequences to find similar-appearing genes and determine whether the function of those genes are similar or different from each other. Scientists also use systems biology to look at how systems behave when they interact with each other, showing why a certain trait might have evolved in some organisms but not others. These are just some of the says scientists have studied gene evolution.