Genomics Flashcards
What is the purpose of sequencing and comparing genomes?
To explore evolutionary relationships, gene functions, and genomic differences.
What percentage of the human genome is made up of genes for proteins and RNA?
1.5%
How many genes does Escherichia coli have?
4,400 genes
How many genes does Homo sapiens have?
21,300 genes
How many genes does Zea mays (corn) have?
32,000 genes
What do gene sequences tell us about evolutionary relationships?
They provide insights into how genomes evolve over time.
What is the evolutionary rate of the elephant shark’s genome?
Slower-evolving genome
What is the evolutionary rate of the tiger tail sea horse’s genome?
Faster-evolving genome
What major project began in 1990 to sequence the human genome?
The Human Genome Project
What was the cost and duration of sequencing the first human genome?
13 years and cost between $500 million and $1 billion
What is the current cost and time to sequence a complete genome as of 2019?
Under $1,000 per genome in 44 hours
What is the whole-genome shotgun approach?
Cloning and sequencing random DNA fragments, then assembling them into a complete genome.
What is metagenomics?
The sequencing of DNA from an entire community of species from environmental samples.
What is the National Center for Biotechnology Information (NCBI)?
A centralized resource for analyzing genome sequences.
What is GenBank?
A database of sequences maintained by the NCBI.
What program allows users to compare a DNA sequence with every sequence in GenBank?
BLAST (Basic Local Alignment Search Tool)
What does the Protein Data Bank maintain?
A worldwide database of experimentally determined three-dimensional protein structures.
What is the role of bioinformatics in genomics?
To analyze and manage large volumes of genomic data.
True or False: The human reference genome is static and not revised.
False
Fill in the blank: The ultimate goal in mapping any genome is to determine the complete _______.
nucleotide sequence of each chromosome
What technological advancement has significantly accelerated genome sequencing?
Next-generation sequencing machines
What is the significance of the WD40 domain?
It is found in various eukaryotic proteins with diverse functions.
What is the structure of cow transducin?
Cow transducin contains seven WD40 domains, one highlighted in gray
The sequence similarity of other proteins to cow transducin suggests their structures are likely similar.
What is gene annotation?
Gene annotation is the process of identifying all protein-coding genes in a DNA sequence and their functions
This process uses evidence from pattern recognition, sequence comparison, and RNA expression confirmation.
What are expressed sequence tags (ESTs)?
Expressed sequence tags (ESTs) are sequences collected from cDNA and cataloged in databases
They are used to identify previously unknown protein-coding genes.
What is the purpose of comparing sequences of suspected genes?
The purpose is to obtain clues about their identities and functions by comparing them to known genes from other organisms.
What is RNA-seq used for?
RNA-seq is used to confirm the identities of genes by showing that the relevant RNA is expressed from the proposed gene.
What is the ENCODE project?
The ENCODE project aims to learn about functionally important elements in the human genome using various experimental techniques
It began in 2003 and has involved multiple phases and extensive data publication.
What was a key finding from the ENCODE project?
About 75% of the human genome is transcribed at some point in at least one cell type studied
However, less than 2% of the genome codes for proteins.
What is systems biology?
Systems biology is an approach that aims to model the dynamic behavior of whole biological systems based on interactions among their parts.
What is proteomics?
Proteomics is the study of sets of proteins, their properties, interactions, and abundance
A proteome is the entire set of proteins expressed by a cell or group of cells.
What is the Cancer Genome Atlas?
The Cancer Genome Atlas is a project that analyzes many interacting genes and gene products to understand how biological systems lead to cancer
It began in 2007 and culminated in 2018 with the Pan-Cancer Atlas.
How does systems biology contribute to cancer treatment?
It allows for the analysis of gene expression patterns to tailor treatments to individual patients’ genetic makeups.
What technology is used to analyze gene expression patterns?
DNA microarrays and RNA-seq are used to analyze gene expression patterns in patients with various diseases.
What potential does personalized medicine hold?
Personalized medicine holds potential for disease prevention and treatment based on individual DNA sequences.
Fill in the blank: The process of identifying all protein-coding genes in a sequence is called _______.
gene annotation
True or False: Systems biology only focuses on individual genes.
False
What is the goal of characterizing the epigenome in the Roadmap Epigenomics Project?
To focus on the epigenetic features of the genome of hundreds of human cell types and tissues.
What experimental technique is used to block gene function?
The CRISPR-Cas9 system
What is the significance of the findings regarding cancer epigenomes?
The original tissue in which a cancer arose can be identified in cells of a secondary tumor based on their epigenomes.
What is the significance of the arrangement and interactions of components in genetic systems?
They deepen our understanding of whole organisms.
This reflects the foundational concept in systems biology.
How many genomes have been completed and what are the categories of these genomes?
Approximately 137,500 bacterial genomes, 1,200 archaeal genomes, and 430 completed eukaryotic species.
There are also about 22,000 metagenomes and 4,500 permanent drafts.
What is the typical genome size range for most bacterial genomes?
Between 1 and 6 million base pairs (Mb).
For example, E. coli has a genome size of 4.6 Mb.
How does the genome size of eukaryotes generally compare to prokaryotes?
Eukaryotic genomes tend to be larger than prokaryotic genomes.
For instance, the human genome is about 3,000 Mb.
What is the estimated genome size of the Japanese canopy plant Paris japonica?
149 billion base pairs (149,000 Mb).
This is an example of the enormous range of genome sizes among plants.
What is the difference in the number of genes between prokaryotes and eukaryotes?
Bacteria and archaea generally have fewer genes than eukaryotes.
Free-living bacteria and archaea have 1,500 to 7,500 genes, while eukaryotes range from about 5,000 to over 40,000.
How many genes does the human genome contain according to the latest estimates?
Around 21,300 genes.
This number is much lower than the initial expectations of 50,000 to 100,000 genes.
What process allows vertebrate genomes to utilize fewer genes while producing more proteins?
Extensive alternative splicing of RNA transcripts.
This process allows for multiple polypeptides to be generated from a single gene.
What is gene density and how does it differ between prokaryotes and eukaryotes?
Gene density is the number of genes per given length of DNA; eukaryotes generally have larger genomes but lower gene density.
Humans have a lower gene density compared to bacteria.
What percentage of the human genome codes for proteins or is transcribed into rRNAs or tRNAs?
About 1.5%.
This highlights the vast amount of noncoding DNA present in the human genome.
What are transposable elements?
Stretches of DNA that can move from one location to another within the genome.
They play a significant role in the structure and function of genomes.
How much of the human repetitive DNA is made up of transposable elements?
About 75% of human repetitive DNA, which is 44% of the entire human genome.
This indicates the prevalence of transposable elements in the human genome.
Who was Barbara McClintock and what was her contribution to genetics?
An American geneticist who discovered transposable elements in maize and received the Nobel Prize for her work.
Her research provided key insights into genetic mobility.
Fill in the blank: The human genome contains _____ times as much noncoding DNA as bacteria.
10,000.
This significant difference illustrates the complexity of eukaryotic genomes.
Who proposed the idea of mobile genetic elements after observing variegations in corn kernel color?
Barbara McClintock
McClintock’s work was initially met with skepticism but was later validated with the discovery of transposable elements in bacteria.
What are the two types of eukaryotic transposable elements?
- Transposons
- Retrotransposons
How do transposons move within a genome?
By means of a DNA intermediate
What are the two mechanisms by which transposons can move?
- Cut-and-paste mechanism
- Copy-and-paste mechanism
What enzyme is required for the movement of transposons?
Transposase
How do retrotransposons move?
By means of an RNA intermediate
What is the role of reverse transcriptase in retrotransposon movement?
To convert RNA back to DNA
What percentage of most mammalian genomes is made up of transposable elements?
25-50%
What are Alu elements and how much do they account for in the human genome?
They are a family of similar sequences that account for approximately 10% of the human genome.
What is the length of Alu elements?
About 300 nucleotides long
What is the function of LINE-1 retrotransposons in the human genome?
They may affect chromatin structure crucial for early embryonic development
What percentage of the human genome is made up of simple sequence DNA?
3%
What are short tandem repeats (STRs)?
Repeats of short sequences that can vary in number from site to site within a genome
What is the role of simple sequence DNA located at telomeres?
To protect chromosomal ends from degradation
What percentage of the human genome is accounted for by repetitive DNA not related to transposable elements?
About 14%
What is a multigene family?
Collections of two or more identical or very similar genes
What are the two related families of genes that encode globins?
- Alpha-globin gene family
- Beta-globin gene family
What is the primary product of the rRNA gene family?
Ribosomal RNA (rRNA)
How much of the human genome is gene-related DNA, including coding and noncoding sequences?
About 25%
What is the significance of pseudogenes?
They are versions of functional genes that no longer encode functional polypeptides.
What genetic event is suggested by the similarity between human chromosome 2 and chimpanzee chromosomes 12 and 13?
Fusion of two ancestral chromosomes
What underlies much of genome evolution?
Mutation
Fill in the blank: The primary transcript of the rRNA gene family is cleaved to yield _______.
three rRNA molecules
What is the likely characteristic of the earliest forms of life in terms of genes?
Minimal number of genes necessary for survival and reproduction.
What is polyploidy?
A condition resulting from an accident in meiosis that leads to one or more extra sets of chromosomes.
How can polyploidy facilitate the evolution of genes?
One set of genes can provide essential functions, while extra sets can diverge by accumulating mutations.
What is the significance of gene divergence in polyploid organisms?
It can lead to the evolution of genes with novel functions.
Why is polyploidy relatively common among plants?
It’s estimated that as many as 80% of plant species show evidence of polyploidy among their ancestral species.
What evolutionary evidence exists regarding human and chimpanzee chromosomes?
Humans have 23 chromosomes while chimpanzees have 24 due to the fusion of two ancestral chromosomes in humans.
What does the presence of telomeres and an unused centromere in human chromosome 2 indicate?
It supports the model of chromosome fusion in the human lineage.
What was discovered when comparing human chromosome 16 with mouse chromosomes?
Large blocks of genes on human chromosome 16 are found on four mouse chromosomes.
What was the outcome of comparing chromosomes among humans and six other mammalian species?
Researchers reconstructed the evolutionary history of chromosomal rearrangements.
What are some common chromosomal rearrangements observed during evolution?
Duplications and inversions of large portions of chromosomes.
True or False: Polyploidy is common among animals.
False.
Fill in the blank: The accumulation of mutations in extra gene copies can lead to the _______.
[branching off of a new species]
What can the analysis of chromosomal organizations of different species reveal?
Inferences about evolutionary processes that shape chromosomes.
What was a key finding from the Human Genome Project regarding human chromosome 2?
It revealed sequences for telomeres and an extra, unused centromere.
What is the importance of meiotic recombination in chromosomal evolution?
Errors during meiotic recombination can lead to duplications and inversions.
What can mutations in polyploid organisms lead to in terms of phenotype?
Changes in the organism’s phenotype.
What is the relationship between chromosome number and speciation in plants?
Polyploidy can facilitate speciation by providing genetic diversity.
What do the colored areas in the diagram of human and mouse chromosomes represent?
DNA sequences similar to large blocks of human chromosome 16 found on mouse chromosomes 7, 8, 16, and 17
This suggests that the DNA sequence in each block has remained intact in mouse and human lineages since their divergence from a common ancestor.
What mechanism can lead to gene duplication during meiosis?
Recombination between copies of a transposable element flanking the gene
This process can result in one chromatid with two copies of the gene and another with none.
What significant event regarding chromosomal rearrangements occurred around 100 million years ago?
The acceleration of chromosomal rearrangements coincided with the extinction of large dinosaurs and the rapid increase in mammalian species
Such rearrangements contribute to the generation of new species.
True or False: Chromosomal rearrangements can lead to populations that cannot successfully mate with each other.
True
This can occur due to individuals having nonequivalent sets of chromosomes.
What are recombination ‘hot spots’?
Specific sites associated with chromosomal rearrangements that are reused
These hot spots can correspond to locations associated with congenital diseases.
Fill in the blank: Errors during meiosis can lead to the duplication of _______.
chromosomal regions that are smaller than whole chromosomes, including segments the length of individual genes.
What can result from unequal crossing over during prophase I of meiosis?
One chromosome may have a deletion and another may have a duplication of a particular gene or genes.
What is a consequence of template slippage during DNA replication?
A segment of DNA may be deleted or duplicated
This often occurs in regions of repeats, affecting the variable number of repeated units used for STR analysis.
How did the globin genes evolve?
They evolved from one common ancestral globin gene that underwent duplication and divergence
This process occurred about 450-500 million years ago.
What are pseudogenes and how could they have arisen?
Pseudogenes are non-functional gene copies that may have arisen after gene duplication due to random mutations
Over evolutionary time, these mutations can destroy their function.
What is the significance of the lysozyme and a-lactalbumin proteins in mammalian evolution?
Lysozyme protects against bacterial infection, while a-lactalbumin is involved in milk production
Both proteins are similar in amino acid sequences and structures.
What process can lead to the evolution of new proteins via rearrangements of DNA sequences?
Exon duplication and exon shuffling
This can occur through unequal crossing over during meiosis.
What role do introns play in the evolution of proteins?
They may facilitate the duplication or shuffling of exons, contributing to new protein evolution.
Fill in the blank: The presence of introns may have promoted the evolution of new proteins by facilitating the _______ of exons.
duplication or shuffling.
What is the role of natural selection in the evolution of globin genes?
Natural selection maintains altered genes in the population if they provide a beneficial function without substantially changing the protein’s primary function.
What does the comparison of amino acid sequences of globin family proteins help scientists understand?
It helps reconstruct the evolutionary history of the globin genes.
What are the two proteins compared in the amino acid sequence alignment?
Lysozyme and a-lactalbumin
In the amino acid sequence alignment, what indicates gaps in one sequence?
Dashes
What is the significance of nonidentical amino acids that are structurally and chemically similar?
They may behave similarly
What is the role of duplication in protein-coding genes?
It allows for divergence and the potential for new functions
What type of protein is collagen?
Structural protein
What is exon shuffling?
The mixing and matching of different exons within or between different genes
What gene is used as an example of exon shuffling leading to new proteins?
Tissue plasminogen activator (TPA)
How are transposable elements thought to contribute to genome evolution?
They can promote recombination, disrupt genes, and carry genes to new locations
What can happen when a transposable element jumps into a protein-coding sequence?
It can prevent the production of a normal transcript
What is the main consequence of transposable elements inserting within regulatory sequences?
It may lead to increased or decreased protein production
What was the example provided regarding transposition in McClintock’s corn kernels?
It caused changes in pigment-synthesizing enzymes
What is the significance of genetic diversity provided by transposable elements?
It serves as raw material for natural selection
What do researchers compare to understand evolutionary relationships of globin genes?
Amino acid sequences of the polypeptides
What does a higher percent identity value between globin pairs indicate?
Closer evolutionary relationships
What is the evolutionary relationship between species represented as?
A tree diagram
What can comparisons of genomes of distantly related species reveal?
Ancient evolutionary history
How can conserved genes help in understanding evolutionary relationships?
They indicate how closely related species are
What is the approximate time frame for the divergence of bacteria, archaea, and eukaryotes?
Between 2 and 4 billion years ago
Fill in the blank: Transposable elements can carry entire genes or individual exons to _______.
New locations
What is the significance of comparing gene sequences in distantly related species?
It helps clarify evolutionary relationships among species that diverged long ago.
What do comparative genomic studies reveal about the three fundamental domains of life?
Bacteria, archaea, and eukaryotes diverged between 2 and 4 billion years ago.
What percentage of important yeast genes could be replaced by human versions in an experimental study?
47% of the yeast genes.
What is the expected genomic similarity between closely related species?
Their genomes are likely to be organized similarly with few gene differences.
What can genetic differences between closely related species indicate?
They can be correlated with phenotypic differences.
What does the comparison of the human genome with that of chimpanzees reveal?
It helps identify what genomic information defines humans or chimpanzees.
By what percentage do the human and chimpanzee genomes differ based on single nucleotide substitutions?
1.2%.
What additional percentage difference is observed due to insertions or deletions in the genomes of humans and chimpanzees?
2.7%.
Which gene is associated with the acquisition of speech in humans?
FOXP2.
What did the 2002 research publication reveal about the FOXP2 gene?
It was evolving faster in humans than in other primates.
What evidence supports FOXP2’s role in vocalization across vertebrates?
- Mutations can cause speech impairments in humans. * It’s expressed in the brains of songbirds during song learning. * Knockout experiments in mice show vocalization issues.
What is the result of replacing the FOXP2 gene in mice with a humanized copy?
Mice showed subtle vocalization differences and changes in brain cells associated with speech.
What is a significant finding regarding human genetic variation?
Humans have a small amount of DNA variation compared to many other species.
What are single nucleotide polymorphisms (SNPs)?
Single base-pair sites where genetic variation is found in at least 1% of the population.
What are copy-number variants (CNVs)?
Regions where individuals have one or multiple copies of a gene or genetic region.
How do CNVs potentially impact phenotypic variation?
They are likely to have phenotypic consequences and could play a role in complex diseases.
What was remarkable about the genetic diversity found among four Khoisan-speaking men in a study?
They differed more from each other than a European would from an Asian.
What does the conservation of homeotic genes across species indicate?
There is a widespread conservation of developmental genes among animals.
What represents homeotic genes in the chromosomes of fruit flies?
Colored bands on the chromosomes
Each colored band indicates the expression in different parts of the embryo and the resulting adult body regions.
In which organism are all homeotic genes found on one chromosome?
Fruit flies (Drosophila melanogaster)
In mice and other mammals, these genes are distributed across four chromosomes.
What is the primary aim of evolutionary developmental biology (evo-devo)?
To understand how developmental processes have evolved and how changes can modify organismal features
This field compares developmental processes among different multicellular organisms.
What significant molecular feature do homeotic genes in Drosophila share?
A 180-nucleotide sequence called a homeobox
This sequence codes for a 60-amino-acid homeodomain in the encoded proteins.
What are Hox genes?
Homeobox-containing genes in animals
They were named because they were the first genes found to contain the homeobox sequence.
What is the role of the homeodomain in homeobox-encoded proteins?
It binds to DNA when the protein functions as a transcription factor
The homeodomain coordinates the transcription of developmental genes.
Fill in the blank: Homeobox sequences have been found in regulatory genes of _______.
Eukaryotes, including plants and yeasts
True or False: The same genes can be involved in the development of animals with vastly different forms.
True
What can small changes in regulatory sequences lead to in terms of body form?
Major changes in body form
For example, changes in Hox gene expression patterns can account for variations in leg segments in related animals.
What do sea urchins demonstrate about Hox genes?
Hox genes are expressed during their embryonic and larval stages despite having different body plans from insects and mice.
What was the Human Genome Project’s main achievement?
Completion in 2003 with advances in sequencing technology
What does the whole-genome shotgun approach involve?
Cutting the whole genome into many small, overlapping fragments for sequencing
Computer software assembles these fragments into a complete genome sequence.
What percentage of the human genome codes for proteins or gives rise to rRNAs or tRNAs?
1.5%
What are the two types of transposable elements in eukaryotes?
- Transposons (move via a DNA intermediate)
- Retrotransposons (move via an RNA intermediate)
What is the significance of repetitive DNA in multicellular eukaryotes?
It includes transposable elements and plays structural roles in chromosomes
These repetitive sequences are especially prominent in centromeres and telomeres.
What evolutionary process occurs more often among plants than animals?
Polyploidy
What do chromosomal rearrangements contribute to in evolution?
The emergence of new species
How do scientists use bioinformatics in genomics?
To analyze genomes and study sets of genes and proteins as whole systems
Fill in the blank: The ENCODE project focuses on _______.
Functional elements in the genome
Comparing genome sequences from different species can provide clues about what?
Ancient and recent evolutionary history
What provides valuable information about ancient and more recent evolutionary history?
Comparisons of genomes from widely divergent and closely related species.
What analysis can shed light on the evolution of a species?
Analysis of single nucleotide polymorphisms (SNPs) and copy-number variants (CNVs).
What do homeotic genes and some other genes associated with animal development contain?
A homeobox region whose sequence is highly conserved among diverse species.
What is bioinformatics?
Using DNA technology to clone genes, align DNA sequences, inform medical decisions, and amplify DNA segments.
What do homeotic genes encode?
Transcription factors that control the expression of genes responsible for specific anatomical structures.
Which process is most likely to have contributed to the similarity of two eukaryotic proteins with one domain in common?
Gene duplication.
Fill in the blank: Homeotic genes are found only in _______.
[Drosophila and other arthropods]
What is the significance of Hox gene products in modern insects?
They inhibit wing formation on the first thoracic segment.
How long ago did primates and rodents diverge?
About 65 million years ago.
How long ago did chimpanzees and humans diverge?
About 6 million years ago.
What observation was made regarding groups of SNPs in the human genome?
They tend to be inherited together in blocks known as haplotypes.
Fill in the blank: Mutations in protein-coding genes and regulatory DNA contribute to _______.
[evolution]
What evolutionary role do transposable elements play?
They drive evolution.
What is hypothesized about the rate of evolution of the FOXP2 gene based on amino acid differences?
It can be inferred from the number of differences across species.
True or False: The continuity of life is based on heritable information in the form of RNA.
False
What can changes in gene regulation lead to in terms of evolutionary structures?
The evolution of structures like the ornate helmet of the treehopper insect.
