Genomes Flashcards
What is genomics?
- Every cell in the organism contains a complete copy of the genome.
- Genomics is the study of an organism’s complete set of genes, known as its genome, including all of its DNA sequences.
- Genomics explores (1) the organization, (2) function, (3) evolution, and (4) interactions of genes within an organism.
- It provides a comprehensive view of an organism’s genetic makeup, allowing us to understand the basis of life.
Genome
an organism’s complete set of DNA
an organism’s complete set of DNA
Genome
What does genomics explore within an organism? [4]
- Genomics explores the (1) organization, (2) function, (3) evolution, and (4) interactions of genes within an organism.
- It provides a comprehensive view of an organism’s genetic makeup, allowing us to understand the basis of life.
Advances in Genomics have revolutionized various fields (some examples are): [4]
- Medicine: Personalized medicine, genetic disease diagnosis, and drug development.
- Evolutionary Biology: Understanding species evolution and relationships.
- Biotechnology: Engineering organisms for various applications.
- Forensics: DNA profiling for crime solving.
In general, genomics helps in unraveling the complexity of life and offers insights into human health, biodiversity, cell biology.
How can genomics improve crop production?
- Crop Yield Enhancement: Identification of genes responsible for desirable traits such as high crop yield, disease resistance, and tolerance to environmental stressors.
-
Precision Breeding: Selection of specific genes, breeding programs can create new crop varieties with
improved characteristics.
How does genomics contribute to food quality?
-
Enhancing Taste and Texture : Genomics helps developing food products with improved taste, texture, and
sensory qualities by identifying genes associated with these attributes. - Shelf Life Extension : Understanding the genetics of spoilage and deterioration processes can lead to the development of foods with longer shelf lives.
How does genomics contribute to food safety?
- Pathogen Detection : Genomic analyses are used to detect and identify foodborne pathogens like Salmonella, E. coli, and Listeria in food products.
- Tracing Contamination Sources : Genomics helps trace the sources of foodborne outbreaks, enabling quick interventions and recalls.
How does genomics contribute to nutrition science?
- Personalized Diets : Genomics research helps in understanding how an individual’s genetic makeup influences their nutritional needs. Helps developing personalized diets.
- Nutrigenomics : Studying how specific nutrients interact with genes to impact health and metabolism.
How does genomics help with allergen detection?
Genomic techniques can be used to detect and identify potential allergens in food items, which is crucial for labeling and ensuring food safety for individuals with allergies.
What is the structure and variation of the nuclear genome in eukaryotes?
- DNA in different organisms is made from the same molecules.
- In eukaryotes, the nuclear genome is split into a set of linear DNA molecules, each contained into a chromosome.
- Chromosomes are always linear.
- Chromosome number varies among organism but is unrelated to the complexity (yeast=16, human 23, walnut 32, fruit flies=4).
The 30 nm chromatin fiber
the major type of chromatin in the nucleus during interphase, the period between nuclear divisions
How is it that the chromosomes are much shorter than the DNA they contain?
- The genome is packed through DNA binding proteins called Histones
Describe DNA during nuclear division.
- more compact packaging (metaphase chromosomes)
- The two copies of chromosomes are held together at the centromere (in plants 0.4-3Mb made up largely of 178-180 bp repeat sequences; in yeast is short, a single copy sequence), which has a specific position within each chromosome.
- The arms of the chromosome, which are called chromatids and have terminal structures called telomeres (made up of hundreds of copies of a repeated motif, 5ʹTTAGGG 3ʹ in humans)
Describe gene distribution.
Genes appear to be distributed at random with variations in gene densities along the chromosome
Describe the genomic regions in this 50kb segment of chromosome 12 of the human genome.
- 4 genes (discontinuous from presence of exons and introns)
- 88 genome wide repeat sequences (transposable elements) including:
- LINEs=long interspersed nuclear elements
- SINEs=short interspersed nuclear elements
- LTR=long terminal repeats
- DNA transposons
- 7 microsatellites (short motif, CA, CAAA, CCTG, CTGGGG, etc. is repeated in tandem)
5’CACACACACACACACACA 3’
3’GTGTGTGTGTGTGTGTGT 5’ - 30% of nongenic , nonrepetitive DNA, single copy DNA of no function
Describe the composition of the human genome.
In the genome exons are 48Mb, 1.5% of the total.
44% is taken by genome wide repeats.
What is genic DNA?
- “Single” copy genes
- Duplicated genes
- may occur at a single or several loci on different chromosomes
- functional multi gene families with same function (e.g. 5S ribosomal RNA in human is in 2000 copies - probably because cells need a lot of ribosomes, and so they need a lot of sources of the code for efficiency)
- functional multi gene families with slightly different function (biochemical, developmental, tissue specific)
What is a pseudogene?
Genes that are not functionally active (evolutionary relics)
- Pseudogenes are DNA sequences that resemble functional genes but have lost their ability to produce proteins or functional RNA.
What are genes?
Genes are segments of DNA that contain the instructions for building proteins or functional RNA molecules.
What is alternative splicing?
- Alternative splicing is a post transcriptional mechanism in eukaryotes that allows a single gene to generate multiple different messenger RNA (mRNA) transcripts and, consequently, multiple protein isoforms.
- This process enhances the diversity and complexity of the protein produced by a genome without requiring an increase in the number of genes.
How does alternative splicing of the calcitonin/CGRP gene result in different proteins?
- The human calcitonin/CGRP gene has two splicing pathways that give rise to different proteins.
- In the thyroid, exons 1-2-3-4 are spliced together to give the mRNA for calcitonin, a short peptide hormone that regulates calcium ion concentration in the bloodstream.
- In nerve tissue, exons 1-2-3-5-6 are joined to give the calcitonin gene-related peptide (CGRP), a neurotransmitter active in sensory neurons and involved in the pain response.
How do pseudogenes arise?
Pseudogenes often arise through evolutionary processes, such as (1) gene duplication or retrotransposition, and (2) accumulation of mutations that render them nonfunctional.
What is a conventional pseudogene?
- The gene is inactivated because of mutations.
- Conventional pseudogenes usually arise from functional genes that have experienced mutations, deletions, or insertions, which disrupt their ability to produce a functional protein or RNA product.
What is a processed pseudogene?
- Originates from a process called retrotransposition .
- These genes cannot be expressed because of a lack of promoter.
What is retrotransposition?
- Retrotransposition is a mechanism by which a functional mRNA (messenger RNA) transcript is reverse transcribed back into DNA and then inserted into the genome, creating a DNA copy of the original RNA.
- This process can lead to the formation of a processed pseudogene, which is a non-functional copy of a gene.
What is a truncated gene or gene fragment?
- Only parts of the gene are present.
- Gene fragments are smaller sections or remnants of genes found within a genome.
This can occur for example if a transposon is integrated in the middle of a gene, separating its components and rendering it non-functional.
What are the two major categories of the repetitive DNA content of eukaryotic nuclear genomes?
- Interspersed repeats
- Tandemly repeated DNA
What are interspersed repeats?
- Interspersed repeats (LINEs, SINEs, LTRs, Transposons) some are descended from transposable viruses
- e.g. 150-300+ bases repeated 103-104 times throughout genome
- Types of repetitive DNA sequence found throughout the genome that are characterized by their scattered or interspersed distribution rather than being organized into tandem repeats (repeating sequences found adjacent to each other).
What is tandemly repeated DNA?
- Satellite DNA: Up to hundreds of kb in length, repeat units from 5 to 200 bp in length (see centromeric regions)
- Minisatellites : Up to 20kb in length , repeat units up to 25bp in length (see telomeric regions)
- Microsatellites: Up to 150bp in length , repeat units up to 13bp in length, widespread in the genome
What are the steps of retrotransposition? [3]
1) The retrotransposon is initially transcribed into RNA by the host cell’s RNA polymerase.
2) The retrotransposon is reverse transcribed into DNA by the reverse transcriptase enzyme, producing a DNA copy called cDNA.
3) The cDNA is integrated into a new genomic location
by another enzyme called integrase. This integration results in the retrotransposon’s insertion.
What is the key enzyme involved in the movement of DNA transposons and what is its function?
Transposase
It catalyzes two essential reactions:
1) excision and 2) insertion.
Transposons and Retrotransposons do not codify for key enzymes for the eukaryotic cells; however, they play a key role in […]
Transposons and Retrotransposons do not codify for key enzymes for the eukaryotic cells; however, they play a key role in affecting the phenotypes (e.g., crop composition/quality)
“How is red pigmentation in grapes regulated by the flavonoid pathway?”
- The red pigmentation in grapes is due to the synthesis of anthocyanins in the berry skin.
- Anthocyanins are produced through the flavonoid pathway.
- UFGT is the key enzyme for their synthesis (glycosylates the anthocyanin group).
- When UFGT is expressed, anthocyanins are produced.
- MYBA is a gene that codifies for the MYBA transcription factor that by binding to the promoter of UFGT induces the expression of the UFGT gene.
- When MYBA is expressed, then UFGT is expressed and anthocyanins are produced.
- These genes are located in various part of the genome, not in the same region.
Why do white grapes not produce anthocyanins?
- UFGT is not expressed even though the gene is functional
- Its lack of expression is due to the lack of expression of its transcription factor MYBA
- MYBA1 sequences are more similar from either red or white alleles.
- But the retrotransposon prevents the expression of the gene.
- MYBA2 red encodes a protein of 344 amino acids.
- MYBA2 white has two mutations in the coding region; the second mutation determines a non functional allele and is the deletion of a dinucleotide (CA) in the white allele altering the reading frame at amino acid 258, terminating the protein.
What is the relationship between the genome size, the
number of genes, and the complexity of an organism in
eukaryotes?
The complexity of an organism is not related to the size of its genome.
Describe the variation of genome size in plants.
Compare the genome of humans, yeast, fruit flies, and maize
- Space is saved in the genomes of less complex organisms because the genes are more closely packed together
- Gene density is higher in yeast than in humans. Yeast have very few introns and interspersed repeats.
- Gene number vary among organisms. Yeast have a low gene number, plants and humans a higher gene number.
What is the relationship between genome size and number of genes?
There is no relationship between the genome size and the number of genes in eukaryotic genomes.
Genome size is proportional to the gene number in prokaryotes!
How is the physical organization of a prokaryotic genome different from eukaryotes?
- The singular, circular DNA is localized in the nucleoid (no spatial separation of genome in a nucleus like in eukaryotes).
- Circumference is 1.6mm. Cell is 1x2um
- DNA gyrases (DNA topoisomerases) are the enzymes that help forming this structure and the DNA replication.
- Other proteins (HU) help packaging the DNA (structurally different but act as the histones).
- 60,000 HU in each E.coli cell
Some linear version of the chromosome has been found in some bacteria (Borrelia burgdorferi, Lyme disease agent; Agrobacterium tumefaciens)
While most prokaryotes (like bacteria) typically have a single circular chromosome, some prokaryotes can have more than one chromosome or even linear chromosomes.
What are some variations in bacterial genomic structures beyond the typical circular chromosome and plasmids?
Generally bacteria have a circular chromosome and plasmids, however there are many genomic features that can be found in the different species.
E.g., more than one chromosome, or a combination of chromosome, megaplasmid (a big plasmid), and plasmid. Chromosomes can also be linear in some exceptions.
What are plasmids and how do they differ from chromosomal DNA?
- Plasmids normally carry non essential genes for the bacterium.
- Plasmids are physically separate from chromosomal DNA and replicate independently.
Describe prokaryotic gene density.
- Complete genome of E.coli K12 (4405 genes).
- 11% non coding distributed in small segments in the genome.
- Very little space is wasted - very high density of genes
Describe prokaryotic gene organization. [4]
- No introns (generally speaking, some exceptions exist)
- Genes are 2/3 in length of the eukaryote ones
- Infrequent repetitive elements (insertion sequences=IS, < 1%)
- Presence of operons
What are operons?
- Operons are very common in prokaryotes
- Groups of genes located closed to each other with a single promoter.
- Belong to the same pathway and are expressed in conjunction.
- This feature allows to save space as genes are close to each other.
- The expression is also efficient as all (or several of) the genes needed for a given biological function are expressed at the same
What comprises the lactose operon?
- Lactose operon contains three genes involved in conversion of the disaccharide lactose into its monosaccharide units, glucose and galactose.
How does genome size and gene density in prokaryotes compare to eukaryotes?
- Prokaryotes have generally smaller genomes than eukaryotes
- Genome size is proportional to the gene number (950 genes/1Mbp) in prokaryotes.
- The average gene density is 87%, with most genomes in the range 85 90%.
- Smaller genomes for parasites and larger for free living species.
What is genome size proportional to in prokaryotes?
Genome size is proportional to the gene number
What is the pan-genome?
the entire set of genes from all strains within a clade
What is lateral gene transfer?
movement of genetic material between species; non sexual movement of genetic information between genomes)
What is unique about the genomes of eukaryotic organelles like mitochondria and chloroplasts?
- Mitochondria and chloroplasts have their own genomes, independent and distinct from the nuclear genome.
- Separate transcription and translation machinery for each organelle.
How does the size and compactness of mitochondrial genomes vary across organisms?
- Mitochondrion genome size is variable but does not correlate with the complexity of organism
- In yeast and plants - less compact mitochondrial genome
What are the key features of the chloroplast genome across plants?
- Chloroplast genome is similar in size and structure across plants
- Circular genome
- Approximately 200 genes - mostly related to photosynthesis
What was Barbara McClintock awarded the Nobel Prize for?
- Nobel Prize in Physiology or Medicine, awarded to her in 1983 for the discovery of genetic transposition.
- Elected a member of the National Academy of Sciences in 1944.
- During the 1940s and 1950s, McClintock discovered transposons and used it to demonstrate that they affect the phenotype.
- She developed a theory by which these mobile elements regulated the genes by inhibiting or modulating their action.
Barbara McClintock studied the cytogenetics of maize:
https://www.nature.com/scitable/topicpage/barbara-mcclintock-and-the-discovery-of-jumping-34083/
What are transposable elements (TEs), and how do they affect genes in plants?
- Most TE families have fully intact (autonomous) copies that encode all of the element specific activities, such as transposase for cut and paste elements, and reverse transcriptase for retroelements.
- How TE insertion specificities are generated in plants is unknown; however, there are preferences of the transposable element families for some sites (outside or inside the gene, close or far to the gene or another element).
- Transposable elements can be inserted in genes. Most of the insertions in genes are probable detrimental.
