Week 10 Flashcards
Genome
All genetic material of an organism
- coding and no-coding DNA
- Nuclear and organelle genomes
Genomics
- Genome structure: chromosome number, structure, gene order
- Genome sequence: entire DNA sequence of the genome
- Genome function: annotation and confirmation
- Genome evolution: comparisons within and among species
What is the relationship between genome size and gene content?
- Bacteria and archaea have a positive linear relationship between genome size and gene content
- eukaryotes are not linear, as genome size increases gene content experiences ceiling effect
Whole genome sequencing by primer walking
- Primers, initially based on vector sequences, allow ends of clone to be sequenced from both sides
- New primers are designed based on newly obtained sequence
- Procedure is reiterated until sequence from both ends overlaps
Whole genome shotgun sequencing
- Fragment into smaller lengths and clone using plasmid vectors
- Sequence ends of clones
- Assemble sequences into contiguous sequences by computer
- Use PCR (with primers based on flanking sequences) to close remaining gaps
What is a draw back and solution in WGS
- Drawback: Repetitive DNA
- Solution: Sequence large insert library
What is genome annotation
Annotation is the process of attaching biological functions to DNA sequences
Objectives of annotation
- Identify the location of genes and functional sequences within the genome sequence
- Describes the biochemical, cellular, and biological function of each gene product
Approaches of annotation
- Computational analysis
- Experimental evidence: transcriptome, gene knock-out and knock-in
Bioinformatics
Computational annotation
- Identify open reading frames, exon, introns and splice sites
- Define threshold: ORF greater than a minimum size
- Compare with confirmed annotations in databases
- Assume genes with similar sequences likely have similar biochemical functions
- Compare sequences at AA level
How does experimental validation work
- gene functional analyses through knock-out and knock-in experiements
- RNA-sequencing cDNA library to confirm exons, introns, splice junctions, and tissue specificity
Gene families
groups of genes that are evolutionarily closely related, containing similar protein domains and motifs
What is comparative genomics
Comparing genomes from within and between species
- Intraspecific comparisons: Population genomics
- Interspecific comparisons: Phylogenomic/ evolutionary genomics
What are the major goals of intra-species comparisons
Identify allelic differences (by comparing to reference genome)
- SNPs
- Insertions/deletions
- Copy number variations
- Chromosomal structural changes
Address questions in;
- history of an individual, population or species
- the genetic bases for phenotypic variation
What are the major goals of interspecific genome comparisons?
- Construct the tree of life
- origin and evolution of genes and gene families: gene duplication
- Genetic bases of phenotypic differences among species and evolutionary lineages
Use of interspecific genome comparisons in determining the tree of life
- Basic local alignment search tool (BLAST) is commonly used to identify homologous sequences
- Genome sequences alignments - closely related species often have very similar genome sequences and structures
- Compare how similar
Interspecific genome duplication and divergance
Gene duplicated and either;
a. pseudogene: inactivation of mutation
b. subfunctionalization: mutation and original combine to produce full function
c. Neofunctionalization: mutation acquires new function
Homologs
Descended from common ancestral gene
Orthologs
genes in different species that are derived from single ancestral gene in the species last common ancestor and perform the same function
Paralogs
originated by duplication event; distinct but related function
lateral gene transfer
the transfer of genetic material between species
- about 1.5 - 14.5% of gene in any genome are the result of lateral gene transfer
- More common for genes encoding proteins for secondary metabolic functions than those coding informational processing proteins
Metagenome
the complete DNA sequences from natural communities
Metagenetics
the study of metagenome; providing information on species and functional diversity
Sub-cellular physiological functions of mitochondria
- ATP synthesis through oxidative respiration
- Metabolic biosynthesis
- Ion homeostasis
Organismal functions of mitochondria
- Fungal pathogens: resistance to drugs, host defense and virulence
- Plants: male sterility in plants - hybrid varieties
- Humans: diabetes, neurodegenerative disorders, cancer, fertility
Nobel prizes in mitochondrial research
- Mitochondria were associated with cellular respiration
- localizing the enzymes in the citric acid cycle
- developing a method for isolation
- Chemiosmotic theory for ATP synthesis that linked the electron transport chain, proton gradient formation, oxidative phosphorylation and ATP biosynthesis
- Structures of the complexes involved in oxidative phosphorylation - ATP synthesis complex
What are the major differences between nuclear and mitochondrial genomes
- Mito. much smaller - one circular molecule
- Mito. many more copies
- Mito. variable number of replication
- Mito. Uniparental inheritance - maternal
Approximately what size is an animals mito. genome
16000 bp
Human Mitochondrial gemone structure
- contains 37 genes
- 13 polypeptides
- 22 tRNAs
- the small and large rRNA subunits
Human mitochondrial genome transcription and translation
- Only three promotors
- Two heavy strand and one light strand
- HS; one full length, other only rRNA transcribed
- LS goes in opposite direction on inside of circle
- Protein encoding mostly on HS, tRNA on both
Mitochondrial tRNA genes
- fewer mt tRNA than nuclear
- A few unique: genetic code is not universal
Chloroplasts
enclosed by a double membrane, and possess a third membrane system, the thylakoid membranes, where photosynthesis complex are resided
Chloroplast genome structure and content
- circular
- typically 120-200 kb, encoding 100-250 genes
- has own tRNAs and rRNA genes
- proteins involved in photosynthesis are located on chloroplast genome
Endosymbiosis theory
free-living bacteria infected ancient eukaryotic cells and then evolved along with the hosts to produce the organelles
What is the evidence for the endosymbiosis theory
- Double membrane system
- Organelle size
- Organellar genome structure has no histone
- similarities in transcription and translational machineries to bacteria
Nuclear mitochondrial sequences
mito. to nucleus
Nuclear plastid sequences
chloroplasts to nucleus
Homoplasmy
same mtDNA molecules within a cell/individual
Heteroplasmy
difference mtDNA molecules within a cell/indivdual
Factors influencing mitochondrial inheritance during mitosis
- Within each mitochondrion, different mitochondrial DNA molecules replicate at different speed
- different replicated genomes do not segregate evenly among daughter mitochondria - Within each cell, different mitochondria replicate at different speed
- parental mito. do not segregate evely - Per base mito. DNA mutation rate in animals is 10x higher than their nuclear genomes
How is uniparental/maternal mtDNA inheritance achieved
- differential contribution in parental mito.
- Selective degradation of whole mito
- selective tagging and degradation of mito DNA
Muller’s Ratchet
The irreversible increase of deleterious mutations over time in small, asexual populations, leading to steady decline of fitness
