LC 03: Genomes and Chromosomes

• Genome is the entirety of an organism's hereditary information, typically composed of DNA, but for some viruses, it can be RNA
• Sequencing a genome is a significant achievement, with hundreds of different species having been sequenced, and getting published in top journals like Nature or Science can greatly impact a scientist's career
• The T4 bacteriophage is a virus that infects E. coli, with a genome size of 169,000 base pairs
• Genome size can be measured in base pairs, which is equivalent to the number of nucleotide pairs
• The T4 bacterial Fage virus that infects E. coli has a genome length of 169,000 kilo base pairs, which is the same as 169,000 nucleotide pairs
• E. coli is a model prokaryotic system with a genome size of 4.6 million nucleotide pairs
• Human mitochondrial genome is about 16,000 base pairs long, while the chloroplast genome is 121,000 base pairs long
• Human genome has three billion base pairs per genome, with 23 pairs of chromosomes containing around 20,000 protein-coding genes
• 50% of the human genome is repetitive DNA, while less than 1% encodes proteins
• Non-repetitive DNA includes sequences that help cells determine which RNAs to transcribe and how much RNA to transcribe, including promoters and regulatory sequences
• Sequences in DNA help determine the amount of RNA transcribed by the cell, including promoters and regulatory sequences
• Protein-coding exons are transcribed and translated, while introns are transcribed but not translated
• Repeated sequences in DNA include segment duplications, where thousands to hundreds of thousands of base pairs are duplicated
• Simple repeats, like CAG repeated 30 times, are examples of repeated sequences in DNA
• Mobile genetic elements are sequences that can cut themselves out over long periods, make a copy, and paste themselves back in
• DNA-only transposons remain as DNA throughout the process, while retrotransposons get made into RNA
• Long interspersed nuclear elements (LINEs) are greater than or equal to 500 base pairs, while short interspersed nuclear elements (SINEs) are less than 500 base pairs
• In prokaryotes, DNA is condensed through folding and twisting about a thousandfold and complexed with proteins to form the nucleoid
• The human genome, with 6 billion base pairs per cell, is packaged into the nucleus, which is about 6 micrometers in diameter
• Chromosomes are used to package the eukaryotic genome into cells
• Fluorescence in situ hybridization (FISH) is a diagnostic technique for detecting the presence of particular DNA sequences
• FISH (Fluorescence In Situ Hybridization) is a technique where a probe binds to a specific DNA sequence, labeled with a fluorescent dye, allowing visualization under a microscope
• In FISH, after heating to separate DNA strands and cooling to allow binding, excess probe is washed away to ensure specificity
• Probes used in FISH are easily made by chemists or automated systems, with the aim of detecting specific gene sequences in samples
• Chromosome Painting Hybridization (CPH) is a subcategory of FISH where probes of different colors bind along different chromosomes, allowing visualization of the entire set of chromosomes
• A karyotype is an ordered array of chromosomes in a cell, used as a diagnostic tool to analyze an individual's chromosomes
• In a karyotype, chromosomes are arranged from longest to shortest, with sex chromosomes typically placed at the end
• Each chromosome in a karyotype contains a single long linear DNA molecule and associated proteins called chromatin, which must remain accessible for transcription, replication, and repair
• During the cell cycle, in interphase, chromosomes duplicate, forming sister chromatids, which are separated during mitosis to form individual chromosomes
• Chromatin, consisting of DNA and proteins, is the material chromosomes are made of, with chromatin being tightly packaged but dynamic for cellular processes
• Chromatin is DNA and some proteins, not just DNA alone
• Nucleosome: composed of protein beads, DNA wrapped around the beads, and linker DNA
• Nucleosome core particle: the central part of a nucleosome, consisting of the protein bead and the DNA wrapped around it
• Linker DNA: the DNA between nucleosomes, can vary in length up to about 80 nucleotide pairs
• 30 nanometer fiber: formed by packing nucleosomes together, can be folded into loops to create a mitotic chromosome
• Chromatin compaction levels can change, DNA is flexible and can be compacted differently
• Genome size is not always correlated with the number of genes or organism complexity
• Human complexity is influenced by factors like alternative splicing, non-repetitive DNA sequences, and protein regulation
• Understanding genome complexity involves considering various factors, not just genome size
• Nucleosome:

  • 200 nucleotide pairs of DNA wrapped around protein beads
  • Linker DNA can vary up to about 80 nucleotide pairs long