Genome Study Guide

📖 Core Concepts Genome – the complete set of genetic material (DNA or RNA) in an organism or cell. Nuclear vs. organellar genomes – Nuclear genome holds most genes (coding, non‑coding, regulatory); mitochondria and chloroplasts each carry a small, usually circular, genome. Ploidy – number of chromosome sets per cell; most eukaryotes are diploid (2 copies of each chromosome). Human diploid set = 22 autosome pairs + XY/XX. Types of genomes – Viral (RNA or DNA, single‑ or double‑stranded, segmented or not); Prokaryotic (usually a single circular chromosome, may have plasmids); Eukaryotic (multiple linear chromosomes; chromosome number varies enormously). Genome composition – Coding sequences: DNA that encodes proteins. Non‑coding sequences: introns, ncRNA genes, regulatory regions, repetitive DNA. 98 % of the human genome is non‑coding. Tandem repeats: microsatellites (2–5 bp unit) and minisatellites (30–35 bp unit). Transposable elements (TEs): “copy‑and‑paste” retrotransposons (LINEs, SINEs) and “cut‑and‑paste” DNA transposons. Genome size – total base‑pairs in a haploid set; human nuclear genome ≈ 3.1 × 10⁹ bp. Size is driven mainly by expansion/contraction of repeats and TEs. Dynamic processes – Somatic mutations, V(D)J recombination (immune diversity), meiotic recombination (genetic shuffling). Evolutionary forces – Gene/whole‑genome duplication, horizontal gene transfer (HGT), TE‑mediated rearrangements, organellar gene transfer to the nucleus. Applications – Genomic medicine uses genome data for disease‑risk prediction and precision therapies. --- 📌 Must Remember Genome = all genetic information (DNA or RNA). Nuclear genome = protein‑coding + non‑coding + regulatory + junk DNA. Organellar genomes are usually circular (mitochondrial, plastid). Diploid = two chromosome copies; human: 22 autosomes + X/Y. Human genome: 3.1 Gb; 98 % non‑coding. Microsatellite repeat unit: 2–5 bp; minisatellite: 30–35 bp. Retrotransposons = copy‑and‑paste (RNA intermediate). DNA transposons = cut‑and‑paste (transposase enzyme). LINEs = long interspersed nuclear elements; SINEs = short interspersed nuclear elements. HGT = transfer of genetic material between unrelated species (common in microbes). Meiosis creates unique gametes via homologous recombination. --- 🔄 Key Processes | Process | Step‑by‑step outline | |---------|----------------------| | Reference‑based resequencing | 1. Obtain DNA reads (high‑throughput). 2. Align reads to a reference genome. 3. Call variants (SNPs, indels). 4. Annotate polymorphisms. | | V(D)J recombination | 1. RAG1/2 proteins cleave DNA at recombination signal sequences. 2. Random joining of V, D, J gene segments. 3. Junctional diversity added by TdT‑mediated N‑nucleotides. 4. Result = unique antibody/TCR exon. | | Meiotic recombination | 1. Pair homologous chromosomes. 2. Form double‑strand breaks (Spo11). 3. Strand invasion & Holliday junction formation. 4. Resolution → crossover or non‑crossover. 5. Segregation → four genetically distinct gametes. | | Retrotransposition (LINE/SINE) | 1. Transcribe TE DNA → RNA. 2. Reverse‑transcribe RNA back to DNA (via reverse transcriptase). 3. Integrate new copy elsewhere (target‑primed reverse transcription). | | DNA transposon “cut‑and‑paste” | 1. Transposase binds inverted terminal repeats. 2. Excises TE from donor site. 3. Inserts TE into new genomic locus. | | Horizontal gene transfer (bacterial) | 1. DNA uptake (transformation) or phage‑mediated transduction or conjugative plasmid transfer. 2. Integration into recipient genome (recombination). 3. Expression of new genes. | --- 🔍 Key Comparisons RNA virus vs. DNA virus – RNA viruses use RNA as genetic material (often single‑stranded); DNA viruses use DNA (often double‑stranded, can be circular). Microsatellite vs. Minisatellite – Microsatellite: 2–5 bp repeat unit; Minisatellite: 30–35 bp repeat unit. Retrotransposon vs. DNA transposon – Retrotransposon: copy‑and‑paste via RNA intermediate; DNA transposon: cut‑and‑paste using transposase, no RNA step. Prokaryotic chromosome vs. plasmid – Chromosome: essential, usually single circular DNA; Plasmid: auxiliary, often circular, can be transferred between cells. Linear vs. Circular genome – Linear genomes have ends (telomeres) and are typical of eukaryotic nuclear DNA; circular genomes lack ends (mitochondria, many bacteria, most organelles). Coding vs. Non‑coding DNA – Coding: contains open reading frames for proteins; Non‑coding: introns, regulatory regions, repeats, and “junk” DNA. --- ⚠️ Common Misunderstandings “Junk DNA is useless.” – Much non‑coding DNA includes regulatory elements, introns, and TE‑derived sequences that affect gene expression. All repeats are harmful. – Tandem repeats can serve as useful genetic markers (e.g., forensic microsatellites) and may have structural roles. Ploidy equals chromosome count. – Ploidy refers to sets of chromosomes; a diploid organism can have many chromosomes (e.g., 46 in humans). All viruses have the same genome type. – Viral genomes are highly diverse (RNA vs DNA, single vs double, segmented vs non‑segmented). Organellar genomes act independently of the nucleus. – Most organellar genes have been transferred to the nucleus; organelles rely heavily on nuclear‑encoded proteins. --- 🧠 Mental Models / Intuition Genome as a library – Coding books (genes) tell the cell how to build proteins; the rest (non‑coding) are reference manuals, index cards, and filler pages that still guide where and when to read the books. Transposable elements = “genome’s mobile apps.” – They copy or cut‑paste themselves, sometimes delivering new “features” (exons, regulatory sites) to different pages. Ploidy = two copies of a textbook – Diploid cells have two editions of each chromosome, providing backup and allowing recombination to generate new editions. Repeats = “stamps” – Microsatellites are tiny stamps repeated many times; the pattern of stamps can be read quickly (useful for fingerprinting). --- 🚩 Exceptions & Edge Cases Haploid eukaryotes – Some ants and nematodes have only one chromosome set. Linear bacterial chromosomes – A few bacteria (e.g., Borrelia) possess linear chromosomes. Circular DNA viruses – Some DNA viruses (e.g., papovaviruses) have circular genomes. Extremely high chromosome numbers – Certain ferns have > 700 chromosome pairs. Transposable element inactivity – Some TEs are “dead” (mutated, no longer transpose). --- 📍 When to Use Which Variant detection – Use reference‑based resequencing when you have a high‑quality reference genome and need SNP/indel calls. Genome assembly of a small virus – Direct PCR and Sanger sequencing works; high‑throughput short‑read sequencing is overkill. Genetic marker selection – Choose microsatellites for fine‑scale population studies (high polymorphism, short repeats); use minisatellites for broader phylogenetic signals. Studying immune diversity – Apply V(D)J repertoire sequencing for B‑cell/T‑cell receptor analysis. Investigating genome expansion – Examine TE content when a species has an unusually large genome. --- 👀 Patterns to Recognize Large genomes → high repeat/TE content (e.g., mammals). Inverted terminal repeats flanking a sequence → likely a DNA transposon. LINE‑like structure (5′UTR, ORF1/2, 3′ poly‑A) → retrotransposon. Presence of both mitochondrial and nuclear copies of a gene → recent organellar‑to‑nuclear transfer. Segmented viral RNA genomes → look for multiple distinct RNA segments in sequencing data. --- 🗂️ Exam Traps Confusing genome size with chromosome number – Size is total base pairs; chromosome count is the number of physical DNA molecules. Assuming all non‑coding DNA is “junk.” – Many non‑coding regions have regulatory or structural functions. Mixing up retro‑ vs. DNA transposon mechanisms – Retrotransposons need an RNA intermediate; DNA transposons do not. Thinking diploid means only two chromosomes total – Diploid means two sets of chromosomes; humans have 46 total. Believing all viruses have RNA genomes – DNA viruses exist and often have circular genomes. Attributing every large genome to polyploidy – Many large genomes are enlarged by repeat/TE expansion, not extra chromosome sets. ---