Genes, Genomes And Genomics Flashcards
(49 cards)
What is a genome?
A genome is the full set of hereditary genetic material (DNA or RNA) within a cell, organelle, or organism. It includes all the genes and non-coding sequences necessary for life, development, and reproduction
What are the universal features of genomes?
They are made of nucleic acids (DNA or RNA).
They are self-replicating.
They encode instructions for the production of proteins and RNAs via transcription and translation
What are the features of viral genomes?
Can be DNA or RNA, single- or double-stranded, linear or circular, and segmented or unsegmented.
Structure depends on the viral life cycle.
Name 5 viruses and their genomes?
Tobacco Mosaic Virus (RNA, helical)
Adenovirus (dsDNA, linear)
Influenza Virus (segmented RNA)
Bacteriophage T4 (dsDNA)
PhiX174: first genome sequenced, notable for overlapping genes
Why study viral genomes?
To track disease outbreaks (e.g. SARS-CoV-2 sequencing helped monitor variants and inform vaccine design).
To understand how viruses evolve, adapt, and interact with hosts (e.g. HIV).
What are the key features of prokaryote genomes?
Prokaryotes (bacteria and archaea) have compact genomes with high gene density.
Key features:
Typically circular, double-stranded DNA
Non-segmented with a single chromosome plus plasmids
Highly efficient: ~85% of genome codes for proteins or RNA
Prokaryotes are haploid—one copy of the genome per cell
How is the DNA organised in prokaryotes?
Compact DNA via supercoiling and nucleoid-associated proteins (NAPs)
Enzymes like DNA gyrase and topoisomerases manage DNA tension
Chromosome organized into a nucleoid (dense protein-DNA complex)
Why study prokaryotic genomes?
Metagenomics: sequencing all DNA in microbial communities (e.g. gut microbiota)
Found links between microbiome diversity and health conditions (obesity, IBD, mental health)
What are the key features of eukaryotic genomes?
Eukaryotes have larger, more complex genomes spread across multiple linear chromosomes inside a nucleus.
Key features:
Double-stranded, linear DNA, usually segmented into multiple chromosomes
DNA is packaged into chromatin with histone proteins
Eukaryotes have organelles (e.g., mitochondria, chloroplasts) with their own genomes
What are the 2 different chromatin types?
Euchromatin: active, loosely packed
Heterochromatin: inactive, tightly packed
Constitutive: always condensed
Facultative: variably condensed (e.g. X-inactivation)
What is the epigenome?
Heritable chemical modifications (e.g. DNA methylation, histone acetylation)
Regulate gene expression without changing the DNA sequence
Example: X-chromosome inactivation in females
Why study genomes and genomics?
Gene number and function – understand what genes do and how they’re regulated
Disease understanding – many diseases have a genetic or epigenetic component
Breeding and agriculture – manipulate genomes to improve traits
Genome evolution – track how organisms adapt and diversify
Evolutionary relationships – trace ancestry and lineage
What is DNA packaging in eukaryotic genomes?
DNA wraps around histones → forms nucleosomes
Nucleosomes coil to form chromatin fibers
These fold into looped domains and compact further during mitosis
How are genomes measured?
Measured in base pairs (bp) or by C-value:
What is the C value?
C-value: the amount of DNA in a haploid genome (measured in picograms; 1pg ≈ 1Gbp).
Human genome ≈ 3.2pg ≈ 3.2 billion bp.
What is the c-value paradox?
Genome size does not correlate with organism complexity.
Some simple organisms have much larger genomes than humans.
Most DNA in large genomes is non-coding (e.g., introns, repetitive elements).
What is gene density?
Varies widely: Humans have ~20,000 genes, but only ~1.5% of DNA codes for proteins.
Includes coding genes and non-coding RNA genes (rRNA, tRNA, lncRNA)
What is a gene? How does you go from a gene to a protein?
A gene is the basic unit of heredity.
Classic model: “One gene – one enzyme”.
Modern definition (ENCODE project): a gene is a union of sequences that encode potentially overlapping functional products.
From DNA to Protein:
DNA → RNA → Protein
(Transcription → Translation)
How are prokaryotic genes organised? Key features?
Often organized into operons (e.g., tryptophan operon).
May be polycistronic (one RNA codes for several proteins).
Key features:
Single transcription start site (TSS)
Shine-Dalgarno sequence aligns ribosome
Start/stop codons define open reading frames (ORFs
How are genes regulated in prokaryotes?
Promoter regions: -35 and -10 boxes (Pribnow box)
Operators: regulate operon activity
Terminators: hairpin loops or Rho factor-mediated
How are eukaryotic genes organised?
Generally monocistronic (one gene = one RNA = one protein).
Genes include exons (coding) and introns (non-coding).
Also contain 5’ and 3’ untranslated regions (UTRs):
5’ UTR includes Kozak sequence (ACCATGG)
3’ UTR includes polyadenylation signal
How are genes regulated in eukaryotes?
TATA box: common core promoter (bound by TBP)
Initiator (Inr): can initiate transcription without a TATA box
Enhancers: distant sequences that boost transcription
Transcription factors (TFs): protein families like zinc finger, leucine zipper
What are gene families?
Genes with similar sequences and functions, descended from a common ancestor.
Examples: globin genes (different forms during embryonic, fetal, and adult life)
May be clustered or dispersed across the genome
