Lecture 2 - Genome diversity and DNA organisation Flashcards
What is the structure of a viral genome?
Genomes of viruses and bacteriophages are relatively small but there is significant size variation between different viruses.
* Viral genomes may be DNA or RNA
* Viral genomes may be single-stranded or double-stranded
* Viral genomes may be cellular or linear
* Viral genes may overlap
There is a large amount of variation - diverse genomes
Describe the variation in genome size and gene number in different organisms.
Single-celled eukaryotes generally have fewer genes than multicellular organisms. There is no simple correlation between genome size, gene number and organism complexity.
The density of genes is lower in eukaryotic genomes.
What is the C-value paradox?
(used interchangeably with genome … paradox)
* Genome size doesn’t consistently correlate with organism complexity
* Similar organisms can show a large range in genome size
Genomes often have transposable elements- pieces of DNA that copy themselves within a genome and lead to increases in genome size.
What DNA is found within the eukaryotic chromosome classified?
The genome consists of genes and intergenic regions that do not appear to contain ‘typical’ gene units - Historically ‘junk’ DNA.
* A gene is a region that controls a discrete hereditary characteristic, usually a specific product like a protein.
* A large proportion of ‘junk’ DNA (codes for RNA that is not translated - Regulatory) - transposable elements - pieces of DNA that copy themselves within a genome and lead to increases in genome size
* Junk DNA includes coding for RNA species that are not translated.
DNA sequence in genomes are classified by abundance
Unique - One to a few copies/genome
Moderately repetitive - Few to 105 copies/genome
Highly repetitive - 105 - 107 copies/genome
* Prokaryotes have mostly unique sequence of DNA
* Eukaryotes have a mix of unique and repetitive sequences
E.g. The human genome is approximately 50% unique sequence, 50% repeat
DNA is packaged into linear or circular (bacteria) units called chromosomes.
Describe the structure of bacterial chromosomes.
The bacterial genome is usually a single, circular, dsDNA chromosome (also archaea)
In addition to the bacterial genome, bacteria may contain additional, extrachromosomal, small circular DNA molecules - Plasmids. They are non-essential but may confer advantages to host cells.
Exceptions include Borrelia burgdorferi - Lyme Disease
Has one large dsDNA linear chromosome (0.91 MB) - 12 linear, 9 circular extrachromosomal elements/plasmids totalling 0.61 Mb.
How is bacterial DNA compacted and organised?
How is it made to fit into the cell?
Bacterial DNA must be organised and compacted to fit into a cell much shorter than the length of DNA molecule. DNA compaction in bacterial nucleoid is less well-understood than eukaryotic chromosome structure.
* First packing stage - binding of small positively charged proteins that counteract the negative charges on the DNA backbone which normally repels itself making it difficult to compact.
* Bacterial Nucleoid Associated Proteins (NAPS) including Integration Host Factor (IHF) bend DNA to facilitate packaging and supercoiling.
DNA arranged into ~400 independent negatively (to make more compact) looped domains each of ~10 kb. Topoisomerases generate supercoils.
Describe the organisation of Eukaryotic genomes
The genome distributed across multiple, linear chromosomes with varied DNA content, differing gene density. Every genome has a fixed number of chromosomes per cell. Most eukaryotes are diploid (two copies of each chromosome and produce haploid gametes) - and produce haploid gametes
* Each eukaryotic chromosome consists of one linear, double-stranded DNA molecule
* DNA complexed with proteins into chromatin - compacts and organises DNA into a form that fits into a cell
Human cells ~2m of DNA , nucleus 10 µm diameter.
Describe and give the function of histone proteins.
Eukaryotic DNA and histones are packaged into nucleosomes
In eukaryotes, basic binding proteins are histones
* Four core histones – very highly conserved
* Histones - rich in positively charged lysine and arginine which counteract negative charges on phosphate groups on DNA
* Charge interactions stabilize the DNA-histone interaction
* DNA wraps around a histone complex in a left handed manner to form a nucleosome – the histone complex at the center is the histone octamer
The histone octamer has two each of the four core histones H2A, H2B, H3 and H4
Describe the structure of the nucleosome core.
The structure of the nucleosome core
* Two H3-H4 dimers associate with DNA
* Two H2A-H2B dimers then associate to form the octamer
* About 146bp of DNA wraps around the octamer to form the nucleosome
* DNA is wound ~1.75 x around the histone octamer in a left-handed direction - supercoiling
* Removal of histone octamer leaves negatively supercoiled DNA
Negative supercoiling makes strand separation easier, required for replication and transcription
What are varient histones?
Variant histones replace core histones at specific chromatin locations and have special functions
* The four core histones are the most common
* Other histone variants can be incorporated into nucleosomes, and are found at special chromatin locations
* CENP-A (centromere protein-A) is a variant of histone H3 that is incorporated into nucleosomes at centromeres – and is essential for centromere formation and function
* Formation of the 30nm fiber involves histone H1
* H1 is a linker histone that binds to the linker DNA in between successive nucleosomes, helping compaction
The core histone tails are also involved in formation of the 30nm fiber, but it is not fully understood how
Describe chromatin compaction into metaphse chromosmes
Chromatin is further compacted into metaphase chromosomes
1. 20-nm chromatin fibre folded into looped domains via anchoring to a central nonhistone protein chromosome scaffold.
2. Chromosome-level condensation achieved through packaging of 10 nm fibre - without 30 nm fibre intermediate.
Describe the variation in chromatin structure during interphase.
Chromosomes undergo various phases of compaction during the cell cycle
* Interphase - when chromosomes are relatively uncondensed and genes are being transcribed, there is a range of compaction along a chromosome
* Chromatin in relatively decondensed regions stains lightly – euchromatin – actively transcribed genes. (10 nm beads on a string)
* Chromatin in more compacted regions stain more darkly – heterochromatin – less active transcription
why are some regions of chromosomes particularly rich in heterochromatina dn what is the effect of chromatin structure.
Specific regions of chromosomes are particularly rich in heterochromatin
* Special DNA at ends of chromosomes - telomeres
* DNA at or near centromeres
* Regions with highly repetitive DNA sequences
Chromatin structure affects:
* Transcription (translocation of a gene from a euchromatic to heterochromatic region can actively prevent transcription)
* DNA replication (rearrangements that place an origin of replication into heterochromatin result in late replication)
* Recombination (in which DNA is broken and joined to a different DNA molecule, is decreased in heterochromatic regions – protects genome from rearrangements)
* Chromosome transmission (special histone CENP-A is needed to form a functional centromere, which is needed for proper chromosome separation)
How does modification of histones affect chromatin structure and function?
Modification of histones affects chromatin structure and function
* Dynamic changes in chromatin are key to regulation of gene activity
* Amino acid side chains in protruding N-terminal histone tails modified
* Side chains in globular regions of histones can also be modified
* Combination of specific modifications influences function of DNA
* Histone modifications are reversible – specialized enzymes add and remove the chemical groups
* Euchromatin is more acetylated than heterochromatin
Histone modifications are reversible - specialised enzymes add and remove the chemical groups.
* Histone acetyltransferases (HATs) add acetyl groups to lysine side chains
* Histone deacetylases (HDACs) remove acetyl groups
* Histone methyltransferases (HMTs) add methyl groups to lysine and arginine side chains.
* Histone demethylases remove the methyl groups
* Phosphates are added by kinases and removed by phosphatases
Ubiquitin is added by a chain of enzymatic reactions, and removed by a deubiquitinating enzyme
What elements are required for chromsome function.
Origins of replication (ori) are required to initiate replication in bacteria and eukaryotes
In bacteria, sequences near the ori determine distribution of replicated chromosomes to the daughter cells. ter specifies replication termination
In eukaryotes, centromeres direct chromosome segregation.
Telomeres stabilize the ends of chromosomes and help solve the problem of replicating chromosome ends (more in DNA replication lectures)
