Organisation of Eukaryotic Genome Flashcards
define genomes
the genetic material of an organism or virus; the complete complement of an organism’s or virus’s genes along with its non-coding nucleic acid sequences
(DNA or RNA, contains all the genetic information needed to direct the development and maintenance of that organism for all the proteins and RNA that the organism will ever synthesise)
what does the locus of a chromosome mean?
it is the fixed position at which any specific gene is located on the chromosome to specify a particular character of the organism
what does a complete eukaryotic genome comprise of?
one complete copy of genetic information carried by a haploid set of linear chromosomes in the nucleus (nuclear genome) mitochondrial genome (a single small circular DNA molecule) chloroplast genome (in photosynthetic organisms only, a single small circular DNA molecule)
what does the human nuclear genome comprise of?
around 3 x 10^9 DNA nucleotide base pairs
over 22 different autosomes (non-X/Y chromosome) and one of the two sex chromosomes, either X for female, Y for male
*being diploid, a human somatic cell (non-reproductive) contains 46 chromosomes. for humans, haploid is 23, and diploid is 46 (two of each, one per parent)
how is genome size normally expressed, and what is its relationship to the complexity of an organism?
total number of base pairs per HAPLOID genome (gamates), in kilobases (kb) or megabases (Mb)
direct relationship between complexity of organism and genome size
- more complex organisms (like eukaryotes) tend to have larger genome sizes compared to simpler organisms (like prokaryotes)
due to: more gene products required for development and maintenance, increase in proportion of regulatory sequences (eg. alternative splicing)
what is the correlation between biological complexity and the number of genes in organisms?
there is no correlation
what is the percentage of genome containing structural genes for prokaryotes and eukaryotes?
prokaryotes: 85-90%
eukaryotes: 1-5%
what DNA sequences (types of DNA) does a eukaryotic genome comprise of?
gene and gene-related DNA sequences: exons (only coding sequences), introns, promotor, terminator
intergenic DNA: regulatory sequences (distal control elements, enhancer and silencer), repetitive DNA (tandemly repeated DNA [centromere and telomere], transposon [ignore]), other non-coding DNA (eg. spacer, ignore)
describe the first level of condensation of chromosomes
10nm nucleosomes: a molecule of DNA coiled around an octamer of histone proteins (two of each H2A, H2B, H3, H4 histones)
“beads-on-a-string” look
nucleosome core, linker DNA, associated non-histone chromosomal proteins
what are histones, and how do they form an octamer and bond with DNA?
small proteins, high concentration of positively-charged residues (eg. lysine and arginine), form ionic bonds with negatively-charged sugar-phosphate backbone of DNA
octamer forms of core upon which 146 pairs of DNA is bound
describe the second level of condensation of chromosomes
DNA on histone octamer is further folded or coiled to produce 30nm chromatin fibre, known as solenoid (6 nucleosome per turn)
- H1 histone and linker DNA involved
describe the third level of condensation of chromosomes
scaffold proteins (non-histone proteins) condense the 30nm chromatin fibre to form looped domains in mitotic and meiotic chromosomes, looped domains themselves coil and fold, further compacting chromatin to produce metaphase chromosome (chromatid, before replication, is 700nm)
what is the role of condensation
- to organise and pack giant DNA molecules of eukaryotic chromosomes into structure that facilitate their segregation onto daughter nuclei (so DNA molecules of different chromosomes will not be entangled or break during separation at anaphase)
particular genes end up located at the same places, packing steps are highly specific and precise
what does a eukaryotic protein-coding gene require?
transcription unit
- exons
- introns
regulatory sequences
- control elements (promoter-proximal and distal)
- promoter
- untranslated regions (5’ UTR and 3’ UTR)
what is the transcription unit (in prokaryotes and eukaryotes)?
exons interrupted by introns, discontinuous coding DNA sequences
exon codes for particular amino acid sequence, introns not represented
number and sizes of introns per gene varies, more intron sequences than exons
for prokaryotes, genomes arranged in continuous operons, no introns
define regulatory sequences
regions of DNA sequence where gene regulatory proteins bind to control the rate of assembly of protein complexes required for gene expression
what is a promoter?
a series of DNA sequences located upstream of transcriptional start site
RNA polymerase and transcription factors bind to promoter to initiate transcription
what are control elements?
DNA segments that regulate the initiation and rate of transcription by binding particular proteins, promoter-proximal elements and distal elements (near and far from promoter respectively)
compare promoter-proximal elements and distal elements
- similarities: proteins bind to both
- differences:
promoter-proximal initiates transcription, distal controls rate of transcription
promoter-proximal has general / basal transcription factors bound to it, distal has activators bound to enhancers (increases transcription rate) and repressors bound to silencers (decreases transcription rate)
describe the 5’ UTR’s position and function, and what it is translated to on mRNA
starts at the +1 position on DNA template strand (non-coding) where transcription begins and ends one nucleotide before the start codon
transcribed into ribosome binding site on mRNA (regulates mRNA’s stability for translation)
describe the 3’ UTR’s position and function, and what it is translated to on mRNA
starts after stop codon
transcribed into polyadenylation signal on mRNA, for transcription termination
what does repetitive DNA refer to, and what percentage of it comprises of intergenic (non-coding) DNA?
sequences present in multiple copies in the genome
59%
what is tandemly repeated DNA (satellite DNA)
mostly relatively short sequences (1-500bp), repeated many times in tandem to form a long array or cluster in a localised area of genome
preferentially located in regions of heterochromatin including centromeres, telomeres, and specific locations within arms of certain chromosomes
three types, based on length of repeating unit: regular satellite DNA (centromeres), minisatellites (telomeres), microsatellites (ignore)
compare centromeres and telomeres (location and function, form of DNA packaging, nature of DNA sequence, type of satellite DNA)
centromere joins two sister chromatids in a replicated chromosome during cell division, telomere protects the two physical ends of linear chromosome)
both are heterochromatin and consists of tandem repetitive, non-coding satellite DNA
centromere made of regular satellite DNA, telomere made of minisatellite DNA
*prokaryotic genomes are circular and do not contain telomeres or centromeres
describe the structure of a telomere
specialised nucleoprotein: telomeric DNA bound by specific proteins
- telomeric repeat sequence varies between organisms
- 3’ end of G-rich strand extends 12-16 nucleotides beyond 5’ end of complementary C-rich strand: 3’ single-stranded overhang (hairpin loop called telomere / t-loop)
what is telomeric DNA like in humans and other vertebrates?
in vertebrates, long stretches of hundreds to thousands of tandem repeats of a short nucleotide sequence with a high G content
human telomeres have hundreds to 2000 tandem repeats of 5’-TTAGGG-3’
what are the four functions of telomere?
- protective: t-loops protect 5’ and 3’ ends of linear chromosomes from degradation by cellular exonucleases (enzymes that cleave off nucleotides), prevents it from being recognised as damaged DNA
- stability: prevent chromosome tips from fusing to ends of other chromosomes (eg. between homologous chromosomes)
- preventing gene loss: protect organism’s genes by eroding in its place during the end-replication problem, so DNA replication occurs without losing important coding sequences
- regulating replicative cell senescence: when telomeres shortened to critical length (cell reaches Hayflick limit), replication stops
what is the end-replication problem, and why does it arise?
eukaryotic chromosomes are linear, shortening the telomeres with each successive cell division since small section at extreme 3’ end of parental strand does not under replication, since DNA polymerase cannot replicate ends of chromosome
define replicative cell senescence
the period in which a cell withdraws permanently from the cell cycle and hence stops dividing after reaching Hayflick limit of 25-50 cell divisions
what are the factors and effects of replicative cell senescence?
when Hayflick limit is reached and telomere is completely lost, apoptosis (programed cell death) occurs
telomere length regulates cell’s life span: cells with longer telomeres (and bigger T-loops) can have more cell divisions, survive longer (telomere shortening = aging)
germ cells, stem cells, cancer cells have telomerase, can add telomeric repeat sequences to end of chromosome
describe the action of telomerase
telomere length cannot be maintained by normal DNA replication, only by telomerase
does not prevent end replication problem, only lengthens and thereby maintains chromosomal ends after end replication problem
what is the structure of telomerase and where is it found?
ribonucleoprotein (protein-RNA) complex:
- RNA sequence template, 3’-AAUCCC-5’ for mammals, complementary to telomere repeat sequence
- protein component, Telomere Reverse Transcriptase (TERT), provides catalytic action to synthesise RNA from DNA template
found in stem, germline, cancer cells
how does telomerase maintain telomere length?
- telomerase’s RNA template binds complimentarily to 3’ overhang of parental DNA strand
- extends 3’ overhang of parental DNA strand in 5’ to 3’ direction by adding sequence repeats (of 5’TTAGGG3’ in mammals) via complementary base-pairing, so daughter strand synthesised has a longer telomere (still with 3’ overhang)
- maintain the number of repeats at telomeres, delaying senescence of cells and enabling proliferation indefinitely
describe the expression of genes coding for telomeric components in somatic and germ + stem cells
somatic: divide a limited number of times, expression switched off or not fully activated
germ or stem: active, same genes reactivated in most cancer / tumour cells, telomere lengths maintained so cells divide indefinitely or are immortalised, evading apoptosis (programmed cell death)
- inhibitors of human telomerase may treat cancer
describe the structure of centromeres
single centromere not in defined position, unique for each chromosome
made of (alpha, for humans) satellite DNA: short, AT-rich sequences repeated thousands of times in tandem
centromeric DNA sequences vary greatly, more than 40kb long in most eukaryotes
embedded in very large stretch of heterochromatin
centromeric DNA bound by centromere-specific histones to form specialised nucleosomes
specialised nucleosomes + centromere-binding proteins = kinetochore (where mitotic spindle fibres associate with at the centromere during mitosis)
what are histone tails, and how do they aid in the formation of nucleosomes?
N-terminus of each histone group protrudes outwards, forming eight -NH2 groups that form histone tails
histone tails rich in positively-charged residues, form strong ionic bonds with negatively-charged phosphate groups of DNA backbone, increase affinity of DNA for nucleosome surface
