organisation of eukaryotic genome

Question 1

what is a gene?

Answer 1

a gene is a section of the DNA that contains the information in the form of a specific sequence of nucleotides to direct the synthesis of one polypeptide chain or RNA. it is a unit of inheritance located in a fixed position on the chromosome which specifies a particular character of an organism

Question 2

what is a genome?

Answer 2

a genome is the genetic material of an organism or virus; the complete complement of an organism’s/virus’ genes along with its non-coding nucleic acid sequence

Question 3

what is the correlation between complex organisms and genome sizes?

Answer 3

more complex organisms tend to have larger genome sizes, as there is a correlation between an organism’s genome size and its apparent biological complexity.
gene size is typically larger in more complex organisms due to the increase in the proportion of regulatory sequences needed for more complex control of gene expression

genome size is usually expressed as the total number of base pairs per haploid genome

Question 4

what does a complete eukaryotic genome comprise of?

Answer 4

• one complete copy of genetic information carried by a haploid set of linear chromosomes in the nucleus
• the mitochondrial genome, which consists of a single small circular DNA molecule
• the chloroplast genome (in photosynthetic organisms only) which consists of a single small circular DNA molecule

Question 5

is there a correlation between biological complexity and size & number of genes in organisms?

Answer 5

no.

GENOME SIZE IS NOT NECESSARILY PROPORTIONAL TO NUMBER OF GENES IN THE GENOME

Question 6

do prokaryotic genomes or eukaryotic genomes have higher gene densities?

Answer 6

prokaryotic genomes have higher gene densities. (despite some eukaryotes having larger genome size than prokaryotes

gene density is the number of genes per million base pairs

Question 7

do more complex eukaryotes have lower gene density than lower eukaryotes?

Answer 7

yes. higher eukaryotes have decreased gene density mostly due to the large proportion of intergenic DNA relative to genes present

Question 8

what are the 3 levels of condensation in packing of DNA in eukaryotic chromosomes?

Answer 8

1st level: nucleosomes
2nd level: 30nm fiber
3rd level: looped domain

Question 9

nucleosomes

describe the 1st level of condensation in packing of DNA

Answer 9

nucleosome: 1 molecule of DNA coiled around an octamer of histone proteins
1. histones are small proteins with high conc of positively charged residues, which form ionic bonds with the negatively charged sugar-phosphate backbone of DNA
2. histones assemble into an octamer to form a core upon which 146 base pairs of DNA is bound
3. double stranded DNA is coiled around the histone core, forming a nucleosome core
4. the completed chromatin subunit consists of the nucleosome core, the linker DNA and the associated non-histone chromosomal proteins
5. multiple nucleosomes are packed together to produce the 10nm chromatin fiber known as nucleosome fiber

Question 10

30nm fiber

describe the 2nd level of condensation in packing of DNA

Answer 10

1. DNA is further folded or coiled to produce the 30nm fiber known as solenoid
2. histone H1 and linker DNA are involved in this coiling of the 10nm nucleosome fiber to produce the 30nm chromatin fiber

Question 11

describe the 3rd level of condensation in packing of DNA

Answer 11

1. non-histone proteins, aka scaffold proteins, are involved in condensing the 30nm chromatin fibre to form looped domains
2. in mitotic and meiotic chromosomes, the looped domains themselves coil and fold, further compacting all the chromatin to produce the characteristic metaphase chromosome. the width of one chromatid is 700nm

particular genes always end up located at the same places in mitotic and meiotic chromosomes, indicating that the packing steps are highly specific and precise

Question 12

what is the role of condensation of DNA?

Answer 12

• to organise and pack the giant DNA molecules of eukaryotic chromosomes into structures that will facilitate their segregation onto daughter nuclei
• DNA molecules of different chromosomes will not be entangled and won’t break during separation at anaphase

Question 13

what does a eukaryotic protein-coding gene contain?

Answer 13

1. coding exons and non-coding introns, collectively termed the transcription unit
2. non-coding DNA regulatory sequences

Question 14

define non-coding DNA regulatory sequences

Answer 14

regulatory sequences are regions of DNA sequence where gene regulatory proteins bind to control the rate of assembly of protein complexes required for gene expression

Question 15

what is in the transcription unit?

Answer 15

coding exons & non-coding introns

Question 16

what are the 3 types of non-coding DNA regulatory sequences?

Answer 16

promoter, control elements and untranslated regions

Question 17

what is a promoter?

Answer 17

a series of DNA sequences located upstream of the transcriptional start site. RNA polymerase & transcription factors bind to the promoter to initiate transcription

Question 18

what are control elements?

Answer 18

control elements are segments of DNA involved in regulating the initiation & rate of transcription by binding particular proteins. there are 2 types of control elements:
1. promoter-proximal elements are sequences where gene regulatory proteins called general transcription factors bind to initiate transcription. they are located near the promoter
2. distal elements consist of enhancers (that bind to activators) that increase transcription rate and silencers (that bind to repressors) that decrease transcription rate, and are located far from the promoter

Question 19

what are untranslated regions?

Answer 19

untranslated regions are found in the exons (coding regions) of mRNA, but are not translated into the polypeptide sequence.

Question 20

what is the 5’ UTR?

Answer 20

the 5’ UTR
- starts at the +1 position on the DNA template strand where transcription begins and ends 1 nucleotide before the start codon
- contains DNA sequence which is transcribed into a ribosome binding site on mRNA, where ribosomes bind and initiate translation
- contains DNA sequence which is transcribed into binding sites on mRNA for proteins which regulate the mRNA’s stability for translation

Question 21

what is the 3’ UTR?

Answer 21

the 3’ UTR
- starts after the stop codon
- contains DNA sequence which is transcribed into a polyadenylation signal on mRNA, which is needed for termination of transcription

Question 22

what are the differences between centromeres and telomeres?

Answer 22

1. region found: the centromere is the region where 2 sister chromatids are joined in a replicated chromosome during cell division, while the telomere is located at the 2 physical ends/tips of a linear eukaryotic chromosome
2. category of satellite DNA: centromere is regular satellite DNA while telomere is minisatellite DNA

similarities: both are heterochromatin form of DNA packaging and both consist of tandem repetitive, non-coding satellite DNA

Question 23

describe the structure of telomeres

Answer 23

1. consists of specialised nucleoproteins which are complexes composed of telomeric DNA bound by specific proteins
2. telomeric DNA consists of long stretches (hundreds to thousands) of tandem repeats of a short nucleotide sequence with high G content. (human telomeres contain hundreds to as many as 2000 tandem repeats of the sequence 5’-TTAGGG-3’)
3. the 3’ end of the G rich strand extends 12-16 nucleotides beyond the 5’ end of the complementary C-rich strand, forming a 3’ single-stranded overhang.

the overhang folds back on itself to form a hairpin loop called telomere loop (t-loop), which invades an upstream telomeric repeat to displace the same sequence in an upstream region of the telomere

Question 24

what is repetitive DNA and tandemly repeated DNA?

Answer 24

repetitive DNA refers to sequences present in multiple copies in the genome.
tandemly repeated DNA consist of DNA sequences repeated multiple times and arranged adjacent to one another in a head-to-tail fashion
the most highly repeated tandem sequences, simple sequence/satellite DNA, make up about 3-6% of the human genome

satellite DNA is usually located in regions of heterochromatin including centromeres and telomeres

Question 25

what are the functions of telomeres?

Answer 25

1. protective function: (telomeric DNA forms t-loops with telomere specific proteins forming a cap that) protects the 5’ ends and 3’ single-stranded overhangs of linear chromosomes from degradation by cellular exonucleases AND prevents it from being recognised as a damaged DNA molecule by the cell’s repair machinery
2. maintains stability: telomeres confer stability to linear chromosomes as the t-loops prevent the chromosome tips from fusing to the ends of other chromosomes, ensuring that the ends of homologous chromosomes don’t spontaneously fuse
3. prevents loss of genes: telomeres protect the organism’s genes from being eroded as the linear chromosome ends shorten with each successive round of DNA replication due to the end replication problem. this ensures that DNA replication can occur without the loss of important coding sequences. without telomeres, vital genetic information that is needed to sustain a cell’s activities will be lost
4. regulating replicative cell senescence: each telomere shrinks with every successive cell division, eventually reaching the hayflick limit and entering a period of replicative cell senescence

Question 26

what is replicative cell senescence?

Answer 26

replicative cell senescence is the period in which a cell withdraws permanently from the cell cycle and stops dividing after reaching hayflick limit, when it has divided for 25-50 cell divisions

once a cell reaches hayflick limit, the cell no longer divides and eventually dies. the complete loss of telomere repeats triggers apoposis

Question 27

what are the characteristics of telomerase?

Answer 27

1. telomerase is generally found only in stem cells, germline cells and cancer cells
2. telomerase is a ribonucleoprotein complex made up of 2 components, the RNA sequence template and a protein component
3. the RNA sequence template is complementary to the telomere repeat sequence, which acts as a template for the insertion of the telomere repeat sequence 5’-TTAGGG-3’ onto the existing 3’ overhang strand, lengthening the overhang
4. the protein component of telomerase is known as TERT (telomere reverse transcriptase)

Question 28

how does telomerase maintain telomere length?

Answer 28

1. telomerase’s RNA template binds complementarily to the 3’ overhang of the parental DNA strand
2. telomerase extends the 3’ overhang of the parental DNA strand in the 5’ to 3’ direction by adding sequence repeats of 5’-TTAGGG-3’ via complementary base-pairing
3. lengthening the 3’ overhang of the parental DNA strand allows the synthesis of the shorter daughter DNA strand to be extended during the next round of DNA replication, resulting in a longer telomere
4. the action of telomerase thus maintains the number of repeats at the telomeres, delaying the senescence of cells and enabling them to proliferate indefinitely

Question 29

describe the structure of centromeres.

Answer 29

1. centromeres are not in a defined position. the position of the centromere is unique for each chromosome
2. centromeres consist of satellite DNA, which consists of short, AT-rich sequences that are repeated thousands of times in tandem. there is no centromere-specific DNA sequence
3. centromeric DNA sequences vary greatly in length in different eukaryotic species
4. centromeres are embedded in a very large stretch of heterochromatin. centromeric DNA is bound by centromere-specific histones to form specialised nucleosomes
5. folding of DNA into specialised nucleosomes facilitates the assembly of other centromere-binding proteins to form the kinetochore

Question 30

what are the functions of the centromere?

Answer 30

1. sister chromatid adhesion: the centromere is the region of a linear chromosome where the 2 sister chromatids join
2. kinetochore formation: the centromere is the site of assembly of the kinetochore
3. proper chromosome segregation: centromeres are essential for the correct segregation of daughter chromosomes after DNA replication, so that 1 copy goes to each of the 2 daughter cells. the presence of only 1 centromere on each chromosome is critical. in the absence of a centromere, the daughter chromosomes segregate randomly, leading to loss or duplication of chromosomes in the daughter cells.