organisation and control of eukaryotic genome

Question 1

what is the definition of a genome?

Answer 1

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

Question 2

what is the function of the genome?

Answer 2

the genome comprises of genetic material (DNA or RNA) that contains all the genetic information needed to direct the development and maintenance of that organism

Question 3

what is the definition of a gene?

Answer 3

a gene is a section of 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 at a locus on the chromosome which specifies the phenotype of an organism

Question 4

what are the properties of the eukaryotic genome?

Answer 4

1. genes are carried on chromosomes, and each gene resides in the gene locus along the chromosome
2. in humans, a complete haploid copy of the nuclear genome comprises of 3 billion nucleotide base pairs distributed over 22 autosomes and one of the two sex chromosomes.
3. more complex organisms tend to have larger genome sizes compared to simpler organisms, because more genes and gene products are required to direct the development and maintenance of more complex organism. there is also an increase in the proportion of regulatory sequences needed for more complex control of gene expression
4. there is no correlation between the biological complexity and the size and number of genes in organisms, as genome size is not necessarily proportional to the number of genes in the genome
5. the human genome has an estimated 100 fold lower gene density than that of a typical prokaryote, despite its approximately 100 times larger genome size, as there is a large proportion of non-coding intergenic DNA relative in eukaryotes, which are less compact and do not encode any expressed protein

Question 5

how does telomerase carry out its activity?

Answer 5

1. a short 3-nucleotide segment of RNA within telomerase binds to part of a DNA repeat in the 3’ overhand by complementary base pairing
2. the adjacent part of the RNA within telomerase is used as a template to synthesise a short complementary 6-nucleotide DNA repeat. telomerase catalyses the formation of phosphodiester bonds between the existing 3’OH group of the existing DNA overhand and 5’ phosphate group of incoming dNTP
3. telomerase then translocates 6 nucleotides to the right in the 5’ to 3’ direction of the DNA overhand and begins a series of tandem repeats which elongates the telomere
4. RNA primer is then made near the end of the telomere, where DNA polymerase adds nucleotides to the 3’OH end of the primer and synthesises a complementary strand. the nick is then sealed by DNA ligase

Question 6

what is the first level of condensation in an eukaryotic genome?

Answer 6

1. histones are small proteins with a high concentration of positively charged residues, which form ionic bonds with the negatively charged sugar phosphate backbone of DNA.
2. histones assemble into an octomer 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, giving rise to a ‘beads-on-a-string’ look with linker DNA joining adjacent nucleosomes

Question 7

what is the second level of condensation in an eukaryotic genome?

Answer 7

histone H1 and linker DNA are involved in the coiling of the 1nm nucleosome fibre to produce the 30nm chromatin fibre, known as the solenoid

Question 8

what is the third level of condensation in the eukaryotic genome?

Answer 8

1. scaffold proteins are involved in condensing the 30nm chromatin fibre to form looped domains
2. in miotic and meiotic chromosomes, the looped domains themselves coil and fold, and further compacting all the chromatin to produce the metaphase chromosome, in a highly specific and precise packing process
3. the width of one chromatid is 700nm

Question 9

what is the role of condensation in a eukaryotic chromosome?

Answer 9

1. to organise and pack the giant DNA molecules of eukaryotic chromosomes into structures that will facilitate their segregation into daughter nuclei
2. to ensure DNA molecules of different chromosomes will not be entangled and as a consequence, break during separation at anaphase

Question 10

what is the structure of the transcription unit?

Answer 10

1. exons, which code for a particular portion of the polypeptide, are interrupted by non-coding introns, and are thus described as discontinuous coding DNA sequences of a eukaryotic gene
2. the number and sizes of introns per gene varies, but in general, the amount of the DNA in the intron sequences is often greater than the exons, with around 98% of DNA being non-coding sequences

Question 11

what is the definition of regulatory sequences?

Answer 11

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

Question 12

what is the structure of the promoter?

Answer 12

1. the promoter is located just upstream of the TSS of a gene
2. the promoter has critical elements like the TATA box, and 2 CAAT and GC boxes

Question 13

what is the function of the promoter?

Answer 13

1. the promoter acts as a recognition and binding site for GTF which then recruits RNA polymerase to form the transcription initiation complex which initiates transcription
2. the TATA box determines the precise location of TSS

Question 14

what is the definition of proximal and distal control elements?

Answer 14

1. proximal control elements are sequences where gene regulatory proteins called GTD bind to initiate transcription
2. distal control elements consist of enhancers, and silencers

Question 15

what is the function of the 5’ UTR?

Answer 15

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

Question 16

what is the function of the 3’ UTR?

Answer 16

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

Question 17

what is the structure of satellite DNA?

Answer 17

1. satellite DNA makes up about 3-6% of the human genome
2. satellite DNA consists of relatively short sequences repeated many times in tandem to form a long array or cluster in a localised area of the genome
3. satellite DNA is preferentially located in regions of heterochromatin, including centromeres, telomeres and specific locations within the arms of particular chromosomes.
4. regular satellite DNA is found in centromeres, while minisatellites are found in telomeres

Question 18

what is the structure of telomeres?

Answer 18

1. telomeres consist of specialised nucleoprotein which are complexes composed of telomeric DNA bound by specific proteins.
2. telomeric repeat sequences vary between organisms, but in human telomeres, they contain hundreds to thousands of 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 overhand, which invades an upstream telomeric repeat to displace the same sequence in an upstream region of the telomere and base pair with the complementary strand, forming a telomere loop, which involves various proteins

Question 19

what is the function of telomeres?

Answer 19

1. the telomere loop protects the 5’ end and 3’ single stranded overhangs of linear chromosomes from degradation by cellular exonuleases
2. telomeres prevent the chromosome from being recognised as a damaged DNA molecule by the cell’s repair machinery
3. telomeres confer stability to linear chromosomes, as the t-loops prevent the chromosome tips from fusing to the ends of other chromosomes, thus ensuring that the ends of homologous chromosomes do not spontaneously fuse
4. telomeres protect the organism’s genes, located within the interior of the linear chromosomes, from being eroded due to the end replication problem, which ensures DNA replication can occur without the loss of important coding sequences
5. when telomeres have shortened to a critical length, the cell reaches the hayflick limit, and enters the period of replication cell senescence, where it withdraws permanently from the cell cycle and stops dividing

Question 20

what is the definition of replication cell senescence?

Answer 20

replicative cell senescence is the period in which a cell withdraws permanently from the cell cycle and hence stops dividing after reaching the hayflick limit when it has divided for 25-50 cell divisions. the complete loss of telomere repeats eventually triggers apoptosis

Question 21

what is the structure of telomerase?

Answer 21

telomerase is a ribonucleoprotein complex that is made up of two components, which is an RNA sequence template, and telomere reverse transcriptase, which provides the catalytic action to synthesise DNA from an RNA template

Question 22

what is the structure of centromeres?

Answer 22

1. the single centromere found in each chromosome is not in a defined position, and the position of the centromere is unique for each chromosome
2. alpha satellite DNA in centromeres consist of short, AT rich sequences that are repeated thousands of times in tandem, but vary slightly from one another in sequence
3. centromeres are embedded in a very large stretch of heterochromatin, and are bound by centromere-specific histones to form specialised nucleosomes, which are heterochromatin in nature

Question 23

what are the functions of centromeres?

Answer 23

1. the centromere is the region of a linear chromosome where the two sister chromatids join
2. the centromere is the site of assembly of the kinetic horse, which attaches to the microtubules of the mitotic/meiotic spindle, and the sister chromatids are in turn joined via the centromere to the kinetochore microtubules. the kinetochore then binds to kinetochore microtubules and is pulled towards one pole of the cell during anaphase. in the absence of a centromere, daughter chromosomes segregate randomly, leading to loss or duplication of chromosomes
3. centromeres are essential for the correct segregation of daughter chromosomes after DNA replication, so that one copy goes to each of the two daughter cells during cell division

Question 24

what is the structure of enhancers and silencers?

Answer 24

enhancers and silencers are usually located far away from the promoter

Question 25

what is the function of enhancers?

Answer 25

enhancers have a recognition and binding site for activators, increasing the frequency of transcription by promoting the assembly of the transcription initiation complex, with the help of DNA bending proteins that bend spacer DNA

Question 26

what is the function of silencers?

Answer 26

silencers have a recognition and binding site for repressiors, which decrease the frequency of transcription by preventing the assembly of the transcription initiation complex