Organisation of Eukaryotic Genome

Question 1

What is genome

Answer 1

The genetic material of an organism or virus. Contains the genetic information for all the proteins and RNA that the organism will ever synthesis.

Question 2

Definition of a gene

Answer 2

A section of the DNA that contains the information in the form of a specific sequence of nucleotides/bases to direct the synthesis of one polypeptide chain or RNA

Question 3

Where are genes found?

Answer 3

Genes are carried on the chromosomes, each gene resides in a specific location along the chromosome called gene locus.

Question 4

What does the complete eukaryotic genome comprises of

Answer 4

A. One complete copy of genetic information carried by a haploid set of linear chromosomes in the nucleus

B. The mitochondrial genome, which consists of a single small circular DNA molecule

C. The chloroplast genome (in photosynthetic organisms only which also consists of a single small circular DNA molecule

Question 5

Relationships that can be observed pertaining to genomes and genes

Answer 5

1. More complex organisms tend to have larger genome size compared to simpler organisms. However, this correlation is not observed in higher eukaryotes.
2. No correlation between biological complexity and size and number of genes in organism
3. Genome size is not necessarily proportional to number of genes in the genome
4. Prokaryotes have much higher gene densities than that of eukaryotes
5. The more complex eukaryotes generally have lower gene density than lower eukaryotes

Question 6

What is the first level of condensation

Answer 6

1. Nucleosomes packing process involves a molecule of DNA coiled around a octamer of histone proteins, 2 each of histones H2A, H2B H3 and H4
2. Multiple nucleosomes are packed together to produce the 10nm chromatin fibre also known as nucleosome fibre

Question 7

What are histones

Answer 7

Small proteins with a high concentration of positively-charged residues which form ionic bonds with the negatively-charged sugar-phosphate backbone of DNA

• Histones assemble into an octamer to form a core upon which 146 DNA base pairs are bound
• DNA coiled around the histone core are known as nucleosome core

Question 8

What do completed chromatin subunit consists of

Answer 8

Nucleosome core, the linker DNA and the associated non-histone chromosomal proteins

Question 9

What is the second level of condensation

Answer 9

1. DNA is further folded or coiled to produce the 30nm chromatin fibre known as solenoid
2. Histone H1 and linker DNA are involved in this coiling

Question 10

What is the third level of condensation

Answer 10

1. Non-histone proteins known as scaffold proteins are involved in condensing the 30nm chromatin fibre (solenoid) to form looped domains
2. In mitotic and meiotic chromosomes, the looped domains themselves coil and fold, further compacting the chromatin to produce the characteristic metaphase chromosome

Question 11

What is the role of condensation

Answer 11

• To organise and pack the giant DNA molecules of eukaryotic chromosomes into structures that will facilitate their segregation onto daughter nuclei. This helps–
• DNA molecules of different chromosomes will not be entangled and as a consequence break during separation at anaphase

Question 12

What DNA sequences does a eukaryotic protein-coding gene require for the proper expression of the gene

Answer 12

A. Coding exons and non-coding introns, collectively termed the transcription unit

B. Non-coding DNA regulatory sequences

Question 13

Some transcription units FYI (idt really impt)

Answer 13

• As exons are interrupted by introns, exons are thus described as discontinuous coding DNA sequences of a eukaryotic gene
• Exons code for a particular portion of the polypeptide while introns are not represented in the amino acid sequence of the protein gene product
• The number and sizes of introns per gene varies
• Usually the number of DNA in the intron sequence is greater than that of exons

Question 14

What is the definition of regulatory sequences

Answer 14

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

They include

• promoters
• Untranslated regions
• Control elements

Question 15

What is a promoter

Answer 15

A series of DNA sequences including the TATA box located upstream of the transcriptional start site. RNA polymerase and transcription factors bind to the promoter to intiate transcription.

Question 16

What are control elements

Answer 16

Segments of DNA involved in regulating the initiation and rate of transcription by binding particular proteins

These include promoter-proximal and distal control elements that are located near to and far from the promoter respectively

Question 17

What are distal elements

Answer 17

It consists of enhancers and silencers.

Enhancers are DNA sequence that bind specific regulatory proteins known as activators to increase transcription rate

Silencers interact with other specific regulatory proteins proteins known as repressors to decrease transcription rate.

Question 18

What are promoter-proximal elements

Answer 18

Sequences where gene regulatory proteins called general transcription factors bind to initiate transcription

They are found between 100 to 200 bp upstream of the transcription start site

They are essential for efficient transcription

Question 19

What are untranslated regions (UTRs)

Answer 19

They are found in the exons of the mRNA, but are not translated into polypeptide sequences. Include:

The 5’ UTR

The 3’ UTR

Question 20

What is the 5’ UTR

Answer 20

It starts at the +1 position on DNA template strand where transcription begins and ends one nucleotide before the start codon

• Contain DNA sequence which is transcribed into a ribosome binding site on mRNA for ribosome to bind and initiate transcription
• 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

Starts after the stop codon

• contains DNA sequence which is transcribed into a polyadenylation signal on mrRNA, which is needed for termination of transcription

Question 22

What is repetitive DNA

Answer 22

sequences present in multiple copies in the genome

Question 23

Structure of telomere??

Answer 23

IDK bout this one

Question 24

State the protective function of telomere

Answer 24

Telomeric DNA forms T-loops with telomere specific proteins forming a cap that:

• Protects the 5’ end and 3’ single stranded overhangs of linear chromosomes from degradation by cellular exonucleases
• Prevents it from being recognised as damaged DNA molecule by the cell’s repair machinery

Question 25

How do telomeres prevent loss of genes

Answer 25

• They protect the organism’s genes from being eroded as the linear chromosome ends shorten after 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

Question 26

State how telomeres maintain stability

Answer 26

They confer stability to linear chromosomes as the t-loops prevent the chromosome tips from fusing to the ends of other chromosomes, thus ensuring that ends of homologous chromosomes do not spontaneously fuse

Question 27

State how telomeres regulate replicative cell senescence

Answer 27

Each telomere shrinks with every successive cell division. When the telomeres, have shortened to a critical length, the cell reaches the hayflick limit and enters a period of replicative cell senescence

Which means the cell withdraws permanently from the cell cycle and stops dividing.

Question 28

Describe the end replication problem (not v difficult)

Answer 28

The chromosomes of eukaryotes are linear and thus DNA polymerase is incapable of completely replicating all the way to the end of the chromosome, leading to shortening of telomeres.

Question 29

Characteristics of telomerase

Answer 29

1. Telomerase is generally found only in stem cell, germline cells and cancer cells
2. It is a ribonucleoprotein (protein-RNA) complex that is made up of 2 components
   
   • an RNA sequence template and
   • a protein component
3. The protein component of telomerase is known as TERT (Telomerase Reverse Transcriptase). It is an enzyme that provides the catalytic action to synthesise DNA from an RNA template

Question 30

How does telomerase maintain telomere length

4 bloody steps (SUPER HARD)

Answer 30

1. Telomerase enzyme recognises and binds to the G rich telomere sequence at the 3’ overhang on the parental strand. The 3’ nucleotides are base paired to the 5’ UAA 3’ sequence in the RNA template of the telomerase
2. Through its reverse transcriptase activity, telomerase adds nucleotides to the 3’ end of the overhang using the bound RNA as template, thereby extending the 3’ end of the parental strand
3. Telomerase is translocated to the end of the extended overhang. The result is that the telomere is extended in a 5’ to 3’ direction, over repeated cycles of elongation and translocation
4. Replication of the incomplete lagging daughter strand is completed by using these extensions as a template for synthesis of the complementary strand by DNA polymerase, leacing a 3’ overhang

Question 31

Describe the structure of centromere

Answer 31

Unlike the telomere, the single centromere found in each chromosome is not in a fixed position but its position is unique for ever chromosome

Centromeres consist of satellite DNA (alpha satellite DNA for humans)

• Alpha satellite DNA consits of short, AT rich sequences that are repeated thousands of times in tandem
• There is no centromere-specific DNA sequence so the numerous repeats vary slightly from one another

Centromeres are embedded in a very large stratch of heterochromatin

• The centromeric DNA is bound by centromere-specific histones to form specialised nucleosomes, which are hetrochromatic in nature

Folding of DNA into these specialised nucleosomes facilitates the assembly of other centromere-binding proteins to form the kinetochore that associates the centromere to the mitotic spindle.

Question 32

How do centromeres ensure proper chromosome segregation

Answer 32

1. The presence of only one centromere on each chromosome is critical
   * Each kinetochore at the single centromere of each sister chromatid of a duplicated chromosome binds to kinetochore microtubules and is oulled towards one pole of the cell during anaphase
2. In the absence of a centromere, the daughter chromosomes segregate randomly, leading to loss or duplication of chromosomes in daughter cells