Pro and Eu 1

What are the differences between pro and eu genome? (size, appearance and association with proteins)

Size

• Pro — Smaller

• Eu — Larger

Appearance

• Pro — Single circular molecule

• Eu — Multiple linear molecules

Association with proteins

• Pro — Relatively less i.e. histone-like proteins

• Eu — Large amounts i.e. histones, scaffold proteins

What are the differences between pro and eu genome? (level of packing/coiling)

Pro — Relatively low

• DNA is folded into chromosomal looped domains by protein-DNA associations

• Supercoiling causes further compacting

Eu — High

• DNA molecules = negatively-charged, histones = positively-charged

• DNA held around histones by electrostatic interactions

• Nucleosomes = DNA wound around octamers of 8 histones, linker DNA joins adjacent nucleosomes

• Supercoiling to produce metaphase chromosome

• Chromatin fibre forms looped domains when associated with scaffold proteins

What are the differences between pro and eu genome? (location, extrachromosomal DNA, no. of genes, ORI)

Location

• Pro — Nucleiod region

• Eu — Nucleus

Extrachromosomal DNA

• Pro — Plasmids

• Eu — No plasmids

No. of genes

• Pro — Fewer

• Eu — Many

ORI

• Pro — 1

• Eu — Many

What are the differences between pro and eu genome? (non-coding regions)

Pro — Not common, no introns, rarely enhancers & silencers, few repeated sequences

Eu — Common; many introns, enhancers & silencers present, many repeated sequences

What is non-coding genome?

Any part of the genome that does not code for proteins or RNA products — large component of eukaryotic genome

What are introns? (structure)

Non-coding sequences found within a gene between exons

What are the functions of introns?

• No involvement in translation of mRNA → excised during splicing with spliceosomes

• Points of excision are very precise and determined by the sequence of nucleotides at intron-exon boundaries

What is alternative RNA splicing?

• Produce different mature mRNA depending on the combination of exons spliced

• Different protein isoforms of one gene ← One gene codes for more than one type of polypeptide

What are promoters? (structure)

Non-coding DNA sequences located just upstream of the transcription start site

• Sequences within determine strength of promoter and hence frequency of transcription

What are the functions of promoters?

Serves as a recognition site for the binding of general transcription factors and RNA polymerase to form the transcription-initiation complex and initiate transcription

What is the critical element and proximal control elements in a promoter?

Critical element — TATA box

Proximal control elements — CAAT and GC boxes

What is the TATA box?

• Critical element on a promoter that determines the precise location of the transcription start site

• Serves as the recognition and binding site for general transcription factors which then recruit RNA polymerase to form the transcription-initiation complex

What are CAAT and GC boxes?

• Proximal control elements that may follow a conserved consensus sequence (most commonly occurring bases within critical elements across promoters)

• Higher resemblance to consensus sequence → Greater binding efficiency → Increase in transcription frequency

What are enhancers and silencers? (structure)

Non-coding DNA sequences usually located far away upstream or downstream the promoter

What is the function of an enhancer?

• Increases the frequency of transcription by promoting the assembly of a transcription-initiation complex

• Binds to specific transcription factors i.e. activators

What is the function of a silencer?

• Decreases the frequency of transcription by inhibiting the assembly of a transcription-initiation complex

• Binds to specific transcription factors i.e. repressors

What is the structure of telomeres?

• Non-coding regions of DNA made of tandem repeat sequences found at both ends of eukaryotic chromosomes

• Single-stranded region of DNA at their 3’ ends known as 3’ overhang

What are the functions of telomeres?

• Prevent loss of vital genetic information

• Protect and stabilise terminal ends of chromosomes

• Allow their own extension

What is the end replication problem?

• RNA primer at the end of DNA strand is removed at the end of DNA replication, creating a 3’ overhang at the end of the chromosome

• No RNA primer to synthesise the free 3’ OH end for the addition of nucleotides

• Ends of chromosomes shorten with every round of DNA replication

How do telomeres prevent the end replication problem?

• Telomeres are non-coding → Chromosomal ends shorten = telomeres shorten

• Genes within chromosome will not be eroded due to DNA replication

What happens when telomeres do not protect and stabilize the terminal ends of chromosomes?

• 3’ overhang of the terminal end of chromosome could potentially anneal to a complementary single-stranded terminal end of another chromosome → Joining of different chromosomes

• May trigger cell cycle arrest and apoptosis

How do telomeres allow their own extension?

• Provide an attachment point for the correct positioning of telomerase

• Telomerase lengthens telomeres and maintains telomere length

What are centromeres? (structure)

• Constricted regions on chromosomes where spindle fibres attach to during nuclear division

• Located anywhere along the length of a chromosome

• Tandemly repeating units of 170 base pairs

• Each sister chromatid has their own centromeric DNA sequence

What is the function of centromeres?

Ensure proper nuclear division by

• Allowing sister chromatids to adhere to each other

• Allowing kinetochore proteins (subsequently spindle fibres) to attach so that sister chromatids can separate to opposite poles

How does telomerase extend a telomere?

1. 3-nucleotide segment of RNA in telomerase binds to a part of the tandem repeat in the 3’ overhang

2. Adjacent part of the telomerase RNA is used as a template to synthesise a 6-nucleotide repeat sequence → Telomerase moves down to make more repeats

3. Using extended 3’ overhang as template, primate synthesizes RNA primer → DNA polymerase adds deoxyribonucleotides to 3’OH end of primer to synthesise a complementary DNA strand

4. Primer is then removed