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Flashcards in 5. Genome Structure Deck (19):

Features of DNA in three dimension

• Two antiparallel strands of DNA
• Bases “stacked”
• Two grooves
- Major
- Minor


DNA packing levels

DNA double helix -> Nucleosomes -> Chromatin fibre - > Extended section of chromosome -> Loops o chromatin fibre -> Metaphase chromosome


Briefly describe the structure of nucelosomes

• Basic proteins that bind DNA
• Eight histones form the nucleosome
• Histone 1 binds the linker DNA


Describe the 3 types of chromosome structure

1) Metacentric ~ the centromere is in the middle of the chromosome and the arms of the chromatids are the same length
2) Submetacentric ~ centromere is off centre and produces a short and a long arm
3) Acrocentric ~ causes a very short arm (satelites)


Function of the primary DNA

• The primary DNA sequence encodes all the gene products necessary for an organism
• The primary DNA sequence also includes a large number of regulatory signals
• Much of the DNA sequence does not have an assigned function as yet


What is the exome?

• The sum of all the gene sequences
• aka the whole genome


What is a gene?

• All of the DNA that is transcribed into RNA plus all of the cis-linked (physically local) control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein
- (not just the bits that code for the protein - the regulation of the gene is also every important)
• Genes are often very different in size


What are intergenic regions?

• Intergenic regions contain sequences of no known function, such as repetitive DNA, endogenous retroviruses, pseudogenes


Why do genes often cluster in families? e.g. globin clusters

• Allows for co-ordinate gene regulation
• May just reflect evolutionary history


What structures are found in genes?

Promoters, UTRS, inrons and exons


What do promoters consist of? and what is the function?

• They contain regulatory element (CAAT box) - needed to regulate recruitment of RNA polymerase
• And TATA box - needed to recruit general transcription factors and RNA polymerase
• Eukaryotic RNA polymerases are unable to recognise promoters efficiently without help


What are the three eukaryotic RNA polymerases? and what is the function of each?

• RNA polymerase I - needed to transcribe rRNA genes
• RNA polymerase II - needed to transcribe mRNA
• RNA polymerase III - needed to transcribe tRNA and other small RNAs


Briefly describe the process of transcription.

1) RNA polymerase is recruited. DNA is a closed complex.
2) DNA helix locally unwound. (open complex).
3) RNA Synthesis begins
4) Elongation
5) Termination
6) RNA Polymerase dissociates


What are introns?

• spliced out
• vary in size and number
• some contain other genes


What are the other regulatory regions besides promoters?

• ENHANCERS - upregulate gene expression – they are short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators).
• SILENCERS - downregulate gene expression. They are also position-independent and are also targets for transcription factors (repressors).
• INSULATORS - short sequences that act to prevent enhancers/silencers influencing other genes


Post-transcription modifications

1) Capped at 5' end - Soon after RNA polymerase begins transcription a methylated cap is added to the 5’ end.

2) Polyadenylated at 3' end - When transcription finishes, the G/U rich region is cleaved off and polyA tail (250 As) is added by polyadenylate polymerase (PAP)

3) Introns are spliced out - the end of the intron forms a 2'-5' linkage with a region of the intron. - the exons on either end then join together and release the intron in a lariat like shape.


What is alternative splicing?

Exons can be skipped or added so variations of a protein (called isoforms) can be produced from the same gene.


What are the other structures found on the mRNA prior to nuclear export, besides the cap and the polyA tail?

• TREX export complex (TRanscription-EXport) ~ enhanced by EJC
• Exon junction complex (EJC) - bound to the message


What are pseudogenes?

• These are genes that have been at least partially inactivated by the loss or gain of sequence that disrupt their correct transcription and/or translation
• Processed pseudogenes have no promoter or introns as they are copied from mRNA by retrotransposition (the reverse transposition of an RNA intermediate)