genome structure Flashcards
Why does DNA have a negative charge?
The phosphate group is negatively charged everything else (sugar and bases) are neutral
major groove
backbones are far apart
minor groove
backbones are close together
structure of dna
nitrogenous base - composed of Nitrogen and C
pentose sugar - 5 carbons form cyclical structure with O bridge between C1 and C4
nitrogenous base at C1
phosphate group at C5 w ester bond
hydroxyl at C3
arrangement of DNA
bases stacked with major and minor groove
how does 2 metres of DNA fit into a cell?!
DNA is bound to histone proteins to form nucleosomes (contains 8 histones)
Nucleosomes are wound further into chromatin and then into extended chromosomes
chromatin fibre then forms loops
they are then compressed and folded to form the most condensed form of DNA, the chromosome
Describe the histone structure DNA wraps around
Eight histones form the nucleosome
2A,2B, 3 & 4 (2 copies of each)
Histone 1 binds the linker DNA (piece of DNA between nucleosomes)
tightness of DNA packing and expression
DNA tightly packed = less accessible so less gene expression
DNA more loosely = more accessible so more gene expression
types of chromosomes
Metacentric - centromere in middle and chromosome arms almost equal
Subcentric - centromere located near middle (sub median) resulting in slightly unequal lengths of chromosomal arms
Acrocentric - centromere located near the end of the chromosome (has little satellites)
genome size and complexity
genome size is not related complexity of organism
what is exome
The coding Genome
sum of all the gene sequences is called the exome
Some definitions just use the coding sequences
Some definitions use the whole gene sequences
what do intergenic regions contain
sequence of no known function, such as repetitive DNA, pseudogenes and may contain regulatory elements
what is gene cluster
two or more genes that code for the same or similar products, found close together in genome
when do genes cluster and why - organisation of genes
in families ie, globin clusters
- allows for coordinated gene regulation
- may just reflect evolutionary history
what are promoter regions
recruit RNA polymerase to DNA template
also binds transcription factors to regulate gene expression
what are the different regulatory regions which affect gene expression
they are position independent
- enhancer sequences: short sequences in gene which are targets for transcription factors (activators) to up regulate expression
- silencer sequences: targets for transcription factors (repressors) to down regulate expression
- insulator sequences: short sequences that prevent enhancers/silencers influencing other genes outside of tehri target ones
what are the diff modifications done to pre mrna to make it mature?
capping
splicing
polyadenilation
capping
methylated guanosine cap added to 5’ end of euk RNAs
5’ cap protects mRNA from degradation
splicing
spliceosome interacts w 3’ ed of exon and 5’ end of the next and breaks the link between intron to first exon
spliced exons are joined together and intron becomes lariat structure
why is splicing needed
so other proteins (exon junction complex and TREX) target spliced mRNA for translation
polyadenylation
addition of many adenine nucleotides to 3’ end of newly synthesized mrna to protect the end from degradation
What are pseudogenes?
genes that have been at least partially inactivated by the loss or gain of sequence that disrupt their correct transcription and/or translation
How does the spliceosome remove introns?
Spliceosome brings the ends of the exons together and cleaves the intron from in between then joining the adjacent exons together.
Lariat structure is then degraded
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 is the role of RNA Polymerase during transcription?
RNA polymerase binds asymmetrically and can only move 5’ to 3’
What two sequences form the gene promoter?
Regulatory CAAT box
Recruiting TATA box
What is the role of the CAAT box?
Regulatory element
regulates the recruitment of RNA Polymerase
What is the role of the TATA box?
Needed to recruit general Transcription factors and RNA polymerase
Outline the process of transcription
- promoter recruist RNA pol 2
- DNA helix locally unwound
- RNA synthesis begins in 5’ to 3’
- RNA poly moves along - elongation occurs
- RNA pol reaches a termination signal and stops
- RNA polymerase dissociates, carrying the pre mRNA with it
What export signals bind to the spliced mRNA?
Exon Junction Complex
TREX export complex
These all signal the compound out of the nucleus and into the ER ready for translation by the ribosomes
