Genomic Structure

Question 1

Describe the structure of DNA from single base to the grooves of the helix

Answer 1

• comprised of ribose sugar, phosphate group and nitrogenous base
• nitrogenous base: A -> T, G -> C purine(2ring) to pyramidine (1 ring) paired via hydrogen bonds
• negatively charged phosphate group forming sugar phosphate backbone
• read in 5’ -> 3’
• two antiparallel strands with bases stacked in the middle
• twisting the ladder = major and minor grooves

Question 2

Describe histones and how they are used to solve the DNA packing problem

Answer 2

Histones act as bead to wrap DNA around (coil) these coil twist around themselves forming nucleosomes
- +tively charged proteins bind to negative backbone
- H1 responsible for binding to linker DNA
- comprised of 8 histones 2x (H2A, H2B , H3, H4)

Question 3

Define the exome and the gene, including regulatory regions

Answer 3

EXOME: coding gene sequences

GENES: sequence of codons which are used to make and regulate a specific polypeptide chain. All DNA including cis-linked control regions which transcribes tissue specific amounts of protein production.

Question 4

Describe the process of transcription in detail

Answer 4

• RNA Pol II recruited
• local unwinding of helix
• asymmetrical binding travels unidirectionally
• elongation of pre-mrna transcript
• regulation of transcript via transcription factors
• stop sequence indicates termination of production
  = pre-mRNA transcript (undergoes post transcriptional modifications adenylating tail/splicing/capping)

Question 5

Describe the three parts of post-translational modification of RNA in detail

Answer 5

• METHYL CAP
  added to 5’ end when 25 - 30 its synthesised. RNA 5’ triphosphotase and guanylyltransferase work using bifunctional capping enzyme (RNA Pol II also involved)
• SPLICING
  Team of 150 enzymes forms splicosome unit. introns are extruded in a lariat (rope like) loop using 2’-5’ linkage and cleaved. Exons are connected.
  Alternative splicing allows exons to be kept removed = various isoforms of protein
• POLY ADENYL TAIL
  AAUAAA sequence identified by CPSF, acting on cleavage site. CSTF recognises a rich GU sequence downstream of pre-mRNA. PAP is recruited to add AAAA bases to cleavage site. PAB, CFIm, CFIIm and Simplekin involved in binding poly-A tail.

Question 6

Describe the process of translation

Answer 6

mRNA processed through ribosome. precursor mRNA read by ribosome and locates start codon.
tRNA precursors are activated via splicing and deliver specific amino acids after reading each codon.
Amino acids form peptide bonds via condensation reactions and ribosome continues along strand, forming a polypeptide chain

Question 7

Describe the process of alternative splicing and explain why it is useful

Answer 7

alternate splicing can skip or include various exons which gives rise to various isoforms of a protein

Question 8

Define the roles of compartments and TADs in 3D arrangement of DNA

Answer 8

topologically associated domains = TADs
are non-interactive sub compartments in the 3D genome. Transcriptional repressors and CTCF proteins separate the domains to allow specific local signalling for smaller section of genome compartments to increase precision.

Question 9

Briefly describe the loop extrusion model of control of transcription

Answer 9

(like a thread loop through a needle)
chromatin loop extrusion via CTCF first uses cohesion complex to thread chromatin through the loop.
In 3D structure, this allows promoter and enhancer signals to be closer which allows their signals to interact.