Cmmb Notes
Essay Preview: Cmmb Notes
Report this essay
05-09-13
CMMB 511
No final exam
Journal based course.
Try to think of everything in terms of GENE EXPRESSION
Biol questions
concepts
strategies and approaches — need cross f(x) or complimentary approaches to develop a compreshensive understanding
techniques — lots of techniques, make sure using appropriate techniques
outcome of results
overall conclusions
DNA content per haploid genome:
Bacteria: 2 x 106 bp
Mammal: 2 x 109 bp
Complexity of the genomes. Important question in biol scinces is
How is the genome organized?
How is gene expression regulated? Very tightly regulated, don’t expect genes to go up or doen. Different mechanisms, remarkable complexity.
These are important questions in the understanding of cellular processes including:
cell differentiation, development, diseases (etc). the study of processes comes down to the two above questions. If you know the basic concepts, can answer anything!
05-09-15
How is the genome organized?
How do we know the presence of the sequences. Will re-visit classic methods to determine the sequence of these genomes.
S(X) of the chromo
Each chromo is a single, linear DNA molecule
At the ends are the telomeres — f(x) in the repication, make the chromosome tips inert to chemical interactions and the enqumatic attach
A chromo is divided in to 2 arms by the centromere — the position at which spindle microtubule attach to the chromosome during cell division
Chromo have sites serving as replication origins
Chromatin — (DNA and PROTEIN ) organization of the chromosomes
Genome activity — linear CHROMATIN that is tc’d not the DNA
Morphological complexity — determined by the DNA content in the haploid genome (AKA genomic complexity) , simplest is the micoplasma very complex are flowering plants. The nubmer of bp present in E.coli I sfar less than that in flowering plants, therefore when we talk about genomic complexity — it’s the number of bp present. The point — in terms of technology it’s complex
How do we know this is the case (study done in the 70’s) — back then what did they use to determine this? Extract DNA from the organism. DNA is ds, so can denature. Take DNA chop into pieces by sonication and do denaturing and renaturing (to similar bp)
Take two different sequences, denature with heat (or alkaline) пє ss пє renature (cool, or neutralize)
Cot curves — if start with DNA, make ss — ss can renature (but will depend on time) the time it takes for ss to form a duplex, the product (cot) . then carry out complex DNA analysis . plot against time, when ss, absorption of light increases (almost two fold) . Melting temperature (important) or TM is a function of the G & C content.
Back to the question — if an org just has unique sequence (NO repeats of several times in the genome), cut into pieces (~1000bp), denature, then the renaturation will take a long time for those 2 complimentary strands to come together (Cot value will be large). However if sequences are repeated several times, then the renaturation will be rapid (the cot value will be small (assumption) — DIAGRAM 1 tells you molecule is 30X more complex
DIA 2 — 1. reassoc rapidly (lots of repeating sequences), 2. reassociates moderately, 3. reassociates slowly. Notice the length or the steepness ( can tell you the relative allocation of the genome to that particular complexity)
DIA 3 — Cot = DNA [ ] (m) x time (s)
Cot ÐÐ – calue of ÐÐ… reassociation
The diagram shows that 60% is highly repeated, 25% moderately repeated, 15% unique
Ecoli seq are unique where as mouse DNA is highly repetitive (106 copies, 300 bp average, 15%) , 25% mod repetitive (103 tp 104 copies) several seeuees, 60% are unique, single or few copies, genes coding for mRNAs (how do we know this?? пє use mRNA — DNA hybridization — so when you go to the cyto you’ll find mRNA — convert them to ***cDNAs or the mRNA tagged. mRNA will compete with antisense , tagged mRNA will bind to sense DNA. Do Cot curves and will find silimiar to Dia 3.
Repetitive DNA
DNA is present in > one copy
families of coding genes (+ pseudogenes — genes part of a family and present but some reason do not f(x), or maybe noe splicing on mRNA, or promoter no there and cannot be tc’d) Lots in the human genome
— dispersed gene families
— tandem gene gamilies
non-coding functional sequences
— telomeric
— centromeric
Organ of coding seuence
# of genes for various RNA tags
in lower euk (yeast) ~5000
in higher euk ~ 100,0000
mRNA coding genes: – represent about 80% of genomic sequences (mRNAs of different kinds)
coding