Cmmb Notes

05-09-13

CMMB 511

No final exam

Journal based course.

Try to think of everything in terms of GENE EXPRESSION

Biol questions

1) concepts

2) strategies and approaches вЂ" need cross f(x) or complimentary approaches to develop a compreshensive understanding

3) techniques вЂ" lots of techniques, make sure using appropriate techniques

4) outcome of results

5) 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

1) How is the genome organized?

2) 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 вЂ" 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 вЂ" the position at which spindle microtubule attach to the chromosome during cell division

Chromo have sites serving as replication origins

Chromatin вЂ" (DNA and PROTEIN ) organization of the chromosomes

Genome activity вЂ" linear CHROMATIN that is tc’d not the DNA

Morphological complexity вЂ" 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 вЂ" it’s the number of bp present. The point вЂ" in terms of technology it’s complex

How do we know this is the case (study done in the 70’s) вЂ" 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) пÑ" ss пÑ" renature (cool, or neutralize)

Cot curves вЂ" if start with DNA, make ss вЂ" 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 вЂ" 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) вЂ" DIAGRAM 1 tells you molecule is 30X more complex

DIA 2 вЂ" 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 вЂ" Cot = DNA [ ] (m) x time (s)

Cot Ð'Ð... - calue of Ð'Ð... 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?? пÑ" use mRNA вЂ" DNA hybridization вЂ" so when you go to the cyto you’ll find mRNA вЂ" 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

a) families of coding genes (+ pseudogenes вЂ" 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

a. вЂ" dispersed gene families

b. вЂ" tandem gene gamilies

b) non-coding functional sequences

a. вЂ" telomeric

b. вЂ" 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