Dosage compensation in a chromosome?

What is done to female chromosomes?

Adjusts number of sex cells

X inactivation of 1 X chromosome randomly (called a barr body)

Are there any genes active on the Y chromosome? If so, what are they??

Yes. Pseudoautosomal regions at the tips, gives X-Y homologity. Passed down to generations of sons just like any autosomal trait would be.

Also, SRY genes (testes determining factor) which gives rise to male characteristics

Usually use SSRs (simple sequence repeats)

Men have recent common ancestor with these

Genghis Khan-> large percentage of descendants in Asia

Not having the same number of each chromosome

Trisomy= third copy of 1 chromosome

Monosomy= only 1 particular copy

result of trisomy 21

Usually caused by translocations in which genes move around positions to other chromosomes.

2 chromosomes try to pair up with 1 chromosome

vs

1 chrom left along

chromosome which is pure breeding but has deletions will let the recessive only show

E.G Normally: ABCDE and abcde

now: ABC and abcde

Unequal crossing over

in which one chromosome gets more genes from the other chromosome than should have

What causes inversions? What is the problem with them

What happens with this problem?

Breaks in DNA

Fine in mitosis

Cause problems in meiosis. Form loops since opposite sides of those genes trying to attach. Everything's fine if there's no crossing over.

Translocations

and reciprocal translocations

Problems with the latter?

chromosomes break and fragments join to other chromosome

2 non homologous chromosomes break and exchange parts; problems with fertility

Robertsonian translocations

related to what disease?

fusion of acrocentric chromosomes (centromere on an extreme side)

Down syndrome, since this happens with chromosome 21

1 of each chromosome vs half the number of total chromosomes

if tetraploid= 36, haploid= 18, monoploid= 9

Purine vs Pyramidine bases?

Also, # of hydrogen bonds between each nitrogenous base pair?

Purine= 2 ring (A and G) Pyramidine= 1 ring (T and C)

AT= 2

GC= 3

Structural differences between A, G, C, and t

2 rings

A- NH2 on top

G- C=O and NH2

1 ring

C- C=O NH2

T- C=O, C=O, CH2

Direction of prokaryotic dna replication?

This vs eukaryotic replication?

Bi-directional. Forked, and then replicates both ways

Euk: also has a fork and is bi-directional. Can start another fork/replication process simultaneously; eventually these bubbles can fuse.

leading= newly synthesized DNA strand that is doing things smoothly

lagging= due to okazaki fragment

Method of identifying bases + sequencing the strand

Get newly synthesized dna + template

Primer kept there as a "visible" marker

place each in a tube with dNTPs, individual ddntps (end the sequence) and dna polymerase

can help sequence out where bases are individually

amplification of a small segment of DNA

add dntps, dna template, dna polymerase, and a buffer (adjusts ph and provides Mg++)

denature, anneal, extend-> all based on temperature; do for several cycles till you have a high amount of target dna (exponential increase)

exponential= increasing growth

stationary= pop stabilizes due to less resources

can grow in presence of ampicilin

can't synthesize methionine and therefore require it in media

can grow fine on plates with glucose but can't synthesize lactose

dormant cells that are not killed by most antibiotics which are targetting dividing cells

these are NOT mutant cells; just regular cells chilling out

once antibiotic is removed, the ones surviving can reestablish the infection and biofilm of cells

"extra" DNA elements, aka plasmids

Most of genome contained in original circular dna

pick up DNA from environment

usually remnants of dead bacteria (like smooth vs rough staph cells)

Are most plasmids conjugative?

If not, what helps them to become conjugative?

No, but can "hitch a ride" with conjugative plasmids via recombination...if they're small enough

transposable elements + recombination helps switch gene parts around to make non conjugative plasmids conjugative (called a cointegrate)

this is a plasmid that has many genes, ensures its own maintanence in the cell and that it will move from cell to cell

directs f pilus formation

"rolling circle" replication so it can keep rolling out copies. nuclease makes a nick in the dna befre this process

new dna gets f factor, replicated, then both cells seperate

still, highly selected against as a form of balance

Tranduction?

generalized transducing phage vs specialized?

tranducing phage (virus) can transfer pieces of dna between bacteria

transfers dna by accident vs tries to transfer its own genome + specific other dna

phage dna enters cell + integrates itself into bacterial genoome (called a prophage); these are called temperate phages cuz they don't attack immediately

prophages can be activated, excise themselves from genome, and begin lytic phase

but before then, basically a part of the bacterial genome

steps for transcription in prokaryotes?

are there introns?

see promoter region (beginning of gene), chain initiation (start transcribing here), chain elongation (make rna molecule), chain termination (stop at right place); then termination happens where end of mRNA are repeats so form "stem loop"/hair pin to signal end

all done by rna polymerase

no introns. primary transcript...that's it. ends are just untranslated regions

RNA polymerase binds to promoter, dna seperates, keeps transcribing then in a 5->3 fashion; chain initiation and elongation; then termination

also promoter regions/enhancers much more complicated here;

5' cap and poly-A tail at ends for stability

RNA strands that fold up on their own + catalyze on their own

e.g. self splicing introns

Hydrolysis

Also becomes O=C-N-H

prokaryotes.

eukaryotes- they occur in seperate domains of the cell

initiation- ribosome assembles, initiation factors bind the mrna (attach at 5' cap) and help start translation at start codon

elongation- A= active sight for trna; moves and waits in p area then leaves aa behind to the growing chain

termination- stop codon, release factors recognize + help ribosome dissociate

sequence which helps bacteria recruit ribosome to mrna to begin protein synthesis

kozak does the same but in euks

charged; has 3 loops and bottom has the anticodon, aa attached at CCA 3' end of trna

Okay so...

5'CAU'3 = 5'AUG'3

so look at 3-> 5 of anticodon: 3'UAC'5, and then find 5'-3' corresponding codon

1. all genes are turned "on' and "off" as a unit

2. these are the mrna's that undergo this type of regulation

positive regulation and positive feed back

also what does "off" really mean?

by default, genes in operon are "off" unless an activator turns them "on"

protein expressed turns its own genes ON-> amplifies a weak signal

mrna still being made, just at a realllyyyy small amount

Explain the lac operon

Lac Z? (along with what enzyme)? what brings lactose into the cell? what does i, p, o, y, a, and z do? LacI?

what is an inducer and what is it in this case?

beta-galactosidase

these two turn lactose into gluc and glyc

lactose permease does that

i= encodes repressor

p= promoter where rna polymerase binds to

o= operator where the repressor, LacI, binds to, z/y/a= genes for sugar metabolism

this entire thing works if lactose is present

inducer turns off repressor (done to help save energy)-> this is what lactose does to LacI

trp operon: similar to lac?

what type of pathway is this? what is the corepressor?

what senses the level of tryptophan and how?

the opposite: if trp is present, operon does not work because naturally it wants to produce trp

aporepressor

it is anabolic

trpL (the leader sequence; part of mRNA)

trp-TRNA is an anticodon which binds to trpL only if tryptophan levels are high...if not, this doesn't happen

LOW TRYPTOPHAN LEVELS:

ribosome stalls...will not see trp-trna, and anti-terminator loop will form; transcription will continue

HIGH LEVELS:

ribosome not stalled; terminator stem loop will form (which looks like a typical terminator loop lol); trp-trna abundance; transcription terminated

Yes

the difference in function is due to genetic expressibility

general and transcriptional activators and repressors

the second does either to specific genes; the first is just generally interacting with the operon

domains of a protein

DNA binding specifically binds to sequences of DNA near regulated genes; activating= interacts with other proteins to regulate transcription 

gal3 binds with galactose and gal80, and goes to the cytoplasm; galactose metabolism continues with the other 3 enzymes

otherwise, no galactose means that gal 80 can inhibit gal 4, and cannot complete the full process

Transcriptional activation requires the activating transcription factor, the basal transcription factors and...