All morphologically complex organisms are eukaryotic - why?
Lecture 10: Evolution of Eukaryotes
1. meaning of endosymbiosis, cyanobacteria, lateral gene transfer
endosymbiosis: mitochondria and chloroplast derived from free living prokaryotic cells
cyanobacteria: only group of peokaryotes have a photosynthetic structure.
lateral gene transfer: organelle genes relocated to the nucleus, puts them under much tighter
nuclear control; the function of the gene is retained
2. origin of endomembrane system, nuclear membrane, ER etc.
driven by infolding plasma membrane
3. origin of mitochondria and chloroplasts
Mitochondria is derived from an aerobic bacterium, one of these bacteria that can
undergo oxidative phosphorylation. Chloroplasts is derived from cyanobacterium.
Aerobic bacterium is taken first.
4. evidence supporting theory of endosymbiosis
Morphology: look like a bacteria
Formation/division: the way it diis very much like the way a bacteria divides.
Electron transport chains: the only organelles within the eukaryotic cells that have electron
Genome: have their own genomes
Transcription/translation machinery: have their own machinery
5. factors driving development of early eukaryotic cells
the ability to use oxygen, oxidative phosphorylation provides huge amounts of ATP, the cell can grow
bigger, more proteins can be used, genome is bigger…
6. why eukaryotic cells can be larger and more complex than prokaryotic cells
eukaryotic cells have mitochondria that can produce lots of energy and support an increasing volume 7. evidence for lateral gene transfer from organelles to the nucleus
use southern blot to detect lateral gene transfer between three related species (plant A, B, C); detect
the location of oxidase3 gene
8. general idea about how lateral gene transfer is detected (Southern blot)
In a southern blot, run genomic DNA on the gel, DNA single stranded, single strand probe,
hybridized, if hybridization occurred, on the membrane you have a sequence similar to your
9. Hypotheses for why genes move to the nucleus from organelles (lateral gene transfer)
10. Possible reasons why certain genes have NOT moved to the nucleus from organelles
11. Role of cpn60 in tracing endosymbiotic and lateral gene transfer event in eukaryotes.
a mitochondria protein, essential for mitochondria to work
found in the human nuclear genome
showing lateral gene transfer has occurred The evolutionary process of endosymbiosis created organisms with typically "prokaryotic"
genes in organelles and typically "eukaryotic" genes in the nucleus. Wow.
Lecture 11: Intro to Prokaryotic Gene Structure
1. relative sizes of typical mitochondrial, chloroplast and nuclear genomes
70 linear chromosomes in the nucleus
Circular chromosomes in the mitochondria and chloroplast
2. rubisco structure and assembly from components coded by different genomes
some components of rubisco components are coded by nucleus DNA, some are coded by
3. possible reasons why modern organelle genomes have become dramatically smaller over
Chloroplast and mitochondria lose the gene coding for things like flagella, hexokinase,
cell division. (something need in prokaryotes but not in eukaryote)
The genes are been deleted by mutation and deletion. When the organelles have
smaller genomes, they are easier to be replicated. That’s a selective advantage.
Lateral gene transfer (gene transferred to the nucleus)
4. possible reasons why genes have moved to the nucleus from organelles over evolutionary
The nucleus could have more control.
These organelles are involved electron transport. Oxygen metabolism, generate
reactive oxygen species, O2+e-=reactive oxygen species, ros is very reactive and very
mutagenic creating all kinds of damage in your DNA. Get your DNA out of organelles
into the nucleus to get away from ROS.
Nuclear DNA can participate in sexual recombination, while organelle DNA can’t.
5. possible reasons why certain genes have not moved to the nucleus from organelles
Need local control. Need too much time to transfer proteins out of cytosols into the
organelle. The gene products are too hard to transport into the organelle.
Genes Doesn’t work in nucleus
Don’t have enough time. Evolution hasn’t stopped.
6. basic mechanism of transcription and translation in prokaryotic organelles vs. eukaryotic
mitochondria and chloroplast have their own gene expression machinery. Transcription and
translation happen inside the organelle. Ribosomes are inside the organelle. 7. basic structure and function of RNA polymerase and ribosome
RNA polymerases catalyze the assembly of nucleotides into an RNA strand, rather than the
DNA polymerases that catalyze replication.
To initiate transcription, RNA polymerase binds to the promoter, unwinds the DNA in
that region, and starts synthesizing an RNA molecule at the transcription start point.
As RNA polymerase moves along the DNA, unwinding it at the forward end of the enzyme,
the new RNA molecule elongates as nucleotides are added one by one
The new RNA molecule winds temporarily with the template strand of the DNA into a hybrid
RNA–DNA double helix. Beyond this short region of pairing, the growing RNA strand
unwinds from the DNA and extends from the RNA polymerase as a single nucleotide chain.
As the RNA polymerase passes, the DNA double helix reforms. Elongation of the RNA chain
continues until the end of the transcription unit, at which point, RNA synthesis terminates, and
the completed RNA transcript and RNA polymerase are released from the DNA
With the help of another protein, RNA polymerase recognizes key DNA sequences in the
promoter, binds, and begins transcription of the mRNA. Since all the other types of genes
in prokaryotes (for example, tRNA and rRNA genes) have similar promoters, the
same RNA polymerase complex can transcribe them all.
In eukaryotes, there are different polymerases for transcribing different types of
genes. RNA polymerase II transcribes protein-coding genes. RNA polymerases I and III
transcribe genes for non-protein-coding RNAs.
A key element of the promoter of most eukaryotic protein-coding genes, the TATA box,
is important in transcription initiation. RNA polymerase II itself cannot recognize the promoter
sequence. Instead, proteins called transcription factors recognize and bind to the TATA
box and then recruit the polymerase. Once the RNA polymerase II–transcription
factor complex forms, the polymerase unwinds the DNA and transcription begins. Ribosome structure
A finished ribosome is made up of two parts of dissimilar size, called the large and small
ribosomal subunits. Each subunit is made up of a combination of ribosomal RNA (rRNA)
and ribosomal proteins.
The A site (aminoacyl site) is where the incoming aminoacyl–tRNA (carrying the next
amino acid to be added to the polypeptide chain) binds to the mRNA. The P site (peptidyl
site) is where the tRNA carrying the growing polypeptide chain is bound. The E site (exit
site) is where an exiting tRNA binds as it leaves the ribosome.
8. examples of complementary base pairing in gene expression
DNA base pair mRNA, transcription
mRNA base pair with itself: once mRNA is produced, it can fold, band, and make base pair
on itself; hairpin loop
tRNA base pairs with itself: form 3D structure
tRNA (anti codon) base pairs with mRNA: translation
ribosomal RNA base pairs with itself: 3D structure in order to be catalytic
SD box base pair with rRNA in ribosome
mRNA base pair with snRNA: during mRNA splicing
miRNA/pre-miRNA base pair with itself
snRNA base pair with itself (sn: small nuclear)
snRNA base pair with either the end of intron DNA contains many types of information. But how is it all "understood" by the cell?
Lecture 12: Prokaryotic Gene Function
Independent Study Outcomes
1. identify the sequence of standard "start" and "stop" codons
start codon/ initiator codon”: AUG
stop codons/ nonsense or termination codons: UAA, UAG, and UGA
2. identify the function of "start" and "stop" codons
The start codon attracts the first initiator tRNA that codes for methionine and initiates the
process of translation.
There is no tRNA binds stop codon. The release factor (protein) always try to get in there, but it
is always outcompeted by tRNA. But in this case, there is no competing tRNA. The release
factor is able to bind. And translation stops. The release factor is a protein.
3. compare the overall gene expression of prokaryotic vs. eukaryotic cells.
1. relative location of such DNA sequence “signals” as promoter, 5’ and 3’ UTR, “SD box”, start
codon, stop codon, transcription terminator etc. 2. mechanism by which each signal is interpreted, or understood, by the cell
promoter attracts attention of RNA polymerase, RNA polymerase interact with DNA and
template strand gets transcribed (transcription starts) (but promoter is not transcribed)
terminator sequence in the DNA get transcribed in the mRNA, make a loop structure
(pair with itself), and the loop causes destabilize mRNA binds with DNA. mRNA falls off
and stops transcribing (transcription ends) (terminator is transcribed, not translated)
start codon of mRNA attracts the first initiator tRNA that codes for methionine and initiates the
process of translation. (translation starts) (start codon is transcribed and translated)
SD box is region under DNA, once transcribed into mRNA, the sequence base pair with
rRNA, to help the initiation of translation. Not understood by (SD box is
transcribed, not translated)
Stop codon can’t bind tRNA, but binds the release factor (a protein, so not base pairing), and
translation stops. (Stop codon is transcribed, not translated)
3. relationship between DNA sequence of signals and their function (ie. how would low
efficiency promoters be different than high efficiency promoters?
Promoters have a general common sequence/structure, but they are also quite variable
and can drive transcription at different rates. Some promoters are very attractive. The
sequence of some promoters is such that polymerase makes a very stable bind and
initially transcription very frequently. But other promoters have variable sequences here.
They are less and less attractive and less and less efficient at transcription.
A particular terminator stops transcription 60% of the time. Another terminator stops
transcription only 40% of the time. Why? Maybe the terminator sequence is longer,
makes the bonds in the loop longer and more stable, and therefore termina