CBG Lecture 1: Prokaryotes and Eukaryotes Flashcards
what is an UTR
untranslated region, found at 3’ and 5’ mRNA
targeting sequences that are temporal and spatial: how long and where mRNA should stay/go
how to change DNA code from plus sense to - sense
leave labels but reverse the letters, the complementary base pair
eg. 5’ CGT 3’ DNA (+) as written
1. swap labels and reverse: 5’ TGC 3’
2. complementary base pair 5’ ACG 3’
how many possible codons are there
64 - 3 stop, 61 aa coding, start codings
what is the central dogma of biology
sequential info in protein cant flow back to nucleic acid
TRANSLATION IS IRREVERSIBLE
phenotype back to protein is irreversible
no such thing as an anti ribosome
what is a prion
an infectious agent composed of protein in a misfolded form. there is no nucleic acid element to their structure
prions disease
(protein and infection)
what are planctomycetes
a phylum of aquatic bacteria that tend to enclose tehir nuclear material within a double membrane
what is reverse transcription
RNA back to DNA
what are planctomycetes
a phylum of aquatic bacteria that tend to enclose their nuclear material within a double membrane
compare nucleus and time of arising in proks and eukaryotes
o PROK: no nucleus, arose 3000MYA
EUKS: nucleus, arose 1500MYA
outline prokaryotic cell structure
simple cell structure, naked DNA with a simple path from DNA to proteins
circular chromosome in nucleoid (area within the cytoplasm holding the DNA)
only essential organelles: ribosome, mitochondria
rotating flagellum
binary fission
small and diffusion limited:1micrometre
have plasmalemma
have pilli
have capsule
what is a nucleoid
where found
area within the cytoplasm holding the DNA
what can prokaryotes be divided into
bacteria and archaea
what subdivision of prok’s is related closer to eukaryotes
archaea
outline PROK’s molecular biology
'junk' free genome (most is transcribed and translated) nacked DNA lacking histones one RNAP using sigma factor tRNAi formylmethionine start codon small 70s ribosomes
what is S (wrt. ribosome size)
sedimentation coefficient in Svedbergs
outline EUKARY’s cell structure
linear chromosomes in nucleus - with ssSNA ends (telomeres)
complex endomembranes and endosymbionts
prominent cytoskeleton and up-down flagellum (9+2 tubulin rubbing)
complex mitotic division (using microtubule tracks)
large cytplasmic screening 100micrometre
outline eukaryotic molecular biology
junk in genome dna bound by histones into nucleosomes 3 RNAPs using TBP (TATA binding protein) tRNAiMETHIONINE start codon large 80s ribosomes
what size ribosomes present in EUKS
80s
how does DNA packaging in EUKS compare to PROKS
no DNA packaging in PROKS, but DNA bound by histones into nucleosomes in EUKS
what tRNAi start codon do EUKS use
methionine
what tRNAi start codon do PROKS use
formylmethionine
what RNAPs do EUKS use? and use what initiate transcription
3 type RNAPS and TBP (TATA binding protein)
what RNAPs do PROKS use? and use what initiate transcription
one type RNAP use sigma factor
what did Woese propose
3 domains of life based on rDNA sequences - bacteria, archaea, eukarya
the prokaryotes are not a monophyletic group and are sometimes split into archaeabacteria and eubacteria
archaea are a polyphyletic group
what is rDNA
the DNA that encodes rRNA - these genes tend to be highly conserved and mutate rather slowly becaUSE theyre so essential to the cell
why did Woese base domain theory on rDNA
because the genes encoded tend to be highly conserved and mutate rather slowly, as they are essential to the cell
what grp (phylogenetically) are archaea
polyphyletic group
what relation exists between archaea and eukaryotes
archaea are eukaryotes in a bacterium’s clothing
why are archaea said to be eukaryotes in a bacterium’s clothing
they have a prokaryotic cell structure (no nucleus/no endosymbionts/no skeleton) but they have eukaryotic molecular biology (histone bound DNA, tRNAmet start codon, RNAP using TBP)
give example of an archaea
halobacterium
what did Margulis propose
that eukaryotes contain endosymbionts of bacterial origin
- -> Mitochondria (proteobacteria : Rickettsia)
- -> Plastids (cyanobacteria)
the mitochondria merged from the bacteria line into the eukaryotic line, hence the commonalities between them
why is it not sensible to say that archaea are more closely related to eukaryotes than bacreria
due to gene transfer from the endosymbiont to the host nucleus. if you look at individual genes, some of the eukaryotic genes are of clearly (proteo/cyano-)bacteria origin: the eukaryotic genome is loads of genes from different sourcesa
what is the following archaea feature more similar to BACTERIA or EUK??
aa attached to initiator tRNA
eukaryote
what is the following archaea feature more similar to BACTERIA or EUK??
start codon identification by ribosome
bacteria
what is the following archaea feature more similar to BACTERIA or EUK??
binding of RNAP to promoter
euk
what is the following archaea feature more similar to BACTERIA or EUK??
number of different RNAPs
bacteria
what is the following archaea feature more similar to BACTERIA or EUK??
cytoskeletal architecture and composition
bacteria
what is the following archaea feature more similar to BACTERIA or EUK??
dna packaging
eukaryotes
what is the following archaea feature more similar to BACTERIA or EUK??presence/absence of introns
absence of introns - bac
what is the following archaea feature more similar to BACTERIA or EUK??
no. rRNAs in large subunit
bacteria
how does flagellum of bacteria move?
give an exception
movement by PMF
Oscillatoria: use gliding for movement, lack flagellum
how does flagellum of EUKS move?
rotating flagellum-structurally similar to bacterium but analogous
what is max size bacteria can grow? why not bigger?
1 micrometre
size is limited by the fact they rely on diffusion for nutrients and survival so cant grow bigger
why can eukaryotic cells be bigger than archaea/bac
the cytoskeleton allows mixing up of the cytosol which means substances can be transported intracellularly easily
therefore can grow bigger
also, cytoskeleton forms a framework for movement of organelles
what is ENCODE
Encyclopedia of DNA Elements
30 research papers, decade long project
hypothesized that around 80% of genome serves a biochemical purpose
what were the main outcomes of the ENCODE project
showed DNA bases not only define proteins but
- specify landing spots for proteins that influence gene activity
- strands of RNA have many roles
- places where chemicals
