Replication, Transcription and Translation Flashcards
Reasons why Eukaryotes are Monophyletic?
Bacteria and Archaea use horizontal gene transfer- DNA passes from one to another no matter how unrelated.
Eukaryotes all have bacterial DNA in mitochondria & plastids.
What is the Central Dogma?
Sequential information in proteins cannot flow back to nucleic acid (DNA and RNA bases).
DNA can be TRANSCRIBED to RNA which can then be TRANSLATED to Proteins.
DNA can be produced from DNA using DNA polymerase, or reverse transcription (i.e. telomerase) from RNA.
RNA can be produced from DNA or by self-replication (viral, with RNA dependent RNAP) BUT RNA can’t be produced from proteins.
Proteins can be produced from RNA and prions.
REVERSE TRANSLATION DOESN’T EXIST.
Watson said only half the processes happen, Crick said all happened.
What is the difference between the start codon and the Promotor?
The promoter is a sequence base that the RNA polymerase recognises to bind to. It is only involved with TRANSCRIPTION.
The start codon codes for the amino acid methionine, so is present on mRNA and is used in TRANSLATION, for the ribosome to bind to.
SImilarly with the stop codon which signals the RIbosome to detatch (so is only involved in translation.
Why does every peptide start with methionine?
As this is the amino acid that the start codon codes for.
It is later removed.
How is Lamarkism relevant in the Central Dogma?
He suggested that proteins could be produced from the phenotype. This protein -> phenotype relationship isn’t reversible and the central dogma shows he was wrong.
Differences between prokaryotes and eukaryotes and the evidence to support this?
Prokaryotes:
No nucleus
Arose 3000 Ma
Eukaryotes:
Nucleus
Arose 1500 Ma
Evidence: Molecular Fossils (lipid characteristics)- hopanoids found in modern bacteria / cholesterol found in eukaryotes. Can date with ecological effects- Evidence for great oxygenation event = min clade of cyanobacteria.
What are the prokaryotic cell structure and molecular biology?
Circular chromosome
Not membrane-bound simple organelles
Rotating flagellum - powered by PMF in bacteria (axle and flagellin, homologous to F type ATPase) and ATP in archaea.
Binary fission cell division - with cytoskeletal elements (FtsZ and MreB homologous to actin and tubulin), chromosomes don’t condense.
Diffusion limited due to small size (1 micrometre) - Doesn’t need motor proteins so no stirring of cytoplams and molecules move only by diffusion. Cytoplasmic membrane = site of transduction (ATP needs correspond to cell size)
No ‘junk’ in genome
No histones- Bacteria are v. lightly packed (with proteins like catabolic activator protein for regulation), some archaea do have nucleosomes though
RNAP uses sigma factor (protein to find promotor) in bacteria (must EXCLUDE ARCHAEA from this as they use TATA binding protein).
tRNAi (start codon) translates to formlymethionine (must again EXCLUSE ARCHAEA as use just methionine like eukaryotes)
70S ‘small’ ribosomes
What are the eukaryotic cell structure and molecular biology?
Double membrane bound nucleus
Linear chromosomes
endomembranes (e.g. Golgi apparatus)
endosymbionts (e.g. mitochondria)
Cytoskeleton and 9+2 flagellum/cillia - membrane tube with 9+2 ring of tubulin microtubules so goes side to side
mitosis cell division - cytokinesis controlled by tubulin microtubulesof spindles.
Cytoplasmic streaming as are large (100 micrometres) - cytoplasm with many fibril forming proteins (tubulin and actin), distributes between endosymbionts
Parasitic 'junk' in genome Histones bind DNA RNAP uses TBP (TATA binding protein) tRNAi produces methionine start codon 80s large ribosome
Woese proposed what and what contradicts him?
The 3 domain theory, that prokayotes weren’t monopyletic to eukaryotes, based on rRNA (highly conserved through evolution so mutated slowly).
Some sequences don’t agree; (even informational genes= transcriptional and translational) Use gram negative bacteria in phylogentic tree as outgroup.
Characteristics of Archaea
No nucleus
no endosymbionts
no cytoskeleton
(All characteristics of Bacteria)
Histone bound tRNAi with methionine RNAP uses TBP (Eukaryotic characteristics) Use terpenoid ether lipids. Pseudopeptidoglycan cell wall
Also see archaea mind map.
Margulis propose what with what evidence for and against?
Eukaryotes contain endosymbionts of bacterial origin.
Evidence FOR:
- Have DNA inside: sequence of mitochondria similar to Richettsia (disease/parasite to eukaryotic cells) is artefactual (could be inaccurate findings). Mitochondria could have taken up DNA so look alike.
- Endosymbionts have bacterial, viral and eukaryotic systems for replication and sequencing. Uses viral RNAP, bacterial tRNAi and 70S ribosome, mitochondria use 22 mt-tRNA’s. Uses neither TBP or sigma.
- Hydrogen hypothesis: mt may have arose within a Hydrogen-dependent archaeon giving rise to a symbiotic relationship which could account for eukaryotes.
Evidence AGAINST:
- DNA passed to nucleus over evolutionary time: so can’t say in archaea are more closely related to Eukaryotes (informational genes are though)
Why is the 3 domain theory falling apart?
- Contradicting phylogenies: between those done with amino acids and small rRNA subunits (prone to long branch attraction artefacts more than the aa one). DUe to lateral gene transfer, the phylogeny of the species deviates from the gene history, Interspecies interaction (bacteria and archaea swap).
- Have had whole genome fusions and selective loss of half the genes: archaebacteria (archaea) and bacteria fuse, gets rid of one of the 3 domains (disproves 3 domain theory)
- ATPase shows evidence against 3 domain (originally thought to show strong argument for)
- HSP70, v. highly conserved. Shows conflict to RNA phylogenies and 3-domain theory.
Shows eukaryotes= monophyletic and archaea and bacteria forming a clade= 2 domains as archaea intergrated into bacteria.
What genes do 1. mitochondria and 2. chloroplasts have?
Proteobacteria
cyanobacteria
Why was Margulis wrong about the cytoskeleton being of endosymbiotic origin?
Flagella don’t have DNA
Cytoskeleton have different structure to bacteria and archaea
Can distinguish between endosymbionts and organelles by length of genome: transfer some of the genome to host cell.
What is very specific about the Archaea membranes?
They don’t have cardiolipin (which both bacteria and eukaryotes have= convergent evolution as use different enzymes families to get the same product). They do however have phosphatidlyglycerol (isoprenoid chains ether links to sn-glycerol-1-phosphate). These stabilise the oxphos machinery formed with 2 different pathways. (convergent)
Exception to haloarchaea which have cardiolipin.
