cycle 6

• three domains of life

  bacteria, archaea, eukarya
• rRNA gene sequencing (& what is the goal of it)

  sequence the gene that encodes for RNA on the small subunit

  - goal is to identify between the three domains
• did all origins of life lead to LUCA (last universal common ancestor)

  no, they didn't all lead to LUCA
• earliest life was _____

  anaerobic
• why was the earliest life anaerobic?

  because there was no oxygen before PSII (which makes O2) = before eukaryotes
• what group used oxygenetic photosynthesis first


  cyanobacteria
• GOE (great oxygenation event)

  event when PSII was first evolved to create O2
• why are eukaryotes more complex? (3 points)

  they are...

  
  

  - larger cells, have more genes, have larger genomes
• how do you measure complexity

  the more O2 you have, the more complex you are
• origin of endomembrane system, nuclear membrane

  1) Starts with ancestral prokaryotic cells that unfold to create ER and nucleus

  
  

  2) aerobic bacterium gets engulfed and stays in cell with mito

  
  

  3) cyanobacterium gets engulfed and stays in cell with chloroplast
• endosymbiosis


  an idea that mitochondria and chloroplast were their own aerobic bacterium
• evidence for endosymbiosis:


  - Morphology

  - Reproduction

  - Genetic information

  - Transcription and translation

  - ETC

  - Sequence analysis

  
  

  MRGTES

  MaRGariTas Every Sunday
• Relative sizes of typical mitochondrial, chloroplast (compared to bacterial ancestor)

  The genome sizes of the modern mitochondria (ones today) and chloroplast are significantly SMALLER than the genome sizes of the ancestral organisms they originate from
• Why have the genomes shrunk compared to ancestors?

  - redundancy

  - horizontal gene transfer (HGT)
• redundancy


  Many genes found in aerobic bacteria and cyanobacteria are already found in the host cell; why keep redundant genes?
• horizontal gene transfer (HGT) - does anything change?

  Overtime, genes of one genome can move to another genome

  
  

  - Gene function DOESN'T change, only the location of the gene changes
• why do we think HGT (horizontal gene transfer) occurs between mitos/chloros and the nucleus (why does it happen?)

  - integrative control

  - safety
• integrative control


  - more genome/genome = control = boss
• safety


  nucleus is much safer than highly reactive environments of mitochondria and chloroplast
• how do you detect horizontal gene transfer using DNA hybridization? how do you interpret the data?

  Technique: DNA hybridization (sees where gene of interest is and if it has it)

  
  

  - Labeled probe is part of a gene... where is the gene located??

  - If gene of interest is present in genome, labeled probe will bind to the SS DNA
• how do you know if the gene of interest is present?

  Gene of Interest Present = BAND

  Gene of Interest NOT Present = NO BAND
• Role of the signal peptide in trafficking nuclear-encoded proteins that end up in the mitochondria or chloroplasts

  The signal peptide on the protein will be recognized by the organelle and then cleaved so it can be used by that organelle
• how do proteins target to organelles via a signal peptide

  Signal peptides tracks DNA to mitochondria and directs it to the right place
• Three domain vs two domain tree of life...Eukaryotic signature proteins and Archaea (Asgard)

  We used to think we had three domains

  Now we discovered we only have 2

  
  

  - States eukaryotes evolved from archaea having common ancestor of "Asgard"

  - It has many signature eukaryotic proteins and high sequence similarity
• what are eukaryotic signature proteins (ESPs)

  Proteins that have no homologs in bacteria or archaea
• chimera


  mixture of bacteria and archaea
• endomembrane is a mixture of...

  bacteria and archaea
• nucleus is a mixture of...

  NONE! it is uniquely eukaryotic
• what is a surprising thing about the origin of the membrane lipids in eukaryotes?

  membrane lipids in eukaryotes are passed down from ARCHAEA
• BIG PICTURE.....Three genomes in Chlamy....what does that mean??

  = three compartments need transcription/translational machinery!
• what does this include? ^^^ (what needs transcription/translational machinery?)

  This includes chloroplast, mitochondria, and nucleus = need transcription/translational machinery
• Bacteria need genes for...

  for metabolism
• archaea need genes for...

  for information-processing & structure (central dogma)
• what is an antibiotic

  organic compound that can either kill bacteria or inhibit bacterial growth
• what are the major aspects of bacterial cell structure

  - have circular chromosomal DNA

  - have plasmids (non-chromosomal DNA)

  - have cell walls
• gram +


  - stains purple

  - when antibiotics CAN get into cell membrane

  - thicker wall

  - hydroPHILIC
• gram -


  - stains pink

  - when antibiotics CANNOT get into cell through its cell membrane

  - hydroPHOBIC

  - have extra outer membrane
• what does the peptidoglycan cell wall consist of?

  - peptide chains

  - polysaccharides (sugars)
• what is the role of transpeptidase in peptidoglycan cell wall synthesis? what is it?

  - an enzymes that cross links the peptide chains together in a peptidoglycan

  - this golds up the cell wall and makes it rigid (strong)
• what is penicillin considered as

  an IRREVERSIBLE competitive inhibitor