Lecture Cycle 6

• What are the three domains of life? What are some differences?

  1. archaea

  2. eukarya

  3. bacteria

  differences: chromosome structure, ribosomes, membrane lipids
• What is the role of rRNA gene sequencing?

  to sequence the gene that codes for the small subunit of ribosomes
• What was LUCA? What are some common characteristics found across all domains?

  - Last Universal Common Ancestor

  - DNA, RNA, ribosomes, ATP, glycolosis
• What did the origin of life look like that led to LUCA?

  unsure, it could have looked various different ways
• What is the basic evolution of life from anaerobic to aerobic?

  anaerobic, great oxidation event / PSII, cyanobacteria, aerobic
• Why are eukaryotes more complex?

  because they are bigger, they generate more ATP which enables them to do more, increasing complexity
• How does the Great Oxidation Event and organism complexity relate?

  after the GOE complexity drastically increased
• Why don't prokaryotes have larger genomes?

  they don't have the energy
• What is the origin of the endomembrane system? The nuclear membrane?


  infolding of the plasma membrane of ancesteral prokaryotic cells
• What is endosymbiosis?


  the origin of the mitochondria and chloroplasts which evolved from free-living prokaryotes
• What are the six lines of evidence of endosymbiosis?

  1. morphology

  2. reproduction

  3. genetic information

  4. transcription and translation

  5. electron transport

  6. sequence analysis
• What are the relative sizes of the mitochondrial and chloroplast genome compared to bacterial ancestors?

  much smaller
• What are factors that have caused a shrinking in genomes compared to ancestors?

  - redundant genes disapper because parent fenome already has them

  - the nucleus has genes as well

  - moved location
• What is horizontal gene transfer?

  the movement of genes from one genome to another
• Why do we think that HGT occurs between the mitochondria/ chloroplast and the nucleus?

  - the nucleus must have total control over the whole cell

  -semiautonomous organelles
• How can you detect horizontal gene transfer? How would you know if it has or hasn't occurred?

  - detect using DNA hybridization: single stranded DNA probe, single stranded DNA target, complimentary base pairing

  - if present in nuclear but no longer present in mitochondrial
• What is the role of the signal peptide in trafficking nuclear encoded proteins that end up in the mitochondria or chloroplasts?


  the signal peptide takes the protein to the mitochondra once it is coded by the nuclear genes
• What are the basics of protein targeting to organelles using a signal peptide?

  signal peptide attaches to protein, takes to organelle by the receptor protein, once in the organelle, the signal sequence is cleaved
• What separated the three domain tree of life and the two domain tree of life?


  the two domain tree is different becausre it recognizes common ESPs in a group of Archaea called asgard, eukarya are descendents of Asgard
• What is meant when we refer to a eukaryotic cell as a chimera? What are the basic contributions from archaea and bacteria?

  - eukaryotic cells are composed of two genetically distinct cells, archaea and bacteria

  - archaea: genes for information processing and structure

  - bacteria: lipids, and genes for metabolism
• What is interesting about the origin of membrane lipids in eukaryotes?

  they are bacterial
• What is the significance of chlamy having three genomes? What does this mean?

  - allows for both autotrophic and heterotrophic growth

  - why it is a good model system, are able to study through all three genomes
• What is an antibiotic?

  organic compound that either kills or inhibits bacterial growth
• What are the major aspects of bacterial cell structure?

  - hydrophobic cell membrane

  - membrane proteins

  - peptidoglycan
• What is a plasmid?

  non-chromosomal DNA
• What are the key differences in the Gram+ vs Gram- bacteria?

  1. dye can get into Gram+ easily, stain doesn't take up in Gram-

  2. Gram- is hydrophillic

  3. Gram- is hard to treat because antibiotics are water soluble
• What is the structure of a peptidoglycan cell wall?

  cross-linked peptide chains
• What is the role of transpeptidase in the synthesis of peptidoglycan?

  cross links the peptide chains
• What does penicillin block? How does it do this?

  - blocks the function of transpeptidase

  - it is an analog of the substrate
• Penicillin is a...

  irreversible competitive inhibitor of transpeptidase
• What are the modes of action of major antibiotics?

  1. metabolic pathways

  2. cell wall formation

  3. DNA replication/transcription

  4. protein synthesis
• What causes antibiotics to not kill us?

  they target the cell wall (peptidoglycan) which human cells do not have
• Are mitochondria prokaryotic or eukaryotic?

  eukaryotic
• How to detect antibiotic resistant bacteria?

  place paper disks with antibiotics on an agar plate with a bacterial lawn
• What are the two ways antibiotic resistance phenotype is acquired?

  1. Random mutation

  2. DNA from an elready resistant cell
• Is antibiotic resistance a phenotype or genotype?

  phenotype
• What is meant by random mutation?


  occur randomly, without pattern, cannot be predetermined
• What is the difference between deleterious, neutral, and advantageous mutations?

  - deleterious: harmful

  - neutral: no affect, amino acid sequnce is the same

  -advantageous: provides some advantage
• What happens during the process of bacterial conjugation?

  plasmids cause themselves to be replicated and transferred from one bacterium to another (type of HGT)
• What are the major mechanisms of antibiotic resistance?

  1. inactivation of antibiotic

  2. target site modification

  3. target bypass

  4. active efflux

  5. downregulation of porin