Cycle 6: Endosymbiosis and Antibiotics

Question 1

Three domains of life….appreciate all the differences know 3 of them. Role of rRNA gene sequencing

Answer 1

Three domains of life:
- Bacteria
- Archaea
- Eukarya

These are identified by rRNA sequencing for molecular evidence (e.g. sequence information).

While bacteria and archaea are simple life forms, they can be chemically complex.

Question 2

What was LUCA….common characteristics that are found across all domains.

Answer 2

LUCA is the last universal common ancestor between the three domains of life and while there’s no physical evidence for existence, but they share DNA, RNA, proteins, etc.

Question 3

Could have been many “origins of Life” not all led to LUCA.

Question 4

Basics of evolution of life…anaerobic….to aerobic…

Answer 4

Earliest life forms were anaerobic. Then, cyanobacteria evolved oxygenic photosynthesis during the Great Oxygenation Event (GOE) - they are the first life froms to use oxygen as proton donors for photosystem II. Subsequently, there was a rise in the prevalence of aerobic bacteria, which consume oxygen and perform OxPhos.

Question 5

Idea behind why eukaryotes are more complex: role of O2 and mitochondria

Answer 5

Aerobic bacteria tend to be simple, because unlike eukaryotic cells, which are much bigger and so have MANY mitochondria, they are unable to generate the large amounts of ATP required for complexity. Oxygen is required for complexity! (higher ATP yield)

Question 6

Link between Great Oxygenation Event and increase in organism complexity (cell types, genes, genome size).

Answer 6

During the GOE, there was a significant rise in eukaryotic complexity in terms of three main metrics:
1) # cell types
2) # genes
3) genome size
see figure on slides?

Question 7

Why don’t prokaryotes have bigger genomes…more complex?

Answer 7

Prokaryotes don’t have bigger genomes and aren’t more complex because there’s an energetic cost associated with maintaining a giant genome. elaborate

Question 8

Origin of endomembrane system, nuclear membrane.

Answer 8

An anaerobic ancestral prokaryotic cell is the origin of an infolding of the plasma membrane and the formation of the nucleus and ER (also nuclear membrane).

Question 9

What is endosymbiosis and what the 6 lines of evidence (Section 1.6b)

Answer 9

Endosymbiosis is where one organism (e.g. mitochondria and chloroplasts) lives within another (i.e. eukaryotic cells).

Six lines of evidence for endosymbiosis:
1. Morphology
2. Reproduction
3. Genetic Info
4. Transcription and Translation
5. Electron Transport (has its own electron transport chain, since it was once free living)
6. Sequence Analysis

elaborate!!!!!!!!

Question 10

Relative sizes of typical mitochondrial, chloroplast (compared to bacterial ancestor)

Question 11

Why have the genomes shrunk compared to ancestors (redundancy and horizontal gene transfer).

Answer 11

There’s a huge reduction in genome size from prokaryotic ancestors to its current form as organelles. This is because the many tasks required for a free-living cell are redundant/obsolete since the cell that engulfed it already has those genes (e.g. protein transportation). Otherwise, many genes moved to the nucleus via horizontal gene transfer (HGT), with no change to gene function.

Question 12

What is horizontal gene transfer (HGT) and why do we think it occurs between mitos/chloros and the nucleus.

Answer 12

Horizontal gene transfer refers to the relocation of genes from one genome to another.

Question 13

Detecting horizontal gene transfer using DNA hybridization…Can you interpret the pattern of the result?

Question 14

Role of the signal peptide in trafficking nuclear-encoded proteins that end up in the mitochondria or chloroplasts.

Question 15

Basics of protein targeting to organelles via a signal peptide.

Question 16

Three domain vs two domain tree of life…Eukaryotic signature proteins and Archaea (Asgard)

Question 17

The eukaryotic cell is a chimera…what does that mean….basic contributions from bacteria and archaea.

Question 18

Surprising thing about the origin of the membrane lipids in eukaryotes.

Question 19

BIG PICTURE…..Three genomes in Chlamy….what does that mean….three compartments need transcription/translational machinery!

Question 20

What’s an antibiotic

Question 21

Major aspects of bacterial cell structure….e.g. cell wall and presence of plasmid

Question 22

Structural differences in the cell surface of Gram+ versus Gram- bacteria and the easy of entry of antibiotics.

Question 23

Structure of peptidoglycan cell wall and specific role of transpeptidase in its synthesis

Question 24

How penicilin acts to block cell wall biosynthesis

Question 25

Mode of action of major antibiotics.

Question 26

Why don’t antibiotics kill us.?

Question 27

Mitochondria are prokaryotic!

Question 28

Assay to detect antibiotic resistant bacteria

Question 29

Two ways antibiotic resistance is acquired

Question 30

Random mutation…what does that term mean

Question 31

Understand distinction between deleterious, neutral and advantageous mutations

Question 32

What happens during bacterial conjugation

Question 33

Major mechanisms of resistance (two are INTRINSIC….Efflux pump, downregulation of porin).

Question 34

Role of loss of porin in acquisition of resistance in Klebsiella.