Week 2 Review

Why are Asgard Archaea important?

they are relatives of eukaryotes and their genomes encode typical eukaryotic systems

What is episymbiosis vs endosymbiosis?

episymbiosis: where one organism lives on the surface of another (the host) for survival

endosymbiosis: where one organism lives inside another (the host)

Which 2 microorganisms utilize episymbiosis?

DPANN archaea and CPR bacteria

Which features of eukaryotes are absent in bacteria but present in archaea?

key biosynthetic pathways that makes nucleotides, amino acids, and lipids

bacteria cannot replicate or survive on their own for this reason

What are characteristics of CPR Bacteria?

• small genomes

• small cell sizes

• mostly symbiotic

• found in anaerobic environment (no oxygen)

What are characteristics of DPANN archaea?

• small genoms

• small cell sizes

• mostly episymbiotic

• found in extreme ennvironments

What are hami?

unique surface attaching grappling hooks for cell adhesion located on the outer membrane of DPANN arachaea

What are the similarities between CPR bacteria and DPANN archaea?

• small genoms

• small cell size

• limited metabolic abilities (cant make nucleotides/amino acids/lipids)

• symbiotic/episymbiotic

What are differences between CPR and DPANN?

• they are different phylla

  • CPR = bacteria

  • DPANN = archaea

• have different genetic codes

• CPR are missing some ribosomal proteins

What are the names of the pathways used by CPR vs DPANN for making their membranes?

• DPANN → MVA pathway

• CPR → MEP pathway

How are CPR bacteria different from previously known symbiotic bacteria?

CPR has gaps in their metabolic capacities unlike other bacteria

Define homology

derived from common ancestor

Define divergence

related species become increasingly different over time

Define similarity

look or behave alike but may not share common ancestor

Define analogy

similarity in function or appearance but NOT due to a common ancestor

Define convergent evolution

unrelated organisms evolve similar traits/features from living in same environment → NOT due to common ancestry

What is ASD?

Autism spectrum disorder that is highly multi-factorial (impacted by genetic and environmental factors)

What are the molecular correlates of autism spectrum disorders?

• GI microbiota

• metabolism

• Nervous system

• immune system

• neurotransmitters

• maternal microbiota

• epigenetics

How does the microbiome impact the intestinal barrier?

it strengthens its integrity

What is the impact of the microbiota and CNS on homeostasis?

it can directly or indirectly impact homeostasis

Describe the impact of dysbiosis

dysbiosis = gut imbalance

can cause disease and disorders (like ASD)

How does metabolism impact the microbiota?

production of metabolites like tryptophan/serotonin/short chain fatty acids can generate neurotoxic products and impact that state of the microbiome through the microbiota-gut-brain-axis

What are the 3 nervous sytems/axis that interact with the vagus nerve to mediate gut-brain connection?

• ANS

• ENS - enteric NS

• HPA - hypothamalic-pituitary-adrenal axis)

Which NT cant cross the BBB?

GABA → only acts locally

What is the impact of maternal gut microbiota on the fetus?

it modulate growth and fetal brain development → can upregulate expression of tight junction proteins and decrease permeability

What is vertical transmission?

transfer of infection or disease from mother to child during birth or pregnancy → birth method can have a significant difference in the microbiome diversity

How does epigenetics work?

changes acetylation and deactylation

What does deacetylation do to chromatin?

causes gene inhibition by condensing the chromatin

How does food selectivity impact ASD and the gut microbiota?

• picky eating and severe food selectivity are seen in pts with ASD → this consumption of a particular diet alters the gut microbiota to favor specific bacteria

• a less diverse diet = reduces microbiome diversity

How can pro and prebiotics help deficits in social behavior?

they can reverse the deficits

What are the 2 main divisions of the immune system?

• innate = fast and general

• adaptive = slow and specific

What substances does the gut microbiome produce?

• short chain fatty acids and tryptophan

What are germ-free mice?

germ free mice are essentially sterile so they are used to study microbiota impacts

What are social behaviors like in GF animals vs normal?

they have social behavioral problems → tells you healthy microbiota is important

What are the 5 microbiome compartments?

1. intestinal

2. mouth

3. skin

4. respiratory

5. vaginal

What is the role of bacteria on host health/behavior?

a good microbiome (from good bacteria) means good health while a deficient microbiome could cause deficits in health and behavior

What is a wobble position?

a codon (typically the 3rd) that is more flexible for tRNA binding

Which positions are wobble positions for initiation codons vs. elongation codons vs. termination codons

initiation: P1

elongation/termination: P3

What is the importance of the P2 nucleotide?

P2 specifies the TYPE of amino acid → it has the least amount of variance (it is the most conserved position)

What type of amino acid would we have if we had a “T” in P2?

hydrophobic

What type of amino acid would we have if we had “A” in P2?

hydrophilic W

What type of amino acid would we have if we had “C/G” in P2?

semipolar

How does selection pressure interact with expression level?

genes expressed at:

• HIGH levels → increased selection pressure

• LOW levels → weak selection pressure

Are codon preferences different across species?

yes → each species has its own codon preferences

Which nucleotide bases are PURINES?

A and G → 2 rings

Which nucleotide bases are PYRIMIDINES?

C and T → 1 ring

Which nucleotide base pairs are WEAK and why?

T:A or A:U are WEAK

they form 2 H bonds between them, making them easier to break

Which nucleotide base pairs are STRONG and why?

C:G are STRONG

they form 3 H bonds between them, making them harder to break

Is purine:pyrimidine mRNA:tRNA base pairing energetically different

from pyrimidine:purine mRNA:tRNA base pairing?

Yes → a T:A is stronger than A:T mRNA:tRNA

a C:G is stronger than G:C

What is the current view on early life forms?

cooperation may be the true driving force for survival and evolution → not competition

How does evolutionary complexity change over time?

through mutations, selection, symbiosis

Why does complexity increase over time?

evolution builds on what ALREADY works and exists → why things become more complex as evolution continues

What are the different forms of symbiosis?

• mutualism → both organisms benefit

• parasitism → one benefits, one harmed

• commensalism → one benefits, one unaffected