BSCI330 Final Part 1 - Evolution

Why do different length scales and time scales of processes in living systems matter?

Why do different length scales and time scales of processes in living systems matter?

Length scales represent the hierarchy of biological organization.

• organelles

• cells

• tissues

• organs

Time scales provide an understanding of the temporal regulation of cellular processes

Evolution requires a geological time scale as noticeable changes take a long time.

What did evolution do to increase the rates of transport and the speed of movement and signaling? (think of a few examples)

Variations in hormones that affect signals

Coupled transport

origination of master regulator molecules

new ways of intercellular communication 

replacement of old housekeeping mechanisms (frozen accidents) with quickly developing signaling mechanisms, which remarkably accelerated evolution.

Ameboid and flagellar motion

What are the principal differences between pro- and eukaryotes?

Prokaryotes lack membrane bound organelles such as a nucleus. Prokaryotes also lack compartmentalization. For example, the DNA of a prokaryote is localized to a region without a membrane, called a nucleoid.

Eukaryotes are compartmentalized and contain a nucleus

Bacteria: Gram-positives and Gram-negatives

Gram positive means thick peptidoglycan layer on outside, Gram negative means thin peptidoglycan layer in inner membrane layers

What uniquely bacterial components are recognized by our innate immune system (PAMPAS)?

PAMPAS = Pathogen Associated Molecular Patterns.
Components Recognized = Lipopolysaccharides (LPS), peptidoglycan, zymosan, bacterial flagella, etc.

What is peptidoglycan?

Peptidoglycan is a sugar (NAM and NAG)- and peptide- containing substance that forms the cell wall of bacteria

 What is the turgor (hydrostatic) pressure inside a typical Gram- bacterium?

4.8 atm - lecture 2 slide 27

How do beta-lactam antibiotics (penicillin) kill bacteria?

Beta-lactam targets peptidoglycan synthesis. This weakens the peptidoglycan membrane, leading to blebbing due to the internal hydrostatic pressure.
—> cleaves peptidoglycan structure, weakening cell wall, bacteria blebs and dies

How does ciprofloxacin stop bacterial growth?

Ciprofloxacin inhibits bacterial DNA gyrase and topoisomerase IV. It binds to bacterial DNA gyrase with 100 times the affinity of mammalian DNA gyrase.

Stops Type II and IV topoisomerase in the bacteria

Topoisomerase needed to relax supercoil during DNA replication. Without topoisomerase, DNA replication cannot occur

How does tetracycline act on bacteria?

Tetracycline inhibits protein synthesis. It binds to the 30S ribosomal subunit and prevents the amino-acyl tRNA from binding to the A site of the ribosome. It also binds to some extent to the 50S ribosomal subunit.

—> Passively diffuse through membrane and destroy bacteria proteins

Opportunistic pathogenicity: how does switching to a virulent behavior occur?

Opportunistic pathogenicity means that when a host is immunocompromised, virus or pathogen invades. Stops peptidoglycan from strengthening the bacteria

Bacteria proliferate in an exponential manner while simultaneously producing autoinducers, signaling molecules that control the genetic expression of bacterial genes. At a critical threshold of cell density, the concentration of autoinducers becomes enough to achieve recognition by cell receptors and become transcription factors. The emergent transcription factors regulate the transcription of virulence genes. The virulence genes induce colonization of bacteria and immunosuppression. At this stage, the number of bacterial cells becomes flattened.

How different is LPS from a regular phospholipid? What do the phosphate groups on LPS do?

LPS is much larger than regular phospholipids. Increase negative charge of the cell and ionically bond to Mg2+ or Ca2+.

N- Acetyl glucosamine backbone (normal glycerophospholipids have a glycerol backbone)

Phosphate groups interact with cations to form salt bridges and cause crosslinkage to prevent cell leakage

What is the typical structural motif making proteins in the outer membrane?

Beta-barrels

Most of the basic biochemistry, protein structural motifs and energy production pathways (electron-transport chain, rotary ATP synthases photosynthesis) are fruits of bacterial evolution. Bacteria strictly rely on the closeness of their cytoplasmic compartment (H+ - leak-proof)

What do bacteria use as the central bioenergetic intermediate?

ATP

Why is the integrity of the cytoplasmic membrane critical?

maintains a proton gradient: H+ concentration higher on the outside

Membrane is permeable, allowing the passage of specific molecule via diffusion while others must use transporters

Importing nutrients and exporting waste

What two critical bioenergetic processes have evolved within the bacterial world?

1) Photosynthesis (cyanobacteria) and 2) electron transport and oxidative phosphorylation (aerobic oxidation)

What is special about the branch of Archaea called Asgard?

closest genetic relatives to eukaryotes from archaeal kingdom

What two separate endosymbiotic events happened in the course of eukaryotic evolution?

1) alpha proto bacteria was engulfed by eukaryotic cell eventually forming the mitochondria

2) cyanobacteria was engulfed by eukaryotic cell and eventually formed the chloroplast

What is the evidence that mitochondria and chloroplasts have endosymbiotic origin?

1) they have DNA plasmids (circular DNA, characteristic of bacterial cells)

2) they have their own genome, ribosomes, and RNA polymerases. For DNA, they require both DNA from the cell’s nucleus and its own DNA

What two different ways of handling osmotic forces and locomotion arose within Protozoans?

Ways of handling Osmotic forces:
1) cell wall with tubulin cytoskeleton
2) no cell well but excess membrane area and actin cytoskeleton

Locomotion
1) flagellar motion - dynein
2) ameboid motion - acto-myosin

How did the two motility paradigms shape the animal world? What groups of organisms retained the ability to employ both types of locomotion?

• the two motility paradigms allowed for adaptation and survival

Who retained this?

• Homosapeins - Humans

• Nematostella - Anemone

• physarum - slime mold

When a primitive animal with a digestive chamber formed, what three types of tissues arose?

• Endoderm - secretory (external)

• Ectoderm - sensory (external)

• Mesoderm - internal (organs and blood vessels etc.)

Note three differences between the Protostome and Deuterostome. When did this division occur?

Protostome:

• spiral cleavage

• mouth of primary animal turns into mouth

• neural cord on bottom and gut in the middle

Deuterosome:

• radial cleavage

• mouth of primary animal turns into anus

• gut on bottom and neural cord on top

600 million years ago

What drives modern evolution?

(1) slowly evolving (almost constant) house-keeping genes
(2) quickly evolving signaling and cell-to-cell communication systems, including master plan regulation genes

Examples:

• origination of master regulator molecules

• new ways of intercellular communication 

• replacement of old housekeeping mechanisms (frozen accidents) with quickly developing signaling mechanisms, which remarkably accelerated evolution.

Clonal growth provides almost no variation. What advantages are provided by polyploidy and sexual reproduction?

1) un-even cell division - daughter cells vary in cellular content

2) different gene expression - drives formation of distinct cell types and allows for adaptation to environmental stimuli

OVERALL -  recombination and segregation can lead to increased biodiversity/genetic diversity