# Outline

1.  Beyond the Central Dogma
2.  Transcription Factors
3.  Pseudomonas Aeruginosa
4.  Proposal

# **Beyond the Central Dogma**

## Levels of Organization

- Hierarchical structure
- Increasing in complexity
  - Each "layer" composed of the previous level's basic unit

### Biosphere

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Remarks:

All of the world's ecosystem
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Example:

Earth
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![](images/paste-1.png){fig-align="center"}

### Ecosystem

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Remarks:

Interacting community of organisms (tree, people, fungi, etc...)
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Example:

Forest
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![](images/paste-2.png){fig-align="center"}

### Organism

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Individual in a species
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Example:

Human
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![](images/paste-3.png){fig-align="center"}

### Organ

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Remarks:

Group of tissues that carry out functions
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Example:

The eye
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![](images/paste-6.png){fig-align="center"}

### Tissue

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Homogeneous group of cells
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Example:

Retina
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![](images/paste-7.png){fig-align="center"}

### Cells

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Remarks:

Composed of organelles
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Example:

Photoreceptors
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![](images/paste-8.png){fig-align="center"}

### Organelles

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Composed of molecules
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Example:

Nuclei
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![](images/paste-9.png){fig-align="center"}

### Molecules

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Composed of atoms
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Example:

Nucleic acids
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![](images/paste-10.png){fig-align="center"}

## Hierarchical Causation

![Bottom-up and top-down causation from the quantum level up to the organism level and down again](images/paste-4.png){fig-align="right"}

## Causation at the Molecular level

![Systems biology view of upward and downward causation in biology as a feedback diagram. While the upward causation is well known (black links), some of major downward causation (blue links) elements include TFs, epigenetic regulators, reverse transcriptases, DNA_polymerases † , and recombinases.](images/paste-5.png)

# **Transcription Factors**
## Characteristics
- Proteins that bind specific DNA sequences to activate or repress transcription

- Two Domains:

  - **Binding Domain (DBD):** This region identifies and binds to specific nucleotide sequences within promoter or enhancer regions.
  - [**Effector Domain**](https://www.google.com/search?q=Effector+Domain&client=ubuntu-sn&hs=afh&sca_esv=b05c8d9632b51df6&channel=fs&biw=1268&bih=1013&sxsrf=ANbL-n5PxsJdooNEkz2Dn1nwdzl_NKkUcw%3A1773944558164&ei=7j68abHgCb7a1e8P0ZzMgQo&ved=2ahUKEwix54PFyqyTAxVZYfUHHYL1BNsQgK4QegQIBBAC&uact=5&oq=transcription+factors+binding+and+effector&gs_lp=Egxnd3Mtd2l6LXNlcnAiKnRyYW5zY3JpcHRpb24gZmFjdG9ycyBiaW5kaW5nIGFuZCBlZmZlY3RvcjIFECEYoAEyBRAhGKABMgUQIRigAUjYKFCKC1iBJnAAeAKQAQCYAYABoAGpEKoBBDE4LjS4AQPIAQD4AQGYAhegAuUSwgIEEAAYR8ICBhAAGBYYHsICCxAAGIAEGIYDGIoFwgIFEAAY7wXCAgsQABiABBiRAhiKBcICCxAuGIAEGJECGIoFwgIFEAAYgATCAggQABgWGAoYHsICBxAhGKABGArCAgUQIRifBcICBBAhGBWYAwDiAwUSATEgQIgGAZAGCJIHBDguMTWgB6aaAbIHBDcuMTW4B8kSwgcIMC4zLjYuMTTIB9oBgAgA&sclient=gws-wiz-serp) **(ED):** This portion interacts with the transcriptional machinery (like [RNA polymerase II](https://www.google.com/search?q=RNA+polymerase+II&client=ubuntu-sn&hs=afh&sca_esv=b05c8d9632b51df6&channel=fs&biw=1268&bih=1013&sxsrf=ANbL-n5PxsJdooNEkz2Dn1nwdzl_NKkUcw%3A1773944558164&ei=7j68abHgCb7a1e8P0ZzMgQo&ved=2ahUKEwix54PFyqyTAxVZYfUHHYL1BNsQgK4QegQIBBAD&uact=5&oq=transcription+factors+binding+and+effector&gs_lp=Egxnd3Mtd2l6LXNlcnAiKnRyYW5zY3JpcHRpb24gZmFjdG9ycyBiaW5kaW5nIGFuZCBlZmZlY3RvcjIFECEYoAEyBRAhGKABMgUQIRigAUjYKFCKC1iBJnAAeAKQAQCYAYABoAGpEKoBBDE4LjS4AQPIAQD4AQGYAhegAuUSwgIEEAAYR8ICBhAAGBYYHsICCxAAGIAEGIYDGIoFwgIFEAAY7wXCAgsQABiABBiRAhiKBcICCxAuGIAEGJECGIoFwgIFEAAYgATCAggQABgWGAoYHsICBxAhGKABGArCAgUQIRifBcICBBAhGBWYAwDiAwUSATEgQIgGAZAGCJIHBDguMTWgB6aaAbIHBDcuMTW4B8kSwgcIMC4zLjYuMTTIB9oBgAgA&sclient=gws-wiz-serp)) or other coregulatory proteins to modulate the speed and occurrence of transcription.

## Mechanism & Classification

## (Many) Responsibilities

# **P. Aeruginosa**

# Proposal