vault backup: 2026-09-24 11:50:31

.obsidian/workspace.json

@@ -125,30 +125,58 @@
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-              "title": "Classifying Organic Compounds"
+              "title": "3 Classification of Prokaryotes"
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-              "title": "root"
+              "title": "5 Classification (taxonomy) and Kingdoms"
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+              },
+              "icon": "lucide-file",
+              "title": "7 Species concepts and Evidence for Relatedness"
+            }
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+              "title": "8 Kingdom Protista"
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@@ -332,35 +360,37 @@
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-    "biology/G11 Pre-AP Biology/2 Prokaryotic vs. Eukaryotic Cells.md",
+    "biology/G11 Pre-AP Biology/8 Kingdom Protista.md",
-    "biology/G11 Pre-AP Biology/1 Viruses.md",
+    "Assets/Pasted image 20260924105525.png",
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+    "biology/G11 Pre-AP Biology/5 Classification (taxonomy) and Kingdoms.md",
+    "biology/G11 Pre-AP Biology/7 Species concepts and Evidence for Relatedness.md",
     "biology/G11 Pre-AP Biology/3 Classification of Prokaryotes.md",
-    "biology/Chemistry of Life/Proteins.md",
+    "biology/G11 Pre-AP Biology/2 Prokaryotic vs. Eukaryotic Cells.md",
-    "biology/Chemistry of Life/Carbohydrates.md",
+    "biology/G11 Pre-AP Biology/G11 Pre-AP Biology.md",
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-    "biology/Chemistry of Life/Lipids.md",
-    "biology/Chemistry of Life/Macromolecules.md",
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-    "literacy/fallacies.md",
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-    "physics/Electric Force, Field, and Potential/Electric Force, Field, and Potential.md",
     "literacy/buzzwords.md",
-    "math/linear algebra.md",
+    "literacy/fallacies.md",
+    "literacy/literacy.md",
+    "biology/Chemistry of Life/Proteins.md",
+    "biology/Chemistry of Life/structure of water and hydrogen bonding.md",
+    "biology/Chemistry of Life/Nucleic Acids.md",
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+    "biology/Chemistry of Life/Lipids.md",
+    "physics/Modern Physics/Bohr Model of Atomic Structure.md",
+    "root.md",
+    "biology/Cell Structure and Function/Membrane Transport.md",
+    "biology/G11 Pre-AP Biology/1 Viruses.md",
+    "chemistry/Organic Chemistry/Classifying Organic Compounds.md",
+    "biology/Cell Structure and Function/Origins of Cell Compartmentalization.md",
+    "biology/biology.md",
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     "physics/Oscillations",
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     "physics/Torque and Rotational Dynamics",
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biology/G11 Pre-AP Biology/1 Viruses.md

@@ -1,18 +1,20 @@
 c[[G11 Pre-AP Biology]]
 
 * Non-living
-	* Not capable of surviving on its own
+	* Not capable of surviving on its own.
-	* Acellular (Not made of cells)
+	* Acellular.
 	* No cytoplasm, ribosomes, or membrane bound organelles.
-	* Doesn't produce energy.
+	* Doesn't produce energy (no metabolism).
-* Essentially structures with genetic material (nucleic acid) and protein coating (capsid)
+	* No self reproduction.
+	* No homeostasis.
+* Essentially structures with genetic material (nucleic acid) and protein coating (capsid).
 * Shapes:
 ![[Pasted image 20260911203414.png|336]]
 * Bacteriophages are complex viruses which attach to bacteria.
-* Replicates doesn't reproduce
+* Replicates doesn't reproduce.
 * Instructs host cell to make copies of virus DNA
-* Viroids are viruses without capsoids
+* Viroids are viruses without capsids.
-* Prions are proteins that cause cells to misfold
+* Prions are proteins that cause cells to misfold.
 # Lytic and Lysogenic Cycles
 * Lytic:
 	* Cycle:

biology/G11 Pre-AP Biology/2 Prokaryotic vs. Eukaryotic Cells.md

@@ -33,14 +33,16 @@ Prokaryotic Cell
 | Exchanges information with other cells through conjugation | Genetic variation through meiosis |
 
 # Endosymbiotic theory
-Theory that eukaryotic cells evolved from symbiotic theory between 2 or more prokaryotic cells. Larger cell engulfed a smaller cell, engulfed cell (endosymbiont) became an internal part of engulfing cell (host cell). Mitochondria and chloroplast originated from bacteria.
+Theory that eukaryotic cells evolved from symbiotic theory between 2 or more prokaryotic cells. Larger cell engulfed a smaller cell, engulfed cell (endosymbiont) became an internal part of engulfing cell (host cell). MAC[^1] originated from bacteria.
 
 Ancestral prokaryote engulfed aerobic bacterium. Lived symbiotically.
 Other ancestral prokaryotes engulfed photosynthetic bacterium. Lived symbiotically.
 
 Evidence:
-* Mitochondria and chloroplast have a outer and inner membrane, theorized one from new, one from when it was independent.
+* MAC[^1] have a outer and inner membrane, theorized one from new, one from when it was independent.
-* M and C have their own DNA.
+* MAC have their own DNA.
-* M and C can divide on their own independent of host cell.
+* MAC can divide on their own independent of host cell.
 
 [More Information](obsidian://open?vault=obbyvault&file=biology%2FCell%20Structure%20and%20Function%2FOrigins%20of%20Cell%20Compartmentalization)
+
+[^1]: Mitochondria and chloroplast

biology/G11 Pre-AP Biology/7 Species concepts and Evidence for Relatedness.md

@@ -0,0 +1,16 @@
+[[G11 Pre-AP Biology]]
+Species is a group in organism that interbreed in nature and produce fertile offspring. Gaps though, bacteria don't sexually reproduce, and there are separate species that are able to mate and create fertile children. 
+
+Three types of species.
+* Morphological Species:
+	* Studies shape, size, physics, structural features.
+	* Simple, quick.
+	* Most populations have variation.
+* Biological Species:
+	* Ability to reproduce in nature and produce fertile offspring.
+	* Most commonly accepted definition, objective.
+	* Can't test on asexually reproducing, extinct, and/or physically separated organisms.
+* Phylogenetic:
+	* Studies evolutionary history and relationships among organisms.
+	* Can be applied to extinct species.
+	* Not all evolutionary histories are known.

biology/G11 Pre-AP Biology/8 Kingdom Protista.md

@@ -0,0 +1,50 @@
+[[G11 Pre-AP Biology]]
+Characteristics:
+* Mainly unicellular
+* Under Eukarya domain.
+* Eukaryotic cells.
+* Reproduces sexually and/or asexually.
+* Diverse, not closely related.
+
+Classification:
+* Animal-like (protozoans):
+	* Heterotrophs.
+	* Can move.
+* Plant-like:
+	* Autotrophs, can photosynthesize.
+	* Photoautotrophs.
+	* Some are capable of consuming other organisms when light is unavailable.
+	* Can be unicellular or multicellular.
+* Fungus-like:
+	* Absorbs nutrients from other organisms.
+	* Heterotroph/decomposers, outer digestion.
+	* Cell wall is not chitin.
+	* Examples are slime moulds and water moulds.
+
+
+| Phylum        | Characteristics                                                                                        | Example                             |
+| ------------- | ------------------------------------------------------------------------------------------------------ | ----------------------------------- |
+| Cercozoan     | Pseudopods, temporary cytoplasmic extension for movement/feeding.                                      | *Amoeba proteus*                    |
+| Cilliophora   | Cilia, short hair like extensions for sweeping food or movement.                                       | *Paramecium caudatum*               |
+| Zoomastigma   | Flagella, long tail like whip.                                                                         | *Trichonympha*                      |
+| Sporozoa      | Vector, uses living organism to transmit infection from one organism to another. Parasitic to animals. | *Plasmodium vivax* (causes malaria) |
+| Myxomycpta    | Many nuculei, engulfs like amoeba.                                                                     | Plasmodia                           |
+| Acrasiomycota | Individual amoeboid cells, one nuculeus.                                                               | Cellular slime mold                 |
+| Oomycota      | Filamentous, resemble fungi, release enzymes to absorb nutrients.                                      | *Water mold*                        |
+Paramecium:
+* Cilia.
+* Asexual (binary fission/sexual.
+* Gullet.
+* Outer protein covering.
+* Lives in water.
+![[Pasted image 20260924105000.png|371]]
+Amoeba:
+* Pseudopods.
+* Extension of cytoskeleton.
+![[Pasted image 20260924105030.png]]
+Euglenoids/Euglena:
+* Plant-like protista.
+* Flagella.
+* Unicellular.
+* Capable of ingesting nutrients.
+![[Pasted image 20260924105525.png]]

literacy/fallacies.md

@@ -1,6 +1,6 @@
 [[Literacy]]
 
-| NAME                             | MEANING                                                                                                                                     |
+| NAME                             | DESCRIPTION                                                                                                                                 |
 | -------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------- |
 | Ad Hominem                       | Insulting opposition without argument.                                                                                                      |
 | Ad Lapidem (Appeal to the stone) | Saying no without an argument.                                                                                                              |

root.md

@@ -1 +1,13 @@
-"Excess is easy, anyone can do it. What's beyond most… is making it succinct—the art of abbreviation."
+"*Excess is easy, anyone can do it. What's beyond most… is making it succinct—the art of abbreviation.*"
+
+# Terminology
+
+| NAME         | DESCRIPTION                                       |
+| ------------ | ------------------------------------------------- |
+| Child        | File parented to working file.                    |
+| Parent       | File working file is parented to.                 |
+| Subject File | A child representing a sub-subject of the parent. |
+
+# Rule of Thumb
+* Notes should be concise.
+* Common sense.