Biology

Subjects to add/finish: Anatomy, Botany, Cell Biology, Ecology, Epidemiology
Anatomy
guhh

Botany
Generic Plant Dichotmous Key
1 Has seed, may have fruit

Sporophyte/Gametophyte (unfern-like)

May have flowering, conical, or scaley parts.

2 Has either scales or cones, style/stigma absent
Gymnosperm
2' Has flowering parts (petals), reproductive parts present around ovary
Angiosperm
1' Has spores, fruitless

Tracheophyta (fern-like)

Possesses rhizoid structures


Cell Biology
Prokaryotic and eukaryotic cells

Organelles (of the typical mammalian cell)
Subcellular structures and their jobs
Nucleus - The Genetic Guardian
- The Nuclear membrane: has a double membrane (phospholipid bilayer)
- Attached to the Endoplasmic Reticulum; has ribosomes
- Nucleoplasm has many nuclear bodies
- Cajal
- Gemini
- Polycomb
- Nucleolus: "nucleus" of the nucleus and site of ribosomal biogenesis; not comparted
- Chromatid and chromosomes stored here
- Chromosomes are arranged in specific territories inside the nucleus

Mitochondia - Mommy Powerhouse
- Interacts heavily with the Endoplasmic reticulum and Golgi apparatus
- Can be fissured and fissioned
- Double membrane: phospholipid bilayer + cristae (oxidative metabolism)
- Crista: fold in the inner membrane of a mitochondrion
- Respiratory chain (ATP): Complexes I, II, III, IV, V (phosphorylation)
- Coenzyme 10 + Cytochrome C
- Mitochondrial matrix contains mitochondrial genome
- mRNA, tRNA, electron transport chains, enzymes, acids, catalysts, ribosomes, matrix granules, etc.
- Calcium regulation for membrane constipation
- Apoptosis: Mitochondrial outer membrane permeabilization releases cytochrome C

Endoplasmic Reticulum (ER)
- Has rough and smooth components
- Rough: Protein synthesis, folding, management, glycosylation
- Smooth: Synthesizes lipids and phospholipids, calcium ions
- Cisternae: sac like structures
- Has protruding tubes to increase surface area
- Chaperones enzymes that are sent to the golgi apparatus

Golgi Apparatus (GA) - Traffic Control Center
- Lipid synthesis
- Receives endoplasmic reticulums vesicles
- Fused, charged, organized
- Facilitates phosphorylation
- Has direct access to the plasma membrane

Lysosomes - The Recycling Plant
- Breaks down cellular waste
- Phospholipid bilayer sphere
- Full of enzymes that digest and hydrolyze
- Autophagy: cell component turnover

Plasma Membrane + Extracellular Matrix
- Semipermeable phospholipid bilayer
- Cytoskeleton
- Fibrous proteins: Collagen, elastin
- Glycoprotein: signaling, migration
- Peptidoglycan
- Active & passive transport chains
- (facilitated) diffusion, endo/ectocytosis
- Ligand binding sites, antigen markers (ID)
- Ion dynamic , lipid homeostasis, cell signaling

Microfilament - The Skeleton
- Organelle anchors and general cell structure
- Transportation
- Cytoskeleton
- Charged: one positive and one negative end
- Actin: Thin, flexible, fibrous

Centrosomes + Microtubules
- Cytoskeleton's primary contribution
- Cell's physical structure, mobility, polarity
- Meiosis and mitosis facilitators
- Have some DNA in them
- Help arrange, anchor, and connect organelles
- Centrosomes duplicate for cell division
- Mother and Daughter centrosomes
- Mother has tubule appendages


The Cell Cycle (Eurakyotic Cells)
The life (and death?) of the cell
G1 Phase
The first growth phase
- During late G1, proteins for chromosome replication are activated

G0 Phase
Quiescent phase
- Metabolically inactive cells wait here until they are needed

G1 Checkpoint
DNA damage checkpoint

S Phase
Synthesis phase
- There is some “S” factor that can trigger the chromosomes to replicate prematurely
- Contains DNA polymerase and other enzymes required for DNA synthesis, histones and non-histone proteins and the enzymes to make the deoxyribonucleotides
- Condensation of the chromosomes and the break down of the G2 nucleus are delayed until the S phase chromosomes have completed their replication

G2 Phase
The second growth phase
- Chromosome liscensed: fail safe or check system to ensure that the DNA is replicated only one time during a single cell cycle (license removed during M or early G1)

G2 Checkpoint
DNA damage and size checkpoint

M Phase
The factor in M phase cells predominates over every other cell cycle factor. We call this M phase factor MPF(mitotic promoting factor).
Mitosis - Cell replication and segregation
Prophase:
- nuclear envelope still intact
- spindle developing
- chromosomes condensing
- two chromatids held together by kinetochores (near the center)
Prometaphase:
- nuclear envelope fragments
- spindle pole established (orientation)
Metaphase:
- chromosomes align at the equator
Anaphase:
- chromatids separate towards poles
- inner spindle lengthens, outer spindle shortens
Telophase:
- nuclear envelope begins developing around separated chromatids
- chromosomes unravelling
Cytokinesis:
- nuclear envelope completes
- polar spindle cleaves and forms two cells

M Checkpoint
Spindle attachment checkpoint

Mitosis Deep Dive: Interphase through Cytokinesis
Interphase
Nucleation
- microtubules assemble from the centrosome towards the kinetochores
Nucleation from chTOG module
- gamma tubulin ring complex provides nucleating center for microtubule assembly and chTOG complex traps
- brings tubulin to initial (positive) end of microtubules
Nucleation from centrosome mediation
- pericentrin, CEP192, CDK5RAP2 proteins bind to gamma tubulin ring complex
Nucleation from CPC at the kinetochore
- CPC: chromosome passenger complex
- formation and localization of CPC activates Aurora B kinase
- Aurora B phosphorylates and inactivates MCAK (microtubule destabilizing protein) and stathmin (tubulin-sequestering protein)
- microtubule polymerizes towards kinetochores


Proteins, enzymes, factors & drugs, oh my!
Kinases
- enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates
p34 kinase
- requires correct phosphorylation for MPF activation

Cyclins (proteins) and their dependent kinases (enzymes)
regulated by the binding of cyclically synthesized proteins

CyclinD/CDK4
- exists in the G phase
- destroyed at the end of the G phase
CyclinE/CDK2
- exists in the G phase
- stays for the S phase to start chromosome replication
Cyclin A/CDK2
- required to complete chromosome replication
CyclinB/CDK1
- produced during the G2 phase
- threshold triggers mitosis
p34 kinase
- requires cyclin, so p34 falls under CDK

Chromatins: euchromatin, heterochromatin
- DNA and protein complex. On/off

Microtubule Motor Proteins
Dyneins (towards negative)
- retrograde cargo
- heavy + light chains
- cytoskeletal motor proteins that move along microtubules in cells
- convert the chemical energy stored in ATP to mechanical work

Kinesins (towards positive)
- anterograde cargo
- heavy chain + flexible hinge + light chains
- motor protein associated with microtubule transport
- andocytotic vesicle + cargo receptor


Lamin
- Protein that supports the nuclear cytoskeleton

Drugs/Inhibitors
Colcemid (M)
- inhibits microtubule assembly, disassembles microtubules
- nuclear cycle continues until M where the mitotic spindle cannot form and the chromosome cycle is arrested (metaphase/anaphase block)

Aphidicolin (S)
- inhibits DNA polymerase a
- directly prevents replication at the replication fork

Hydroxyurea (S)
- inhibits the ribonucleotide reductase (enzyme that generates the deoxyribonucleotides required to synthesize new DNA)


Chemistry

Subjects to add/finish: Chemicals, General, Organic, Inorganic
General Chemistry

[summary of gen chem]

Hypotheses, theories, facts and law

Definitions to know

Fact: True under any and all conditions

Hypothesis

Theory

Law

Belief

Hypotheses, theories, facts and law


Organic Chemistry


List of Chemicals (I like)
Pyridine

(Molecular formula: C5H5N)

Nitrogen (N) makes the world go round! Pyridines are present in alkaloids (plant aroma and poison), histamines (allergen mediator) and many neurotransmitters (norepinephrine, dopamine, epineprhine). Pyridine as a structure includes any aromatic heterocyclic chain that has five carbons and a nitrogen; substituents would include only organic elements. It is used in various water repellents, bactericides, herbicides medicines, vitamins, food flavorings, pesticides, paints, dyes, adhesives, and waterproofing for fabrics.

General chemistry uses

- mix with ethanol (EtOH; molecular formula: C2H6O) => strong basic solvent that facilitates acyl substitutions

Biochemical uses

- sulfapyridine (M&B 693), a drug active against bacterial and viral infections

- pyribenzamine is an old antihistamic that was used to treat asthma, hay fever, rhinitis, and urticaria. is still used relatively frequently in cough/repiratory medication

- piperidine (C5H11N) is the representative structure for many alkaloids. it is used in rubber processing and as a chemical raw material

- present in the following vitamin Bs: niacin and pyridoxal

- isoniazid, an antitubercular drug

- it is found in nicotine, fried bacon, fried chicken, and cheese!


Bases
Lithium Diisopropyl Amide

(Molecular formula: C6H14LiN)

Really strong base of a hindered lithium diorganylamides that is excellent for deprotonization at the alpha point in carbonyls.

Lithium Diisopropyl Amide

(Molecular formula: C6H14LiN)

Really strong base of a hindered lithium diorganylamides that is excellent for deprotonization at the alpha point in carbonyls.

Lithium Diisopropyl Amide

(Molecular formula: C6H14LiN)

Really strong base of a hindered lithium diorganylamides that is excellent for deprotonization at the alpha point in carbonyls.