1. DNA is not able to undergo transcription as well as translation. As a result, the genes are unable to be expressed.
2. the response that the signal molecule produces is important because it is what allows DNA to replicate and genes to be expressed.
2.1. genes turned on
2.1.1. allows for DNA to be replicated, increases transcription and transltion factors which lead to cell growth and an overall higher metabolism
2.2. genes turned off
3. Photosynthesis (Isaac)
3.1. Photoautotrophs
3.1.1. Plants
3.1.2. Cyanobacteria
3.1.3. Multicellular Alga
3.1.4. Purple Sulfur Bacteria
3.1.5. Unicellular Eukaryotes
3.2. Chloroplasts
3.2.1. Located in the leaves
3.2.2. Stomata
3.2.2.1. Pores that aid in the flow of CO2 and O2
3.3. Light Reactions
3.3.1. Photosystem II
3.3.1.1. H2O is split
3.3.1.2. O2 is released
3.3.1.3. Excites electrons to produce ATP in electron transport chain
3.3.2. Photosystem I
3.3.2.1. Excites electrons to produce NADPH via electron transport chain
3.3.3. Non-cyclic vs Cyclic Electron Flow
3.3.3.1. Non-cyclic
3.3.3.1.1. AKA linear flow
3.3.3.1.2. Incorporates both photosystems and produces both ATP and NADPH
3.3.3.2. Cyclic
3.3.3.2.1. Photosystem I sends electrons back through the first electron transport chain to produce ATP
3.3.3.2.2. No NADPH produced
3.3.3.2.3. Photosystem II is not utilized
3.3.4. Photophosphorylation
3.3.4.1. ATP produced via ATP synthase
3.3.4.1.1. Powered by the electrochemical proton gradient
3.4. Calvin Cycle
3.4.1. Phase 1
3.4.1.1. Carbon fixation via enzyme Rubisco
3.4.1.2. Creates a 6 carbon intermediate
3.4.1.3. Split into two 3 carbon molecules
3.4.2. Phase 2
3.4.2.1. Reduction phase
3.4.2.2. A sugar is produced
3.4.3. Phase 3
3.4.3.1. Regeneration phase
3.4.3.2. The 5 carbon molecule CO2 acceptor is regenerated to restart the process
3.5. Alternative Methods
3.5.1. C3 Plants
3.5.1.1. Photorespiration
3.5.1.1.1. In the absence of CO2, O2 is fixated instead of CO2
3.5.1.1.2. CO2 is released and O2 is consumed
3.5.1.1.3. No ATP or sugar products created
3.5.2. C4/CAM
3.5.2.1. CO2 is fixated into 4 carbon molecules
3.5.2.2. Cell-Separation
3.5.2.2.1. Bundle-Sheath Cells
3.5.2.2.2. Mesophyll Cells
3.5.2.2.3. C4
3.5.2.2.4. CAM
4. DNA Replication (sammy)
4.1. semi conservative
4.1.1. One complete strand from parent DNA is conserved
4.2. enzymes/proteins involved and functions
4.2.1. Helicase
4.2.1.1. nwinds double helix at replication forks
4.2.2. SSB
4.2.2.1. protein binds and stabilizes DNA so it can be used as a template strand
4.2.3. Topoisomerase
4.2.3.1. relieves stress near replication forks
4.2.4. Primase
4.2.4.1. synthesizes RNA primer at 5’ end of leading strand and okazaki fragments and end of lagging strand
4.2.5. DNA pol 3
4.2.5.1. synthesizes new DNA template strand by adding nucleotides to the 3’ end of a pre-existing DNA strand or RNA primer
4.2.6. DNA pol 1
4.2.6.1. replaces RNA nucleotides from primer at 5’ end with DNA
4.2.7. DNA ligase
4.2.7.1. joins 3’ end of DNA that replaced primer and joins okazaki fragments of lagging strand
4.3. where it occurs
4.3.1. Prokaryotes-cytoplasm
4.3.2. Eukaryotes-nucleus
5. Cell Signaling(sammy)
5.1. signaling through signal molecules
5.1.1. with use of a signal molecule (polar/hydrophilic)
5.1.1.1. G protein receptor
5.1.1.1.1. response
5.1.1.1.2. transduction
5.1.1.1.3. reception
5.1.1.2. Tyrosine kinase receptor
5.1.1.2.1. Signal molecule binds to signal-binding site, creating dimers each containing 3 unphosphorylated tyr.
5.1.1.3. Ion channel receptor
5.1.1.3.1. a signal molecule (ligand) attaches itself to a Ion channel receptor, which opens the gate and allows for ions to pass through and triggering a cell response.
5.1.2. local signaling
5.1.2.1. paracrine signaling
5.1.2.1.1. cell produces a signal to induce changes in nearby cells, altering the behaviour of those cells
5.1.2.2. synaptic
5.1.2.2.1. only occurs between cells with the synapse between the cell originating and the cell receiving the signal
5.1.3. long-distance signaling
5.1.3.1. hormonal
5.1.3.1.1. long distance signaling often having to go through bloodstream
5.2. how cells communicate with each other
5.2.1. physical cell-to-cell interaction
5.2.1.1. cell-to-cell contact
6. Concept map
6.1. Arthur Williamson
6.1.1. Chemistry
6.1.2. Mitosis
6.2. Isac Dominguez
6.2.1. Respiration/Fermentation
6.2.2. Photosynthesis
6.3. Samuel Liu-zarzuela
6.3.1. DNA replication
6.3.2. Cell signaling
7. Water
7.1. High heat of vaporization
7.1.1. Change from liquid to gas
7.1.2. Without this property all the water in our cells would evaporate
7.1.3. The amount of energy needed to change 1 gram of substance into a gas at a constant temp
7.1.4. high humidity on a hot day prevents evaporation
7.2. Cohesion
7.2.1. The H bonds in water are strong and allow for a high water surface tension
7.3. High density
7.3.1. Water is denser as a liquid
7.4. High boiling point
7.4.1. The waters hydrogen bonds need a lot of energy to break
7.5. High specific heat
7.5.1. Can absorb a lot of energy before the bonds break due to H bonds
7.5.2. This is how oceans regulate heat
7.6. Adhesion
7.6.1. Water attaches itself to polar molecules over itself
7.6.1.1. this allows capillary action (water going up the plant) to occur when paired with the high cohesion properties
7.7. Hydration shells
7.7.1. Water molecules come between the two atoms of a molecule and separate it
7.8. universal solvent
7.8.1. uses hydration shell to do so
7.9. expansion upon freezing
8. Chemistry
8.1. Bonds
8.1.1. Intermolecular forces
8.1.1.1. Hydrogen bonds
8.1.1.1.1. Strong polar bonds between molecules
8.1.1.1.2. Only involve O, N, and F
8.1.1.2. Dipole dipoles
8.1.1.2.1. Bond formed through partial charges between molecules
8.1.1.3. Van Der walls
8.1.1.3.1. Short weak interactions between molecules
8.1.1.3.2. momentary dipole
8.1.1.4. Ion-ion interactions
8.1.1.4.1. Bond formed between ions
8.1.1.5. Ion-dipole
8.1.1.5.1. Bond formed between the partial charge if a dipole and a ion
8.1.1.6. Dipole
8.1.1.6.1. A partial charge due to the unequal electronegativity
8.1.2. Intramolecular forces
8.1.2.1. Polar
8.1.2.1.1. Unequal sharing of electrons between atoms with very different electronegativity
8.1.2.2. Non polar
8.1.2.2.1. sharing of electrons between atoms with equal electronegativity
8.2. Acid
8.2.1. substance that increases the H+ concentration of a solution
8.3. Base
8.3.1. Substance reduces the H+ concentration of a solution
8.4. Types of isomers
8.4.1. Structural
8.4.1.1. Different arrangements of their atoms
8.4.1.2. have the same atoms
8.4.2. Geometry
8.4.2.1. Same covalent arrangements but different in spacial arrangements
8.4.2.1.1. Cis isomer
8.4.2.1.2. Trans isomer
8.4.3. Enantiomers
8.4.3.1. mirror images of eachother
8.4.3.2. none of the 4 can have the same molecule
8.5. Functional Groups
8.5.1. hydroxyl
8.5.1.1. OH
8.5.2. carbonyl
8.5.2.1. >C=O
8.5.3. carboxyl
8.5.3.1. -COOH
8.5.4. amino
8.5.4.1. -NH2
8.5.5. sulfhydryl
8.5.5.1. -SH
8.5.6. phosphate
8.5.6.1. -OPO3
8.5.7. methyl
8.5.7.1. -CH3
9. Respiration and Fermentation (Isaac)
9.1. Redox Reactions
9.1.1. Transfer of electrons
9.1.2. Releases energy used to synthesize ATP
9.1.3. Oxidation
9.1.3.1. Substance loses electrons
9.1.4. Reduction
9.1.4.1. Substance gains electrons
9.2. Electron Shuttles
9.2.1. NAD+
9.2.2. FAD
9.3. Cellular Respiration
9.3.1. Glycolysis
9.3.1.1. Glucose => 2 Pyruvate
9.3.1.1.1. Step 1
9.3.1.1.2. Step 3
9.3.1.2. Use 2 ATP, Produce 4 ATP (Net 2 ATP)
9.3.1.3. Produce 2 NADH
9.3.2. Pyruvate Oxidation
9.3.2.1. 2 Pyruvate => 2 Acetyl CoA
9.3.2.2. Produces 2 NADH (one per pyruvate)
9.3.2.3. Produces CO2
9.3.3. Citric Acid Cycle
9.3.3.1. 2 Acetyl CoA enter
9.3.3.2. Produces 2 ATP
9.3.3.3. Produces 6 NADH
9.3.3.4. Produces 2 FADH2
9.3.4. Oxidative Phosphorylation
9.3.4.1. Produces 26 to 28 ATP
9.3.4.2. Electron Transport Chain
9.3.4.2.1. Consists of 4 complexes
9.3.4.2.2. Uses electrons from electron carriers (NADH and FADH2)
9.3.4.2.3. Creates proton gradient
9.3.4.3. Chemiosmosis
9.3.4.3.1. Creates ATP
9.3.4.3.2. Utilizes proton gradient as energy source
9.3.4.3.3. Protein called ATP synthase
9.4. Phosphorylation
9.4.1. Substrate-Level
9.4.1.1. An enzyme catalyzed, close proximity reaction to produce ATP
9.4.2. Oxidative
9.4.2.1. Gradient-driven, chemiosmotic production of ATP
9.5. Control of Respiration
9.5.1. Phosphofructokinase
9.5.1.1. ATP Inhibits
9.5.1.2. Citrate Inhibits
9.5.1.3. AMP Stimulates