BIO 2
1/11/23:
Binomial Nomenclature: The way we identify plants with two terms the first being genus and the second epithet.
Carolus Linnaeus published system of taxonomy based on resemblances.
The Epithet is unique for each species within genus
Both parts together name the species (not the epithet alone)
Hierarchical Classification
Linnaeus introduced a system for grouping species in categories
Broad to narrow groups are: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
The Energy of Life
Living cell is a miniature chemical factory where thousands of reactions occur
Cellular respiration extracts energy stored in sugars and other fuels.
Cells apply this energy to do work
Some organisms convert energy to light
Metabolism: the totality of an organisms chemical reactions
Metabolic pathway: begins with a specific molecule and ends with a product
Each step is catalyzed by a specific enzyme
Chemistry of Life
Catabolic pathways: release energy by breaking down complex molecules into simple compounds
Anabolic pathways: consume energy to build complex molecules from simpler ones
Energy
Is the capacity to do work
Energy exists in various forms: potential & kinetic energy
Kinetic: energy in motion
Potential: energy that matter possesses because of its location and structure.
1.13.22 Cellular Respiration and Fermentation Part 1
Cellular respiration: series of chemical reactions to break down glucose or sucrose to produce ATP.
Energy flows into an ecosystem as sunlight and leaves as heat.
Photosynthesis generates O2 and organic molecules, which are used for cellular respiration
Cells use chemical energy stored in organic material
Light Energy (sun) → Organic Molecules + 02 → Cellular respiration in mitochondria → Releases ATP and releases heat energy → Co2+ H20 → Ecosystem → back to light energy.
Organic molecules are very important because they come from the sun. The organic compounds (mostly glucose) break down either in the presence or absence of oxygen to release energy in ATP and produce water & carbon dioxide.
Catabolic pathways: release stored energy by breaking down complex molecules.
The breaking down of the molecules release ATP (exergonic)
Fermentation: is a partial degradation of sugars that occurs without 02
Aerobic respiration: consumes organic molecules and 02 yields ATP.
Anaerobic respiration: is like aerobic but consumes compounds other than O2.
Electron transfer: play a major role in these pathways.
Redox reactions: chemical reactions that transfer electrons between reactants
Some redox reactions: change the degree of electron sharing in covalent bonds
Oxidizing: to remove one or more electrons
Reduction: to gain one or more electrons
NAD+: used to extract electrons from organic compounds. NAD+ accepts an electron and becomes NADH which represents stored energy that is tapped to synthesize ATP.
NADH passes the electrons to the ETC. Then passes electrons in a series of steps instead of one explosive reactions.
O2 pulls electrons down the chain in an energy yielding tumble,
The energy yielded is used to generate ATP
O2 is able to pull more electrons due to its electronegativity.
3 Stages of Cellular Respiration
Glycolysis (break down glucose into two molecules of pyruvate)
The citric acid cycle (completes breakdown of glucose)
Oxidative phosphorylation (accounts for most of the ATP synthesis)
Cytosol through active transport needs energy to go inside the mitochondrion.
Substrate-level phosphorylation: process that generates 90% of the ATP because its powered by redox reactions.
Smaller amount of ATP is formed in glycolysis and the citric acid cycle by substrate-level phosphorylation.
1/18/23
What goes in comes out in the process of energy investment phase
Glucose → 2 Pyruvate + 2 H20
4 ATP formed - 2 ATP used → 2 ATP
2 NAD+ + 4e- + 4H- → 2 NADH + 2H+
Enzymes are necessary for reactions to speed up. They lower the activation energy so that it can start.
Glycolysis happens outside of the mitochondria → Pyruvate Oxidation → Citric Acid Cycle → Oxidative Phosphorylation (needs 02 to yield tumble).
Pyruvate oxidation to acetyl coenzyme A is carried out by a multienzyme complex that catalyzes 3 reactions.
- Oxidation of Pyruvate and release of CO2
- Reduction of NAD+ to NADH
- Combination of the remaining two-carbon fragment and coenzyme A to form acetyl CoA
Citric Acid Cycle/ Krebs Cycle- Oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH, and 1 FADH2 per turn - later fed into electron energy chain.
Citric acid cycle has 8 Steps each catalyzed by a specific enzyme.
The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate
Next seven steps decompose the citrate back to oxaloacetate making the process a cycle.
NADH and FADH2 produced by cycle relay electrons extracted from food to the electron transport chain.
Cellular respiration can create carbon skeletons for other organisms
After glycolysis and the citric acid cycle, NADH and FADH2 account for most of the energy extracted
These two electron carriers donate electrons to the transport chain, which powers ATP synthesis
It breaks the large free-energy drop from food to O2 into smaller steps that release energy in manageable amounts.
Chemiosmosis: The Energy-Coupling Mechanism
Energy released as electrons pass down the electron chain is used to pump H+ from the mitochondrial matrix to the intermembrane space
H+ then moves down its concentration gradient back across the membrane, passing through protein complex ATP synthase.
Protein will pass from higher concentration to lower concentration.
proton-motive force, H+ gradient in the electron transport chain
Energy stored in H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis
Cellular respiration energy flow: glucose → NADH → Electron → transport chain → proton motive force → ATP
Energy that is not used s lost as heat energy.
Fermentation consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis. (alcohol fermentation and lactic acid fermentation)
Fermentation has no electron transport chain involved.
ATP yield per glucose molecule
32 for Cellular respiration
2 for fermentation
1.20.23
Photosynthesis Feeds the biosphere
Photosynthetic organisms contain organelles called chloroplasts
Photosynthesis is the process that converts solar energy into chemical energy within chloroplasts
Autotrophs are "self-feeders”
Autotrophs are the producers of biosphere
Almost all plants are photoautotrophs using the energy of sunlight to make organic molecules
Leaves are the major sites of photosynthesis in plants
Chloroplasts are found mainly in cells of mesophyll
Co2 enters and O2 exits the leaf through microscopic pores called stomata
Thylakoids: sacs in chloroplast that compose a third membrane system
Chlorophyll resides in the thylakoid membranes
The direct product of photosynthesis is glyceraldehyde 3-phosphate
Chloroplasts Split H20 into hydrogen and oxygen, incorporating the electrons of hydrogen into sugar molecules and releasing oxygen.
Photosynthesis reverses the direction of electron flow compared to respiration
Photosynthesis consists of light reactions and Calvin Cycle
Light reactions: split h20 release o2 reduce the electron acceptor NADP+ to NADPH, Generate ATP from ADP by photophosphorylation
Calvin Cycle: forms sugar from Co2, using ATP and NADPH,
Calvin Cycle begins with carbon fixation incorporating Co2 into organic molecules
Light is electromagnetic energy/radiation that travels rhythmic waves
Wavelength is the distance between crests of electromagnetic waves and it determines the type of electromagnetic energy
Pigments are substances that absorb visible light
wavelengths that are not absorbed are released
spectrophotometer measures a pigment’s ability to absorb light of various wavelengths
1.23.23- Photosynthesis Part 11-Light Reactions
Pigments are important because they absorb the light energy.
Chlorophyll A has a CH3 group change in structure change in function
Chlorophyll B has a CHO group change in structure change in function
Carotenoids- accessory pigments that broaden the spectrum of colors that drive photosynthesis.
Some carotenoids function in photoprotection, they absorb excessive light that would damage chlorophyll or react with oxygen.
When a pigment absorbs light it goes from ground to excited state which makes them unstable. They quickly fall to ground state releasing heat energy.
The energy is also released as fluorescence.
Photosystem consists of a reaction-center complex surrounded by light-harvesting complexes
reaction-center complex is a protein complex holding a special pair of chlorophyll a molecules and a primary electron acceptor
Photosystem 2 function first and has P680
Photosystem 1 functions last and has P700
Linear electron flow, the primary pathway, involves photosystems and produces ATP and NADPH using light energy.
Cyclic electron flow, photoexcited electrons flow back from FD to the PS 1 reaction center via a plastocyanin molecule it produces ATP, but not NADPH. No Oxygen is released.
1.25.23
Water must be split in photosynthesis to allow electrons to continue in the cycle. it also releases O2.
Living stones ~37 Species (in 98 varieties and forms) in genus Lithops
Chloroplasts and mitochondria generate ATP by chemiosmosis but use different sources of energy
ATP is taken out of the thylakoid space to the Stroma where the Calvin cycle can take place.
Carbon enters the cycle as Co2 and leaves as a sugar named G3P
The Calvin Cycle- has three faces. 1 Carbon fixation 2. Reduction 3. Regeneration of the Co2 Acceptor
To make 1 G3P need 3 Co2 molecules and 1 krebb cycle.
In some weather conditions plants will close their stomata
The closing of stomata reduces access to CO2 and causes O2 to build up-favor photorespiration
Photorespiration- add O2 to RuBP via Rubisco allowing the the Calvin Cycle to produce a two-carbon compound.
PR limits damaging products of light reactions that build up in the absence of the Calvin Cycle
C4 plants minimize the cost of photorespiration by incorporation CO2 in to 4 carbon compounds.
Bundle-Sheath cells- tightly packed sheaths around veins of leaf
Mesophyll cells- loosely packed between bundle sheath
CO2→ PEPC → 4C → Pyruvate → Bundle Sheath cell → Calvin Cycle→ Sugar → Vascular tissue
CAM plants- open stomata at night, incorporating Co2 into organic acid stored in vacuoles
Stomata close during the day and Co2 is released from organic acids and used in the Calvin Cycle
C4 pathway are structurally separate
CAM pathways are separate by temperature