Study Guide 3 (Thur 3/27)

1. What is ATP? What is ATP hydrolysis?

• ATP (Adenosine Triphosphate): Cell’s energy currency. Composed of ribose (sugar), adenine (base), and three phosphate groups.

• ATP Hydrolysis: Releases energy by breaking a phosphate bond (ATP → ADP + Pi).(pi is an inorganic phosphate)

• assembles polymers, membrane transport (facilitated diffusion), and moving and reproducing.

2. What is energy? What are the different types/forms of energy?

Energy is the ability to do work or capacity to cause change

• Kinetic Energy: Energy associated with motion.

• Potential Energy: Stored energy based on position or structure.

• Thermal Energy: Kinetic energy of atoms or molecules in motion.

• Heat: Transfer of thermal energy between objects.

• Chemical Energy: Potential energy for release in chemical reactions. (food)

3. Endergonic Reactions and Exergonic reactions. Breaking bonds vs. Building bonds (energy requirements)

• Negative - ΔG: Spontaneous reaction (exergonic, releases energy). broken bonds= releasing energy, from polymers to monomers

• Positive + ΔG: Non-spontaneous reaction (endergonic, requires energy) from monomers to polymers.

• Endergonic Reactions build bonds and require energy and is nonspontaneous

• Exergonic Reactions break bonds and release energy, no external energy input. spontaneous

4. Entropy? Activation energy? Catalyst?

• Second Law of Thermodynamics (Entropy Increase): Energy transfer increases disorder/chaos, with some energy lost as heat. (aka entropy)

• Activation Energy (E_a) is the initial energy required to start a reaction. Has to be less than or equal to energy being released.

• Catalysts: Speed up reactions by lowering activation energy

• Entropy randomness/chaos

5. Active site, allosteric site, and inhibitors. Metabolism, catabolism vs anabolism.

• Active Site: The region on an enzyme where substrate molecules bind and undergo a chemical reaction.

• Allosteric Site/Regulation: Molecule binds to a site other than the active site to activate/inhibit enzymes.

• Metabolism is the totality of an organism’s chemical reactions.

• Inhibitors: molecules that reduce or prevent enzyme activity by binding to the active site. (stops chemical reaction)

  • Competitive Inhibitor: Binds and blocks active site to prevent substrates from completing chemical reaction.

  • Noncompetitive Inhibitor: Binds at allosteric site, altering enzyme shape.

• Catabolism - releases energy by breaking bonds of complex molecules to simpler molecules.

  • Example: Cellular Respiration, digestion

• Anabolism—consumes energy to build complex molecules/bonds from simpler molecules

  • Example: Building the proteins of muscles by joining
    together of amino acids. and photosythesis

• How Enzymes Work:

  • Bind to substrates at the active site. (where reaction

  • Lower activation energy.

  • Follow an induced fit model /ER complex (enzyme shape adjusts to fit the substrate).

  • Product is then created and enzyme separates and is free to do it all again.

6. Oxidation/Reduction reactions. Hydrolysis? Decarboxylations? Laws of
Thermodynamics?

Thermodynamics: Study of energy transformations.

• First Law of Thermodynamics (Conservation of Energy): Energy cannot be created or destroyed, only can be transferred or converted to a different energy.

• Second Law of Thermodynamics (Entropy Increase): Energy transfer increases disorder/chaos (entropy), with some energy lost as heat.

• Hydrolysis: breaking bonds with water

• Decarboxylation: Losing carbon dioxide (CO₂)

• Oxidation is when you lose electrons.

• Reduction is when you gain electrons.

• Phosphorylation: The addition of a phosphate group to a molecule, often activating or deactivating its function.

• ATP stands for Adenosine Triphosphate

• ADP stands for Adenosine Disphaosphate

• ATP Hydrolysis: happens when energy is released by breaking a phosphate bond (ATP → ADP + Pi).

• PI are inorganic phosphates

Electron transfer releases energy used for ATP synthesis. It transfers through redox reactions.

• Molecule/electron donor that loses an electron is the reducing agent and molecule/electron receptor that gains an electron is the oxidizing agent. It’s called reducing because wit gains an electron.

(when you give, you are the reducer. when you gain you’re the oxidizer)

7. Compare autotrophs, phototrophs, and heterotrophs.

• Autotrophs - Plants produce their food by photosynthesis (producers).

• Fungi absorb nutrients (decomposers/also applies to bacteria).

• Phototrophs are organisms that use light energy to produce organic compounds and carry out cellular processes. (bacteria, plants, and algae) 

• Heterotrophs: Animals ingest their food (consumers).

  • We have to get our food elsewhere, cannot make it ourselves

8. What is the formula for calculating the Free energy of a chemical reaction?
Determine if a reaction will be spontaneous or non-spontaneous if given
the energy profile of that reaction?

• ΔG is free energy change

• Formula for free energy change is ΔG = ΔH - TΔS

• Negative - ΔG: Spontaneous reaction, exergonic

• Positive + ΔG: Non-spontaneous reaction, endergonic

9. What is the notion of energy coupling?

Energy Coupling is when one reaction provides an exergonic reaction (ATP breakdown) to drive another endergonic reaction. (exergonic energy supporting endergonic reaction)

10. What are kinases? What are phosphatases?

• Kinase is an enzyme that adds phosphates to a molecule.

• Phosphatases remove phosphate groups from a molecule.

11. What makes an enzyme a catalyst? What does it do to the chemical
reaction?

An enzyme is a catalyst because it lowers a reactions’ activation energy and as a result, speeds up the reaction.

12. What conditions may affect the function of an enzyme?

• Temperature

• pH

• inhibitors

• activators

13. What is feedback inhibition?

Feedback Inhibition is the end product of a pathway that inhibits an earlier enzyme, preventing wasteful overproduction.

For example, if you take vitamins and your body no longer needs to produce them because you have enough, there will be too much.

14. Know the formula for cellular respiration and photosynthesis.

• Photosynthesis occurs in the chloroplasts of plant cells converting light energy from the sun to chemical energy/glucose in the leaves of a tree.

  • Photosynthesis formula: CO₂ + H₂O + light energy _———> C₆H₁₂O₆ + O₂

(Carbon dioxide + water + light energy = glucose + oxygen)

(substrates/reactants) —→ (products)

• Cellular respiration occurs in the mitochondria, converting chemical energy (glucose) to cellular energy (ATP).

  • Cellular respiration formula: C₆H₁₂O₆ + O_{2 ———>} CO₂ + H₂O + ATP

glucose + oxygen = Carbon dioxide + water + cellular energy (ATP)

(substrates/reactants) —→ (products)

15. Know the different biochemical pathways for cellular respiration (glycolysis,
pyruvate oxidation, Krebs cycle, and Electron transport chain/chemiosmosis) and where do they take place in the cell. Know the substrates for starting each reaction and the products.

• Biochemical Pathways:

  • Glycolysis - occurs in the cytoplasm -

    • Substrates: Glucose and ATP

    • Products: Pyruvate, ATP, NADH and H₂O

  • Pyruvate Oxidation - loses electrons, occurs in mitochondria

    • Substrates: pyruvate and Coenzyme A

    • Products: CO₂, NADH, Acetyl CoA

  • Kerbs Cycle (AKA citric acid cycle) - occurs in the mitochondria matrix (the cytoplasm of the mitochondria).

    • Substrates: Acetyl CoA

    • Products: ATP, CO₂, NADH and 1 FADH₂

  • Electron transport Chain- electrons being passed from protein to protein, producing ATP through oxidative phosphorylation.

    • occurs in the inner membrane of the mitochondria,

    • pumps out hydrogen portions to the inner membrane space

    • Substrates: NAHD, Oxygen,FADH2

    • Product: water and ATP

  • Chemiosmosis/electron transfer chain: the transport of hydrogen protons across the membrane that produces ATP.

    • ATP Synthase - the part that pumps hydrogen protons across the membrane, turning ADP to ATP.

electron transport chain and chemiosmosis are one reaction just the two steps

*Energy investment (gross) = amount of energy required to start breaking bonds

*Energy payoff (net) = amount of energy left over after the energy investment has been accounted for, resulting in the total ATP gain from the process.

1. Glycolysis

• Occurs in cytoplasm, whether or not O₂ is present!!! Breaks glucose into pyruvate.

• Substrates are glucose, ATP

• Products are pyruvate, ATP, NADH and H₂O.

• Energy Investment: Uses 2 ATP.

• Energy Payoff: Net gain = 2 ATP. Produces 4 ATP, 2 NADH, and 2 pyruvate.

2. Pyruvate Oxidation

• Occurs in mitochondria in eukaryotic cells (only can occur with O₂/oxygen present).

• Converts/oxidizes pyruvate by releasing CO₂ and producing NADH then adding Coenzyme A to make → Acetyl CoA.

  • Substrates: pyruvate and Coenzyme A.

  • Products: CO₂, NADH and Acetyl CoA.

3. Citric Acid Cycle aka Krebs Cycle

• Occurs in mitochondria - completes the breakdown of pyruvate to CO_2. Only can occur with oxygen!

• Process is as follows:

  • Oxaloacetate and acetyl-CoA combine to form Citrate.

  • Decomposing/oxidizing citrate back to oxaloacetate to continue the cycle.

  • As a result, oxidation reactions generate NADH and FADH₂.

• The substrate is Acetyl CoA.

• Products are ATP, CO₂, NADH, and FADH₂.

4. Oxidative Phosphorylation (90% of ATP Production) - all stages

• Electron Transport Chain (ETC):

  • Located in the inner mitochondrial membrane, it can only occur with oxygen.

  • Electrons from NADH reduces Complex I and FADH₂ reduces Complex II move through protein complexes, donating electrons to the Electron Transport Chain (ETC).

  • The final electron acceptor is O₂, forming H₂O.

• Chemiosmosis:

  • H⁺ ions are pumped into the inner membrane during the chain, creating a gradient (proton-motive force).

  • H⁺ flows back to the outer membrane via facilitated diffusion via the protein ATP synthase, generating ATP.

  Total ATP yield:

  • Glycolysis: ~2 ATP

  • Krebs Cycle: ~2 ATP

  • Oxidative Phosphorylation: ~26-28 ATP

  • Total ATP per glucose: ~32 ATP

16. Know the electron carriers of cellular respiration and photosynthesis and
when they are produced.

• Cellular Respiration Electron Carriers

  • NADH is produced in glycolysis, pyruvate oxidation and krebs cycle.

  • FADH₂ is produced during the Krebs cycle only, FADH2 serves as an electron carrier that donates electrons to the electron transport chain.

• Photosynthesis electron carriers

  • NADPH is produced

Order Photosynthesis Electron Transport Chain:

• Light comes in hitting Chlorophyll A & B and Carotenoids.

• Energy is transferred to an electron from the Reaction Center to the electron center.

• Moves from photosystem 2 to Plastoquinone.

• Passes to the cytochrome complex BCF.

• Then, it passed to Plastocyanin.

• Makes its way to Photosystem 1.

• Then to Ferredoxin to NADP Reductase.

• Finally the NADPH. final electron acceptor

17. Know aerobic respiration vs anaerobic respiration vs fermentation.

• Aerobic respiration is a process of oxidizing(breaking bonds) glucose to produce ATP with the final acceptor being organic.

• Anaerobic breaks down glucose to great ATP with the final electron accepted being inorganic

• Fermentation is a type of anaerobic process that breaks down sugars (still goes through glycolysis).

• The 2 Types of Fermentation:

  • Alcohol fermentation (yeast & bacteria) – Converts pyruvate to ethanol in two steps.

    • First, it releases CO₂ through decarboxylation, then produces NAD+ and ethanol.

    • yeast

  • Lactic acid fermentation (fungi, muscle cells, and bacteria): NADH reduces pyruvate by giving it electrons, resulting in lactate, which produces lactic acid.

    • humans go through

      For example, when your cells frun out of oxygen it creates lactic acid fermation.

  • The difference between the two types:

    • Yeast has DNA that human cells don’t, so they can carry out decarboxylation. Human cells lack this ability, which is why they rely on lactic acid fermentation instead.

18. Know the enzymes/electron carriers of ETC/Chemiosmosis of both
photosynthesis and cellular respiration. (is this a repeat of #16 or not? Do we need to know the enzymes of each complex?)

Enzyme/Electron Carriers of ETC/Chemiosis: in order

1. Complex I - NADH dehydrogenase

2. Complex II - Succinate dehydrogenase

3. Q Enzyme

4. Complex III - Cytochrome bc₁ complex

5. Cytochrome C

6. Complex IV - Cytochrome c oxidase

Photosynthesis enzymes in order

1. Photosystem II (can oxidize water)

2. Plastoquinone

3. Cytochrome complex bcf

4. Plastocyanin

5. Photosystem I

6. Ferredoxin

7. NADP+ reductase

19. Know the different structures of a leaf and the chloroplast.

• Leaf structure:

  • Stomata: tiny openings on the leaf's surface that facilitate gas exchange, allowing carbon dioxide to enter and oxygen to exit during photosynthesis.

• Chloroplast structure:

  • Thylakoids: membrane-bound sacs where the light-dependent reactions happen; these disc-like stacks are known as grana.

  • Stroma: a semi-fluid surrounding thylakoids where light-independent reactions (Calvin cycle) take place.

  • Chlorophyll: the pigment located within the thylakoid membranes that captures light energy.

20. Define photons. What are pigments? What are the colors of the light
    spectrum?

    • photons: small bundles of light energy

    • Pigments: living organisms that contain chlorophyll and other pigments

      • all pigments absorb light energy

      • and absorb wavelengths of light to convert solar energy into chemical energy.

    • Colors of light spectrum: ROYGBIV

      • Geen reflects energy in plants - red, orange, yellow, blue, and indigo. and violet absorbs energy

      • In white – all colors are reflected – no energy is absorbed.

      • In black – all colors are absorbed – all energy is absorbed.

      • The color you see in an item is reflected; the ones you don’t see are absorbed.

21. Know the difference between Light-dependent and Light-independent
reactions. What happens in each stage?

• Light Dependent Reaction:

  • captures light energy and converts it into ATP and NADPH (light energy to chemical energy)

  • Water is split to release electrons (which is called oxidation) and produce oxygen

  • pumps out hydrogen proteins from the stroma into the thyokoids

  • ATP synthase pumps out the hydrogen protons across the membrane and produces ATP

  • assists light-independent reactions

• Light Independent reaction:

• An endergonic Reaction that drives the completion of the endergonic process is called Energy Coupling.

  • requires light energy

  • uses ATP and NADPH to convert CO2 into glucose

  • carbon fixation occurs via the enzyme rubisco (combines CO2 with ribulose/RuBP

  • CO2 is used to make C₆ H₁₂ O₆ (glucose and other carbs).

  • Goes from a one-carbon molecule (CO2) to a six-carbon molecule (C6H12O6 glucose).

    22. What pigments are found in green plants?

• Chlorophyll A - main pigments

• chlorophyll B - accessory pigment

• Carotenoids - accessory pigment

23. Know the different proteins that participate in the Electron Transport Chain
in the Light-dependent reactions.

Proteins in Light Dependent Reactions:

• Photosystem II (can oxidize water)

• Plastoquinone

• Cytochrome complex bcf (BeCause Fuck)

• Plastocyanin

• Photosystem I

• Ferredoxin

• NADP+ reductase

24. What is the role of the Calvin Cycle? What are the three phases? What is
carbon fixation?

• The Calvin Cycle converts carbon dioxide into glucose.

• The three phases of the Calvin Cycle are:

1. Carbon fixation - adding smaller carbon compounds to make larger carbon compounds

2. Reduction - Adding CO2

3. Regeneration of RuBP

   
   25. What enzyme is responsible for beginning the Calvin Cycle?

Rubisco 9Rubp combined with CO2)

26. How does CO2 contribute to Climate Change, and how do trees help
prevent this from occurring?

• CO2 contribution to climate change:

  • Increasing CO2 levels, like fossil fuel combustion and deforestation, are major contributors to climate change

• temperatures rise

• the sun's radiation gets trapped in the atmosphere and gets stored by greenhouse gases.

• Prevention:

  • Trees absorb CO2 during photosynthesis, effectively reducing the amount of greenhouse gases in the atmosphere and helping mitigate the effects of climate change.

Photophosphorylation - ATP production resulting from the capture of light energy by chlorophyll

• energy is finite, not infinite