bio 2 exam

Kinetic Energy:

The energy of motion (e.g., thermal energy, light/photons, movement of molecules across a membrane).

Potential Energy:

Stored energy based on location or structure (e.g., chemical energy stored in covalent bonds of glucose or ATP; concentration gradients across a membrane).

First Law (Law of Conservation of Energy):

Energy cannot be created or destroyed; it can only change form.

• Example: Plants convert radiant solar energy into chemical energy in glucose; muscles convert chemical energy from ATP into kinetic mechanical energy.

Second law

Every energy transfer or transformation increases the entropy (disorder/randomness) of the universe. No energy conversion is 100% efficient; some energy is always lost as non-usable heat.

• Example: As you exercise, your cells break down glucose to do mechanical work, releasing body heat into the surrounding environment.

High Entropy:

Disordered, dispersed, simple structures (e.g., individual CO2 and H2O molecules floating freely; high temperature).

low Entropy:

Highly ordered, organized, complex structures (e.g., a glucose molecule held together by tight covalent bonds; a steep ion gradient across a membrane).

Metabolism:

The sum total of all chemical reactions that occur within an organism.

Anabolic Pathways:

Synthesize complex molecules from simpler ones. Require energy input (endergonic). Example: Photosynthesis, protein synthesis.

Catabolic Pathways:

Break down complex molecules into simpler ones. Release energy (exergonic). Example: Cellular respiration, digestion.

Endergonic Reactions

-Absorbs/requires free energy (Delta G > 0)

-Non-spontaneous

-Products have more potential energy than reactants

-Anabolic (Building)

Exergonic Reactions

-Releases free energy (Delta G < 0)

-Spontaneous

-Products have less potential energy than reactants

-Catabolic (Breaking down)

Endergonic Graph:

Starts low on the Y-axis (Energy) and ends high. The line goes UP overall from reactants to products.

Exergonic Graph:

Starts high on the Y-axis and ends low. The line goes DOWN overall from reactants to products.

Activation Energy (Ea):

The initial energy hump required to start both types of reactions.

ATP

Adenine base + Ribose sugar + 3 Phosphate groups Pi.

Hydrolysis (Exergonic):

ATP + H_2O ——→ADP + Pi + Free Energy (cleaving the terminal high-energy phosphate bond releases energy).

Synthesis/Phosphorylation (Endergonic):

ADP + Pi + Energy——>ATP + H_2O (energy from food or sunlight builds ATP back up).

• exergonic and endergonic

• coupled reactions

• An x reaction (usually ATP hydrolysis) is paired directly with an x reaction so the overall net free energy change ($\Delta G$) remains negative/spontaneous.

• Example: Sodium-Potassium Pump ($Na^+/K^+$ ATPase). The hydrolysis of ATP transfers a phosphate group (energy) to the channel protein, changing its shape to pump $Na^+$ out against its gradient.

Function of Enzymes:

Biological catalysts (proteins) that speed up chemical reactions by lowering the activation energy ($E_a$). They do not change the overall $\Delta G$ of a reaction.

induced fit model

Substrates bind to the enzyme's active site forming an enzyme-substrate complex

Competitive Inhibition:

The inhibitor directly mimics the substrate and binds to the active site, blocking substrate access. High substrate concentrations can overcome this type of inhibition.

• Non-Competitive (Allosteric) Inhibition:

• The inhibitor binds to an allosteric site (a location other than the active site), causing a conformational shape change in the active site so the substrate can no longer fit. Increasing substrate concentration does not reverse this effect

Feedback Inhibition:

The final end product of a metabolic pathway binds to and inhibits an early enzyme in the pathway, preventing overproduction.

denature

Every enzyme has an optimal temperature and pH range. Beyond these ranges, hydrogen bonds break, causing the enzyme to x (lose shape and function).

Substrate Concentration:

Rate of reaction increases as substrate is added until saturation is reached (all active sites are occupied, hitting V_max).

celluar respiration goal

Extract chemical potential energy stored in organic molecules (glucose) to synthesize ATP for cellular work.

cellular respiration equation

$$\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2O + \sim 30\text{--}32\text{ ATP}$$

• Organisms that Perform Respiration:

• All eukaryotes (plants, animals, fungi, protists) and prokaryotes (prokaryotes perform it across their plasma membrane/cytoplasm).

Step 1: Glycolysis

• Location:

• Cytoplasm (Cytosol).

tep 1: Glycolysis

• Process:

• Anaerobic breakdown of 1 glucose (6C) into 2 pyruvate (3C).

Step 1: Glycolysis

• Inputs:

1 Glucose, 2NAD^+, 2 ADP + 2Pi

Step 1: Glycolysis

• Outputs:

• 2 Pyruvate, 2 NADH, 2 ATP (net, via substrate-level phosphorylation).

Step 1: Glycolysis

• Destination of Products:

• Pyruvate and NADH move to the mitochondria; ATP is used immediately by the cell.

Step 1: Glycolysis

• Redox:

• Glucose is partially oxidized; NAD^+ is reduced to NADH.

Step 2: Pyruvate Oxidation (Transition Step)

• Location:

• Mitochondrial Matrix.

Step 2: Pyruvate Oxidation (Transition Step)

process

2 Pyruvate molecules are converted into 2 Acetyl-CoA (2C).

Step 2: Pyruvate Oxidation (Transition Step)

• Inputs:

• 2 Pyruvate, 2NAD^+, 2 Coenzyme A.

Step 2: Pyruvate Oxidation (Transition Step)

• Outputs:

• 2 Acetyl-CoA, 2CO_2, 2 NADH.

Step 2: Pyruvate Oxidation (Transition Step)

Destination of Products:

Acetyl-CoA enters the Citric Acid Cycle; $CO_2$ diffuses out as waste; NADH goes to Electron Transport Chain (ETC).

Step 2: Pyruvate Oxidation (Transition Step)

• Redox:

• Pyruvate is oxidized; NAD^+ is reduced to NADH.

Step 3: Citric Acid Cycle (Krebs Cycle)

• Location:

• Mitochondrial Matrix.

Step 3: Citric Acid Cycle (Krebs Cycle)

• Process:

• Complete breakdown of acetyl groups into carbon dioxide. Runs twice per glucose molecule.

Step 3: Citric Acid Cycle (Krebs Cycle)

inputs

2 Acetyl-CoA, 6NAD^+, 2FAD, 2 ADP + 2Pi

Step 3: Citric Acid Cycle (Krebs Cycle)

output

4CO2, 6 NADH, 2 FADH2, 2 ATP (via substrate-level phosphorylation).

Step 3: Citric Acid Cycle (Krebs Cycle)

Destination of Products:

CO2 is released as waste; NADH and FADH_2 transport electrons to the ETC; ATP is used by the cell.

Step 3: Citric Acid Cycle (Krebs Cycle)

redox

Acetyl group is fully oxidized to $CO_2$; $NAD^+$ and FAD are reduced to NADH and $FADH_2$.

Step 4: Oxidative Phosphorylation (ETC & Chemiosmosis)

• Location:

• inner Mitochondrial Membrane (Cristae).

Step 4: Oxidative Phosphorylation (ETC & Chemiosmosis)

process

NADH and $FADH_2$ donate high-energy electrons to the ETC. As electrons move down the chain, $H^+$ ions are pumped into the intermembrane space, creating a proton gradient. $H^+$ flows back into the matrix through ATP Synthase (Chemiosmosis) to generate ATP.

Step 4: Oxidative Phosphorylation (ETC & Chemiosmosis)

inputs

0 NADH, 2FADH2, 6O_2, ~ 26-28 ADP + Pi

Step 4: Oxidative Phosphorylation (ETC & Chemiosmosis)

outputs

~26-28 ATP, 6H_2O, 10NAD^+, 2FAD.

Step 4: Oxidative Phosphorylation (ETC & Chemiosmosis)

Destination of Products:

ATP Powers cellular work; H_2O is metabolic waste; NAD^+ and FAD recycle back to earlier steps.

Step 4: Oxidative Phosphorylation (ETC & Chemiosmosis)

redox

NADH and FADH_2 are oxidized; O_2 is the final electron acceptor and gets reduced to H_2O.

Anaerobic Respiration:

Used by certain prokaryotes in oxygen-deprived environments; utilizes an ETC with an alternative final electron acceptor (e.g., $SO_4^{2-}$, $NO_3^-$).

Fermentation:

Operates when $O_2$ is absent. Allows Glycolysis to continue making 2 ATP by recycling NADH back to $NAD^+$.

Lactic Acid Fermentation:

Pyruvate is reduced directly by NADH to form Lactate (occurs in animal muscle tissue, yogurt cultures).

Alcohol Fermentation:

Pyruvate is converted into Ethanol and CO_2 (occurs in yeast).

photosynthesis goal

Convert solar energy into stored chemical energy in carbohydrate molecules (G3P/Glucose).

photosynthesis equation

$$6\text{CO}_2 + 6\text{H}_2O + \text{Light Energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$$

Organisms that Perform Photosynthesis:

Photoautotrophs (plants, algae, cyanobacteria).

chlorophyll harvest soloar energy by

Pigments in the thylakoid membranes absorb specific wavelengths of light (blue/red) and reflect green light. Excited electrons are passed to a primary electron acceptor in Photosystem II and Photosystem I.

Step 1: Light-Dependent Reactions

• Location:

• Thylakoid Membrane (inside the Chloroplast).

Step 1: Light-Dependent Reactions

process:

• Light energizes electrons in Photosystem II (PSII). Water photolysis splits $H_2O$ to replace lost electrons, releasing $O_2$. An ETC creates a proton gradient across the thylakoid membrane to drive ATP Synthase. Photosystem I (PSI) re-energizes electrons to reduce $NADP^+$ to NADPH.

Step 1: Light-Dependent Reactions

inputs

Light Energy, H_2O, NADP^+, ADP + Pi

Step 1: Light-Dependent Reactions

outputs

O2, NADPH, ATP

Step 1: Light-Dependent Reactions

Destination of Products:

O2 diffuses out of stomata into the atmosphere; ATP and NADPH move to the Stroma for the Calvin Cycle.

Step 1: Light-Dependent Reactions

redox

H_2O is oxidized into O_2; NADP^+ is reduced to NADPH.

Step 2: Calvin Cycle (Light-Independent / Dark Reactions)

• Location:

• Stroma (fluid inside Chloroplast).

Step 2: Calvin Cycle (Light-Independent / Dark Reactions)

process

• Carbon Fixation: $CO_2$ is attached to RuBP by the enzyme RuBisCO.

• Reduction: ATP and NADPH reduce 3-PGA to form high-energy G3P molecules.

• Regeneration: Remaining G3P molecules use ATP to regenerate RuBP.

Step 2: Calvin Cycle (Light-Independent / Dark Reactions)

inputs

CO_2, ATP, NADPH.

Step 2: Calvin Cycle (Light-Independent / Dark Reactions)

outputs

G3P (precursor to Glucose), ADP + Pi, NADP^+

Step 2: Calvin Cycle (Light-Independent / Dark Reactions)

Destination of Products:

G3P forms glucose/sucrose; ADP and NADP^+ recycle back to the Light Reactions.

Step 2: Calvin Cycle (Light-Independent / Dark Reactions)

redox

CO_2 is reduced to form sugars; NADPH is oxidized to NADP^+

Cellular Respiration

-Breakdown sugar to extract energy (ATP)

-Exergonic ($\Delta G < 0$), Catabolic

-Cytoplasm & Mitochondria

-NAD^+ / NADH and FAD / FADH_2

-O_2 (forms H_2O)

-Products of respiration ($CO_2, H_2O$) are reactants for photosynthesis!

Photosynthesis

-Capture light energy to synthesize sugar

-Endergonic ($\Delta G > 0$), Anabolic

-Chloroplasts

-NADP^+ / NADPH

-NADP^+ (forms NADPH)

-Products of photosynthesis (O_2, Glucose) are reactants for cellular respiration!

Direct Cell Communication

Physical connections allowing cytosol and signaling molecules to pass freely between neighboring cells without crossing membranes

• Plasmodesmata

• Plant Cells

• Microscopic channels passing through cell walls that physically connect adjacent plant cells.

Gap Junctions

Animal Cells

Protein channels (made of connexins) connecting adjacent animal cells for rapid chemical and electrical communication (e.g., cardiac muscle synchronizing heartbeats).

Autocrine Signaling:

A cell targets itself by secreting a signal that binds to its own receptors.

Example: Cancer cells releasing growth factors to self-stimulate replication; immune T-cells releasing interleukins.

Paracrine Signaling:

Signals target nearby cells through diffusion across local extracellular space.

Example: Neurotransmitters diffusing across a synaptic cleft; inflammatory response via histamine.

Endocrine Signaling:

Signals (hormones) travel long distances through the bloodstream to reach target cells throughout the body. Example: Insulin released by pancreas regulating blood sugar in liver and muscle cells.

Direct Signaling Across Plasma Junctions:

Signaling via direct contact (e.g., cell-cell recognition via surface proteins in immune responses).

Membrane-Bound Receptors (Hydrophilic / Water-Soluble Signals)

• Signal Characteristics

Large or polar molecules (e.g., peptide hormones like Insulin, Epinephrine) that cannot cross the hydrophobic phospholipid bilayer.

Membrane-Bound Receptors (Hydrophilic / Water-Soluble Signals)

• Mechanism

1. Signal acts as a first messenger and binds to an extracellular domain of a membrane receptor (e.g., G-Protein Coupled Receptor - GPCR, Receptor Tyrosine Kinase).

2. Receptor undergoes a conformational shape change, activating intracellular pathways.

3. Triggers a Signal Transduction Cascade utilizing second messengers (e.g., $cAMP$, $IP_3$, $Ca^{2+}$) and protein kinases (phosphorylation cascades).

4. Response: Rapid, short-term cellular response (e.g., enzyme activation, opening ion channels).

Cytosolic / Intracellular Receptors (Hydrophobic / Lipid-Soluble Signals)

• Signal Characteristics:

• Small or nonpolar molecules (e.g., steroid hormones like Estrogen, Testosterone, Cortisol) that easily cross the lipid bilayer.

Cytosolic / Intracellular Receptors (Hydrophobic / Lipid-Soluble Signals)

• Mechanism:

1. Hormone diffuses directly across the plasma membrane into the cytoplasm/nucleus.

2. Binds to a cytosolic or nuclear receptor to form a Hormone-Receptor Complex.

3. The complex translocates into the nucleus and acts directly as a transcription factor.

4. Response: Binds to specific DNA promoter regions to stimulate or inhibit target gene expression (protein synthesis). Response is slower but long-lasting.