General Biology: Cellular Energy, Photosynthesis, and DNA Structure Study Notes

Cellular Energy and Metabolism

Kinetic vs. Potential Energy

Energy in biological systems exists in two main forms: kinetic (energy of motion) and potential (stored energy). Understanding the distinction is crucial for studying cellular processes.

• Kinetic energy: Energy associated with movement, such as molecules moving across membranes.

• Potential energy: Stored energy, such as chemical energy in bonds or concentration gradients.

Oxidation and Reduction Reactions

Redox reactions are fundamental to energy transfer in cells. They involve the transfer of electrons between molecules.

• Oxidation: Loss of electrons; often associated with loss of hydrogen or gain of oxygen.

• Reduction: Gain of electrons; often associated with gain of hydrogen or loss of oxygen.

• Example: In cellular respiration, glucose is oxidized and oxygen is reduced.

Thermodynamics in Biology

Cells obey the laws of thermodynamics, which govern energy transformations.

• First Law: Energy cannot be created or destroyed, only transformed.

• Second Law: Every energy transfer increases the entropy (disorder) of the universe.

• Application: Heat lost in metabolism is an example of increased entropy.

Endergonic vs. Exergonic Reactions

Chemical reactions in cells can either require energy (endergonic) or release energy (exergonic).

• Endergonic reactions: Products have more energy than reactants; require input of energy.

• Exergonic reactions: Products have less energy than reactants; release energy.

• Example: ATP synthesis is endergonic; ATP hydrolysis is exergonic.

ATP and Coupled Reactions

ATP (adenosine triphosphate) is the primary energy currency of the cell. It couples exergonic and endergonic reactions.

• ATP structure: Adenine base, ribose sugar, three phosphate groups.

• Energy release: Hydrolysis of ATP to ADP + Pi releases energy.

• Equation: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

• Phosphorylation: Transfer of phosphate group to a protein or molecule, often activating it.

Enzymes and Biological Catalysts

Enzymes are proteins that speed up chemical reactions by lowering activation energy, but do not affect the overall energy change.

• Active site: Region where substrate binds.

• Substrate specificity: Determined by enzyme structure.

• Inhibition: Competitive (active site) and noncompetitive (allosteric site).

Cellular Respiration

Autotrophs vs. Heterotrophs

Organisms are classified by how they obtain energy.

• Autotrophs: Produce their own food (e.g., plants via photosynthesis).

• Heterotrophs: Obtain energy by consuming other organisms.

Electron Carriers and Redox Reactions

Electron carriers like NAD+ and FAD are essential for transferring energy in cells.

• NAD+ (Nicotinamide adenine dinucleotide): Accepts electrons to become NADH.

• FAD (Flavin adenine dinucleotide): Accepts electrons to become FADH2.

• Role: Carry electrons to the electron transport chain (ETC).

Stages of Aerobic Respiration

Aerobic respiration consists of several stages, each producing different products.

Process	# ATP	# NADH	# FADH2	# CO2
Glycolysis	2	2	0	0
Pyruvate Oxidation	0	2	0	2
Krebs Cycle	2	6	2	4

Additional info: Table summarizes net products and products used in next steps for each stage.

Electron Transport Chain (ETC) and Oxidative Phosphorylation

The ETC uses electrons from NADH and FADH2 to pump protons and generate ATP.

• Oxygen: Final electron acceptor in the ETC.

• ATP yield: NADH yields about 2.5 ATP, FADH2 yields about 1.5 ATP.

• Equation: $\text{NADH} + \text{H}^+ + 1/2\text{O}_2 \rightarrow \text{NAD}^+ + \text{H}_2\text{O}$

Electron Carrier	# ATP formed per molecule
NADH from glycolysis	2.5
NADH from pyruvate oxidation and Krebs	2.5
FADH2 from Krebs	1.5

Additional info: Table used to calculate total ATP produced by aerobic respiration.

Anaerobic Respiration and Fermentation

When oxygen is absent, cells use fermentation to regenerate NAD+ and produce ATP.

• Lactic acid fermentation: Occurs in muscle cells; produces lactate.

• Alcoholic fermentation: Occurs in yeast; produces ethanol and CO2.

• Fermentation yields less ATP than aerobic respiration.

Photosynthesis

Connection to Respiration

Photosynthesis and respiration are interconnected; products of one are reactants for the other.

• Photosynthesis: Converts CO2 and H2O into glucose and O2 using light energy.

• Respiration: Breaks down glucose to produce CO2, H2O, and ATP.

Light-Dependent and Light-Independent Reactions

Photosynthesis occurs in two stages: light-dependent reactions and the Calvin cycle (light-independent).

• Light-dependent reactions: Occur in thylakoid membranes; produce ATP and NADPH.

• Calvin cycle: Occurs in stroma; uses ATP and NADPH to fix CO2 into glucose.

Chlorophyll and Light Absorption

Chlorophyll is the main pigment that absorbs light for photosynthesis.

• Chlorophyll a: Primary pigment; absorbs blue and red light.

• Accessory pigments: Carotenoids and others broaden the spectrum of absorbed light.

Photosystems and Electron Flow

Photosystems I and II are complexes that capture light and transfer electrons.

• Photosystem II: Splits water, releases O2, and passes electrons to ETC.

• Photosystem I: Transfers electrons to NADP+ to form NADPH.

• Equation: $2\text{H}_2\text{O} + 2\text{NADP}^+ + 3\text{ADP} + 3\text{P}_i + \text{light} \rightarrow 2\text{NADPH} + 2\text{H}^+ + 3\text{ATP} + \text{O}_2$

Calvin Cycle

The Calvin cycle fixes carbon dioxide into organic molecules.

• Key steps: Carbon fixation by Rubisco, reduction of 3-phosphoglycerate, regeneration of RuBP.

• Product: G3P (glyceraldehyde-3-phosphate), a precursor to glucose.

C3, C4, and CAM Pathways

Plants have evolved different mechanisms to fix carbon depending on their environment.

• C3 plants: Use Calvin cycle directly; most common.

• C4 plants: Spatial separation of steps; adapted to hot, dry environments.

• CAM plants: Temporal separation; fix CO2 at night, adapted to arid conditions.

DNA Structure and Replication

Nucleotides and DNA Backbone

DNA is composed of nucleotides linked by phosphodiester bonds, forming a sugar-phosphate backbone.

• Nucleotide: Deoxyribose sugar, phosphate group, nitrogenous base.

• Phosphodiester bond: Links 3' carbon of one nucleotide to 5' phosphate of the next.

Base Pairing and Complementarity

DNA strands are held together by hydrogen bonds between complementary bases.

• Adenine (A) pairs with Thymine (T) (2 hydrogen bonds).

• Guanine (G) pairs with Cytosine (C) (3 hydrogen bonds).

• Chargaff's rule: %A = %T, %G = %C in double-stranded DNA.

Watson-Crick Model and DNA Replication

The double helix model explains how DNA replicates and stores genetic information.

• Antiparallel strands: One runs 5' to 3', the other 3' to 5'.

• Semiconservative replication: Each new DNA molecule has one old and one new strand.

• Enzymes: DNA polymerase synthesizes new DNA; helicase unwinds the helix.

Transcription and Translation

Genetic information flows from DNA to RNA to protein.

• Transcription: DNA is copied into messenger RNA (mRNA).

• Translation: mRNA is decoded by ribosomes to synthesize proteins.

DNA Synthesis and Proofreading

DNA polymerase adds nucleotides in the 5' to 3' direction and proofreads for errors.

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized in Okazaki fragments.

• Proofreading: DNA polymerase has 3' to 5' exonuclease activity to correct mistakes.

Discontinuous Replication

On the lagging strand, DNA synthesis is discontinuous, resulting in short fragments that are later joined.

• Okazaki fragments: Short DNA segments synthesized on the lagging strand.

• Ligase: Enzyme that joins Okazaki fragments.

Additional info: Academic context and explanations have been expanded for clarity and completeness. Tables have been recreated and equations provided in LaTeX format as required.