exam review 3-4

Metabolism

• Metabolism is the sum of all anabolic and catabolic reactions in a cell, connected in a network of reaction pathways
• Anabolic reactions synthesize or "build" molecules with more bonds, using energy and reducing entropy (endergonic and non-spontaneous)
• Catabolic reactions degrade or "break" molecules to make lower free energy products with fewer bonds, releasing energy and increasing entropy (exergonic and spontaneous)

Thermodynamics

• The First and Second Laws of Thermodynamics state that energy is transformed in many ways, but always at the cost of energy lost through entropy that is not available to do work
• Free energy (G) is chemical energy available to do work and is expressed as the difference between enthalpy (total energy) and entropy
• Any reaction involves a change in free energy, ∆G, between reactants and products
• The direction of change in free energy tells if it is positive or negative ∆G (anabolic or catabolic)

Enzymes

• Enzymes are proteins that reduce the activation energy of a reaction
• Enzyme specificity and function are the result of the structure (shape) of the protein
• Substrates interact with enzymes at the active site, forming an enzyme-substrate complex with a close interaction through induced fit

Cellular Respiration

• Cellular respiration is the process of breaking down glucose to make ATP using substrate level and oxidative phosphorylation
• Glycolysis: uses glucose as its preferred substrate to make 2 ATP (Net, via substrate level phosphorylation), 2 NADH, and 2 pyruvate
• Pyruvate oxidation: converts 2 pyruvates into 2 acetyl-CoA, making 2 NADH and 2 CO2
• Citric acid cycle: oxidizes acetyl-CoA to CO2, making 2 ATP (via substrate level phosphorylation), 6 NADH, and 2 FADH2
• Oxidative phosphorylation: uses the energy from NADH and FADH2 to pump H+ into the intermembrane space, generating proton motive force (PMF) across the inner membrane

DNA Structure and Replication

• DNA is a polymer of the four nucleotides A, C, G, and T with the sugar deoxyribose
• Nucleotides can be either purines (A and G) or pyrimidines (C, T, and U)
• The Watson-Crick Model of DNA has four main features:
  • Double helix with sugar-phosphate backbone outside
  • Antiparallel strands
  • Strict base-pairing of nucleotides (A:T; C:G)
  • Two strands held together by hydrogen bonding between bases
• DNA replication involves semi-conservative replication: each parental strand from a double helix is used as a template to make a daughter strand along its entire length

Photosynthesis

• Photosynthesis transforms light energy into chemical energy, synthesizing new carbon backbones from CO2 released when cellular respiration breaks down carbon backbones
• The light reactions use two photosystems to capture light and generate high energy electrons
• Electrons leave the light reactions in NADPH, and new electrons are obtained by the splitting of water through photolysis by PSII
• The flow of H+ from high concentration in the lumen to low concentration in the stroma powers the enzyme complex ATP synthase, resulting in the formation of ATP in the stroma (=photophosphorylation)

Central Dogma

• The Central Dogma states: DNA is used to make RNA is used to make Protein
• The information encoding proteins is organized as genes on DNA, and all genes have the same basic structure:
  • A transcription start site denoted as "+1" corresponding to the first nucleotide at the 5' end of the RNA product
  • A transcribed region that acts as the template for the transcribed RNA, located "downstream" of the transcription start site (base positions denoted by positive numbers)
  • A regulatory domain called a promoter located "upstream" of the transcription start site (base positions denoted by negative numbers)

Translation

• Translation occurs in the ribosome, a large multi-protein complex that interacts with mRNA and enzymatically assembles polypeptides
• Initiation of translation occurs when the small ribosomal subunit binds to mRNA near the 5'-end
• During elongation, a charged tRNA enters the A-site, and the ribosomal enzymes cut the growing polypeptide free from the P-site tRNA, and attach it to the new amino acid on the tRNA in the A-site with a peptide bond
• The process repeats until a stop codon lines up with the A-site and binds to a release factor, halting translation

Test your knowledge on metabolism, energy, and enzymes in cellular reactions. Learn about anabolic and catabolic reactions, free energy, and entropy in biological systems.