Biomolecules and ATP - Practice Flashcards

Biomolecules

  • Biomolecules are made by living organisms.
  • All biomolecules contain carbon; therefore, they are organic.
  • Inorganic compounds do NOT contain carbon (examples: water, sodium chloride).

Monomers and Polymers

  • Organic compounds in the body (carbohydrates, lipids, proteins, nucleic acids) are polymers built from monomer subunits.
  • Monomers are single subunits that can be linked into polymers via dehydration synthesis, an anabolic reaction that forms water in the process.
  • Hydrolysis is a catabolic reaction that uses water to break polymers into smaller subunits.
  • Dehydration synthesis: monomer + monomer → polymer + H2O.
  • Hydrolysis: polymer + H2O → monomer1 + monomer2 (or more).

Carbohydrates: Monosaccharides

  • Monosaccharides are simple sugars that serve as the building blocks of carbohydrates.
  • Pentoses (five-carbon sugars): ribose (C5H10O5) and deoxyribose (C5H10O4).
    • Deoxyribose: C5H10O4
    • Ribose: C5H10O5
  • Hexoses (six-carbon sugars): glucose (C6H12O6), fructose (C6H12O6), galactose (C6H12O6).
  • Glucose, fructose, and galactose are isomers with the same molecular formula but different structures.
  • Glucose is a reference hexose; isomers differ in the arrangement of hydroxyl groups.
  • Isomers of glucose include fructose and galactose (structural isomers).
  • Chemical formulas to remember:
    • Glucose: extC<em>6extH</em>12extO6ext{C}<em>6 ext{H}</em>{12} ext{O}_6
    • Fructose: extC<em>6extH</em>12extO6ext{C}<em>6 ext{H}</em>{12} ext{O}_6
    • Galactose: extC<em>6extH</em>12extO6ext{C}<em>6 ext{H}</em>{12} ext{O}_6

Carbohydrates: Disaccharides

  • Formed by dehydration synthesis linking two monosaccharides.
  • Example: Sucrose (glucose + fructose) formed by dehydration synthesis; hydrolysis breaks disaccharides back into monosaccharides.
  • Dehydration synthesis connects two sugar units with the elimination of a water molecule (H2O).
  • Hydrolysis uses water to separate the disaccharide into its constituent monosaccharides.
  • Example pathway:
    • Glucose + Fructose --dehydration synthesis--> Sucrose + H2O
    • Sucrose --hydrolysis--> Glucose + Fructose

Carbohydrates: Polysaccharides

  • Polysaccharides are polymers of many glucose units (100s or 1000s of monosaccharide units).
  • Biological roles vary by organism:
    • Animals: glycogen (animal storage polysaccharide).
    • Plants: starch and cellulose (structural and storage roles).
    • Yeasts and bacteria: dextran (a storage polysaccharide; context varies).
    • Chitin (invertebrates only) is another polysaccharide.
  • Glycogen and starch are glucose polymers, whereas cellulose is a structural polymer of glucose with different linkages.
  • Note: The only difference between glucose and galactose is the spatial arrangement of the hydroxyl groups.

Lipids in the Human Body: Fatty Acids and Triglycerides

  • Triglyceride: three fatty acids linked by dehydration synthesis to a modified 3-carbon carbohydrate, glycerol; storage polymer for fatty acids.
  • Fatty acids + glycerol form triglycerides, which serve as energy storage molecules.

Lipids in the Human Body: Phospholipids

  • Phospholipid: amphiphilic molecule with a hydrophilic (water-loving) head and a hydrophobic (water-fearing) tail.
  • Phospholipid bilayers are the main component of cell membranes.

Lipids in the Human Body: Steroids

  • Steroids: nonpolar; share a four-ring hydrocarbon structure called the steroid nucleus.
  • Cholesterol forms the basis for all other steroids; derivatives include testosterone and others.

Lipids in the Human Body: Eicosanoids

  • Eicosanoids: cell communication molecules involved in inflammation and feedback loops.
  • Prostaglandins are examples of eicosanoids.

Proteins

  • Proteins are macromolecules with multiple roles:
    • Function as enzymes
    • Structural roles
    • Involvement in movement
    • Defenses (immunity)
    • Can be used as fuel (energy source) when needed
  • Proteins are built from amino acids (20 different amino acids) connected by peptide bonds into polypeptides.
  • Amino acid structure:
    • Amine group
    • Carboxylic acid group
    • Hydrogen atom
    • R group (side chain; one of 20 different structures)
  • Peptides: formed when two or more amino acids are linked by peptide bonds through dehydration synthesis.
    • Example: Dipeptide (two amino acids)
    • Peptide bond forms via condensation reaction; water (H2O) is released.
  • Protein structure is organized into four levels of complexity:
    • Primary structure: amino acid sequence of the polypeptide chain.
    • Secondary structure: segments of the primary structure folded in specific ways; stabilized by hydrogen bonds.
    • Alpha helix: coiled spring
    • Beta-pleated sheet: Venetian blind appearance
    • Tertiary structure: three-dimensional shape of the polypeptide, including secondary structures; stabilized by hydrogen bonds and other interactions.
    • Quaternary structure: linkage of more than one polypeptide chain in a specific arrangement; crucial for overall protein function.
  • Conjugated proteins: combined with carbohydrates (glycoproteins) or lipids (lipoproteins).
    • Examples include glycoproteins and lipoproteins; transmembrane proteins and peripheral proteins can be embedded in a phospholipid bilayer with cholesterol and glycolipids.
  • Protein denaturation: destruction of a protein’s shape due to heat, pH changes, or exposure to chemicals; disrupts hydrogen bonding and ionic interactions that stabilize structure and function.

Nucleotides and Nucleic Acids

  • Nucleotides: monomers of nucleic acids; abundant in cell nuclei; form genetic material.
  • Nucleotide structure:
    • Nitrogenous base with a hydrocarbon ring structure
    • Five-carbon pentose sugar (ribose or deoxyribose)
    • Phosphate group
  • Two types of nitrogenous bases: purines and pyrimidines
    • Purines: double-ringed molecules; adenine (A) and guanine (G)
    • Pyrimidines: single-ringed molecules; cytosine (C), uracil (U), thymine (T)
  • Adenosine triphosphate (ATP): potential energy stored in a high-energy bond; energy can be released as kinetic energy to perform work.
    • Production of large quantities of ATP requires oxygen; that’s why we need air.
  • DNA (deoxyribonucleic acid): extremely large molecule in nuclei; composed of two long chains that twist to form a double helix; contains genes that provide the recipe or code for protein synthesis.
    • DNA contains the sugar deoxyribose.
  • Structural features of DNA:
    • Complementary base pairing: purine A pairs with pyrimidine T; purine G pairs with pyrimidine C.
    • A = T (two hydrogen bonds)
    • C ≡ G (three hydrogen bonds)
  • RNA (ribonucleic acid): single-stranded molecule; moves between nucleus and cytosol; critical to protein synthesis.
    • RNA contains the sugar ribose and the nitrogenous base uracil (U) instead of thymine; A pairs with U (A = U).
  • Functions of RNA:
    • RNA copies the recipe from a DNA gene (transcription) for a specific protein.
    • RNA exits the nucleus to the cytosol where it directs protein synthesis (translation).
  • Visuals in sequence:
    • RNA (single-stranded): includes the 5' phosphate group and 3' hydroxyl group; the backbone consists of sugar-phosphate linkages.
    • DNA (double-stranded): backbone is sugar-phosphate with two strands held together by hydrogen bonds between bases (A-T, G-C).

ATP Generation and Use

  • ATP is produced and used as follows:
    • ATP formation (endergonic reaction): energy from fuel molecules (e.g., glucose) is stored in ATP by forming the triphosphate group.
    • ATP splitting (exergonic reaction): ATP is hydrolyzed to release energy that powers cellular processes (e.g., muscle movement).
    • Schematic idea: Energy-rich phosphate bonds in ATP act as energy currency; breakdown yields energy available for work.
  • Structure of ATP: triphosphate group attached to ribose and adenine.

Electron Carriers and Metabolism

  • The ability to use chemical energy in nutrients to make ATP depends on transferring electrons via electron carriers.
  • Oxidation-reduction (redox) reactions: when fuel is oxidized, electrons are transferred to another molecule; energy release drives work.
  • OIL RIG mnemonic:
    • Oxidation Is Loss of electrons
    • Reduction Is Gain of electrons
  • During catabolism, nutrient molecules are oxidized and their electrons are transferred to another molecule which is reduced.
  • Flow of electrons through the electron transport chain (ETC) powers cellular work, including ATP synthesis.
  • Electron carriers involved include NAD+/NADH (and others). See NAD+ cycle described below.

What is an Electron Carrier?

  • NAD+/NADH example:
    • NAD+ accepts electrons and a proton to become NADH; NADH carries electrons to later stages of respiration and is oxidized back to NAD+.
    • Stepwise process:
      1) NAD+ within the cell accepts electrons and a hydrogen ion from fuel; becomes NADH.
      2) NADH carries electrons to a later stage of respiration and drops them off, becoming NAD+ again.
  • This shuttle system enables energy extraction from nutrients across metabolic stages.

Energy Requirements of Metabolic Reactions

  • Exergonic catabolic reactions release energy from nutrients (e.g., glucose, fatty acids, amino acids).
  • This released energy is used to drive endergonic anabolic reactions, including ATP synthesis.
  • Schematic relationships:
    • Nutrients (glucose, fats, amino acids) → exergonic catabolic reactions → ADP + P_i (energy release) → ATP (endergonic synthesis) → drives anabolic reactions (e.g., glycogen, phospholipids, proteins) -> more energy output or storage.

Introduction to Glucose Catabolism

  • Core question: How does glucose get turned into ATP?
  • Pathways involved:
    • Glycolysis: occurs in the cytosol; anaerobic; glucose → pyruvate; net yield of ATP and NADH.
    • Oxidative phosphorylation: occurs in mitochondria; uses NADH and FADH2 to drive ATP synthesis via the electron transport chain (ETC).
  • Major stages in brief:
    • Glycolysis → ATP and NADH production in cytosol.
    • Pyruvate oxidation (between glycolysis and the citric acid cycle) to acetyl-CoA in mitochondria.
    • Citric acid cycle (Krebs cycle) in mitochondria; generates NADH, FADH2, and a small amount of ATP.
    • Electron transport chain and oxidative phosphorylation in the mitochondria; produces a large amount of ATP from NADH and FADH2.
  • Location highlights:
    • Glycolysis and the intermediate step occur in the cytosol.
    • Citric acid cycle and ETC occur in mitochondria.
  • Net energy flow concept:
    • Energy in glucose is converted into ATP through a series of controlled redox reactions and phosphate transfers.

Overview of Glucose Catabolism and ATP Synthesis

  • Two broad classes of reactions break down glucose to produce energy:
    • Glycolytic (anaerobic) catabolism: occurs in the cytoplasm; glycolysis uses 2 ATP to produce 4 ATP (net gain = +2 ATP).
    • Oxidative (aerobic) catabolism: requires oxygen; includes the citric acid cycle and ETC; net yield ~34–36 ATP from the ETC.
  • Overall schematic for one glucose molecule (illustrative numbers):
    • Glycolysis: glucose → 2 pyruvate; 2 ATP produced (net) and 2 NADH.
    • Intermediate step: 2 pyruvate → 2 acetyl-CoA; 2 NADH produced.
    • Citric acid cycle: 2 acetyl-CoA → 6 NADH, 2 FADH2, 2 ATP (or GTP).
    • Electron transport chain: NADH and FADH2 donate electrons; oxidative phosphorylation yields ~32–34 additional ATP.
    • Net total: typically cited as 36–38 ATP per glucose, depending on shuttle systems and cell type.
  • Specific number notes from the slides:
    • Some slides state a maximum of 36 ATP per glucose molecule.
    • Other slides state 38 ATP per glucose molecule (accounting for different ATP yields from NADH/FADH2 shuttles).
    • Breakdown example (as per slide details): 2 ATP (glycolysis) + 2 ATP (Krebs) + 34 ATP (ETC) = 38 ATP total.
  • Illustrative overall equation (cellular respiration):
    • ext{C}6 ext{H}{12} ext{O}6 + 6 ext{O}2
      ightarrow 6 ext{CO}2 + 6 ext{H}2 ext{O} + 36 ext{ATP}
    • Note: The exact ATP total can be cited as 36–38 depending on conditions; the slides present both figures in different sections.

Fate of Pyruvate: Oxygen or No Oxygen?

  • Intermediates between anaerobic glycolysis and aerobic respiration include pyruvate.
  • Anaerobic fate (in cytosol): 1 glucose → 2 pyruvate → 2 lactate (lactic acid) under anaerobic conditions.
  • Aerobic fate (with oxygen): 1 glucose → 2 pyruvate → move into mitochondria → 2 acetyl-CoA → two rounds of the citric acid cycle and subsequent electron transport chain.

Cellular Respiration: Glycolysis, the Krebs Cycle and the Electron Transport Chain

  • Overall cell respiration equation (as summarized in slide):
    • ext{C}6 ext{H}{12} ext{O}6 + 6 ext{O}2 + 36 ext{ADP} + 36 ext{P}i ightarrow 6 ext{CO}2 + 6 ext{H}_2 ext{O} + 36 ext{ATP}
  • Functional parts:
    • Glycolysis in cytosol: glucose → 2 pyruvate; net 2 ATP and 2 NADH.
    • Krebs cycle in mitochondria: acetyl-CoA oxidation yields NADH, FADH2, and ATP/GTP.
    • Electron transport chain in mitochondria: NADH and FADH2 donate electrons; proton pumping creates proton gradient used by ATP synthase to generate ATP; oxygen is the final electron acceptor forming water.

Food to Energy Pathways in Cellular Respiration

  • Different macromolecules enter the respiration pathway at different points:
    • Carbohydrates: mostly enter via glycolysis.
    • Glycerol (a fat component) can enter glycolysis.
    • Fatty acids: enter via β-oxidation to acetyl-CoA and feed into the citric acid cycle.
    • Proteins: amino acids can be transaminated and enter respiration at various points (as intermediates or via pyruvate, acetyl-CoA, or TCA cycle intermediates).
  • Rationale for varying efficiency: fats yield more ATP per carbon because fatty acids are more reduced than carbohydrates and provide more acetyl-CoA units per molecule.

Overview of Nutrient Catabolism

  • β-oxidation converts fatty acids into acetyl-CoA, generating NADH and FADH2 in the process.
  • Lipids contribute to energy production through the steps that feed into the citric acid cycle and ETC.
  • Carbohydrates feed directly into glycolysis and then into the mitochondria for full oxidation.
  • Proteins contribute amino acids that can be deaminated and fed into glycolysis, the acetyl-CoA pool, or the citric acid cycle.
  • Urea is produced from amino acid catabolism as a byproduct of nitrogen disposal.
  • Overall pathway flow: Nutrients → glycolysis/β-oxidation/amino acid catabolism → NADH and FADH2 → ETC → ATP.

Overview of Nutrient Anabolism

  • Anabolic pathways build complex molecules from simpler ones, using ATP as energy input:
    • Gluconeogenesis: synthesis of glucose from non-carbohydrate precursors.
    • Glycogenesis: synthesis of glycogen from glucose for storage.
    • Lipogenesis: synthesis of lipids from acetyl-CoA (and glycerol from glycolytic intermediates).
    • Protein synthesis: assembly of amino acids into proteins using ribosomes.
  • Common feed-ins and outputs:
    • Glucose can be converted into glycogen for storage.
    • Fatty acids can be assembled into triglycerides (lipogenesis).
    • Amino acids can be used to synthesize proteins or be converted into other molecules after deamination.

Notes and connections

  • The energy currency of cells is ATP, produced via glycolysis, the Krebs cycle, and the electron transport chain; the overall process is tightly coupled through redox reactions and phosphate transfer.
  • NAD+/NADH functions as a key electron shuttle in metabolism; NAD+ is reduced to NADH during oxidation steps and NADH delivers electrons to the ETC to produce ATP.
  • The distinction between pentose and hexose sugars explains the diversity of carbohydrate chemistry; key sugars (ribose, deoxyribose) form the backbone of RNA and DNA, respectively.
  • The DNA/RNA base-pairing rules (A-T with 2 H-bonds; C-G with 3 H-bonds; A-U pairing in RNA) underpin genetic transcription and replication.
  • The concept of denaturation emphasizes that protein function is intimately tied to structure; changes in environment can disrupt this structure and function.
  • The steroid nucleus and cholesterol serve as scaffolds for steroid hormones, influencing many physiological processes.
  • Ethico-Philosophical/Practical implications: understanding energy metabolism informs medical contexts (e.g., metabolic disorders, athletic performance, nutrition strategies).