LC

Comprehensive Biology Notes: Atoms to Cell Membranes

Atoms and Subatomic Particles

  • Three main components of every atom: protons, neutrons, and electrons.
  • Protons are positively charged; electrons are negatively charged; neutrons are uncharged (neutral).
  • The number of protons defines the atomic number, often written as Z.
  • In a neutral atom, the number of electrons equals the number of protons, so E = Z and the net charge is zero. If the atom is charged, the number of electrons differs from Z, giving the atom a positive or negative charge.
  • The protons in a specific atom never change; neutrons can vary, giving different isotopes.
  • Common biological examples mentioned: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), with phosphorus (P) occasionally noted.
  • Memory aid mentioned: "CHOP" (C, H, O, N; sometimes P) as the most prevalent atoms in the body.
  • Isotopes vs. Isomers:
    • Isotopes: variants of the same element with different numbers of neutrons but the same number of protons. Example: carbon-12 (^12C) and carbon-14 (^14C).
    • Mass number relation: A = Z + N where A is the atomic mass number and N is the number of neutrons.
    • Protons (Z) and neutrons (N) determine the isotope; electrons contribute negligible mass.
    • Example: For ^{12}C, Z = 6, N = 6, so A = 6 + 6 = 12.
    • Carbon-14: Z = 6, A = 14, so N = A − Z = 8 neutrons.
  • Isomers (briefly mentioned): different orientation/arrangement of atoms in molecules with the same formula; not the same as isotopes and not emphasized for this topic.
  • Electron configuration and bonding (overview):
    • Ionic bonds: transfer of electrons, typically between a metal and a nonmetal (example: NaCl). Metals tend to lose electrons to reach a full shell; nonmetals tend to gain electrons to complete their shell.
    • Covalent bonds: sharing of electrons between atoms (often nonmetals). Example discussed: covalent bonding in hydrocarbons and water.
    • Ionic vs Covalent distinctions rest on whether electrons are transferred (ionic) or shared (covalent).
    • Water (H₂O) is polar due to uneven electron distribution, giving it partial charges and influencing bonding and solubility.
  • Bohr model vs Lewis structures vs modern orbital theory (brief awareness):
    • Bohr model emphasizes energy levels and valence electrons.
    • Lewis structures focus on valence electrons as dots around atoms to show bonding.
    • Modern orbital theory discusses electron arrangement in orbitals and subshells in more detail (not deeply covered here).
  • Electron configuration and bonding examples and notes:
    • Ionic bond example: metal/nonnmetal transfer leads to electrostatic interaction and salt formation (e.g., NaCl).
    • Covalent bond example: nonmetals share electrons; joint custody over electrons.
    • In water, polar covalent bonds (O–H) create a bent molecular geometry contributing to polarity.

Water, Polarity, and Hydrogen Bonding

  • Water (H₂O) is polar due to its bent shape and unequal electron distribution; this polarity allows hydrogen bonding between water molecules.
  • Hydrogen bonds are weak individually but collectively strong; key for biomolecules (e.g., DNA base pairing).
  • Cohesion: water molecules stick to each other via hydrogen bonds (e.g., droplets forming due to cohesive forces).
  • Adhesion: water sticks to polar surfaces (e.g., glass, plant tissues) due to hydrogen bonding with surfaces.
  • Physical properties of water discussed:
    • High specific heat: water requires a large amount of energy to change its temperature, helping organisms regulate temperature.
    • High heat of vaporization: water absorbs a lot of energy when it vaporizes, providing cooling (e.g., sweating).
    • Ice is less dense than liquid water due to hydrogen bonding; generally ice floats on water.
    • pH = 7 is neutral at standard conditions; acids increase hydrogen ion concentration, bases increase hydroxide; pH scale typically ranges from 0 (acidic) to 14 (basic).
  • Hydrophilic vs hydrophobic:
    • Hydrophilic: water-loving, polar substances that dissolve in water.
    • Hydrophobic: water-fearing, nonpolar substances that do not mix well with water (e.g., oils).
  • Specific properties of water referenced:
    • pH-related behavior (acidic vs basic): acids increase [H⁺]; bases decrease [H⁺] by increasing [OH⁻].
    • Acids; bases; pH values (example: lemon is acidic with pH < 7).
  • Water’s role in biological systems and macromolecules:
    • Water is a major component of cells and cytosol; this environment drives folding and interactions in biomolecules.

Acids, Bases, pH, and Functional Groups

  • Definitions:
    • Acids increase hydrogen ion concentration in solution; bases decrease hydrogen ion concentration or increase hydroxide.
    • pH is a measure of acidity/basicity with pH 7 considered neutral under standard conditions; pH < 7 is acidic; pH > 7 is basic.
    • Simple example relationships: acids have lower pH values; bases have higher pH values.
  • Functional groups discussed (structure and implications):
    • Hydroxyl group: -OH
    • Found in alcohols and carbohydrates; contributes to polarity and water solubility.
    • Carbonyl group: C=O
    • Found in aldehydes and ketones; important for reactive chemistry.
    • Carboxyl group: -COOH
    • Found in carboxylic acids; acidic; involved in peptide bond formation; in peptides and proteins.
    • Amino group: -NH₂
    • Found in amino acids; essential for peptide bond formation.
    • Phosphate group: -PO₄ (phosphates)
    • Found in ATP and nucleotides; energy-related roles in metabolism.
  • Note on monomer/polymer context following functional group discussion (to be expanded below).

Monomers, Polymers, and Macromolecules

  • Polymers are large molecules composed of repeating subunits (monomers).
  • Monomer vs polymer:
    • Monomer: single subunit (e.g., a single sugar unit like glucose).
    • Polymer: many subunits linked together in a particular arrangement (e.g., polysaccharides like starch).
    • Prefixes: poly- = many; mono- = one.
  • Proteins as polymers:
    • Protein = polymer of amino acids; a polymer of amino acids forms a polypeptide chain.
    • Peptide bonds connect amino acids via dehydration synthesis (removal of water):
    • Example dehydration reaction:
      ext{amino acid}1- ext{COOH} + ext{amino acid}2- ext{NH}2 ightarrow ext{amino acid}1- ext{CO-NH–amino acid}2 + H2O
  • Protein structure levels:
    • Primary structure: linear sequence of amino acids.
    • Secondary structure: local folding patterns stabilized by hydrogen bonds; main forms are:
    • Alpha helix
    • Beta-pleated sheet
    • Tertiary structure: overall 3D folding of a single polypeptide, stabilized by several interactions, including:
    • Hydrogen bonds
    • Disulfide bonds (between cysteine residues, involving sulfur)
    • Hydrophilic vs hydrophobic effects (hydrophobic amino acids tend to be buried inside; hydrophilic on the outside in aqueous environments)
    • Van der Waals interactions
    • Quaternary structure: multiple polypeptide subunits (subunits) assembled into a functional protein.
  • Isomer clarification (brief): isomers discussed in chemistry are not the same as isotopes; isomers refer to different arrangements of atoms with the same formula in a molecule.
  • Chaperone proteins: assist folding of other proteins; misfolding can lead to diseases (e.g., prions, mad cow disease) when chaperones are insufficient or misfolding occurs.
  • Functional implications:
    • Protein folding relies on intermolecular forces; misfolding can disrupt function and lead to disease.

Nucleic Acids: DNA and RNA; Replication, Transcription, and Translation

  • Nucleic acids and bases:
    • DNA bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).
    • RNA replaces thymine with Uracil (U).
  • Base pairing: A with T (in DNA) and A with U (in RNA); C pairs with G.
  • DNA structure and replication context (as discussed):
    • Template strand orientation: discussed as 3' to 5' for the template strand; the complementary strand is 5' to 3'.
    • Helicase separates the two strands; DNA polymerase synthesizes new strands.
    • Leading strand vs lagging strand:
    • Leading strand synthesized continuously in the 5'→3' direction toward the replication fork.
    • Lagging strand synthesized discontinuously in Okazaki fragments (short segments) also in the 5'→3' direction but away from the fork.
    • Okazaki fragment synthesis requires ligase to seal nicks and produce a continuous strand.
  • Transcription and translation flow (overview from lecture):
    • RNA is produced from a DNA template to form mRNA, which exits the nucleus and is translated by ribosomes into a polypeptide chain (protein).
    • The coding strand concept: in transcription, the RNA sequence is complementary to the template strand and matches the coding strand sequence (with U in place of T for RNA).
  • Role of transcription/translation in protein synthesis: mRNA is processed by ribosomes to build polypeptides from the genetic code.
  • Functional roles of nucleic acids (briefly): genetic information storage (DNA) and protein synthesis (RNA and ribosomes).

Metabolism, Cells, and Energy Transfer: Redox and Bioenergetics

  • Redox concepts:
    • Oxidation: loss of electrons; reduction: gain of electrons.
    • Mnemonic: Oil Rig — Oxidation Is Loss; Reduction Is Gain.
  • Redox in biological processes:
    • Cellular respiration and photosynthesis involve electron transfer and redox reactions.
    • In photosynthesis, light energy drives electron transfer from water to carbon dioxide; water is oxidized (loses electrons) and CO₂ is reduced (gains electrons) to produce glucose; overall equation includes water oxidation and CO₂ reduction.
  • Electron carriers and energy production:
    • NAD⁺/NADH and FAD/FADH₂ shuttle electrons (and protons) during metabolism; in cellular respiration, NADH and FADH₂ donate electrons to the electron transport chain (ETC).
    • The ETC creates a proton gradient across a membrane (mitochondrial inner membrane) by pumping protons as electrons pass through the chain.
    • ATP synthase uses the proton gradient to drive the phosphorylation of ADP to ATP:
      ext{ADP} + ext{P}_i
      ightarrow ext{ATP}
    • ATP is a energy-storage molecule; energy is released when the bond between the second and third phosphate is cleaved.
  • Important note on the speaker’s example (NaOH + HCl):
    • The transcript describes a redox interpretation for a neutralization reaction, but standard chemistry considers NaOH + HCl as an acid-base (neutralization) reaction, not a redox reaction. The output of this reaction is NaCl + H₂O; it does not inherently illustrate electron transfer between redox partners, unlike typical redox examples.
  • Water, protons, and energy carriers are all connected in cellular energy workflows, as the electron transfers power the proton pumps that generate ATP.

Acids, Bases, pH, and Hydrogen Bonding in Biological Contexts

  • pH and hydrogen ions:
    • pH is a log scale: ext{pH} = -
      \, ext{log}_{10} [H^+].
    • Acids increase hydrogen ion concentration; bases increase hydroxide, shifting pH upward.
  • Hydrogen bonds in biological structures:
    • Hydrogen bonds form between polar molecules and within macromolecules (e.g., DNA base pairing, secondary structures in proteins).
    • They are relatively weak individually but collectively stabilize many structures.
  • Hydrophilic vs hydrophobic context in biomolecules:
    • Hydrophilic amino acids tend to be on the exterior of proteins in aqueous environments; hydrophobic amino acids tend to be buried inside.
    • This drives protein folding (tertiary structure) and membrane protein organization.

Membranes, Lipids, and Transport

  • Cell membrane composition:
    • Phospholipid bilayer with polar (hydrophilic) heads and nonpolar (hydrophobic) tails.
    • Tails face inward; heads face outward toward aqueous environments.
  • Membrane permeability basics:
    • Small nonpolar molecules diffuse readily through the membrane without channels.
    • Large or highly polar molecules require channels or transporters to cross.
  • Passive vs active transport:
    • Passive transport occurs along a concentration gradient (high to low) and can involve channels or simple diffusion; no energy input required.
    • Active transport moves substances against the gradient (low to high) and requires energy input (e.g., ATP or another energy source).
  • Aquaporins and osmosis:
    • Water can diffuse through the membrane via aquaporin channels; osmosis is diffusion of water across a semipermeable membrane.
  • Lipid saturation and membrane fluidity:
    • Saturated fatty acyl tails are straight, stack easily, and make membranes more rigid.
    • Unsaturated tails contain double bonds that bend, reducing packing and increasing fluidity.
    • Membrane fluidity is essential for proper function and is driven by lipid composition and temperature.

Practical Concepts and Biological Relevance

  • Isotopes and dating:
    • Carbon-14 (C-14) is used in radiocarbon dating because it provides a differing neutron count while keeping the same protons (Z = 6).
    • The example ^{14}C has Z = 6 and N = 8, giving A = 14.
  • Isomer, ions, and covalent vs ionic concepts reinforced:
    • Isomers involve different spatial arrangements of atoms in molecules; not the same as isotopes.
    • Ionic bonds involve transfer of electrons (metal + nonmetal); covalent bonds involve sharing electrons (nonmetal + nonmetal).
    • Water’s polarity arises from the unequal sharing of electrons between O and H in the O–H bonds.
  • Biochemical energy and disease implications:
    • Chaperone proteins assist proper protein folding; lack of chaperone function can contribute to misfolding diseases (e.g., prions causing neurodegenerative conditions).
  • Typical multiple-choice exam expectations (as discussed):
    • The instructor indicated that questions may be multiple choice; focus on understanding concepts, reactions, structures, and pathways described above.

Quick Reference Formulas and Concepts

  • Atomic and isotopic relations:
    • Z = ext{number of protons}
    • E = Z\quad (\text{in a neutral atom})
    • A = Z + N where A = mass number, N = number of neutrons
  • Charge of an ion:
    • Q = Z - E
  • Bonding distinctions:
    • Ionic: transfer of electrons (metal + nonmetal)
    • Covalent: sharing of electrons (nonmetal + nonmetal)
  • Water chemistry:
    • Water formula: H_2O
    • Hydrogen bonding enables cohesion/adhesion and influences solvent properties
  • pH and acidity/basicity:
    • ext{pH} = -\log_{10} [H^+]
  • Dehydration synthesis (peptide bond formation):
    • Two amino acids produce a dipeptide + water:
    • \text{Amino acid}1 - \text{COOH} + \text{Amino acid}2 - \text{NH}2 \rightarrow \text{Amino acid}1 - \text{CO-NH-}\text{Amino acid}2 + H_2O
  • Protein structure hierarchy:
    • Primary, Secondary (\alpha-helix, \beta-pleated sheet), Tertiary, Quaternary
  • DNA replication essentials (conceptual):
    • Helicase separates strands; leading strand synthesized continuously; lagging strand in Okazaki fragments; ligase seals gaps
  • Energy carriers and ATP production:
    • NADH and FADH₂ donate electrons to the electron transport chain
    • Proton gradient drives ATP synthase to produce ATP: \text{ADP} + P_i \rightarrow \text{ATP}
  • Lipids and membrane structure:
    • Phospholipids: polar head groups, nonpolar tails; saturated vs unsaturated tails affect fluidity
  • Key terms to know for exams:
    • Atomic number (Z), mass number (A), isotopes, ions, Bohr model, Lewis structures, bonding types, hydrogen bonds, cohesion/adhesion, specific heat, vaporization, pH, functional groups, polymers/polymerization, monomers, amino acids, peptide bonds, chaperones, prions, DNA/RNA basics, replication/transcription/translation, protein structure levels, phosphorylation concepts, ATP, NADH/FADH₂, electron transport chain, osmosis, aquaporins, passive vs active transport, and membrane fluidity.