Biology Chemistry Essentials: Atoms, Bonding, Air, Water, and Biomolecules

Atoms and Bonding

• Atoms are the basic units of matter; they come together to form molecules.
• Structure of an atom:
  • Nucleus contains protons (positive charge) and neutrons (neutral).
  • Electrons surround the nucleus and can be gained, lost, or shared.
• Key identifiers:
  • The number of protons identifies the element (atomic number).
  • Example: an atom with 6 protons is carbon.
• Ions:
  • Gaining or losing electrons creates charged atoms/molecules (ions).
  • More electrons than protons → negative ion; fewer electrons than protons → positive ion.
• Bonding basics:
  • Atoms bond by pairing unpaired electrons (sharing electrons) to form molecules (covalent bonding).
  • Covalent bonds involve sharing electrons between atoms (often shown in Lewis structures).
• Example: water molecule (H2O)
  • One oxygen atom with two hydrogens forms two covalent bonds (O forms two bonds; H forms one bond each).
• Key mnemonic for covalent bonding patterns (HONKP):
  • H = 1 bond; O = 2 bonds; N = 3 bonds; C = 4 bonds; P = 5 bonds; but phosphorus can sometimes form three bonds as well.
  • HONKP stands for Hydrogen, Oxygen, Nitrogen, Carbon, Phosphorus.
  • Human relevance: these elements are central to biology and the major bond patterns in biomolecules.
• Mass and essential elements:
  • Sulfur (S) is another important bioelement to add to the list of H, O, N, C, P; together with S, these elements make up about 98% of body mass.
• Drawing molecules (practical sketching tips):
  • You’ll be asked to draw molecules (e.g., four hydrogens, one oxygen, one carbon).
  • Rule of thumb: start with the largest number of bonds first (carbon forms 4, oxygen forms 2, hydrogens form 1).
  • Example workflow to build a methanol molecule (CH3OH):
  • Step 1: place carbon (forms 4 bonds).
  • Step 2: attach oxygen (forms 2 bonds) to carbon, leaving one bond to satisfy.
  • Step 3: attach hydrogens to satisfy remaining single bonds (usually save hydrogens for the end).
  • Outcome: methanol with carbon bonded to three H and one O; oxygen bonded to carbon and to one hydrogen (O–H) structure.
• Key takeaways:
  • Covalent bonds arise from sharing electrons to satisfy outer-shell needs.
  • The HONKP pattern helps predict how many bonds common elements tend to form.

The Chemistry of Air

• Major components of the air you breathe:
  • ~78% nitrogen (N₂): chemically nonreactive due to a very strong triple bond between the two N atoms.
  • ~21% oxygen (O₂): highly reactive and essential for respiration.
  • ~0.04% carbon dioxide (CO₂): small fraction, yet important for climate and atmospheric chemistry.
• Water vapor in air (humidity):
  • Water in the air varies; temperature affects humidity.
  • Warmer air can hold more water vapor than cooler air.
• Significance:
  • Even small changes in CO₂ levels can have large effects on climate and atmospheric processes.

Water and pH

• Water molecule: H₂O
  • Oxygen end is slightly negative; hydrogen ends are slightly positive due to differences in electronegativity.
  • This polarity drives water’s solvent properties and interactions with other molecules.
• Water autoionization (acid-base behavior):
  • Water can split and re-form: $\mathrm{H_2O} \rightleftharpoons \mathrm{H^+} + \mathrm{OH^-}$
  • The balance between H⁺ and OH⁻ in a solution determines acidity/basicity.
• pH scale:
  • Measures how acidic or basic a solution is.
  • Lower pH means higher acidity (more H⁺).
  • Higher pH means higher basicity (less H⁺).
  • Neutral pH is 7.
  • Typical relation: if [H⁺] increases, pH decreases, and vice versa.
  • Commonly, $\mathrm{pH} = -\log_{10}[\mathrm{H^+}]$.
• Buffers and pH stability:
  • Buffer systems maintain pH within a narrow range.
  • One important buffer system is the carbonate buffer system, discussed next.
• The carbonate buffer system (blood buffering focus):
  • Reaction network (simplified to key species):
  • $\mathrm{CO<em>2} + \mathrm{H</em>2O} \rightleftharpoons \mathrm{H<em>2CO</em>3}$
  • $\mathrm{H<em>2CO</em>3} \rightleftharpoons \mathrm{H^+} + \mathrm{HCO_3^-}$
  • The reverse can also occur: $\mathrm{H^+} + \mathrm{HCO<em>3^-} \rightleftharpoons \mathrm{H</em>2CO<em>3} \rightleftharpoons \mathrm{CO</em>2} + \mathrm{H_2O}$
  • Practical focus: water, carbon dioxide, hydrogen ion, bicarbonate ion (carbonate system) governs blood pH.
  • Blood pH is normally about $\mathrm{pH} \approx 7.40\, (\approx 7.4)\,$
  • The intermediate carbonic acid (H₂CO₃) is part of the equilibrium, but for these notes we emphasize the water–CO₂–H⁺–HCO₃⁻ relationships.

Biomolecules

• What biomolecules are: the chemical basis of life; four major categories compose all living things.
• Four categories:
  • Carbohydrates
  • Proteins
  • Nucleic acids
  • Lipids
• Common subunits and composition:
  • Carbohydrates: subunit is sugar; examples include glycolytic carbohydrates and starches; cellulose (fiber) is a carbohydrate and is not digestible by humans.
  • Carbohydrates are composed of hydrogen, oxygen, and carbon (H, O, C). They are often represented by empirical formula CH₂O (or (CH₂O)ₙ).
  • Proteins: subunit is amino acids; proteins perform enzymes, structural roles, and regulation; proteins frequently regulate chemical reactions as enzymes and serve structural roles.
  • They contain hydrogen, oxygen, nitrogen, and carbon (HONC). Nitrogen content is particularly important for nutrition, agriculture, and health.
  • Nucleic acids: subunit is nucleotides; DNA and RNA store and transmit genetic information, ATP stores and transfers energy.
  • They contain hydrogen, oxygen, carbon, nitrogen, and phosphorus (H, O, C, N, P).
  • Lipids: subunit composition is more variable; lipids are carbon-hydrogen compounds that may also include oxygen and sometimes phosphorus (phospholipids).
  • Lipids form fats, oils, and steroids (rings); they are used for energy storage and for membrane structure.
• Food context: how biomolecules relate to eating and health
  • Carbohydrates as energy sources; simple sugars are rapidly absorbed and used for quick energy.
  • Starches act as energy sources, rapidly broken down to simple sugars like glucose and absorbed.
  • Cellulose (fiber) is indigestible; passes through the digestive system and aids in digestion/pooping.
  • Fats and oils are energy-dense biomolecules; also used to build lipid-based structures.
  • Proteins eaten are digested into amino acids and reused to build the body's own proteins; the nitrogen in amino acids is a critical nutritional consideration.
  • Nucleic acids (DNA, RNA) are consumed in small amounts in foods; they are digested into nucleotides and used as building blocks for own nucleic acids and energy carriers like ATP; eating DNA from other organisms does not transfer their information to you (no cross-species genetic information transfer in that sense).
  • In nucleic acids, nitrogen and phosphorus are key elements in addition to H, O, and C.
• All biomolecules contribute to structure and function in living organisms; nitrogen presence in proteins is particularly important for growth and metabolism.
• Quick note on digestion and information transfer:
  • When you eat DNA or RNA, your body breaks them down into nucleotides and reassembles them using your own genetic information; there is no transfer of functional genetic information from the food’s DNA to your genome.
• Key elemental composition highlights:
  • Major atoms in biomolecules: H, O, C, N, P (and often S for proteins and other biomolecules).
  • Sulfur (S) is the other important element that contributes to biological mass and function (e.g., in certain amino acids like cysteine and methionine).
• Summary of roles:
  • Carbohydrates provide quick and stored energy; some serve structural roles (e.g., cellulose in plants).
  • Proteins perform catalysis, structural roles, signaling, transport, and more; nitrogen-containing.
  • Nucleic acids store genetic information (DNA), participate in gene expression (RNA), and transfer cellular energy (ATP as a nucleotide).
  • Lipids form membranes, store energy, and include steroidal compounds; include phospholipids containing phosphorus.

Quick recap and connections

• Core ideas:
  • Atoms bond by sharing electrons; patterns of bonding follow the HONKP mnemonic to predict valence (H=1, O=2, N=3, C=4, P=5; P can sometimes form three bonds).
  • The air composition (N₂, O₂, CO₂) influences chemistry and climate; humidity depends on temperature.
  • Water’s polarity and its autoionization drive pH; bicarbonate and carbonate buffering stabilize pH in biological systems (most notably blood at ~7.4).
  • Biomolecules are built from three simple elements (H, O, C) plus N and P (and S in some cases); each category has a distinct subunit and function.
  • Digestion transforms biomolecules into usable components (sugars, amino acids, nucleotides) for growth, energy, and maintenance; digestion does not transfer genetic information from food DNA to our genome.

Equations and key symbols (for quick reference)

• pH equation: $\mathrm{pH} = -\log_{10}[\mathrm{H^+}]$
• Water autoionization: $\mathrm{H_2O} \rightleftharpoons \mathrm{H^+} + \mathrm{OH^-}$
• Carbonate buffering (simplified):
  $\mathrm{CO<em>2} + \mathrm{H</em>2O} \rightleftharpoons \mathrm{H<em>2CO</em>3}$
  $\mathrm{H<em>2CO</em>3} \rightleftharpoons \mathrm{H^+} + \mathrm{HCO_3^-}$
• Biomolecule subunits and composition (conceptual):
  • Carbohydrates: sugar units; empirical formula typically $\mathrm{CH<em>2O}$ (or $(\mathrm{CH</em>2O})_n$).
  • Proteins: amino acids; elements $\mathrm{H, O, N, C}$; nitrogen-rich.
  • Nucleic acids: nucleotides; elements $\mathrm{H, O, N, C, P}$.
  • Lipids: fatty acids and/or glycerol backbones; elements $\mathrm{H, O, C}$ (and sometimes $\mathrm{P}$ in phospholipids).

Closing note

• This lecture emphasizes the foundational chemistry necessary to understand biology: atoms and bonding, the chemistry of air and water, pH and buffering, and the four biomolecule classes along with their foods-related roles and digestion implications. It also highlights practical drawing strategies for molecules and the importance of nitrogen-containing biomolecules in health and nutrition.