Foundations of Chemistry in Biology: Atoms, Bonds, and the Cell

Atoms and the Hierarchy of Biological Organization

• Biology can be viewed hierarchically: from big to small or small to big. In BIO 181 (companion to BIO 182), we start with small stuff and build up: fundamental units of matter -> how atoms bond into molecules -> the functionality of those molecules -> organelles within cells (mitochondria, Golgi, endoplasmic reticulum) -> cell function and gene expression -> tissues and their interactions. In BIO 181, life’s fundamental unit is the cell; in BIO 182, you expand to tissues, organ systems, ecosystems, and evolution.
• Life is organized around molecules and their interactions, and big-picture organization emerges from small parts working together.

Matter, Chemistry, and Life

• Chemistry is the study of matter and chemical reactions; life is a vast network of ongoing chemical reactions inside every cell.
• You are a “big bag of chemical reactions” as reactions occur trillions of times each second in your cells; if these reactions stop, the organism dies.
• To understand biology, you must understand chemistry because matter and reactions underlie all biological processes.

Fundamental Unit of Life: The Cell

• The cell is the fundamental unit of life.
• Cells contain organelles (e.g., mitochondria, Golgi, endoplasmic reticulum) built from molecules that have specific functions.
• Different tissues share common functional themes (e.g., neurological, respiratory, muscular tissues) and work together within organ systems.
• Some organisms are unicellular (e.g., bacteria, protozoa); others are multicellular with trillions of cells.
• Human body cell count: about
  • On average, roughly $10^{13}$ cells (about 10,000,000,000,000), though it varies by person.
  • Cell numbers increase with growth from baby to adult height and size.
• Tissues organize into organ systems; tissues talk to one another and coordinate function.

Chemistry: Matter and States of Matter for Biology

• Matter exists in four states, but biologically relevant states are typically three:
  • Solid (e.g., ice under cold conditions for some substances)
  • Liquid (water is the primary biological liquid)
  • Gas (vapor phase; water vapor in the air at sufficient temperature)
• In biology, plasma is not a typical state for common biomolecules in cells.
• Water has standard phase transitions: solid to liquid to gas occur with changes in thermal energy (temperature). In Celsius terms:
  • Ice ↔ Water occurs around 0°C; Water ↔ Steam occurs around 100°C.
• Other elements (e.g., nitrogen, mercury) can also change phase under extreme conditions, but biological systems rely on liquid water at around 0–100°C and stable molecular forms under physiological conditions.
• Quick practical note: in chemistry class you may be asked to memorize precise melting/boiling points; in biology, the big idea is that matter changes state with energy input/output and can transition between solid, liquid, and gas depending on temperature and pressure.

Atoms, Elements, and the Periodic Table

• Matter that composes everything is made of atoms; the periodic table organizes elements by proton count (atomic number) and electron configuration.
• Protons and neutrons reside in the nucleus; electrons orbit in shells around the nucleus.
  • Protons: positive charge; determine the element by their count in the nucleus.
  • Neutrons: neutral; contribute to atomic mass.
  • Electrons: negative charge; orbit in electron shells and determine chemical behavior.
• Element example basics:
  • Hydrogen: $1$ proton (atomic number $Z=1$)
  • Helium: $Z=2$
  • Carbon: $Z=6$, common isotope masses include $^{12}C$ (mass number 12) and $^{14}C$ (mass number 14)
  • Oxygen: $Z=8$, common isotope $^{16}O$ (mass 16)
• Atomic mass notation and isotopes:
  • Carbon-12 vs Carbon-14 differ in the number of neutrons while having the same number of protons: $^{12}<em>{6}C ext{ vs } ^{14}</em>{6}C$ with 6 protons in both, but 6 vs 8 neutrons respectively.
• Human body elemental composition (roughly):
  • Major elements: $ext{O} <br /> ightarrow ext{65 ext{ extperthousand}}$, $ext{C} <br /> ightarrow ext{~18 ext{ extperthousand}}$, $ext{H} <br /> ightarrow ext{~10 ext{ extperthousand}}$, $ext{N} <br /> ightarrow ext{~3 ext{ extperthousand}}$ (percentages approximate; the transcript notes ~65% O, ~18% C, ~10% H, ~7% other).
  • Earth's crust composition: ~26 ext{ extpercent}$ ext{Si}, 8 ext{ extpercent} ext{Al}, 3 ext{ extpercent} ext{Ca}, 5 ext{ extpercent} ext{Fe}, 8 ext{ extpercent} ext{others}.
• The four big elements that make up about $96.3 ext{ extpercent}$ of you and me are O, C, H, and N; the remaining roughly $3.7 ext{ extpercent}$ come from seven trace elements (examples include Ca, P, K, S, Na, Mg, Cl, plus others like Fe, Zn, Mn, Cu, I, F, B, Cr, Li, Sn, Si, etc.).
• The idea is that carbon-based chemistry drives biology because carbon can form up to four covalent bonds, enabling complex and diverse molecular structures.
• Atmospheric composition (air we breathe): primarily nitrogen and oxygen; roughly ~$78 ext{ extpercent}$ N and ~$21 ext{ extpercent}$ O with other gases making up the rest.

Bonding and Molecular Shape

• Bonding principle: Shape dictates function. The 3D arrangement of atoms in a molecule determines its behavior and role in biology.
• Isomers illustrate how same atoms and counts can yield different shapes and functions:
  • Structural isomers (e.g., butane vs isobutane): both have the same number and type of atoms, but are connected differently, leading to different properties (e.g., ignition temperature, fuel characteristics).
  • Enantiomers (mirror images like left vs right hands): same bonding pattern and connectivity but non-superimposable; can have different biological activities.
• Bond formation basics:
  • Atoms seek full outer electron shells (octet rule) or full shells depending on the context.
  • First electron shell capacity: $2$ electrons; second shell: $8$ electrons; third shell: $8$ electrons (for biology-focused shells).
  • Octet rule: most stable configurations have full outer shells (eight electrons in outermost shell) or a full first shell (2 electrons) if that is the outermost. Partially filled outer shells are unstable.
• Example of ionic bonding (NaCl):
  • Sodium has $11$ electrons: two in the first shell, eight in the second shell, and one in the third shell.
  • Chlorine has $17$ electrons: two in the first shell, eight in the second shell, and seven in the third shell.
  • Sodium tends to give up its one outer electron to chlorine, yielding Na⁺ and Cl⁻, achieving full shells for both and forming stable ions.
  • Overall reaction: $ext{Na} <br /> ightarrow ext{Na}^+ + e^-$ and $ext{Cl} + e^- <br /> ightarrow ext{Cl}^-$, leading to $ext{Na}^+ ext{Cl}^-$ and often salt (NaCl).
• Electronegativity:
  • Trend: more electronegative to the top-right of the periodic table; less electronegative toward the bottom-left.
  • Highly electronegative nonmetals (in biology-relevant elements) include chlorine (Cl), fluorine (F), and oxygen (O).
  • Electronegativity drives how atoms attract electrons in bonds and helps determine bond type (ionic vs covalent) and polarity.
• Electron affinity, while a chemistry term, is related to the energy released when atoms gain electrons; biology-focused discussions often emphasize how electron distribution and energy relate to metabolism rather than the numerical values.
• Ion formation and metabolism:
  • Gaining or losing electrons changes the charge state of atoms (e.g., O gaining an electron becomes O⁻ in a negatively charged ion), which drives bonding and energy flow in metabolism.
  • In cellular respiration, high-energy electrons are transferred and processed to extract usable energy (glycolysis → TCA cycle → electron transport chain), highlighting the role of electron energy in biology.

The Octet Rule, Shells, and Stability

• Shells and energy: inner shells are lower in energy; outer shells are higher in energy and determine reactivity.
• Electron capacity per shell (biology-focused):
  • First shell: max $2$ electrons
  • Second shell: max $8$ electrons
  • Third shell: max $8$ electrons
• Stability and electron transfer:
  • Atoms seek to fill shells to be stable; they may gain or lose electrons to achieve full shells.
  • When electrons move to fill a lower-energy shell (e.g., from the second to the first), energy is released.
• Example explanation: sodium (Na) and chlorine (Cl) achieve octets via electron transfer, leading to stable ions and ionic bonding in NaCl.

The Periodic Table and Biology-Relevant Trends

• Biology relies on a subset of elements that appear in the body and in biological molecules.
• Biological relevance by position:
  • Left side: metals (often reactive, forming cations in biology)
  • Right side: nonmetals (often anions or covalently bonding partners)
  • The very rightmost noble gases are largely inert and not reactive under normal biological conditions.
• Common biological trends discussed:
  • First-row elements (H, Li, Na, K) often form positive ions (plus-one in their outer shell).
  • Alkaline earth metals (e.g., Ca, Mg) commonly form plus-two species.
  • Halogens (e.g., Cl, F, I) tend to need one more electron to fill their outer shell (often forming negative ions or covalent bonds with other atoms).
• The four major elements critical to biology: O, C, H, N (together make up the vast majority of body mass).
• The other seven essential elements (trace nutrients) support various physiological processes (Ca, P, K, S, Na, Mg, Cl, plus others like Fe, Zn, Mn, Cu, I, B, Cr, Li, etc.). They come from diet and water.
• Practical dietary takeaway:
  • You obtain most trace elements through foods and water; vegetables are especially valuable for micronutrients.
  • Dairy products provide calcium; eggs provide sulfur; potassium comes from bananas; iron from meat and fortified foods; zinc from spinach or other sources; magnesium from greens and supplements; phosphorus from many foods; chlorine mainly comes from water and food usage.
  • Ultra-purified water can be low in trace minerals; regular water and a balanced diet support micronutrient intake.
• Composition of the air we breathe: mostly nitrogen and oxygen, with trace amounts of other gases.

Energy in Biological Molecules: Where Is the Energy?

• Carbohydrates, lipids, and proteins all store energy; energy content comes from the bonds in these molecules.
• Calories are a measure of energy content; the energy available from nutrients comes from the electrons and the bonds they form.
• The energy resides primarily in the bonds of molecules; when bonds break and rearrange, energy is transferred or transformed in metabolic processes.
• In essence: energy in macromolecules is stored in chemical bonds, which involve electrons and their arrangements.

Energy Levels and Electron Movement in Biological Contexts

• The energy value of electrons depends on which shell they occupy:
  • Electrons in the inner shells have lower energy; outer-shell electrons have higher potential energy.
  • When electrons move from a higher-energy shell to a lower-energy shell (e.g., 3rd to 2nd, 2nd to 1st), energy is released as photons or heat.
• If a shell is not full, atoms are reactive and will either gain electrons from or donate electrons to other atoms to achieve stability (full outer shell or full first shell).
• The octet rule and shell filling drive chemical bonding and reactions that power biological processes.

Nutritional Elements and Human Health

• Major elements and their roles (examples):
  • Oxygen (O): ~65% of body mass; vital for respiration and energy production.
  • Carbon (C): ~18%; backbone of organic molecules.
  • Hydrogen (H): ~10%; participates in water and organic molecules.
  • Nitrogen (N): ~3%; essential for amino acids and nucleic acids.
• Trace elements and dietary sources (illustrative list):
  • Calcium (Ca): dairy products; important for bones and signaling.
  • Phosphorus (P): dairy, meat; part of ATP and nucleic acids.
  • Potassium (K): bananas; essential for nerve function and fluids balance.
  • Sulfur (S): eggs; present in some amino acids (cysteine, methionine).
  • Sodium (Na): table salt; critical for fluid balance and signaling.
  • Magnesium (Mg): found in vitamins and greens; cofactor for enzymes.
  • Chlorine (Cl): from salt and water; important for osmotic balance and digestion.
  • Iron (Fe): in meats and fortified foods; essential for hemoglobin to carry oxygen.
  • Zinc (Zn), Manganese (Mn), Copper (Cu), Iodine (I), Fluorine (F), Boron (B), Chromium (Cr), Lithium (Li), Tin (Sn), Silicon (Si), etc.
• The key takeaway: a balanced intake of essential and trace elements is necessary; deficiencies can have severe health consequences (e.g., insufficient copper or iron disrupts life-sustaining processes).

The Cell, Tissues, and Real-World Relevance

• The cell’s energy production is central to life; organelles like mitochondria power the cell by generating ATP through processes including glycolysis, the TCA cycle, and the electron transport chain.
• Tissues and organ systems coordinate to maintain homeostasis and enable complex life.
• Real-world relevance: understanding atoms, bonds, and energy helps explain metabolism, nutrition, pharmacology, and disease mechanisms.

Quick Takeaways and Core Concepts

• Shape dictates function: molecular structure determines biological roles; changing connectivity or spatial arrangement changes function (e.g., butane vs isobutane; enantiomers).
• Octet rule and electron shells govern bonding and stability; atoms seek full outer shells via bonding or electron transfer.
• Energy in biology is stored in chemical bonds; the energy of electrons in different shells contributes to overall metabolic energy flow.
• The four major elements (O, C, H, N) dominate body mass; trace elements support many physiological processes; diet and water are primary sources.
• The basic chemical ideas underpin all biology: atoms, isotopes, bonding, electronegativity, ionic/covalent bonds, energy transfer, and the cellular level of organization.

References and Notable Details Discussed in the Lecture

• Personal/professional context about appearance and respect in academic settings (not exam content): a reminder that presence and engagement can influence recommendations and perceptions by senior faculty.
• Reiteration that “calories = energy” and that energy in macromolecules comes from the bonds, with electrons as the fundamental carriers of energy in chemistry relevant to biology.
• The teacher’s emphasis on repeating the key maxim: "Shape dictates function" and the ongoing repetition of the concept throughout the course.
• Acknowledge that the human body contains about ~$10^{13}$ cells on average, with variations by individual growth and body size.