Miller-Urey and Biochemistry Vocabulary Flashcards

Miller-Urey Experiment and Abiotic vs. Biotic Concepts

The Miller-Urey setup is a repeatable, simplified version of the idea that life’s building blocks can arise from non-living (abiotic) starting materials under conditions thought to resemble primitive Earth.
Process: take simple abiotic compounds (not uniquely tied to living systems) and add ingredients believed to exist on primitive Earth; result is formation of organic compounds.
Outcome: these experiments can produce amino acids; some variations also produce nucleic acids; some even form small peptides by linking amino acids together (two or three amino acids).
Goal: to understand how life began and what constitutes life; still a major open question; Nobel Prize-level significance if a full origin of life were demonstrated, which is why the meta-question remains unresolved.
Common misunderstanding: the question “Your experiment showed that natural forces could make organic compounds. That proves life exists, or all of the above?” The answer emphasized here: it demonstrates abiotic synthesis of organic compounds, not that life itself is created by these processes. So, it demonstrates the first part ( abiotic to organic compounds ), but not definitive proof that life began or that life exists from these processes alone.
Timeline and scope: Miller-Urey experiments began in the 1950s and are still performed today in various forms; they contribute to understanding prebiotic chemistry, but no single experiment has definitively shown the complete origin of life.

Abiotic vs. Biotic: Key Definitions and Examples

Abiotic: defined as not bound to living systems; not produced by living cells; found broadly on Earth and elsewhere; abiotic compounds are not inherently biological.
Biotic: characteristic of or derived from living systems; molecules typically associated with biology.
Overlap with organic compounds: many organic molecules are found both in living systems and can be synthesized abiotically in the lab; the distinction is about typical natural occurrence vs. laboratory production.
Urea: famous as a compound historically used to illustrate that some “biotic” molecules could be made in the lab; not inherently restricted to living systems.
Nucleic acids: almost never found outside living systems in nature, though some have been detected in meteorites; generally considered biotic.
Amino acids: overwhelmingly associated with living systems, but a few have been found outside living systems on Earth; many amino acids have been synthesized abiotically in laboratories and in meteorites.
ATP: energy-carrying molecule that is produced and utilized by living systems; discussed as having analogs or lab syntheses, illustrating abiotic/biotic boundaries.
Overall: the Miller-Urey and related experiments have shown that abiotic starting materials can yield amino acids and other biotic-like molecules, challenging the idea that such molecules could only arise within living cells.

From Abiotic Compounds to Biologically Relevant Molecules

Simple abiotic compounds can give rise to amino acids and, in some experiments, nucleic acids.
Some experiments even show formation of short peptides (links between amino acids).
The broad goal remains: to understand how life could begin from non-living chemistry; this is still an open, Nobel-worthy question.

Hydrocarbons: Structure, Properties, and Energy Content

Definition: hydrocarbons are composed exclusively of hydrogen and carbon.
They are hydrophobic (water-fearing) and generally uncharged; no partial charges typical of polar covalent bonds between C and H.
Energy storage: breaking hydrocarbon bonds releases large amounts of energy; this underlies why fats (long hydrocarbon chains) are energy-dense and why fuels like gasoline and oil store a lot of energy.
Structure: can be planar or nonplanar; many hydrocarbons are arranged in rings or long chains; double bonds introduce planarity in the region around the bond; saturated chains (single bonds) are more flexible and three-dimensional.
Common representation: long chains like ext{CH}2- ext{CH}2- ext{CH}2- ext{CH}2- ext{…} (repeating ext{CH}_2 units).
Hydrophobicity and lack of charge explain why hydrocarbons are not water-soluble and do not participate in hydrogen bonding with water.
Distinction from functional groups: hydrocarbons themselves do not form hydrogen bonds and are not charged; many biological lipids include hydrocarbon tails that are hydrophobic, affecting membrane formation.

Functional Groups: Seven Key Groups and Their Hydrogen-Bonding/Charge Properties

Seven functional groups discussed: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl.
A key takeaway: all but methyl can participate in hydrogen bonding under physiological conditions.
- Hydroxyl (-OH): oxygen can form hydrogen bonds; hydrogen can also participate in hydrogen bonding.
- Carbonyl (C=O): the carbonyl oxygen is a hydrogen-bond acceptor; contributes to polarity.
- Carboxyl (-COOH): combines hydroxyl and carbonyl features; can donate and accept hydrogens; can form multiple hydrogen bonds; can be deprotonated to carboxylate (-COO^-).
- Amine (-NH2): can accept a proton (acts as a base); can be protonated to -NH3^+ in physiological conditions.
- Sulfhydryl (-SH): sulfur is less electronegative than oxygen but can participate in hydrogen bonding to some extent; forms thiols.
- Phosphate (-PO4^{n-}): strongly acidic; bears negative charges under physiological conditions; highly capable of hydrogen bonding due to multiple oxygens and a negative charge.
- Methyl (-CH3): the only group among the seven that does not form hydrogen bonds and remains nonpolar/hydrophobic.
Practical implication: the presence of these groups on larger biomolecules (proteins, nucleic acids, lipids, carbohydrates) largely determines hydrophobicity/hydrophilicity, solubility, and interaction with membranes.
Phosphate is explicitly noted as the functional group that is always charged at physiological pH due to its negative charges.
Some groups are titratable (can gain or lose protons depending on pH): amino (can be protonated to +1), carboxyl (can be deprotonated to -), phosphate (can be deprotonated with pH changes).
Hydrophobic vs hydrophilic classification is driven by surrounding functional groups: methyl drives hydrophobicity; carboxyl and phosphate drive hydrophilicity and potential charge.
Example: a molecule with many methyl groups tends to be membrane-associated (hydrophobic), whereas molecules rich in carboxyl groups are water-soluble and interact with polar surroundings.

Planar vs. Three-Dimensional Carbon Arrangements and Isomerism

Planarity vs. tetrahedral geometry around carbon:
- Double bonds (C=C) create planar regions within molecules.
- Single bonds (C–C) allow sp3 hybridization, yielding three-dimensional, tetrahedral geometries.
Cis-Trans isomerism: configuration around a C=C double bond
- Cis isomer: substituents are on the same side of the double bond.
- Trans isomer: substituents are on opposite sides of the double bond.
Enantiomers: mirror-image isomers around a chiral center or a set of carbon–carbon bonds; important in pharmacology because different enantiomers can have very different biological effects.
Important clinical note: drug side effects often arise from enantiomeric impurities; regulators increasingly require enantiomerically pure drugs for new formulations, though older drugs may still be mixtures.
Example contrasts in steroids: Estradiol and testosterone share a common four-ring hydrocarbon core (orange core in diagrams); modifications (decorating rings with various functional groups) change hormonal activity; these are not true isomers in the strict sense when comparing one molecule to another if the atoms are not the same (e.g., an extra hydrogen can alter atom counts and thus disqualify strict isomer status).
Key takeaway: structural isomers require the same atoms; small changes like adding or removing an H can change whether two molecules are isomers.

Steroids: Estradiol, Testosterone, and Their Core Structure

Estradiol and testosterone are structurally related but not simply isomers in a strict sense; they differ by functional groups attached to the same ring framework.
Core feature: a four-ring hydrocarbon framework (steroid nucleus) with a hydrophobic interior.
Decoration: functional groups added to the rings determine the steroid’s biological role (e.g., female vs. male sex hormones).
The hydrocarbon core is highly hydrophobic; most of the molecule is nonpolar, with only specific functional groups introducing polarity.
Takeaway: in steroids, changing the decorations (functional groups) changes function dramatically, even though the core skeleton is conserved.

Which Functional Groups Cannot Form Hydrogen Bonds?

Answer: Methyl is the primary functional group that cannot form hydrogen bonds in the list of seven.
Other groups (hydroxyl, carbonyl, carboxyl, amine, sulfhydryl, phosphate) are capable of hydrogen bonding either as donors or acceptors.
The ability to hydrogen-bond is tied to electronegativity differences and available lone pairs on electronegative atoms (O, N, S, P in certain contexts).

Charge States and pH: Which Groups Are Always Charged at Physiological pH?

Lead answer: Phosphate is always charged at physiological pH due to its multiple oxygens and resonance; present in ATP, DNA/RNA backbones, etc.
Other groups can be charged depending on pH:
- Amino group can be protonated to a positive charge (base behavior).
- Carboxyl group can be deprotonated to a negative charge (acid behavior).
- Phosphate can be negatively charged (and can act as an acid in certain contexts).
Some groups are titratable: the ability to gain or lose protons depending on pH (e.g., amino, carboxyl, phosphate).
Some groups are rarely or never charged under physiological conditions (e.g., methyl—never charged; carbonyl is generally not charged, though its oxygen can be a hydrogen-bond acceptor).
Important concept: “charged” in biology typically means a net positive or negative charge; “partially charged” refers to polar covalent interactions, not full ionic charges.
Hydration and solubility correlate with charge state, hydrogen bonding capacity, and polarity.

Hydrophobicity, Hydrophilicity, and Solubility: How Functional Groups Shape Behavior

Hydrophobic bonds: methyl groups are the best example among the seven for promoting hydrophobic interactions.
Hydrogen bonding and solubility: groups capable of hydrogen bonding generally increase water solubility and interactions with polar surroundings.
Partial charges can contribute to solubility, but full ionic charges (as seen in phosphate, carboxylates, ammonium salts) strongly enhance water interactions.
Amphipathic molecules (having both hydrophobic and hydrophilic parts) include emulsifiers and membrane-forming lipids; they can stabilize interfaces and enable solubilization of otherwise water-insoluble substances.
Membranes rely on amphipathic properties to form lipid bilayers: hydrophobic tails face inward; hydrophilic heads face water.

Energy and Metabolism: ATP and Hydrocarbon Energy Release

ATP as a high-energy molecule: energy release is associated with removing a phosphate group to form ADP, with subsequent regeneration of ATP by phosphorylation.
In the context of energy release, removing a single phosphate is highlighted as a common metabolic step to release energy in some pathways; the phosphate groups are typically highly charged, contributing to energy transfer and solubility considerations.
If you break a long-chain hydrocarbon completely into atoms, you release a large amount of energy, often more than ATP-derived energy, due to the large number of carbon–hydrogen bonds.
This comparison emphasizes why fats (long hydrocarbon chains) are highly energy-dense foods.

Practical Implications and Real-World Relevance

How to evaluate biomolecules: look for functional groups to infer hydrophobic/hydrophilic nature, hydrogen-bonding capability, and potential charge states at physiological pH.
Drug design considerations: enantiomerism and stereochemistry influence pharmacodynamics and pharmacokinetics; older drugs may be mixtures of isomers; newer regulations push for enantiomerically pure formulations when possible.
Biological membranes and transport: amphipathic molecules are central to membrane structure and function; methyl-rich or hydrophobic regions favor interactions with lipid interiors, while polar groups interface with aqueous environments.
Chapter progression and difficulty: the course notes indicate increasing complexity across chapters, with chapter five presenting higher difficulty than chapters one through four; topics introduced here lay groundwork for later chapters, including lipid membranes and more advanced functional-group chemistry.

Quick Reference: Key Terms and Concepts

Abiotic vs. Biotic: non-living vs. living-system-associated; overlap with organic chemistry.
Abiotic synthesis: formation of organic molecules from inorganic precursors under simulated early-Earth conditions (as in Miller-Urey).
Hydrophobic vs. hydrophilic: water-fearing vs. water-loving; driven by polarity and hydrogen-bonding capability.
Hydrogen bond donors/acceptors: groups like -OH, -NH, -C=O, -SOH, -PO4^{n-} can participate; methyl cannot.
Charge states and pH: acidic (donate H+), basic (accept H+); phosphate, carboxyl, and amino groups are key titratable groups.
Isomers: structural, cis/trans, enantiomers; strict isomerism requires identical atom counts; small changes can remove isomer status.
Steroids: four-ring hydrophobic core with variable decorations; function driven by substituents rather than core skeleton alone.
Amphipathic molecules: molecules with both hydrophobic and hydrophilic parts; critical for membranes and emulsification.
Practical takeaways: functional-group analysis informs solubility and membrane behavior; drug side effects can be tied to enantiomers; aqueous chemistry vs. lipid environments governs biomolecular behavior.

Note: If you want, I can convert any section into flashcards or create a one-page cheat-sheet with the most test-relevant bullets for quick review.