AS

Isomers, Enantiomers, Functional Groups, and ATP - Vocabulary Flashcards

Isomers and Structural Features

  • Isomers are compounds with the same molecular formula but different three‑dimensional structures, leading to different properties and behaviors.
  • Types mentioned:
    • Structural (constitutional) isomers: differ in covalent connectivity/arrangement of atoms (e.g., branched versus linear skeletons).
    • Stereoisomers: same connectivity but different spatial arrangement.
    • Enantiomers: non-superposable mirror images of each other (like left and right hands).
    • Cis–trans isomers: differ in spatial arrangement around a double bond or rigid ring.
  • Importance: small changes in structure can lead to large differences in activity, pharmacology, and biology.

Structural Isomers vs. Stereoisomers

  • Structural isomers:
    • Differ in covalent arrangement of atoms.
    • Examples shown as linear versus branched carbon skeletons.
  • Stereoisomers (enantiomers and diastereomers):
    • Enantiomers are mirror images; not superimposable.
    • Left‑hand (L) and right‑hand (D) designations describe the orientation of a chiral center; these are often used in pharmacology to indicate different activities.
  • Analogy used: left hand vs right hand, which are the same in composition but different in structure; same molecule, different orientation.

Enantiomers and Pharmacology

  • Enantiomers can have markedly different biological effects; one may be active, the other inactive or even harmful.
  • Examples discussed:
    • Ibuprofen: the active component is the S enantiomer in many formulations; the corresponding (R) enantiomer can be less active or inactive in reducing inflammation/pain.
    • Albuterol (a bronchodilator for asthma): enantiomers can have different activity on airway relaxation; the active form can vary by compound.
    • L‑DOPA vs D‑DOPA: L‑DOPA reduces Parkinson’s symptoms; D‑DOPA has no therapeutic effect.
  • General takeaway: organisms are highly sensitive to subtle stereochemical variations; this can be life‑impacting in medicine.

Enantiomers: Practical Takeaways

  • In many drugs, one enantiomer is pharmacologically active while the other is inactive or less effective.
  • The activity can be reversed or differ depending on the specific compound (as with ibuprofen and albuterol examples).
  • Ethical/medical implications: drug design and regulation often require testing and sometimes approving specific enantiomers to ensure safety and efficacy.

A Concrete Look: L‑DOPA and Parkinson’s Disease

  • L‑DOPA (L‑dihydroxyphenylalanine) reduces the symptoms of Parkinson’s disease.
  • R‑DOPA has little to no therapeutic effect for the disease symptoms.
  • This illustrates how the same molecular formula arranged differently can have dramatically different clinical outcomes.

Functional Groups: Structure, Function, and Occurrence

  • Key concept: Functional groups are specific groups of atoms attached to a carbon skeleton that largely determine the behavior and reactivity of a molecule.
  • They can replace hydrogens on carbon backbones and dramatically alter molecular function.
  • Common functional groups discussed:

Hydroxyl Group (–OH)

  • Structure: oxygen bound to hydrogen on a carbon skeleton.
  • Properties: polar; forms hydrogen bonds due to the electronegative oxygen.
  • Example mentioned: ethanol, which contains a hydroxyl group and is the alcohol in beverages.

Carbonyl Group (C=O)

  • Carbonyls can be positioned differently, giving different compounds with the same formula.
  • Types:
    • Aldehyde: carbonyl at the end of the carbon chain.
    • Ketone: carbonyl within the carbon chain.
  • Examples:
    • Acetone: a ketone (often used as nail polish remover).
    • Propanal: an aldehyde.
  • Sugars terminology:
    • Ketose: sugars with ketone groups.
    • Aldose: sugars with aldehyde groups.
  • Mnemonic reminder: position of the carbonyl (end vs middle) helps distinguish aldehydes vs ketones.

Carboxyl Group (–COOH)

  • Structure: a carbonyl attached to a hydroxyl on the same carbon.
  • Behavior: acts as an acid, able to donate a proton (H⁺) in solution.
  • Relevance: carboxylic acids (organic acids) influence acidity and pH of solutions.

Amino Group (–NH₂)

  • Structure: nitrogen attached to one or more carbons with hydrogens.
  • Behavior: acts as a base by accepting a proton (H⁺).
  • Relevance: amino groups are found in amino acids; they are essential to protein building blocks.
  • Example: cysteine as an amino acid containing an amino group.

Sulfhydryl Group (–SH)

  • Structure: sulfur bound to hydrogen.
  • Behavior: can form disulfide cross‑links, which stabilize protein structures (strong bonds between sulfur atoms).
  • Concept: thiol compounds contain –SH groups.

Phosphate Group (–PO₄H₂ or –PO₄)

  • Structure: phosphate group is highly electronegative and participates in energy‑releasing reactions.
  • Relevance: phosphate groups are important in biochemical phosphorylation reactions and energy transfer.
  • Example mentioned: a glycerol phosphate moiety involved in metabolism.
  • General idea: phosphate-containing compounds participate in energy reactions and signaling.

Methyl Group (–CH₃)

  • Structure: a carbon bonded to three hydrogens.
  • Relevance:
    • DNA methylation (e.g., 5‑methylcytosine) can turn genes on or off, affecting gene expression.
    • Methyl groups influence the shape and function of steroids (e.g., estradiol vs testosterone) and other molecules.
  • Example in context: five‑methylcytosine is a DNA modification that can regulate gene expression.

Hormones: Steroid Backbone and Functional Group Variations

  • Hormones like estradiol and testosterone share a common four‑ring steroid skeleton (three six‑member rings and one five‑member ring).
  • What differentiates them are the attached functional groups and their positions:
    • Estradiol vs testosterone: differences in functional group attachments alter the molecule’s shape and function.
    • Presence or absence of methyl groups can dramatically alter behavior and receptor interaction.
  • Takeaway: identical carbon skeletons with different functional groups lead to vastly different biological roles.

Functional Group Summary: Structure–Function–Location

  • For each group, know:
    • Structure: what atoms and bonds define the group.
    • Function: typical chemical behavior (acid/base, polarity, bonding).
    • Common locations: where you’ll most likely find the group in biomolecules.
  • The approach: know structure, function, and common locations to predict behavior in biological systems.

Gene Expression and the Central Dogma

  • Concept introduced: gene expression is the flow of genetic information from DNA to RNA to protein.
  • Central dogma (as presented):
    • \text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}
  • Clarification: DNA is informational; RNA is an intermediate; protein is the final functional product.
  • Practical implication: methylation of DNA (adding methyl groups) can regulate gene expression by turning genes on or off.

DNA Methylation and Gene Regulation

  • Methylation: addition of methyl groups to DNA (e.g., 5‑methylcytosine) can influence gene expression.
  • Effects on genes:
    • Methylation can turn genes on or off, altering transcription and downstream protein production.
  • Broader context: epigenetic regulation via methylation is a major mechanism controlling when and how genes are expressed.

ATP: Energy Currency of the Cell

  • ATP stands for adenosine triphosphate:
    • Structure: adenosine + three phosphate groups (–P–P–P).
    • The three phosphate groups are linked by high‑energy bonds that store potential energy.
  • Energy release via hydrolysis (dephosphorylation):
    • Reaction: \mathrm{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi} + \text{energy}
    • The released energy is used to power cellular processes.
  • Energy storage via phosphorylation (reversible):
    • Reaction: \mathrm{ADP} + \mathrm{P_i} \rightarrow \mathrm{ATP} + \text{energy}
  • Note: ATP is commonly referred to as the energy currency of the cell because many reactions depend on its hydrolysis or recharging through phosphorylation.
  • Visual reference mentioned: ATP consists of an adenosine molecule attached to three phosphate groups; energy release occurs when a phosphate is cleaved.

Connections to Biology and Real-World Relevance

  • The lecture emphasizes how tiny structural differences (isomers, functional groups) have big biological consequences in medicine and physiology.
  • Real‑world relevance includes drug design, pharmacology, and understanding disease mechanisms (e.g., Parkinson’s disease treated with L‑DOPA).
  • Ethical and practical implications: stereochemistry and functional group positioning can determine drug safety and effectiveness; regulatory processes often hinge on these details.

Quick Review Tips

  • Distinguish structural isomers (connectivity) from stereoisomers (3D arrangement).
  • Recognize enantiomers and why one may be pharmacologically active while the other is not.
  • Memorize key functional groups and their general properties: hydroxyl (polar, hydrogen bonding), carbonyl (aldehyde vs ketone), carboxyl (acid), amino (base), sulfhydryl (disulfide bonds), phosphate (energy transfer), methyl (gene regulation, hormone function).
  • Recall the central dogma: \text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}.
  • Understand ATP hydrolysis and phosphorylation as energy transfer processes essential for cellular work.
  • Connect steroid backbone to function via attached groups (estradiol vs testosterone) and the impact of methylation on gene expression and hormone activity.