Biomolecules: Functional Groups, Polymers, and Protein Structure

Carbon Backbone and Bonding

• Carbon as the core of organic molecules: backbone can form long chains, rings, and branches because each carbon can form up to four covalent bonds.
• Why carbon can bond four times: carbon has a nucleus with six protons (Z = 6) and six electrons total; two electrons fill the inner shell and four electrons occupy the valence shell, enabling four covalent bonds.
• Implication: carbon–carbon and carbon–heteroatom bonds create diverse, large organic structures with varying polarity.

Exam logistics and course announcements (from transcript)

• Exam 1 is a week from today (next Thursday).
• If you need to schedule with the DRC, do so today or tomorrow to secure a testing spot.
• A practice exam was posted; some image issues may be fixed later today.
• Practice exam is not identical to the real exam; it includes a mix of applied and recall questions.
• Learning objectives (found on slides or in the textbook) guide what you’re expected to do on the exam.
• A practice quiz for today/tomorrow’s material (biological molecules) will be posted for extra practice.
• Chapter five prereading (Pearson) is due before class on Tuesday; chapter five covers material on the exam.
• Tuesday will include exam review; first case study was due tonight (11:59 PM). The instructor emphasizes sharing thought processes for full credit.
• An explanatory video is posted to show how to approach case study questions; it provides a jump start but isn’t required if you can do the questions independently.
• Slides for today (nine-four) cover functional groups and beginning biological molecules like proteins; a large slide deck titled “Complete Biological Molecules” covers all material before the exam.
• The instructor notes that the “complete biological molecules” deck includes learning objectives for each class of biological molecules, including topics to be tested on Tuesday. Students are encouraged to review ahead, but not all content is required before Tuesday.
• In general, students have 50 minutes for the exam (not the full 1.5 times longer for different class periods).
• If questions come up in class, the instructor will stop and address them.

Functional groups (seven key groups to know)

• Overview: Seven functional groups are essential in predicting behavior when attached to carbon backbones. Flashcards for these groups are highly recommended.

1) Hydroxyl group (–OH)

• Structure: oxygen bonded to hydrogen; resembles most of a water molecule.
• Polarity: highly polar; the oxygen is partially negative, hydrogen partially positive.
• Properties: hydrophilic; water-attracting.
• Common in: alcohols (e.g., ethanol) and sugars (carbohydrates).
• Significance: contributes to polarity and solubility; affects reactivity and hydrogen bonding.

2) Carbonyl group (C=O)

• Structure: carbon double-bonded to oxygen.
• Polarity: highly polar due to electronegativity of oxygen.
• Reactivity: highly reactive due to electron density around the C=O bond.
• Placement: can be at the end of a molecule (aldehyde) or within a molecule (ketone).

3) Carboxyl group (–COOH; carboxylic acid when protonated)

• Composition: carbonyl (C=O) bonded to a hydroxyl (–OH).
• Polarity: polar with high electron density around the oxygens.
• Acidity: can donate a hydrogen ion (H⁺) in solution; becomes negatively charged (carboxylate, –COO⁻) after donation.
• Significance: acidic behavior in cells; contributes to buffering and acidity of solutions.
• Example: glycine (an amino acid) contains a carboxyl group as part of its backbone.

4) Amino group (–NH₂)

• Structure: nitrogen bonded to hydrogens; also attached to the rest of the molecule (R group in amino acids).
• Polarity: polar.
• Basicity: can accept a hydrogen ion (H⁺) to form –NH₃⁺; becomes positively charged when protonated.
• In solution, amino groups can become positively charged due to protonation; important for amino acids and protein structure.

5) Sulfhydryl group (–SH)

• Structure: sulfur bonded to hydrogen.
• Polarity: polar.
• Key function: sulfhydryl groups can form covalent disulfide bridges (–S–S–) between cysteine residues in proteins, helping proteins fold and stabilize three-dimensional structure.
• Significance: disulfide bonds are covalent and strong, contributing to protein stability.

6) Phosphate group (–O–PO₄H₂ or –PO₄²⁻ in deprotonated form)

• Structure: phosphorus atom bound to oxygens; highly oxygenated and large.
• Polarity and charge: negatively charged; highly polar due to electronegative oxygens.
• Acidity: can donate protons (acidic) in solution; often exists as deprotonated phosphate (
  –PO₄^{2-}
  ) in cellular conditions.
• Significance: important in nucleic acids (DNA/RNA) backbones and energy currency (ATP); hydrophilic and involved in metabolism.

7) Methyl group (–CH₃)

• Structure: carbon bonded to three hydrogens.

• Polarity: nonpolar; C–H bonds are nonpolar.

• Hydrophobic: water does not interact favorably.

• Biological significance: influences protein folding and structure; can act as an epigenetic tag when added to DNA, potentially turning genes on or off without changing the DNA sequence.

• Caution: focus on behavior when attached to molecules (nonpolar and hydrophobic) rather than deep dive into epigenetics unless relevant for your course.

• Additional note on polarity and behavior: in practice, when you see a functional group, you should infer its polarity, charge state, hydrophilicity, and potential for hydrogen bonding or ionic interactions. Flashcards can help with quick recognition and prediction of molecular behavior.

Polymers, monomers, and dehydration/hydrolysis reactions

• Polymers and monomers:
  • Polymers are large molecules built by linking repeating subunits called monomers.
  • Examples: carbohydrates (sugars as monomers), proteins (amino acids as monomers), nucleic acids (nucleotides as monomers).
  • Fats do not fit the same polymer pattern as the other three (they can be composed of fatty acids and glycerol but aren’t polymers built by repeating identical monomer units).
• Dehydration synthesis (dehydration reaction): removes water to form a covalent bond between monomers, creating a polymer.
  • General representation: ext{Monomer}1 + ext{Monomer}2
    ightarrow ext{Polymer} + ext{H}_2 ext{O}
  • Mechanism: the hydrogen from one monomer and the hydroxyl (–OH) from the other monomer are removed as water; the remaining ends form a new bond.
• Hydrolysis (reverse of dehydration): adds water to break a bond in a polymer, splitting it into monomers.
  • General representation: ext{Polymer} + ext{H}2 ext{O} ightarrow ext{Monomer}1 + ext{Monomer}_2
• Classes of biological polymers and their specific dehydration-based bonds:
  • Carbohydrates: glycosidic bonds.
  • Proteins: peptide bonds.
  • Nucleic acids: phosphodiester bonds.
• General note: for any large biomolecule, dehydration is the typical process to link monomers; the exact molecules involved determine the specific bond type and name.
• Recognize that fatty molecules (fats) can involve dehydration in their assembly but do not form long repeating polymer chains like proteins or nucleic acids.

Proteins and amino acids: basic building blocks

• Proteins are one or more polypeptides folded into a specific three-dimensional shape, enabling them to perform diverse biological roles.

• Amino acids are the monomers of proteins.

• General amino acid structure:

  • Central (alpha) carbon attached to four substituents: an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and an R group (side chain).
  • In cells, they exist in a zwitterionic form with amino group often protonated (–NH₃⁺) and carboxyl group deprotonated (–COO⁻) depending on pH.

• The R group (side chain) is the only part that varies between amino acids and determines their chemistry and behavior.

• Four categories of amino acids based on R groups:

  • Nonpolar (hydrophobic): side chains largely carbon and hydrogen.
  • Polar but uncharged: side chains contain electronegative atoms (e.g., O, N) but are not charged.
  • Acidic: side chains include a carboxyl group that can lose a proton, giving a negative charge.
  • Basic: side chains include an amino group that can gain a proton, giving a positive charge.

• Glycine as an example: a simple amino acid with an –H as its R group; demonstrates the basic amino acid framework and the presence of amino and carboxyl groups.

• Essential amino acids: humans have about 9 essential amino acids that must be obtained from the diet because they cannot be synthesized internally.

• Peptide bonds: dehydration reactions link amino acids into polypeptides (proteins). The bond is formed between the carboxyl group of one amino acid and the amino group of the next.

  • Example representation: two amino acids linked by a peptide bond, forming a dipeptide; further linking yields longer polypeptides.

• Structural consequences in proteins:

  • Primary structure: linear sequence of amino acids (the order dictated by the R groups).
  • Secondary structure: regular local structures stabilized by hydrogen bonds along the backbone, forming either alpha helices or beta sheets.
  • Tertiary structure: three-dimensional folding driven by interactions among side chains (R groups): hydrogen bonds, ionic bonds, hydrophobic interactions, and Van der Waals forces.
  • Quaternary structure: arrangement of multiple polypeptide chains into a functional protein complex (e.g., collagen, hemoglobin).

• Side-chain interactions and structural stability:

  • Hydrogen bonds: between backbone carbonyl oxygens and amide hydrogens (and sometimes side chains).
  • Ionic bonds (salt bridges): between positively charged and negatively charged side chains (e.g., carboxylate with ammonium groups).
  • Hydrophobic interactions: nonpolar side chains cluster away from water, driving folding toward the interior.
  • Van der Waals forces: weak, cumulative interactions between nonpolar surfaces; generally minor but collectively significant.
  • Disulfide bridges: covalent bonds between sulfhydryl groups (–S–S–) of cysteine residues; contribute greatly to stability.

• Protein stability and environmental sensitivity:

  • Changes in pH, temperature, or salt concentration can disrupt ionic and hydrogen bonds, potentially denaturing proteins (loss of 3D structure).
  • Denaturation impairs function; some organisms rely on chaperone proteins to assist in proper folding and refolding under stress.

• Functional roles of proteins (illustrative examples):

  • Enzymes accelerate chemical reactions.
  • Keratin provides structural support.
  • Hemoglobin transports oxygen in blood.
  • Actin and myosin drive cellular movement.
  • Proteins regulate cellular processes and store molecules.

• Summary principle: structure determines function; the precise 3D shape of a protein enables its specific role, and perturbations to structure can disrupt function.

Epigenetics and the methyl group (brief emphasis from lecture)

• Methyl group (–CH₃) as a small, nonpolar tag can be added to certain regions of DNA.
• Methylation can influence gene expression (epigenetic regulation) without changing the DNA sequence.
• Relevance: in research fields like global change biology, methylation is investigated for its potential to enable rapid gene regulation in response to environmental changes (e.g., ocean acidity, temperature shifts).
• Practical takeaway for viewing molecules: recognize that a methyl group is nonpolar and hydrophobic; it can impact protein interactions and DNA accessibility, sometimes affecting gene expression indirectly.

Concepts tying together: structure, function, and interactions

• The backbone–side chain interplay in amino acids:
  • Backbone (amide linkages) provides a repeating scaffold with polar character due to carbonyl and amide groups.
  • Side chains (R groups) determine the specific interactions and folding tendencies of each amino acid.
• Hierarchy of protein structure emphasizes how local interactions (hydrogen bonds, ionic bonds) and global properties (hydrophobic clustering) build the final 3D shape.
• The five main types of noncovalent interaction (in decreasing strength in typical contexts):
  • Ionic interactions (salt bridges) between charged groups.
  • Hydrogen bonds between polar groups (including backbone and side chains).
  • Hydrophobic interactions clustering nonpolar side chains away from water.
  • Van der Waals forces between nearby nonpolar surfaces (weak, cumulative).
  • Covalent disulfide bridges between cysteine residues (strongest among the listed interactions).
• Final idea: proteins’ diverse functions depend on their ability to adopt and maintain specific shapes; environmental changes can disrupt these shapes and functions, but cellular mechanisms (e.g., chaperones) can mitigate misfolding.

Quick recap: what to remember for exams

• Carbon forms up to four covalent bonds; supports long chains, rings, branches.
• Seven functional groups to know: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl; each has characteristic polarity/charge and typical roles.
• Polymers form via dehydration synthesis; broken by hydrolysis; key bond names: glycosidic (carbohydrates), peptide (proteins), phosphodiester (nucleic acids).
• Amino acids: central carbon with amino group, carboxyl group, hydrogen, and variable R group; four categories by R group; nine essential amino acids in humans.
• Proteins: one or more polypeptides folded into a 3D structure; four structural levels (primary, secondary, tertiary, quaternary).
• Types of interactions shaping proteins: hydrogen bonds, ionic bonds, hydrophobic effects, Van der Waals forces, disulfide bridges (covalent).
• Protein stability depends on environment; denaturation disrupts function; chaperone proteins assist folding.
• Methyl groups can influence gene expression epigenetically; methylation is a focus in environmental biology and gene regulation studies.