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Biomolecules: Carbon, Bonding, and Major Macromolecule Classes

Carbon and Covalent Bonding

  • Methane example: carbon forms covalent bonds that give a tetrahedral shape in 3D, though a 2D structural formula shows a simplified picture. The spatial arrangement (tetrahedron) influences how the molecule behaves.
  • Carbon atom basics:
    • Atomic number: total electrons = 6.
    • Electron distribution: 2 electrons in the first shell; 4 electrons in the outer valence shell.
    • The second shell can hold up to 8 electrons, which underpins carbon’s ability to form up to 4 covalent bonds.
    • This bonding versatility enables formation of very large, complex molecules.
  • Carbon’s bonding leads to diverse macromolecules essential for life: carbohydrates, proteins, lipids, nucleic acids (nucleotides).
  • Covalent bonding among carbons creates backbones that are strongly held together, enabling compatibility with H, O, and N.
  • Carbon can form double bonds, extending possibilities for chains and rings; multiple bond formation allows hydrocarbon structures.
  • The four major classes of organic molecules (macromolecules):
    • Proteins
    • Nucleic acids (DNA/RNA)
    • Carbohydrates
    • Lipids
  • Functional groups (key roles in molecular behavior): hydroxyl, carbonyl, carboxyl, amino, amide, sulfhydryl, phosphate, and methyl groups.

Proteins

  • Proteins account for about 50% dry mass of cells.
  • Structural feature: one or more polypeptides can fold into functional proteins; polypeptides comprise amino acids.
  • Functions of proteins include:
    • Defense, storage, transport
    • Cellular communication, movement, structural support
    • Enzymatic catalysis (enzymes act as catalysts)
  • Protein diversity: thousands of different proteins exist due to different sequences and structures.
  • Insulin (example): a hormone involved in cellular communication.
  • Amino acids:
    • An amino acid is an organic molecule with an amino group, a carboxyl group, an alpha carbon, and an R group.
    • The R group determines the properties of each amino acid.
    • Amino acids are linked by peptide bonds (a covalent bond) to form polypeptides.
  • Polypeptide structure and diversity: sequence and folding determine protein function.
  • About the amino acids encoded by genetic code: there are not 22 amino acids; there are 20 amino acids that are specified by genetic code. A diagram shows the 20 amino acids classified by side-chain properties:
    • Nonpolar (hydrophobic)
    • Polar (hydrophilic)
    • Electrically charged

Nucleotides, Nucleic Acids, and Genetic Information

  • Nucleotides: the building blocks of nucleic acids; each nucleotide consists of:
    • A phosphate group (can be one or more phosphates)
    • A five-carbon sugar
    • A nitrogen-containing base
  • Nucleic acids: DNA and RNA
    • DNA sugar: deoxyribose; RNA sugar: ribose
    • Bases in DNA and RNA include:
    • Pyrimidines: cytosine (C), thymine (T) in DNA, uracil (U) in RNA
    • Purines: guanine (G), adenine (A)
    • DNA contains bases C, T, G, A; RNA contains C, G, A, and U (not T)
    • Purines have a double-ring structure; pyrimidines have a single ring.
  • Base pairing and genetic code:
    • A pairs with T (in DNA) via hydrogen bonds; G pairs with C via hydrogen bonds.
    • These interactions help form the double-helix structure of DNA.
    • Nucleotides are linked by phosphodiester bonds along the backbone:
    • The bond forms between the phosphate group of one nucleotide and the 3' hydroxyl end of the preceding nucleotide.
  • DNA structure:
    • Double helix formed by complementary base pairing (A–T and G–C) and phosphodiester backbone.

Carbohydrates

  • Carbohydrates are sugars and polymers of sugars.
  • Simple sugars (monosaccharides) examples: glucose, galactose, fructose.
  • Complex carbohydrates (polysaccharides) are polymers of monosaccharides.
  • Monosaccharides can exist in ring forms; polysaccharides can form multiple rings.
  • Functional groups in carbohydrates can include aldehyde or ketone groups (e.g., glucose is an aldose; fructose is a ketose).
  • Glycosidic bonds connect monosaccharides to form polysaccharides.
  • Roles of carbohydrates: structure, support, and energy storage.

Lipids

  • Lipids are hydrophobic and tend to be nonpolar, forming mostly hydrocarbon structures; they have little to no affinity for water.
  • Key structural feature: nonpolar covalent bonds (between carbon and hydrogen in hydrocarbon chains).
  • Fatty acids: long chains of carbon with a carboxyl group at one end.
  • Saturated vs. unsaturated fatty acids:
    • Saturated fatty acids: maximum hydrogen atoms, no carbon–carbon double bonds; tend to be solid at room temperature and are common in animal fats (e.g., pork fat).
    • Unsaturated fatty acids: contain one or more carbon–carbon double bonds; tend to be liquid at room temperature and are common in plant and fish fats (e.g., olive oil, canola oil, corn oil).
  • Health implications:
    • If an unsaturated fat is transformed into a saturated fat, it becomes less healthy because saturated fats can contribute to plaque formation, increasing risk of heart attack and stroke.
  • Triacylglycerol (triglycerides): a neutral, hydrophobic fat that forms oil droplets.
  • Steroids: lipids with a four-ring carbon skeleton; cholesterol is a common steroid.
    • Cholesterol is a precursor for the synthesis of hormones such as testosterone and progesterone, and for other biosynthetic pathways.
    • Plant steroids exist as phytosterols.

Functional Groups and Their Roles in Macromolecules

  • hydroxyl (–OH)
  • carbonyl (–C=O)
  • carboxyl (–COOH)
  • amino (–NH2)
  • amide (–CONH2)
  • sulfhydryl (–SH)
  • phosphate (–PO4, involved in nucleotides and energy transfer)
  • methyl (–CH3)
  • These groups determine chemical reactivity, polarity, acid-base behavior, and interactions with other molecules, influencing structure and function of biomolecules.

Connections to Foundational Concepts and Real-World Relevance

  • Structure–function relationship: molecular shape (e.g., methane’s tetrahedral geometry) and bonding patterns determine function and properties of biomolecules.
  • Energy and metabolism: carbohydrates provide energy; lipids store energy efficiently; proteins perform a broad range of cellular tasks.
  • Genetic information flow: DNA stores genetic information through sequence data; transcription and translation rely on base pairing, nucleotides, and amino acids.
  • Health implications: dietary fats influence disease risk; choosing unsaturated fats can be healthier than saturated fats; cholesterol role in hormone synthesis highlights importance of lipid metabolism in endocrine biology.
  • Evolutionary and practical relevance: carbon’s versatility underpins the diversity of life; understanding functional groups and bonding is essential for biochemistry, molecular biology, and biotechnology.

Quick Reference Highlights (Numbers and Key Facts)

  • Carbon: total electrons = 6; first shell holds 2 electrons; second shell can hold up to 8 electrons; carbon can form up to 4 covalent bonds.
  • Amino acids: there are not 22 known amino acids; there are 20 amino acids specified by the genetic code.
  • DNA vs RNA sugars: deoxyribose (DNA) vs ribose (RNA).
  • Bases and families:
    • Pyrimidines: cytosine, thymine, uracil.
    • Purines: guanine, adenine.
  • Base pairing (DNA): A pairs with T; G pairs with C (via hydrogen bonds).
  • Backbone linkage: phosphodiester bonds join nucleotides between the phosphate of one nucleotide and the 3' hydroxyl of the previous nucleotide.
  • Lipids: saturated fats have no C=C bonds; unsaturated fats have one or more C=C bonds; structure drives room-temperature state and health implications.
  • Steroids: four-ring carbon skeleton; cholesterol as a key example and a precursor to steroid hormones; phytosterols exist in plants.