Biomolecules: Functional Groups and Carbohydrates Study Notes

Amino Acids: Structure, Roles, and Basic Concepts

• All amino acids share a common backbone: central carbon attached to an amino group, a carboxyl group, a hydrogen, and a variable side chain (R group).
  • General formula: $\mathrm{NH_2-CH(R)-COOH}$
  • At physiological pH, amino acids exist as zwitterions with charges on amino and carboxyl groups: $\mathrm{NH_3^+-CH(R)-COO^-}$
• Glycine as a reference: its R group is hydrogen (H).
• 20 different amino acids are required to build all cellular proteins.
  • Some are essential (must be obtained from diet); others are nonessential (synthesized by the body).
• All 20 amino acids share the same backbone and act as buffers in solution.
• Importance: amino acids are the building blocks of proteins; their properties (size, charge, hydrophobicity) determine protein structure and function.

Cysteine: Sulfhydryl Group, Disulfide Bridges, and Cross-Linking

• Functional group: sulfhydryl (–SH) on cysteine, i.e., a sulfur linked to hydrogen: $\mathrm{-SH}$.
• Cysteine’s R group is: $\mathrm{-CH_2-SH}$, attached to the central carbon.
• Role in proteins:
  • Sulfhydryl groups can form covalent bonds with other sulfhydryl groups to create disulfide bridges: $\mathrm{R-SH\; \cdots\; HS-R} \;\rightarrow\; \mathrm{R-S-S-R}$.
  • Disulfide bridges contribute to protein cross-linking and conformational stability.
• Concept: altering disulfide bonds can cause conformational shape changes, impacting protein function.
• Terminology: a bond between two sulfurs is a disulfide bridge (two sulfurs, hence “di” sulfur). Cross-linkers help stabilize 3D structure.

Phosphate Groups and Polarity in Biomolecules

• Phosphate group: phosphorus atom bonded to oxygen atoms; highly electronegative oxygens create polar covalent bonds.
• Consequences:
  • Phosphate-containing compounds (e.g., many in nucleic acids) are highly polar and water-soluble.
  • In nucleic acids (DNA/RNA), phosphate groups contribute to the charged backbone and solubility in cytosol/extracellular fluid.
• General observation:
  • Phosphate groups and hydroxyl groups increase polarity of a molecule, promoting water solubility.

Methyl Groups and DNA Methylation: Effects on Structure and Gene Expression

• Methyl groups (–CH3) are nonpolar and hydrophobic; attaching them to DNA can reduce polarity and alter interactions with water.
• DNA methylation: adding methyl groups to DNA (often at cytosine bases) can reduce gene expression by affecting transcription.
• Implications:
  • Epigenetic changes (like methylation) can alter gene expression without changing DNA sequence.
  • Methylation can influence trait expression and has implications for aging and disease through altered transcription.
• Conceptual link: small chemical modifications to macromolecules (e.g., methylation) can have large functional consequences.

Functional Groups: Influence on Water Solubility and Nonpolar Behavior

• Polar functional groups (e.g., hydroxyl –OH, carbonyl C=O, phosphate –PO3^2−) tend to promote water solubility.
• Nonpolar groups (e.g., methyl –CH3) decrease solubility in water and promote association with nonpolar solvents (e.g., oils).
• Summary:
  • Molecules rich in polar groups are hydrophilic;
  • Molecules rich in nonpolar groups are hydrophobic.
• Why this matters: solubility influences where a molecule can function (aqueous cytosol vs lipid membranes).

Functional Groups as Predictors of Molecular Behavior

• By recognizing functional groups on a molecule, you can infer:
  • Water solubility or hydrophobicity
  • Likely interactions with other molecules (e.g., hydrogen bonding, ionic interactions)
  • Potential role in macromolecule structure and function.
• Example logic:
  • Phosphate and hydroxyl groups → highly polar; DNA/RNA, other polar biomolecules dissolve well in water.
  • Methyl groups → nonpolar; can reduce overall polarity when attached to polar backbones, affecting solubility.
• Note on macromolecules: large biomolecules can be categorized by predominant functional groups that guide their behavior in cells.

Macromolecules, Polymers, Monomers, and Metabolism

• Macromolecules overview:
  • Carbohydrates, lipids, proteins, nucleic acids are large polymers built from smaller units (monomers).
• Monomers and polymers:
  • Monomer examples: amino acids (proteins), monosaccharides (carbohydrates), nucleotides (nucleic acids), fatty acids/glycerol (lipids).
  • Polymers built by linking monomers via dehydration synthesis (removing water) and broken down by hydrolysis (adding water).
• Dehydration synthesis (condensation):
  • General form: $\text{Monomer}<em>1 + \text{Monomer}</em>2 \rightarrow \text{Dimer} + \mathrm{H_2O}$ (and extended to longer polymers).
  • Water is a byproduct of bond formation.
• Hydrolysis:
  • General form: $\text{Polymer} + \mathrm{H<em>2O} \rightarrow \text{Monomer}</em>1 + \text{Monomer}_2 + \dots$
  • Water is consumed to break bonds.
• Enzymes:
  • Biological catalysts that speed up dehydration synthesis and hydrolysis, enabling rapid metabolism.
• Metabolism:
  • The sum of all chemical reactions in cells, including both synthesis (anabolic) and breakdown (catabolic) pathways.
• Monomer vs polymer terminology:
  • Monomer: the building block (e.g., amino acid for protein).
  • Polymer: the long chain made of many monomers (e.g., protein, polysaccharide).
• Important analogy used:
  • Polymers are like houses built from building blocks (stones, bricks, logs) — the same concept of building units forming a larger structure, with different building blocks giving different properties.
• Computational biology and bioinformatics:
  • Computer simulations help model macromolecule interactions and biological processes.
  • They are complementary to traditional lab methods and rely on accurate data to avoid oversimplification.
  • This field is growing and offers career opportunities for those interested in biology and computing.

Carbohydrates: Monomers, Linkages, and Polymers

• Monomers: monosaccharides (simple sugars) with carbon, hydrogen, and oxygen in general formula $\mathrm{C<em>nH</em>{2n}O_n}$.
  • They are typically water-soluble due to polar carbonyl and hydroxyl groups.
  • Carbohydrates always have a two-to-one hydrogen-to-oxygen ratio: $\frac{H}{O} = 2$ (i.e., $\mathrm{C<em>nH</em>{2n}O_n}$).
• Carbon skeleton sizes:
  • Triose: $C<em>3H</em>6O_3$
  • Pentose: $C<em>5H</em>{10}O_5$
  • Hexose: $C<em>6H</em>{12}O_6$
• Aldose vs Ketose (location of carbonyl):
  • Aldose: carbonyl group (C=O) at an end carbon (terminal) → aldehyde group.
  • Ketose: carbonyl group inside the carbon skeleton (not at the end) → ketone group.
• Ring structures:
  • Monosaccharides often form ring structures in solution; ring position can differ, leading to isomers (structural isomers and enantiomers like D- and L- forms).
• Isomers:
  • Monosaccharides can have the same chemical formula but different structural arrangements; these are structural isomers and can lead to different properties.
• Disaccharides (two monosaccharides linked):
  • Glycosidic bond is the covalent linkage between two monosaccharides.
  • Common disaccharides:
  • Maltose: glucose–glucose (created via dehydration synthesis)
  • Sucrose: glucose–fructose (table sugar)
  • Lactose: glucose–galactose (milk sugar)
  • Digestion in the body:
  • An enzyme in saliva and the GI tract begins hydrolysis of disaccharides into monosaccharides for absorption.
• Polysaccharides (many monosaccharide units):
  • Not crystalline and not very sweet; generally less soluble in water compared to monosaccharides.
  • Three major polysaccharides to know:
  • Glycogen: highly branched glucose polymer; storage form in animals (muscle and liver).
  • Starch: branched glucose polymer; storage form in plants.
  • Cellulose: unbranched glucose polymer; structural component in plant cell walls.
• Linkages in polysaccharides:
  • All are formed by dehydration synthesis (glycosidic bonds connect monosaccharides).
  • The particular linkage type and branching pattern dictate function (storage vs. structure).
• Functional roles:
  • Energy storage: starch (plants), glycogen (animals).
  • Structural support: cellulose in plant cell walls.
• Digestive considerations:
  • Polysaccharides must be hydrolyzed to monosaccharides to be absorbed and used for energy.
• Practical takeaway:
  • While all carbohydrates have the same basic elements, the ratio, branching, and ring forms lead to a spectrum of properties and roles in biology.
• Exam and lab relevance:
  • Recognize carbohydrates by presence of carbon, hydrogen, and oxygen with a 2:1 H:O ratio and typical ending -ose for many sugars.
  • Identify glycosidic bonds as the linking mechanism between monosaccharides.
  • Distinguish storage polysaccharides (glycogen, starch) from structural polysaccharides (cellulose).

Quick Connections and Real-World Relevance

• Structure–function relationship:
  • Small changes in functional group composition (e.g., hydroxyl vs carbonyl, or adding a methyl group) can dramatically alter biological outcomes (e.g., hormone activity, gender differentiation in embryonic development).
  • Hormones (e.g., estrogen vs testosterone) are structurally related yet produce different developmental outcomes due to small chemical variations.
• Gene expression and epigenetics:
  • DNA methylation showcases how chemical modifications to macromolecules influence gene expression without changing the DNA sequence itself.
• Water’s dual role in chemistry of life:
  • Water acts as a reactant in hydrolysis and as a product in dehydration synthesis, illustrating the central role of water in metabolism.
• Exam focus (based on the lesson):
  • Exam 1 covers chapter 3 up to functional groups.
  • Exam 2 covers carbohydrates, lipids, proteins, and nucleic acids.

Quick Reference: Key Equations and Notation

• Amino acid backbone: $\mathrm{NH<em>2-CH(R)-COOH}$, zwitterion form at physiological pH: $\mathrm{NH</em>3^+-CH(R)-COO^-}$
• Disulfide bridge between cysteine residues: $\mathrm{R-SH + HS-R' \rightarrow R-S-S-R'}$
• Dehydration synthesis (general): $\text{Monomer}<em>1 + \text{Monomer}</em>2 \rightarrow \text{Polymer} + \mathrm{H_2O}$
• Hydrolysis (general): $\text{Polymer} + \mathrm{H<em>2O} \rightarrow \text{Monomer}</em>1 + \text{Monomer}_2 + \dots$
• Carbohydrate formula: $\mathrm{C<em>nH</em>{2n}O_n}$ and ratio $\frac{H}{O} = 2$
• Monomer examples with sizes:
  • Triose: $\mathrm{C<em>3H</em>6O_3}$
  • Pentose: $\mathrm{C<em>5H</em>{10}O_5}$
  • Hexose: $\mathrm{C<em>6H</em>{12}O_6}$
• Glycosidic bond: $\text{Monosaccharide} \leftrightarrow \text{Monosaccharide}$ (via glycosidic linkage)

Notes for Study and Exam Preparation

• Be able to identify functional groups on molecules and predict solubility and potential interactions.
• Distinguish aldoses vs ketoses by carbonyl position and recognize triose/pentose/hexose classifications by carbon count.
• Explain how disulfide bridges contribute to protein structure and how their formation can alter function.
• Describe dehydration synthesis vs hydrolysis, including enzyme roles and the concept of metabolism as the sum of all cellular reactions.
• Recognize schematic relationships among monomers, polymers, and their roles in energy storage, structure, and information (DNA/RNA).
• Practice tracing how a carbohydrate like starch or glycogen is assembled and broken down, including where energy is stored and released.
• Understand how small chemical changes can have large biological outcomes, including developmental and epigenetic processes.