Comprehensive Study Notes: Chemistry of Micro Part II

The four biomolecules (biological building blocks)

• The four major classes of macromolecules

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

• Other building blocks mentioned for context

  • Salts: electrolytes

  • Acids (H+) and Bases (OH−): balance is important for metabolism

  • Water: most abundant substance in organisms

• Core idea

  • Macromolecules are large molecules built from smaller organic molecules

  • Each class has specific monomers, structures, and roles in microorganisms

Carbohydrates

• Roles

  • Store energy

  • Structural components in bacteria (and other organisms)

• Monomer, polymer, and examples

  • Monomer: monosaccharides (3–7 carbons; end with -ose; can be in ring form in solution)

  • Disaccharides: two monosaccharides linked by a glycosidic bond (e.g., lactose, maltose, sucrose; 1,2-glycosidic linkage in sucrose)

  • Polysaccharides: long chains of monosaccharides; branched or unbranched; energy storage and structural roles

  • Examples: starch (plants), glycogen (animals), cellulose (plant cell walls), chitin (arthropods; fungal cell walls)

• Structural and functional notes

  • Glycosidic linkages connect sugars

  • Carbohydrates provide and store energy in the cell (e.g., glucose as energy currency)

• Key structural/compositional themes

  • Carbon, hydrogen, oxygen form ring-structured carbohydrates in aqueous solutions

Nucleic acids

• Core concept

  • DNA and RNA store and transmit genetic information

  • DNA: deoxyribonucleic acid; usually double-stranded; houses cellular genome; blueprint for RNA/protein synthesis

  • RNA: ribonucleic acid; usually single-stranded; involved in protein synthesis and regulation

• Monomers and polymerization

  • Monomers: nucleotides (sugar + phosphate + nitrogenous base)

  • Nucleotides polymerize to form nucleic acids via sugar–phosphate backbone

• Nitrogenous bases

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines: Cytosine (C), Thymine (DNA only) (T), Uracil (RNA only) (U)

• Central dogma of molecular biology

  • DNA is transcribed into RNA

  • RNA is translated into proteins

  • Diagram: DNA → transcription → RNA → translation → protein

• DNA structure details

  • Double helix; bases pair A with T (two hydrogen bonds) and G with C (three hydrogen bonds)

  • Antiparallel strands; 5′ to 3′ orientation

  • The genetic code is read through the sequence of nucleotides

• Nucleotide structure recap

  • Nucleotide components: sugar (deoxyribose in DNA, ribose in RNA), phosphate, nitrogenous base

  • Nucleotides link to form the sugar–phosphate backbone; base pairs project inward

Proteins

• Amino acids

  • Monomers of proteins; there are 20 naturally occurring amino acids

  • Each amino acid has a central (α) carbon, amino group (-NH2), carboxyl group (-COOH), hydrogen, and an R-group (side chain)

  • R groups determine the chemical nature and properties of the amino acid

  • Amino acids are commonly represented by a one-letter or three-letter code

• Protein structure and levels

  • Primary structure: sequence of amino acids in a polypeptide chain

  • Secondary structure: local folding patterns stabilized by hydrogen bonds

  • α-helix: helical structure stabilized by hydrogen bonding between amino acids four residues apart

  • β-pleated sheet: pleated sheet formed by hydrogen bonding between segments of the backbone

  • Tertiary structure: three-dimensional folding of a single polypeptide; stabilized by hydrophobic interactions, hydrogen bonds, ionic interactions, and disulfide bonds

  • Quaternary structure: assembly of multiple polypeptide subunits into a functional protein; stabilizing interactions between subunits

• Functional roles of proteins

  • Structural components (cell walls, membranes, cytoskeleton)

  • Enzymatic catalysis (enzymes accelerate reactions)

  • Regulation (gene expression, enzyme activity)

  • Transportation (membrane transport proteins, channels, carriers)

  • Defense and offense (antibodies, toxins, bacteriocins from some bacteria)

• Protein folding and stability

  • Proper folding is essential for function

  • Denaturation can occur due to pH changes or temperature changes, altering active shape and function

  • Mutations in the amino acid sequence can dramatically affect function (e.g., sickle cell anemia due to a single amino acid change in hemoglobin)

• Important structural features

  • Peptide bonds link amino acids

  • The protein structure is driven by interactions among R-groups (hydrophobic effects, hydrogen bonds, ionic interactions, disulfide bridges)

Lipids

• Four main lipid classes

  • Fats (triglycerides)

  • Phospholipids

  • Waxes

  • Steroids

• General roles

  • Long-term energy storage

  • Cell membrane components (phospholipid bilayers)

  • Involved in cell signaling (hormones and other signaling molecules, including steroids)

• Triglycerides

  • Backbone: glycerol with three fatty acids attached via ester bonds

  • Fatty acids vary in length and degree of saturation

• Fatty acids

  • Long hydrocarbon chains with a terminal carboxyl group (-COOH)

  • Saturated fats: no double bonds between carbon atoms (C–C single bonds); usually solid at room temperature; common in animal fats

  • Unsaturated fats: one/more C=C double bonds; typically liquid at room temperature (oils)

  • Monounsaturated: one double bond; Polyunsaturated: more than one double bond

• Phospholipids

  • Similar to triglycerides but with two fatty acid tails and a phosphate-containing head group

  • Structural basis of cellular membranes: phospholipid bilayers

  • Amphipathic: has both hydrophobic (tails) and hydrophilic (head) regions

  • Bilayer arrangement: outer surface is exposed to aqueous environment (hydrophilic heads), inner region formed by hydrophobic tails

  • Temperature effects: more saturated fats reduce fluidity; unsaturated fats increase fluidity

• Other lipid roles

  • Waxes and steroids contribute to sealing and signaling, respectively

• Essential concepts

  • Lipids are non-polar and hydrophobic, yet phospholipids create membrane interfaces due to their amphipathic nature

  • Energy storage through C–C and C–H bonds in fatty acids

Carbon, organic molecules, and inorganic molecules

• Carbon as the backbone of biology

  • Carbon has four valence electrons and can form up to four covalent bonds

  • Enables formation of diverse and complex organic molecules via carbon–carbon bonding

  • Carbon’s tetravalence allows formation of hydrocarbon chains and ring structures that serve as backbones for macromolecules

• Hydrocarbons

  • Simplest form of organic molecules: carbon + hydrogen

  • Covalent bonds store energy; energy is released when these bonds are broken

• Why carbon is central

  • Its tetravalence supports a vast array of covalent bonds with many elements (O, N, P, S, etc.)

Inorganic vs organic molecules

• Inorganic molecules

  • Often small, simple, and play metabolic roles

  • Typically do not form the primary structural components of cells

  • Water is the most important inorganic molecule in biology

• Organic molecules

  • Contain carbon and hydrogen, often large and complex

  • Frequently include O, N, P, S

  • Form the major cellular components and participate in metabolism

• Quick contrasts

  • Organic: carbon-containing, covalently bonded, often complex

  • Inorganic: lack carbon-hydrogen frameworks or are simple inorganic species

• Common functional groups and their general roles

  • Hydroxyl group: –OH

  • Carbonyl group: C=O

  • Carboxyl group: –COOH

  • Amino group: –NH2

  • Phosphate group: –O–PO3H2

  • Sulfhydryl group: –SH

• Contextual notes

  • These groups contribute to solubility, reactive properties, acid/base behavior, and catalysis in macromolecules

  • Nucleic acids and proteins often feature phosphate, amino, hydroxyl, and other groups essential for function

Central dogma and nucleic acids (in depth)

• Flow of genetic information

  • DNA stores genetic information and directs its own replication and transcription into RNA

  • RNA is translated into proteins

  • Overall sequence: DNA −transcription→ RNA −translation→ Protein

• DNA details

  • Double-stranded, often a right-handed helix; antiparallel strands

  • Bases pair: A pairs with T; G pairs with C

  • Backbone: sugar-phosphate with covalent phosphodiester bonds

• RNA details

  • Usually single-stranded

  • Base pairs can form in intramolecular structures; base U replaces T

  • Roles vary: mRNA (codes for protein sequences), tRNA (brings amino acids), rRNA (ribosome component)

• Nucleotides

  • Monomers of nucleic acids

  • Components: sugar (pentose), phosphate, nitrogenous base

  • Bases: A, G (purines); C, T (DNA) / U (RNA) (pyrimidines)

• DNA structure overview

  • Nucleotides linked by sugar-phosphate backbone

  • Bases pair via hydrogen bonds across the two strands

  • Two strands form a double helix with complementary base pairing

The nature of nucleotides and base pairing – quiz-style highlights

• Monomers of nucleic acids are nucleotides (not amino acids or monosaccharides)

• Nucleotides consist of a nitrogenous base, a sugar, and a phosphate group

• Base-pairing rules (A-T, G-C) are central to DNA structure

• Central dogma order: DNA → RNA → Protein

Protein architecture and folding in depth

• Amino acids as the building blocks

  • 20 standard amino acids with diverse side chains (R groups) determine protein properties

  • R groups drive folding and interactions (hydrophobic, hydrophilic, acidic, basic, polar, nonpolar)

• Protein structure: four levels

  • Primary: amino acid sequence

  • Secondary: local helices and sheets (α-helix and β-pleated sheet) stabilized by hydrogen bonds

  • Tertiary: three-dimensional folding driven by interactions among R groups (hydrophobic effects, hydrogen bonds, ionic interactions, disulfide bridges)

  • Quaternary: assembly of multiple polypeptides into a functional protein

• Protein folding and stability

  • Structures can be disrupted by pH changes or temperature shifts, causing denaturation and loss of function

  • Mutations altering amino acid sequences can drastically impact function (e.g., sickle cell disease caused by substitution affecting hemoglobin)

• Functional diversity

  • Proteins serve as structural components, enzymes, regulators, transporters, defense molecules, toxins, and more

Water and life; important properties for biology

• Water as the solvent of life; polarity and hydrogen bonding

  • Water is polar; molecules form hydrogen bonds with each other

  • Hydrogen bonding underpins many properties of water and the behavior of dissolved substances

• Key life-supporting properties of water

  • Density anomaly: solid water is less dense than liquid water, allowing ice to float

  • High heat capacity and high heat of vaporization help stabilize temperatures in organisms and environments

  • High melting and boiling points for a small, simple molecule among common solvents

• Ice and water behavior

  • Ice expands upon freezing due to stable hydrogen-bond networks

  • Liquid water features constantly breaking and reforming hydrogen bonds, enabling dynamic solvent properties

• Water’s molecular structure

  • Water molecules are small, bent, and polar, enabling extensive hydrogen bonding network

The cell’s major macromolecules in context

• Summary of four major macromolecule classes in cells

  • DNA, RNA, ATP, phospholipids, and cellulose appear as recurring examples in cell biology resources

• Key connections to microbiology

  • Carbohydrates contribute to bacterial structure (e.g., cell wall components)

  • Lipids form membranes in bacteria and archaea; membrane composition affects permeability and signaling

  • Proteins perform enzymatic and regulatory roles essential for microbial metabolism

  • Nucleic acids carry genetic information for replication and transcription in microorganisms