Microbial Biochemistry Complete Biochemistry Comprehensive Notes on Microbial Biochemistry

Organic Compounds and the Role of Carbon

• Definition of Organic Compounds: These are molecules that contain carbon-to-carbon bonds and are produced by living organisms. There are four main categories of organic compounds necessary for life:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

• The Versatility of Carbon: Carbon is a highly versatile molecule because it can share electrons with other atoms in four covalent bonds.

  • Carbon can use one or more of its bonds to attach to other carbon atoms, creating an endless diversity of carbon skeletons.

  • Carbon skeletons vary in size (length) and branching patterns.

  • Skeletons may contain double bonds, which can vary in location.

  • Skeletons may be arranged in linear (unbranched), branched, or ring structures.

• Elemental Bonding: Beyond other carbon atoms, the carbon atoms in organic compounds most commonly bond with:

  • Hydrogen

  • Oxygen

  • Nitrogen

• Methane ($CH_4$): One of the simplest organic compounds. It consists of a single carbon atom bonded to four hydrogen atoms.

  • Methane is abundant in natural gas.

  • It is produced by prokaryotes inhabiting swamps (referred to as "swamp gas").

  • It is also produced within the digestive tracts of grazing animals, such as cows.

• Fuel and Energy: Larger organic compounds serve as the primary molecules in gasoline (e.g., Octane) and as important fuels in the human body. The energy-rich portions of dietary fat molecules possess a chemical structure similar to gasoline.

Functional Groups and Isomers

• Properties of Organic Compounds: The unique properties of any organic compound depend upon its carbon skeleton and the specific atoms attached to that skeleton.

• Functional Groups: These are specific groups of atoms directly involved in chemical reactions.

  • They confer specific chemical properties to the molecules they belong to.

  • The number and arrangement of these groups dictate a molecule's unique properties.

  • Many biological molecules contain two or more functional groups.

• Seven Key Functional Groups:

  1. Hydroxyl Group ($-OH$): Found in Alcohols and Monosaccharides.

  2. Carbonyl Group ($C=O$): Found in carbohydrates.

     • Internal carbonyls (Ketones) have carbon atoms on each side of the R group.

     • Terminal carbonyls (Aldehydes) have a carbon atom on only one side.

  3. Carboxyl Group ($-COOH$): Found in Amino acids, Proteins, and Fatty acids.

  4. Amino Group ($-NH_2$): Found in Amino acids and Proteins.

  5. Sulfhydryl Group ($-SH$): Found in Amino acids and Proteins.

  6. Phosphate Group: Found in Phospholipids, Nucleotides, and $ATP$.

  7. Methyl Group: An additional important functional group in life chemistry.

  • Ether Groups: Found in Disaccharides and Polysaccharides.

  • Ester Groups: Found in Fats and Waxes.

• Isomers: Molecules with the same atomic makeup (molecular formula) but different structural arrangements.

  • Structural Isomers: Compounds with identical molecular formulas but different bonding sequences.

  • Stereoisomers: Molecules with the same bonding sequence but different spatial arrangements.

  • Enantiomers: Stereoisomers that are non-superimposable mirror images of each other.

  • Examples: Glucose, Galactose, and Fructose share the formula $C_6H_{12}O_6$ but are structural isomers of one another.

Macromolecules: Synthesis and Digestion

• Macromolecules: On a molecular scale, many of life's molecules are massive and are categorized into four groups: Carbohydrates, Lipids, Proteins, and Nucleic acids.

• Polymers and Monomers: Most macromolecules are polymers, which are made by stringing together many smaller molecules called monomers.

• Dehydration Synthesis (Dehydration Reaction):

  • This process combines single units (monomers) into chains to create polymers.

  • A molecule of water ($H_2O$) is removed for every bond formed between monomers.

• Hydrolysis:

  • This is the process of breaking down macromolecules (digestion) to make monomers available to cells.

  • Bonds between monomers are broken by adding a molecule of water.

  • It essentially reverses the dehydration reaction.

  • Example: The hydrolysis of Sucrose ($C_{12}H_{22}O_{11}$) plus water ($H_2O$) and energy results in Glucose ($C_6H_{12}O_6$) and Fructose ($C_6H_{12}O_6$).

Carbohydrates

• Composition: Includes sugars and polymers of sugar.

  • Small sugars are found in soft drinks.

  • Long starch molecules are found in foods like spaghetti and bread.

• Monosaccharides:

  • The monomers of carbohydrates that cannot be broken down into smaller sugars.

  • Glucose: Found in sports drinks; the main fuel for cellular work and easily used by the body. Often used in IV solutions for sick or injured patients.

  • Fructose: Found in fruit.

  • Both are present in honey.

• Disaccharides: Double sugars constructed from two monosaccharides via a dehydration reaction that forms a glycosidic bond.

  • Lactose: Found in milk; composed of glucose and galactose.

  • Maltose: Found in beer, malted shakes, and candy; composed of two glucose molecules.

  • Sucrose: Common table sugar; composed of glucose and fructose.

• Polysaccharides: Complex carbohydrates made of long chains of sugar monomers.

  • Starch: Long strings of glucose monomers used by plant cells to store energy. Major sources include potatoes and grains.

  • Glycogen: Used by animal cells to store energy; broken down to release glucose when the body needs energy.

  • Cellulose: The most abundant organic compound on Earth. It forms cable-like fibrils in plant cell walls. Animals do not produce enzymes capable of breaking it down.

Lipids

• Properties: Unlike hydrophilic ("water-loving") carbohydrates, lipids are hydrophobic, meaning they are unable to mix with water (e.g., oil separating from vinegar). They are not necessarily polymers or huge macromolecules like the other three groups.

• Fats (Triglycerides): Consist of one glycerol molecule joined with three fatty acid molecules via dehydration synthesis, forming ester bonds.

  • Functions: Energy storage, cushioning, and insulation.

  • Saturated Fats: Contain the maximum number of hydrogens; no double bonds. Most animal fats are saturated, stack easily, and are solid at room temperature. High intake contributes to atherosclerosis (plaque buildup in blood vessels).

  • Unsaturated Fats: Contain fewer than the maximum number of hydrogens due to double bonds in the carbon skeleton. These are typically liquid plant oils.

  • Hydrogenation: A process that adds hydrogen to unsaturated fats to make them solid at room temperature. This creates trans fats, which are particularly harmful to health.

• Phospholipids: Essential components of cell membranes.

  • Made of two fatty acids and a glycerol (diacylglycerol) attached to a phosphate group.

  • Structure consists of a hydrophilic (polar) head and hydrophobic (nonpolar) tails.

  • In cells, they form a phospholipid bilayer.

• Isoprenoids and Steroids:

  • Isoprenoids: Branched lipids (terpenoids) formed by modifying isoprene molecules. Used in pharmaceuticals, pigments, and fragrances.

  • Steroids: Characterized by a carbon skeleton with four fused rings. Function varies based on the attached functional groups.

  • Cholesterol: A key membrane component and the "base steroid" used to produce estrogen and testosterone. In animal/protozoan membranes, it prevents phospholipid packing to keep membranes fluid at low temperatures.

  • Anabolic Steroids: Synthetic variants of testosterone used to treat cancer/AIDS but often abused by athletes. Can cause serious physical and mental health issues.

Proteins

• Significance: Polymers of amino acid monomers that account for more than 50% of the dry weight of most cells and perform nearly all cellular tasks.

• Major Types and Functions:

  • Structural: Provide support (e.g., actin, tubulin, keratin, cytoskeleton, extracellular matrix).

  • Storage: Provide amino acids for growth (e.g., legume proteins, egg white albumin).

  • Contractile: Help movement (e.g., actin, myosin).

  • Transport: Help move substances in blood/lymph (e.g., hemoglobin, albumin).

  • Enzymes: Catalysts that speed up chemical reactions without being consumed (e.g., amylase, lipase, pepsin).

  • Hormones: Chemical signaling molecules (e.g., insulin, thyroxine).

  • Defense: Protect from pathogens (e.g., immunoglobulins).

• Amino Acids: There are 20 different kinds.

  • Structure: A central carbon atom bonded to a hydrogen atom, a carboxyl group ($-COOH$), an amino group ($-NH_2$), and a variable side chain (R group).

  • Amino acids are amphoteric, functioning as both acids and bases.

  • Glycine is the simplest. Two amino acids contain sulfur.

  • Names often end in "-ine" (e.g., Phenylalanine, Cysteine, Glutamine, Alanine).

• Peptide Bonds: Cells link amino acids via dehydration synthesis to form peptide bonds, creating long chains called polypeptides.

• Protein Structure Levels:

  1. Primary Structure: The unique sequence of amino acids in the polypeptide chain.

  2. Secondary Structure: Local folding into alpha-helices or beta-pleated sheets, maintained by weak hydrogen bonds.

  3. Tertiary Structure: Intricate three-dimensional folding resulting from interactions between R groups (disulfide bridges/covalent bonds between cysteines, hydrogen bonds, and electrostatic attractions).

  4. Quaternary Structure: Results from two or more polypeptide chains acting together as a single functional protein (maintained by disulfide bonds, H-bonds, electrostatic attraction, and hydrophobic forces).

• Protein Shape and Function:

  • The variety of proteins is achieved by varying the sequence of the 20 amino acids (similar to using 26 letters of the alphabet to form words).

  • Structure determines function; most proteins work by binding to other molecules.

  • Denaturation: Unfavorable changes in temperature, pH, or other environment factors can cause a protein to unravel and lose its function.

  • Sickle-cell Disease: Caused by a single amino acid substitution in hemoglobin, changing its shape and function.

Nucleic Acids

• Function: Macromolecules that store information and provide instructions for building proteins.

• Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

  • DNA resides in cells as long fibers called chromosomes.

  • Genes are specific stretches of DNA that program the amino acid sequence of polypeptides.

• Nucleotides: Monomers of nucleic acids consisting of:

  1. A five-carbon (pentose) sugar.

  2. A phosphate group.

  3. A nitrogen-containing base.

• Nitrogenous Bases:

  • Purines: Adenine (A) and Guanine (G).

  • Pyrimidines: Cytosine (C), Thymine (T) [DNA only], and Uracil (U) [RNA only].

• Polynucleotides: Chains formed by dehydration reactions between the sugar of one nucleotide and the phosphate of the next, creating a sugar-phosphate backbone.

• DNA Structure:

  • Double-stranded, forming a double helix.

  • Strands are held together by hydrogen bonds between base pairs.

  • Complementary Pairing: A only pairs with T (2 hydrogen bonds); G only pairs with C (3 hydrogen bonds).

• Differences Between DNA and RNA:

  1. RNA sugar is ribose; DNA sugar is deoxyribose.

  2. RNA has Uracil instead of Thymine.

  3. RNA is usually single-stranded, while DNA is a double helix.

Identifying Microorganisms

• Biochemical tests are identifying tools based on:

  • Phenotypic biochemical characteristics.

  • Genotypic identification methods.

  • Lipid profiles.

  • Analysis of proteins produced under specific growth conditions.