Biochemistry: Biomolecules, Carbohydrates and Lipids

• Biochemistry is the study of chemical processes within and relating to living organisms.

Biomolecules

• Biomolecules are molecules synthesized by living organisms.
• The main classes of biomolecules are carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

• Carbohydrates are composed of carbon, hydrogen, and oxygen atoms.
• Carbohydrates serve as a primary source of energy for living organisms.
• Monosaccharides are the simplest carbohydrates (e.g., glucose, fructose, galactose).
• Disaccharides consist of two monosaccharides joined by a glycosidic bond (e.g., sucrose, lactose, maltose).
• Polysaccharides are complex carbohydrates made up of many monosaccharide units (e.g., starch, cellulose, glycogen).
• Starch is a storage form of glucose in plants.
• Glycogen is a storage form of glucose in animals.
• Cellulose is a structural component of plant cell walls.

Lipids

• Lipids are hydrophobic or amphipathic molecules.
• Lipids include fats, oils, phospholipids, steroids, and waxes.
• Fats and oils are composed of glycerol and fatty acids. Saturated fatty acids contain no carbon-carbon double bonds, while unsaturated fatty acids contain one or more double bonds.
• Phospholipids are major components of cell membranes consisting of a glycerol backbone, two fatty acids, and a phosphate group.
• Steroids have a characteristic four-ring structure (e.g., cholesterol, testosterone, estrogen).

Proteins

• Proteins are composed of amino acids linked by peptide bonds.
• Amino acids contain an amino group, a carboxyl group, and a side chain (R group) that varies among different amino acids.
• The primary structure of a protein is the sequence of amino acids.
• The secondary structure refers to local folding patterns such as alpha-helices and beta-sheets, stabilized by hydrogen bonds.
• The tertiary structure is the overall three-dimensional shape of a protein, determined by various interactions (e.g., hydrophobic interactions, disulfide bonds, ionic bonds, hydrogen bonds) between the amino acid side chains.
• The quaternary structure involves the arrangement of multiple polypeptide chains (subunits) in a multi-subunit protein.
• Enzymes are proteins that act as biological catalysts, accelerating biochemical reactions.

Nucleic Acids

• Nucleic acids include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• Nucleic acids are polymers of nucleotides.
• Each nucleotide consists of a nitrogenous base, a pentose sugar (deoxyribose in DNA, ribose in RNA), and one or more phosphate groups.
• DNA contains the bases adenine (A), guanine (G), cytosine (C), and thymine (T).
• RNA contains the bases adenine (A), guanine (G), cytosine (C), and uracil (U).
• DNA is a double-stranded helix with complementary base pairing (A with T, G with C).
• RNA is typically single-stranded and plays various roles in gene expression including mRNA, tRNA, and rRNA.

Enzymes

• Enzymes are biological catalysts that speed up biochemical reactions by lowering the activation energy.
• The active site is the region of an enzyme where the substrate binds and the reaction occurs.
• Cofactors are non-protein molecules or ions that are required for enzyme activity (e.g., metal ions, coenzymes).
• Coenzymes are organic cofactors (e.g., vitamins).
• Enzyme activity can be affected by factors such as temperature, pH, and substrate concentration.
• Enzyme inhibitors can bind to enzymes and reduce their activity.
• Competitive inhibitors bind to the active site, while non-competitive inhibitors bind to another site on the enzyme.
• Michaelis-Menten kinetics describes the relationship between enzyme activity and substrate concentration.
• The Michaelis constant (Km) is the substrate concentration at which the reaction rate is half of the maximum rate (Vmax).

Metabolism

• Metabolism is the sum of all chemical reactions that occur within a living organism.
• Metabolic pathways are series of interconnected biochemical reactions.
• Catabolism involves the breakdown of complex molecules into simpler ones, releasing energy.
• Anabolism involves the synthesis of complex molecules from simpler ones, requiring energy.

Glycolysis

• Glycolysis is the breakdown of glucose into pyruvate.
• Glycolysis occurs in the cytoplasm.
• Glycolysis involves a series of enzymatic reactions that produce ATP and NADH.
• The net yield of ATP from glycolysis is 2 ATP molecules per glucose molecule.

Citric Acid Cycle (Krebs Cycle)

• The citric acid cycle is a series of reactions that oxidize acetyl-CoA, producing carbon dioxide, ATP, NADH, and FADH2.
• The citric acid cycle occurs in the mitochondrial matrix.
• Acetyl-CoA is formed from pyruvate, derived from glycolysis.

Oxidative Phosphorylation

• Oxidative phosphorylation is the process by which ATP is synthesized using the energy released by the electron transport chain.
• The electron transport chain is a series of protein complexes located in the inner mitochondrial membrane.
• Electrons are transferred from NADH and FADH2 to oxygen via the electron transport chain, creating a proton gradient across the inner mitochondrial membrane.
• ATP synthase uses the proton gradient to drive the synthesis of ATP.

Lipid Metabolism

• Beta-oxidation is the breakdown of fatty acids into acetyl-CoA.
• Beta-oxidation occurs in the mitochondrial matrix.
• Lipogenesis is the synthesis of fatty acids from acetyl-CoA.
• Lipogenesis occurs in the cytoplasm.

Protein Metabolism

• Transamination is the transfer of an amino group from one amino acid to a keto acid.
• Deamination is the removal of an amino group from an amino acid, releasing ammonia.
• The urea cycle converts ammonia into urea, which is excreted from the body.

Photosynthesis

• Photosynthesis is the process by which plants and other organisms convert light energy into chemical energy.
• Photosynthesis occurs in chloroplasts.
• The light-dependent reactions occur in the thylakoid membranes and convert light energy into ATP and NADPH.
• The Calvin cycle (light-independent reactions) occurs in the stroma and uses ATP and NADPH to fix carbon dioxide into glucose.

DNA Replication

• DNA replication is the process by which DNA is copied.
• DNA replication is semi-conservative, meaning that each new DNA molecule consists of one original strand and one newly synthesized strand.
• DNA polymerase is the enzyme that synthesizes new DNA strands.
• DNA replication starts at origins of replication.
• Helicases unwind the DNA double helix.
• Primase synthesizes RNA primers to initiate DNA synthesis.
• Ligase joins the Okazaki fragments on the lagging strand.

Transcription

• Transcription is the process by which RNA is synthesized from a DNA template.
• RNA polymerase is the enzyme that synthesizes RNA.
• Transcription starts at promoter regions on the DNA.
• mRNA carries the genetic information from DNA to ribosomes.

Translation

• Translation is the process by which proteins are synthesized from mRNA.
• Translation occurs on ribosomes.
• tRNA molecules carry amino acids to the ribosome.
• Codons on mRNA specify the sequence of amino acids in the protein.
• The start codon (AUG) initiates translation, and stop codons (UAA, UAG, UGA) terminate it.

Regulation of Gene Expression

• Gene expression can be regulated at various levels, including transcription, translation, and post-translational modification.
• Transcription factors are proteins that bind to DNA and regulate the transcription of genes.
• Activators enhance transcription, while repressors inhibit transcription.
• Epigenetic modifications, such as DNA methylation and histone modification, can also regulate gene expression.

Vitamins and Minerals

• Vitamins are organic compounds that are essential for various biochemical processes.
• Minerals are inorganic elements that are required for various biological functions.
• Vitamins can be water-soluble (e.g., vitamin C, B vitamins) or fat-soluble (e.g., vitamin A, D, E, K).
• Minerals include calcium, iron, potassium, sodium, and zinc.

Acid-Base Chemistry

• pH is a measure of the acidity or basicity of a solution.
• Buffers are solutions that resist changes in pH.
• The Henderson-Hasselbalch equation relates the pH of a solution to the pKa of a weak acid and the ratio of the concentrations of its conjugate base and acid.

Thermodynamics

• Gibbs free energy (G) is a measure of the amount of energy available in a chemical or physical system to do useful work at a constant temperature and pressure.
• A reaction is spontaneous (exergonic) if the change in Gibbs free energy (ΔG) is negative.
• A reaction is non-spontaneous (endergonic) if the change in Gibbs free energy (ΔG) is positive.

Spectroscopic Techniques

• Spectrophotometry measures the absorbance or transmission of light through a sample.
• Beer-Lambert law relates the absorbance of a solution to the concentration of the analyte and the path length of the light beam.
• Mass spectrometry measures the mass-to-charge ratio of ions.
• NMR spectroscopy provides information about the structure and dynamics of molecules.

Chromatography

• Chromatography is a technique used to separate molecules based on their physical and chemical properties.
• Types of chromatography include thin-layer chromatography (TLC), column chromatography, gas chromatography (GC), and high-performance liquid chromatography (HPLC).

Electrophoresis

• Electrophoresis is a technique used to separate molecules based on their size and charge.
• SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) is commonly used to separate proteins.
• Agarose gel electrophoresis is used to separate DNA fragments.

This lesson covers the basics of biochemistry, focusing on biomolecules. It will explore carbohydrates (monosaccharides, disaccharides, and polysaccharides) and lipids (fats, oils, phospholipids). Emphasis will be given on their structure, functions, and biological importance.