Biochemistry Foundations & Fundamentals

Course Overview

• The course is Chem 4: Biochemistry, designed for students in the Bachelor of Secondary Education program.
• This course bridges chemistry and biology, and offers insights into molecular mechanisms of life processes.
• Fundamental aspects of biochemistry, structure, dynamics of cellular components are discussed.
• The course includes structure, properties, functions, and metabolism of carbohydrates, proteins, lipids, and nucleic acids. Includes enzyme kinetics, metabolic pathways, and gene regulation.
• The course is 3 credit units spread over 54 instructional hours.

Course Learning Outcomes (CLOs)

• Students will demonstrate understanding of fundamental aspects of biochemistry.
• Students will show an understanding of structure, properties, functions, and metabolism of biochemical compounds.

Unit 1: Foundations & Fundamentals

• Biochemistry is the study of chemical processes and substances within living organisms. It bridges biology and chemistry.
• Key areas include metabolism, enzymology, molecular genetics, and structural biology.
• The scope encompasses cellular processes, molecular interactions, health and disease, biotechnology and agriculture, and education and research.
• Key milestones in biochemistry include: Eduard Buchner's discovery of enzymatic fermentation, Watson and Crick's DNA structure, Krebs' citric acid cycle, Pauling's protein structure work, and Boyer and Cohen's recombinant DNA technology.

Prokaryotes vs. Eukaryotes

• Prokaryotes: Simple structure, no nucleus, circular DNA in nucleoid, includes bacteria and archaea.
• Eukaryotes: Complex cells, defined nucleus, organelles like mitochondria, linear DNA in chromosomes.
• Energy Production: Prokaryotes use the cell membrane, while eukaryotes use specialized organelles like mitochondria.
• Macromolecule Synthesis: Ribosomal structure impacts protein synthesis, targeted by antibiotics in prokaryotes.
• Cell Size: Prokaryotic cells are smaller (1-10 μm) than eukaryotic cells (10-100 μm or more).
• Prokaryotes lack membrane-bound organelles, while eukaryotes contain them.

Biomolecules: Carbohydrates

• Carbohydrates are essential biomolecules for energy, structure, and signaling.
• Monosaccharides: Simplest form, single sugar unit, formula CnH2nOn (n=3-7), e.g., glucose, fructose, galactose.
• Physical Properties of Monosaccharides: Crystalline solids, sweet, soluble in water.
• Chemical Properties of Monosaccharides: Exists in linear or cyclic forms, cyclic forms predominate in solutions.
• Functions of Monosaccharides: Quick energy, building blocks for complex carbohydrates.
• Disaccharides: Two monosaccharides linked by a glycosidic bond, e.g., sucrose, lactose, maltose.
• Physical Properties of Disaccharides: Typically sweet and water-soluble.
• Chemical Properties of Disaccharides: Undergo hydrolysis, breaking into monosaccharides.
• Functions of Disaccharides: Transportable energy in plants, energy when digested.
• Polysaccharides: Long chains of monosaccharides, linear or branched, e.g., cellulose, glycogen, starch.
• Physical Properties of Polysaccharides: Insoluble or poorly soluble, often lack sweetness.
• Chemical Properties of Polysaccharides: Hydrolyzed into simpler carbohydrates, structural integrity depends on glycosidic linkage.
• Functions of Polysaccharides: Storage (starch, glycogen), structural (cellulose, chitin), signaling and recognition.
• Solubility of Carbohydrates: Monosaccharides and disaccharides are soluble in water due to hydroxyl groups.
• Sweetness intensities: Fructose > glucose > galactose.
• Redox Behavior: Some carbohydrates can donate electrons.

Unit 2: Carbohydrates & Proteins - Carbohydrate Metabolism

• Glycolysis involves breaking down glucose (6-carbon molecule) into two molecules of pyruvate (3-carbon molecules) in the cytoplasm.
• The purpose of glycolysis is to generate ATP and NADH.
• Investment Phase: Uses 2 ATP to phosphorylate glucose.
• Cleavage Phase: Splits 6-carbon intermediates into two 3-carbon molecules.
• Payoff Phase: Produces 4 ATP and 2 NADH, net gain of 2 ATP.
• Key Enzymes: Hexokinase, Phosphofructokinase-1 (PFK-1), and Pyruvate Kinase.
• Glycolysis Regulation: Controlled by ATP and AMP levels.
• Gluconeogenesis is the synthesis of glucose from non-carbohydrate sources, such as lactate, glycerol, and amino acids.
• Gluconeogenesis maintains blood glucose during fasting or low-carbohydrate intake.
• The steps of gluconeogenesis are essentially the reverse of glycolysis.
• Liver and kidneys are the key sites for this process
• Regulation of Gluconeogenesis: Controlled by glucagon (stimulates) and insulin (inhibits).

Cellular Respiration Stages

• Glycolysis generates pyruvate.
• Citric Acid Cycle completes oxidation of glucose derivatives to CO2.
• Oxidative Phosphorylation produces ATP via the electron transport chain and chemiosmosis.
• NADH and FADH2 transfer high-energy electrons to the electron transport chain, driving ATP synthesis.
• Glycolysis produces 2 ATP (net).
• Citric Acid Cycle produces 2 ATP (per glucose).
• Oxidative Phosphorylation produces ~26-28 ATP.
• Allosteric Regulation: Enzymes like PFK-1 are regulated by energy signals.
• Hormonal Control: Insulin promotes glycolysis, Glucagon and epinephrine stimulate gluconeogenesis.
• Energy Demand: High energy demand promotes catabolism, and low demand favors anabolism.

Amino Acids & Peptide Bonds

• Proteins are the workhorses of cells, and have structural, enzymatic, and regulatory functions.
• They are determined by amino acids, their unique bonding, and the hierarchical structure.
• All amino acids share a central carbon atom, amino group, carboxyl group, hydrogen atom, and variable R-group.
• Amino acids can be classified by R-groups: Nonpolar, Polar, Acidic, and Basic.
• Peptide Bond Formation: Formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another.

Protein Structure

• Primary structure is the linear sequence of amino acids, which determines the protein's 3D structure and function.
• Secondary structure involves regular folding patterns stabilized by hydrogen bonds, such as alpha-helices and beta-pleated sheets.
• Tertiary structure is the 3D arrangement of a polypeptide due to interactions between R-groups, like hydrophobic interactions.
• Quaternary structure involves complexes of two or more polypeptide chains (subunits).
• Any alterations of protein structure through mutation or denaturation can lead to loss of function.
• Proteins play various roles such as: structural, enzymatic, transport, and signaling.

Enzymes

• Enzymes catalyze chemical reactions and increase speed, by lowering activation energy.
• Examples of enzyme-mediated reactions include digestion and energy production.
• The lock-and-key model suggests the enzyme's active site fits perfectly with the substrate, while the induced-fit model suggests the enzyme undergoes conformational changes.
• Enzyme activity is influenced by environmental factors.
• Temperature influences enzyme activity because each enzyme has an optimal temperature.
• pH influences enzyme activity because enzymes functions best are specific Ph ranges.
• Inhibitors are molecules that can reduce enzyme activity, such as competitive and non-competitive inhibitors.

Protein production

• Protein synthesis involves two steps of transcription and translation.
• Transcription is when the genetic information in DNA is copied into mRNA.
• RNA polymerase binds to the promoter region of a gene in transcription.
• Elongation occurs where the RNA polymerase synthesizes a complementary strand of mRNA.
• Termination occurs when RNA polymerase reaches a termination signal.
• Outcome: A single-stranded mRNA molecule carries the genetic code for protein synthesis from the nucleus to the ribosome.
• Translation occurs by decoding an mRNA sequence is decoded to assemble a polypeptide chain.
• Ribosomes, tRNA, and mRNA molecules participate in translation.
• The degradation process can either occur in the Ubiquitin-Proteasome or Lysosomal Degradation pathways.
• Protein turnover maintains cell function, regulates metabolism, and provides cell adaptation.

Unit 3: Lipids, Nucleic Acids, Other Biomolecules

• Lipids include fatty acids, triglycerides, phospholipids, and steroids.
• Lipids in energy storage, membrane structure, and signaling.
• Lipid catabolism (beta-oxidation) and anabolism (lipid biosynthesis).
• The regulation of pathways and their connections to carbohydrate metabolism.
• Nucleic acids, compare and contrast DNA and RNA structures and functions,
• DNA replication, transcription and translation
• Discuss how gene expression at different levels
• Explain the importance of gene regulation in development and cellular responses.
• The roles of vitamins, coenzymes, and hormones and laboratory techniques.
• Essential vs. non-essential amino acids must be consumed in the body.

DNA vs RNA

• DNA
  • double stranded
  • deoxyribose sugar
  • bases contain Thymine
  • Stores genetic information
  • Located in the nucleus only
• RNA
  • single stranded
  • ribose sugar
  • bases contain Uracil
  • Translates this genetic information into proteins
  • Located in the nucleus and cyoplasm

Gene Expression

• it occurs in a two stage process
• Transcription: Synthesis of RNA from DNA
• Translation: Synthesis of proteins based on the RNA sequence
• Regulated at different levels:
  • Transcriptional Regulation: Using promoters and enhancers
  • Epigenetic Modifications: Using protein modifications

Enzymes and Hormones

• VItamins and minerals serve as cofactors for enzymes, which is essential for life
• Can be fat or water soluable
• Hormones include Peptide, steriod and amine which are chemical messengers secreted by endocrine glands to regulare physiological and biochemical process
• Hormones influence metabolism, growth, and homeostasis.
• Example: Insulin facilitates glucose uptake by cells and reduction of sugar levels

Unit 4: Applications

• Applications of biochemistry in various fields, including biotechnology, medicine, agriculture, and environmental science.
• Genetically Modified Organisms (GMOs), is the understanding of biochemical principles behind gene editing tools
• Biopharmaceuticals: Recombinant DNA technology to produce insulin and monoclonal antibodies.
• Biofuels: useEnzymatic pathways to produce bioethanol and biodiesel from microorganisms.
• Biochemicals can be used for pathways in disease, drug design, and diagnostic tools for diseases such as diabetes and cancer
• The biochemical basis is used for crop improvement, soil health, and pest control in argiculture
• Biochemicals used for Environmental Monitoring: Use of biochemical sensors for detecting pollutants.