Lesson 2 - Macromolecules 2025 PDF

Lesson 2. What are Cells Made of https://micro.magnet.fsu.edu/cells/ribosomes/ribosomes.html January 10, 2025 Learning Objectives Keywords: Lipids, Carbohydrates, Nucleic acids By the end of this lecture you should be able to 2.1. Distinguish chemical principle...

Lesson 2. What are Cells Made of https://micro.magnet.fsu.edu/cells/ribosomes/ribosomes.html January 10, 2025 Learning Objectives Keywords: Lipids, Carbohydrates, Nucleic acids By the end of this lecture you should be able to 2.1. Distinguish chemical principles critical for the production of cellular building blocks. 2.2. List the major building blocks of cells and describe their chemical natures (covalent bonds). 2.3. Define the terms fatty acid and phospholipid and describe their structure, properties, and functions. 2.4. Describe how biological membranes are assembled without covalent bonding. Types of Chemical Interactions A. Covalent Bonds: strong by sharing electrons (C-H, H-O-H) B. Hydrogen Bonds: polar H with electronegative atom (O, N) C. Ionic Bonds: H+ with OH- D. Van der Waals Interactions: between dipoles E. Hydrophobic interaction Condensation Hydrophobic interaction Hydrophilic: Sticky to water Hydrophobic: Repellent to water  LO2.1 NOTE: CHEMICAL PRINCIPLES OF CELLS A. Covalent Bonds: Strong chemical bonds where atoms share electron pairs. Formation of carbon-based backbones for organic molecules. Links in polymers like proteins (peptide bonds between amino acids), nucleic acids (phosphodiester bonds between nucleotides), and polysaccharides (glycosidic bonds between monosaccharides). Q. Which covalent bonds are frequently found in cellular macromolecules? B. Hydrogen Bonds: Weak bonds between a hydrogen atom covalently bonded to one electronegative atom and another electronegative atom (e.g., oxygen or nitrogen). Essential for base-pairing in DNA (A-T and G-C) and polypeptide and RNA folding into secondary structure.. C. Ionic Bonds: Electrostatic interactions between positively charged (cation) and negatively charged (anion) molecules or atoms. Facilitate enzyme-substrate binding and protein-protein interaction. D. Van der Waals Interactions: Weak, non-specific forces arising from transient dipoles in atoms or molecules. Contribute to the packing of lipids in membranes. Help proteins achieve their final folded structures. E. Hydrophobic Interactions: Nonpolar molecules aggregate in aqueous solutions to minimize exposure to water. Drive the formation of lipid bilayers and protein folding. Q. Which chemical groups in bio-molecules do not form hydrogen bonds? C-H Organic macromolecules into 4 major categories Q. How do cells produce highly organized molecules to form the cell structure and carry out the activities of cells? Solution: Cellular ⇡⇣ macromolecules consists of relatively small# of subunits (building blocks like LEGO). Made of C- skeleton Anabolism (production) of macromolecules Building complex molecules from simple ones Nucleic acids Nucleotides /Sugars (6C, 5C) N+R+C 20 kinds P+S+ (Ala ~ Tyr) Acetyl CoA Bases (G,A,T,U,C) Glutamate + NH3  Covalent bonds in macromolecules Peptide (N to C) Phosphodiester (5 to 3) H OH H Glycosidic Fatty acid Hydrolysis  SUMMARY OF COVALENT BONDS IN MACROMOLECULES Macromolecule Covalent Bond Type Function (To be continued) Proteins Peptide (-C-N-), Structure and stability Disulfide (-S-S-) of proteins Nucleic Acids Phosphodiester (- Form DNA/RNA PO-O-), Glycosidic backbone and nucleotides Carbohydrates Glycosidic (-O-) Energy storage, structural roles Lipids Ester (-CO-O-) Membrane formation, between glycerol energy storage and fatty acids Hydrogen bonding in nucleic acids 1. Chain polymer of nucleotides (5’-3’) and complementary pairing (A:U or A:T and G:C). 2. Differences between RNA and DNA: a) Base usage, AGCU (RNA) vs. AGCT (DNA) b) Ribose vs. Deoxyribose (O missing at C2) Antiparallel complementary DNA double helix 3. Flexible RNA, assuming complex 3D-shape via stem and loop formation, but also forming a double-stranded duplex* *RNA-dependent DNA/RNA polymerases exist. 4. Single-stranded DNA is unstable, forming a Self assembly duplex or binding to single-stranded DNA- of 3D structure binding proteins. of RNA iClicker Question Condensation reactions and hydrolysis reactions are two important (and opposite) classes of chemical reactions performed by cells. Classify each of the reactions described below as either a condensation reaction (C), a hydrolysis reaction (H), or neither (N). Glutamate + ATP + NH3 à Glutamine + ADP + Phosphate Sucrose + H2O à Glucose + Fructose A. C&C B. H&C C. C&H D. N&C E. N&H *BIOL2520 uses the ‘condensation’ term inclusively to any reaction combining two molecules via covalent formation. iClicker-MC Question for your review Single-stranded DNA can be replicated by DNA polymerases. Guanine Predict the replicated product of the following tetranucleotide (GGAA). Guanine A. 5’-GGAA-3’ B. 5’-AAGG-3’ C. 5’-CCTT-3’ Adenine D. 5’-TTCC-3’ E. 5’-CCUU-3’ F. 5’-UUCC-3’ Adenine Q. What if the question asks the product produced by RNA polymerases?  LO2.2 NOTE: BUILDING BLOCKS OF CELLS A. Covalent Bonds in Proteins (in the context of protein structure) Peptide Bonds (C-group of the chain is connected to the next): Formed between the carboxyl group of one amino acid and the amino group of another. These bonds create the polypeptide backbone of proteins (as 1’ structure). Disulfide Bonds (Common in extracellular proteins like antibodies and enzymes) Covalent bonds between the sulfur atoms of two cysteine side chains. Stabilize tertiary and quaternary structures of proteins. B. Covalent Bonds in Nucleic Acids (in the context of base-pairing and directionality) Phosphodiester Bonds (3’ of the chain is connected to the next): Link the 3'-hydroxyl group of a nucleotide’s sugar to the 5'-phosphate group of the next. Form the sugar-phosphate backbone of DNA and RNA. C. Covalent Bonds in Carbohydrates Glycosidic Bonds (many OH available to be linked to the next sugar molecule): Link monosaccharides to form disaccharides or polysaccharides. Examples (do not memorize specific names, but variation exist, alpha/beta/1,3/1,4 etc.) α-1,4-glycosidic bonds in glycogen and starch (energy storage). β-1,4-glycosidic bonds in cellulose (structural support in plants). D. Covalent Bonds in Lipids Ester Bonds: Formed between the hydroxyl group of glycerol and the carboxyl group of fatty acids. C-C and C-H Bonds in long hydrocarbon fatty acids: Nonpolar, releasing energy via oxidation. What drives lipids to self-aggregate in water? Hydrophobic (“water fearing”) or contain significant hydrophobic regions (=nonpolar): Aggregating without covalent bonds. Layer or Micelle – two arrangements of lipids in water Ex. Fatty acid (short- or long-chain)  How to build biological membranes? 1. Glycerol (3X CH2-OH) as backbone: linking two fatty acids (C14-20) and one phosphate (or betaine). 2. Phosphates can be further connected to other polar molecules (ex. choline, serine) 3. Amphipathic: contains both hydrophobic and hydrophilic regions to be sandwiched. *Archaean membranes of glycerol isoprenoids ([ ]n.) Where to find lipids in cells? 1. Source of energy in the diet and energy storage in the cells and body ([CH2]nà nCO2). e.g. fats and oils in adipocytes. Ex. triacylglycerides (TAG) 2. Essential oils: Lipid soluble vitamins: VitA, D, and E - Omega oils: long-chain polyunsaturated fatty acids (good for insulation) - Abundant in the green/algal diet as carotenoids, tocopherol, etc. (light-absorbing/scattering pigments) e.g. pigments in retina and macula as a blackout curtain https://www.the-scientist.com/daily-news/bone-marrow- makes-new-fat-cells-35141 iClicker Question Phospholipids may be self-assembled into a bilayer in water. Which of the following chemical forces is the most critical for the phospholipid bilayer formation? A. Covalent bonds B. Hydrogen bonds C. Ionic bonds D. Van der Waals interaction E. Hydrophobic interaction iClicker-MC  LO2.3-4 NOTE: FATTY ACIDS AND PHOSPHOLIPIDS A. Fatty Acids: long hydrocarbon chains with a carboxyl group (-COOH) at one end. They serve as the basic building blocks of lipids. Functions: Energy Storage: Fatty acids are stored as triglycerides and broken down for energy. (ex. TAG) Membrane Precursors: Serve as components for phospholipids and glycolipids, key parts of cell membranes. (ex. phospholipids) Pigments for light absorption: in green photosynthetic cells and in eyes as shades. B. Phospholipids (many kinds): lipids containing two fatty acid tails and a phosphate- containing group attached to a glycerol backbone. They are primary components of cell membranes. Properties: Amphipathic Nature: Phospholipids have both hydrophobic (nonpolar tails) and hydrophilic (polar head) regions, making them ideal for forming bilayers. Self-Assembling: When in water, phospholipids spontaneously form bilayers or micelles, with hydrophobic tails inward and hydrophilic heads outward. Diverse forms: Phosphates are often linked to additional polar groups (like choline).