BLG143 2024 Lecture Notes on Nucleic Acids PDF

BLG143: BIOLOGY I Chapter 4: Nucleic Acids and the RNA World Faculty of Science Department of Chemistry & Biology THE GENERAL STRUCTURE OF A NUCLEOTIDE Ribonucleotides are monomers of RNA Sugar is ribose Has an –OH group bonded to the 2′ carbon Deoxyr...

BLG143: BIOLOGY I Chapter 4: Nucleic Acids and the RNA World Faculty of Science Department of Chemistry & Biology THE GENERAL STRUCTURE OF A NUCLEOTIDE Ribonucleotides are monomers of RNA Sugar is ribose Has an –OH group bonded to the 2′ carbon Deoxyribonucleotides are monomers of DNA Sugar is deoxyribose (deoxy = “lacking oxygen”) Has an H instead at the 2′ carbon TYPES OF NITROGENOUS BASES 1. Pyrimidines Cytosine (C) Uracil (U)—only in RNA Thymine (T)—only in DNA 2. Purines Adenine (A) Guanine (G) NUCLEOTIDES POLYMERIZE TO FORM NUCLEIC ACIDS A condensation reaction forms a phosphodiester bond between: The phosphate group of one nucleotide The –OH group on the 3′ carbon of another Form a sugar–phosphate backbone DNA AND RNA STRANDS ARE DIRECTIONAL One end has unlinked 5′ phosphate group Other end has unlinked 3′ hydroxyl group Sequence is written in 5′ → 3′ direction Reflects the order that nucleotides are added to a growing molecule LEARNING OBJECTIVES Identify the three basic components of a nucleotide Describe the formation of nucleic acids and the sugar-phosphate backbone Recognize how RNA and DNA differ 6 DNA’S SECONDARY STRUCTURE Chemists knew that DNA has a sugar–phosphate backbone Chargaff’s rule: # of purines = # of pyrimidines Equal number of T’s and A’s; equal number of C’s and G’s Franklin and Wilkins used X-ray crystallography to measure Rosalind Franklin Maurice Wilkins distances between atoms in DNA SECONDARY STRUCTURE: DNA STRANDS FOR ANTIPARALLEL HELIX Watson and Crick determined: Complementary base pairing: A - T, C - G DNA strands run antiparallel Forms double helix. Hydrophilic sugar-phosphate backbone faces exterior Nitrogenous base pairs face interior James Watson, Francis Crick, and Maurice Wilkins won the Nobel. Note who is missing! X-ray crystallography image by R. Franklin DETERMINING COMPLIMENTARY BASE PAIRING  DNA STRANDS FORM AN ANTIPARALLEL DOUBLE HELIX Hydrophobic interactions cause DNA to twist Negatively charged phosphate groups face out, making DNA hydrophilic overall DNA FUNCTIONS AS AN INFORMATION MOLECULE Carries information required for growth and reproduction of all cells Coding language is contained in the sequence of the bases Sequence of bases has meaning, like letters in a word THE DNA DOUBLE HELIX IS A VERY STABLE STRUCTURE Resistant to chemical degradation Makes it a reliable store for genetic information Stable molecules such as DNA make poor catalysts DNA has never been observed to catalyze a reaction REVISITING A PAST QUESTION Last class I asked you: Could a protein have been the initial spark of life? Must possess three attributes: Information Replication Evolution Is DNA a good candidate? Biologists think that the first life form was made of RNA RNA’S SECONDARY STRUCTURE RNA is largely single-stranded Contains short stretches of complementary base pairing on the same strand: A with U, G with C RNA strand folds over, forming a hairpin loop TERTIARY STRUCTURE OF RNA MOLECULES Forms when secondary structures fold into more complex shapes RNA is much more diverse in size, shape, and reactivity than DNA RNA is highly versatile An information-containing molecule Capable of self-replication Capable of catalyzing reactions: ribozymes tetrahymena ribozyme 16 LIFE IN AN RNA WORLD Three characteristics of life are accounted for: ✓ Information processing ✓ Replication of hereditary information ✓ Evolution by random changes in nucleic acids LEARNING OBJECTIVES Describe the structure of DNA Describe the secondary and tertiary structures of RNA and explain how RNA and DNA differ. Explain why DNA is an effective molecule for storing biological information Explain and justify why RNA, and not DNA, was probably the first self- replicating molecule 18  BLG143: BIOLOGY I Chapter 5: An Introduction to Carbohydrates Faculty of Science Department of Chemistry & Biology An Introduction to Carbohydrates Carbohydrates, or sugars, are macromolecules that Play an important role in energy Contribute to cell structure Are involved with cell recognition and identity Carbohydrates include Monosaccharide (“one-sugar”) monomers Oligosaccharide (“few-sugars”) small polymers Polysaccharide (“many-sugars”) large polymers 20 An Introduction to Carbohydrates Carbohydrates have the molecular formula (CH 2 O) n “Carbo” refers to carbon “Hydrate” refers to water “n” can vary from 3 to over a thousand Carbohydrates contains: Many carbon–hydrogen bonds (C–H) A carbonyl group (C=O), A hydroxyl groups (O–H), and Since carbonyl and hydroxyl groups are polar, carbohydrates are hydrophilic 21 The Structure of Disaccharides Two sugars linked together form a disaccharide Monosaccharides polymerize when a condensation reaction occurs between 2 hydroxyl groups A covalent bond called a glycosidic linkage forms The linkages can be broken by hydrolysis reactions 22  The Structure of Disaccharides Glycosidic linkages can form between any two hydroxyl groups Two of the most common: α-1,4-glycosidic linkage β-1,4- glycosidic linkage Linkages between the C-1 & C-4 carbons Geometry is different; hydroxyl groups are on opposite sides of glucose rings 23 Starch and Glycogen: Storage Polysaccharides in Plants and Animals Branched, some α-1,6-glycosidic linkages Unbranched, only α- 1,4-glycosidic linkages Highly branched, many α-1,6 linkages, 24 nearly identical to starch Cellulose and Chitin: Structural Polysaccharides Every other glucose is flipped so it is linear, not helix Similar to cellulose, added acetamido group to monomer 25 Peptidoglycan: A Structural Polysaccharide in Bacteria Peptidoglycan is a structural polymer found in bacterial cell walls Similar to cellulose/chitin: backbone of alternating monosaccharides joined by β- 1,4-glycosidic linkages But has short amino acid chains – form peptide bonds b/w adjacent strands 26 Carbohydrate Function: Indicate Cell Identity Information on the outer surface of cells Glycoproteins—carbohydrates attached to proteins Glycolipids—carbohydrates attached to lipids Key molecules for: Cell–cell recognition: Identify cells as “self” Cell–cell signaling: Communication between cells 27 Carbohydrate Function: Indicate Cell Identity – An Example Human blood cells glycoproteins and glycolipids can display one of three oligosaccharides A, B and H antigen Patients cannot receive blood that has antigens they do not make What can happen if you receive a blood transfusion with a different antigen from your own? A&H B&H A, B & H H Antigen Antigen Antigen Antigen Carbohydrate Function: Store Chemical Energy In photosynthesis, plants harvest energy from sunlight and store it in carbohydrates CO2 + H2O + sunlight → (CH2O)n + O2 Carbohydrates have more energy than CO2 Electrons in C–O bonds are held more tightly and have low potential energy Electrons in C–H and C–C bonds are shared more equally and have higher potential energy Fatty acids hold even more energy because they have more C–C and C–H bonds 29 LEARNING OBJECTIVES List the features shared by all carbohydrates. Describe the type of monomer, the type of linkage, the branching (if any), and the major functions of the following polysaccharides: starch, glycogen, cellulose, chitin, and peptidoglycan. Name and give an example of each of the three major functions that carbohydrates perform in cells. 30  BLG143: BIOLOGY I Chapter 6: Lipids, Membranes & The First Cells Faculty of Science Department of Chemistry & Biology Lipid Structure and Function Lipids are largely nonpolar and hydrophobic Hydrocarbons contain primarily C and H Electrons are shared equally in C–H bonds = non-polar, hydrophobic A fatty acid is a hydrocarbon chain bonded to a carboxyl (–COOH) functional group Can be saturated or unsaturated A Look at Three Types of Lipids Found in Cells Lipids characterized by a physical property: their insolubility in water, not a shared chemical structure Insolubility is based on high proportion of nonpolar C–C and C–H bonds Even if they do have some polar functional groups 33 Types of Lipids Found in Cells: Fats Made of 3 fatty acids linked to glycerol Also called triglycerides When their fatty acids are polyunsaturated, they are liquid and form oils Primary role is energy storage Form by dehydration reactions b/w hydroxyl group of glycerol and the carboxyl group of a fatty acid (ester linkage) 34 Types of Lipids Found in Cells: Steroids Distinguished by bulky, four-ring structure Steroids differ from one another by the functional groups attached to carbons in the rings Examples: Hormones such as estrogen and testosterone, cholesterol 35 Types of Lipids Found in Cells: Phospholipids Contains two hydrocarbon chains Are amphipathic: contain hydrophilic & hydrophobic regions Primary role: cell membranes Think-Pair-Share 2 min What will happen when amphipathic lipids are placed in water? The hydrophilic heads interact with water The hydrophobic tails interact with each other, away from the water They form micelles or lipid bilayers 37 PHOSPHOLIPID BILAYER Hydrophilic heads face solution Hydrophobic tails face one another Form spontaneously → No energy required Bilayers have selective permeability Small molecules move across quickly Nonpolar molecules move across quickly Charged or large polar substances cross slowly, if at all LEARNING OBJECTIVE Describe the structures of steroids, fats, and phospholipids Recognize the difference between saturated and unsaturated fatty acids, and implications for molecular shape Explain why phospholipids spontaneously form bilayers in water. 39 How Does Lipid Structure Affect Membrane Permeability? 1. Number of double bonds in the phospholipid’s hydrophobic tail Double bonds in a hydrocarbon chain: Prevents the close packing of hydrocarbon tails Membranes are much more permeable 2. Length of the hydrocarbon tail Membranes containing phospholipids with longer tails are less permeable How Does Lipid Structure Affect Membrane Permeability? 3. Number of cholesterol molecules in the membrane Adding cholesterol increases the density of the hydrophobic section Cholesterol decreases membrane permeability 4. Temperature Membrane permeability decreases as temperature drops Molecules in the bilayer move more slowly Hydrophobic tails pack together more tightly How Substances Move Across Lipid Bilayers: Diffusion and Osmosis Diffusion Concentration gradient created by a difference in solute concentrations Movement from high-concentration to low-concentration Diffusion is spontaneous Equilibrium occurs when the molecules or ions are evenly distributed Molecules are still moving randomly But there is no net movement 42 How Substances Move Across Lipid Bilayers: Diffusion and Osmosis Osmosis A special case of diffusion Only occurs across selectively permeable membranes Water moves from regions of low solute concentration to high solute concentration This dilutes the higher concentration of solute It equalizes the concentration on both sides of the bilayer How Substances Move Across Lipid Bilayers: Diffusion and Osmosis 45 46 Development of the Fluid-Mosaic Model Some proteins inserted into bilayer, making membrane a dynamic mosaic of phospholipids and proteins Proteins that span the membrane are integral membrane or transmembrane proteins Segments face both interior and exterior surfaces Portions that pass through hydrophobic tails have hydrophobic side chains Peripheral membrane proteins only on inside or outside of bilayer LEARNING OBJECTIVES Describe if/how substances move across the lipid bilayer Understand how saturation, length of fatty acid chains, and temperature affect membrane permeability Predict which way a certain substance will diffuse, given its concentration on either side of a selectively permeable membrane. Predict which way water will move, given the overall solute concentration on either side. 48 49