BSC1010C Chapter 5 PP (Spring 2025) PDF

Chapter 5: The Structure and Function of Large Biological Molecules Dr. Kaitlyn Fulford Valencia College – Downtown Campus BSC1010C – 27267 & 27268 Spring 2025 Disclaimer These PowerPoints (and all other class resources) are made...

Chapter 5: The Structure and Function of Large Biological Molecules Dr. Kaitlyn Fulford Valencia College – Downtown Campus BSC1010C – 27267 & 27268 Spring 2025 Disclaimer These PowerPoints (and all other class resources) are made available as a learning tool only. Do not share or distribute this presentation, or any of the information it contains, to anyone outside of your classmates. Sharing these presentations irresponsibly is a potential copyright infringement violation and will not be tolerated. If this behavior occurs, presentations will no longer be available for download to use as a study tool. Please do not be the one responsible for losing this resource for the rest of your classmates! Concept 5.1: Macromolecules are polymers, built from monomers Figure 5.1 Four important classes of biological molecules: 1. Carbohydrates 2. Proteins 3. Nucleic acids 4. Lipids Concept 5.1: Monomers and polymers Polymers: Long molecules made up of many similar or identical building blocks Blocks are linked via covalent bonds These building blocks (repeating units) are called monomers Each class of polymer consists of different monomers, but the way they are linked together and taken apart are similar across classes. Evolutionary crossover! Concept 5.1: Polymerization (dehydration reaction) Figure 5.2 Polymerization: The linkage of monomers together to create a polymer Dehydration reaction: Type of condensation reaction Two monomers are bound together by covalent bonds Water is lost in the process. One reactant provides —OH, or hydroxyl group The other reactant provides —H Together, this creates water, or H 2O Concept 5.1: Breaking apart polymers (hydrolysis) Figure 5.2 Polymers can be pulled apart into individual monomers (water breakage) Hydrolysis: Water (H2O) splits covalent bonds between monomers in the polymer chain, breaking the chain apart. One monomer gets —H Other monomer gets —OH Ex: digestion of food Concept 5.1: Macromolecules 3 biological macromolecules Macromolecule: 1. Carbohydrates Extremely large molecules Monomer: monosaccharides Made up of polymers! Ex: glucose 3/4 classes of biological 2. Proteins Monomer: Amino acids molecules are macromolecules Ex: enzymes 3. Nucleic acids Monomer: Nucleotide Concept 5.1: Macromolecules (Evolution) Evolution Crossover: So much diversity among biological macromolecules due to wide range of potential polymers that exists. 26 letters in the alphabet can create large amounts of words Diverse range of polymers present in all different kinds of life were built from the same pool of monomers common to all organisms. Pay attention to the emergent properties in each of the macromolecules in the next few slides Concept 5.2: Carbohydrates serve as fuel and building materials Carbohydrates The chemical name will end in ---ose 3 main categories: 1) Monosaccharide: The monomer of a carbohydrate AKA: simple sugars 2) Disaccharide: The combination of 2 monosaccharides joined by covalent bonds AKA: double sugars 3) Polysaccharide: Carbohydrate macromolecule made up of polymers of monosaccharides and disaccharides Concept 5.2: Monosaccharides (basic facts) General Facts: Basic molecular formula: CH2O The most common is glucose, or C6H12O6 Very important in the chemistry of life! Other common examples: fructose, galactose, ribose, ribulose Major nutrients for cells (cellular respiration in upcoming chapters) Especially glucose! Concept 5.2: Monosaccharides (basic facts, continued) Figure 5.4 Forms rings in aqueous solutions, like in the body Broken down by cellular respiration Then, the carbon skeleton can: 1. Become raw materials for other biological molecules Ex: amino acids and fatty acids 2. Incorporation into and creation of other disaccharides and polysaccharides Concept 5.2: Monosaccharide categorization (3 ways) 1. Location of the carbonyl group 2. Size of the carbon skeleton Aldose (at the end) Ranges: 3-7 carbons Ex: glucose Glucose and fructose: 6 carbons Ketose (inside the molecule) Called hexoses Ex: fructose 3-carbon sugars, trioses, and 5 carbon sugars, pentoses Concept 5.2: Monosaccharide categorization (3 ways) continued Figure 5.3 3. Arrangement of parts around asymmetric carbons Asymmetric carbons: Carbon attached to four different atoms or functional groups Sometimes, they differ only in the arrangement of these four different groups. They will have the same groups, bound in different places. Ex: Glucose vs. Galactose Concept 5.2: Disaccharides Figure 5.5 Definition: Two monosaccharides joined together by glycosidic linkage. Glycosidic linkage: A covalent bond formed between two monosaccharides by a dehydration reaction Example: maltose, aka malt sugar (ingredient in beer), is a disaccharide of glucose Disaccharides must be broken down into the basic monosaccharides to be used as energy in the body! Concept 5.2: Disaccharides (continued) The most common disaccharide is sucrose, or table sugar Monomers: glucose + fructose Used in plants as the primary source of transporting sugar! Another common disaccharide is lactose (found in milk) Monomers: glucose + galactose Lactose intolerance: Absence of the enzyme, lactase, that breaks down lactose into its monomers. Instead, it is broken down by bacteria, causing gas, cramping and diarrhea. Treatment: Lactase supplements or drinking lactose-free milk. Concept 5.2: Polysaccharides (basic facts) Definition: Polymers ranging from a few hundred to a few thousand monosaccharides joined by glycosidic linkages Polysaccharides are macromolecules!! Connection to chapter 1: structure and function The types of monosaccharides and the position of its glycosidic linkages determines its function! Some functions include: Structural polysaccharides Storage polysaccharides Concept 5.2: Storage polysaccharides Animals store sugar as glycogen Plants store sugar as starch Monomer: glucose Monomer: glucose Link: Usually 1-6 glycosidic linkages Link: alpha 1-4 glycosidic linkages Stored in liver and muscle cells When animals need energy, When plants needs energy, starch is glycogen is hydrolyzed into glucose hydrolyzed into glucose Glycogen stores last ~1 day if not replenished by food Type of soluble fiber Glycogen is more branched than Enzymes break down alpha starch! Structure and function: More linkages branching  faster breakdown  quick energy Concept 5.2: Structural polysaccharides Figure 5.7 (next slide) Plants structural polysaccharide is called cellulose Think of the tough cell walls of plants! Monomer: glucose Held together by beta 1-4 glycosidic linkages Type of insoluble fiber Lacks the enzyme to break down beta linkages Concept 5.2: Starch vs Cellulose (Figure 5.7) Concept 5.2: Cellulose vs Starch Starch: Cellulose: Alpha 1-4 glycosidic linkages Beta 1-4 glycosidic linkages Shape: helical structures, branches Shape: No branching! Straight molecules. Structure and function: Shape allows for Structure and function: Straight shape  easy storage and breakdown into energy strength for cell walls (function) Humans cannot digest cellulose Humans can break down starch into However, important for gut health and glucose (soluble fiber) passage of stools (insoluble fiber) Cows, termites, and fungi can break down cellulose! Concept 5.2: Chitin Figure 5.8 Arthropods use the structural polysaccharide chitin Makes up their exoskeleton Also used by fungi to make cell walls Has beta linkages, similar to cellulose Difference: The glucose monomer has an attachment containing nitrogen Concept 5.3: Lipids are a diverse group of hydrophobic molecules Lipids: Are not large enough to be a macromolecule Are not made of true polymers Important trait of all lipids: They are hydrophobic They consist primarily of hydrocarbon regions with non-polar bonds. 3 primary biologically significant lipids: 1. Fats 2. Phospholipids 3. Steroids Concept 5.3: Fats (basic facts) Fats: Do not meet criteria for a polymer However, they are large molecules made up of smaller ones created via a dehydration reaction. Other names include: Triacylglycerol Triglyceride STRUCTURE: One glycerol + Three fatty acids Concept 5.3: Fat structure (continued) Figure 5.9 Glycerol: An alcohol 3 carbons, each with a hydroxyl group Fatty Acid: An acid because of its carboxyl group Long carbon chain, ~16-18 carbons One end has a carboxyl group Remainder of chain is a hydrocarbon This is why fats are hydrophobic! Because hydrocarbons are non-polar covalent bonds Fatty acids bind to glycerol by a dehydration reaction The resulting bond is called an ester linkage! Concept 5.3: Fat structure (saturated fats) Saturated Fatty Acid: Saturated Fats: No double bonds between Made from saturated fatty acids carbons in the hydrocarbon + glycerol chain Includes most animal fats Therefore, carbons are Solid at room temperature completely saturated with No kinks in the chain  no hydrogen double bonds (makes it When bound to glycerol, these solid!) result in saturated fats Can contribute to cardiovascular disease (atherosclerosis) Concept 5.3: Fat structure (unsaturated fats) Unsaturated Fatty Acid: Unsaturated Fats: At least one double bond between Made from unsaturated fatty acids carbon atoms in hydrocarbon chain + glycerol One less hydrogen atom for each Includes plant and fish fats carbon double bond. Liquid at room temperature Therefore, carbons are not Due to double bonds in the carbon saturated with hydrogen chain causing kinks When bound to glycerol, these result in unsaturated fats Concept 5.3: Fats (Figure 5.10) Concept 5.3: Fats – hydrogenated vegetable oil Hydrogenated vegetable oil: Unsaturated fats are turned into saturated fats by synthetically adding hydrogens. Solid at room temperature EX: Peanut butter, margarine Also creates trans fats, which contribute to coronary artery disease Concept 5.3: The function of fat FUNCTION: Energy storage Stored in hydrocarbon chains of fatty acids 1g of fat holds more than twice the amount of energy in 1g of a polysaccharide (carbohydrate) Humans store energy in adipose cells Adipose tissue serves a few purposes: Stores energy Cushions vital organs (Ex: kidneys) Insulates the body (Ex: whales, seals) Plus many more….. Concept 5.3: Phospholipids structure Figure 5.11 Purpose: Part of cell membranes! Structure & function (Ch. 1) STRUCTURE: Two fatty acids + One glycerol + phosphate group The last hydroxyl group on glycerol binds to the phosphate group instead of another fatty acid (like fats) Creates a negative charge Different polar molecules can bind to (-) phosphate group  diversity of phospholipids! Concept 5.3: Phospholipids structure (continued) Figure 5.11 Hydrophilic head with hydrophobic tail Hydrophilic head  phosphate group and and its attachments (- charge) Hydrophobic tail  hydrocarbons in the fatty acid tails When mixed with water, fatty acids create a bilayer Hydrophilic head close to the water (outside and inside the cells) Hydrophobic tail in the center and away from the water/aqueous solution Seen in Cell membranes! Concept 5.3: Steroids (cholesterol) Figure 5.12 Definition: Lipid with carbon skeleton made of four fused rings Type of steroid determined by functional groups attached to carbons. EX: Cholesterol Important component of animal cell membranes Precursor for sex hormones and other steroids Synthesized in the liver Obtained in the diet Research inconsistent on its role in atherosclerosis (in addition to saturated fats) Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions Figure 5.13 Protein: A biologically functional molecule made of polypeptides with a specific three- dimensional shape. They are macromolecules!! More than 50% of the dry mass of a cell! Large amount of diversity: Each have a unique structure and function Some proteins are enzymes Proteins that act as catalysts Catalysts: Chemical agents that selectively speed up chemical reactions without being consumed in the reaction Concept 5.4: Protein building blocks Monomer: amino acids There are 20, (9 are essential) Amino acids: An organic molecule with both an amino group and a carboxyl group All share the same general formula/structure: Center: Asymmetric alpha carbon with 4 different attachments 1. amino group 2. carboxyl group 3. hydrogen atom 4. side chain (designated as R) Makes amino acids unique! Concept 5.4: Amino acid functions Function: General Groups: Determined by physical and chemical 1. nonpolar side chains These are hydrophobic!! properties of side chain, or R group 2. polar side chains (Figure 5.14) These are hydrophilic!! Inside cells, amino acids/proteins are 3. electrically charged side chains ionized, meaning they have a charge. Acidic side chains are negative Due to the pH of the cell. Basic side chains are positive Both acidic and basic are hydrophilic Concept 5.4: Amino acid functions (Figure 5.14) Concept 5.4: Protein polymers (polypeptides) They are unbranched Peptide bonds form a polypeptide backbone that builds proteins Linkage between amino acids is called One end has free amino group → a peptide bond N-terminus Other end has free carboxyl group Peptide bonds are covalent bonds → C-terminus formed by a dehydration reaction Chemistry of the polymer is based on the unique side chains from the order Between the carboxyl group of one of the amino acids in the connected to amino acid that is adjacent to the polypeptide backbone. amino group on another amino acid. Concept 5.4: Protein polymers (polypeptides) (continued) Concept 5.4: Protein structure (general) Structure: Structure (contd.): Can be made up of one or more Polypeptide chains can fold polypeptides that is uniquely twisted, spontaneously after being coiled and folded to make the specific synthesized by the cell, depending on protein its amino acid sequence Therefore, a polypeptide is not Globular proteins → spherical the same as a protein Fibrous proteins → long fibers Partly determined by the specific amino acid sequence of the polypeptide backbone Concept 5.4: Protein function (general) Function: Based on 3-dimensional shape Main purpose: recognize and bind to other molecules Examples: 1. Antibodies: proteins that recognize and bind to foreign molecules to help the immune system fight off infection 2. Opioid receptors: Proteins on the brain’s surface that bind to molecules shaped like endorphins, initiating feelings pain relief and euphoria. Concept 5.4: Four levels of protein structure Concept 5.4: Four levels of protein structure 1. Primary Structure The linear chain of amino acid sequences Sequence determined by genes (more on this later) Determines the secondary and tertiary structure Concept 5.4: Four levels of protein structure 2. Secondary Structure 2. Secondary Structure (contd.) Repeated coiling and folding 2 kinds of shapes: patterns within the polypeptide 1. Alpha helix: chain Delicate coil Determined by hydrogen bonds Created by hydrogen that form between the repeated bonds every fourth amino polypeptide backbone (not the acid side chains!) 2. Beta pleated sheet: Specifically, these occur Pleated structure between the oxygen and Hydrogen bonds between hydrogen atoms (attached to two parallel segments of Nitrogen) amino acid chain Concept 5.4: Four levels of protein structure 3. Tertiary Structure Hydrophobic interactions (contd.) Overall shape of the polypeptide due to Held together by van der Waals interactions between side chains/R interactions. groups of the amino acids in the chain. Around the center, side chains of other Disulfide bridges: covalent bonds hydrophilic amino acids form hydrogen between the sulfhydryl groups of bonds and ionic bonds to keep cysteine monomers that help structure. contribute to the overall tertiary Relatively weak interactions in the structure of the protein aqueous cellular environment, but have Hydrophobic interactions: The a stronger cumulative effect to keep the hydrophobic, or nonpolar, side shape. chains cluster inside of the protein, away from water. Concept 5.4: Four levels of protein structure Protein misfolding can cause 4. Quaternary Structure serious diseases, including: When proteins consist of two or Cystic fibrosis Alzheimer’s more polypeptide chains that Parkinson’s aggregate into one functional Mad Cow Disease molecule. Dementia Only occurs in some proteins, not all of them! Ex: Collagen, hemoglobin Concept 5.4: Protein denaturation Denaturation Sickle Cell Disease (contd.) Protein loses its overall structure due to Pathophysiology: changes in the environment’s: Normal RBC: disk-shaped pH Sickle-Cell RBC: sickled/crescent- Temperature shaped High fevers can be fatal! Sickled RBCs can block blood Salt concentration vessels due to its shape, causing Aqueous vs. nonpolar solvent occlusion, rupture, and decreased (Ex: ether, chloroform) blood flow. Other environmental factors… Pain crises When proteins denature, they become Swelling biologically inactive Stroke Example: Sickle Cell Disease Anemia (shorter lifespan) Change in primary structure of hemoglobin Only one amino acid is different!) Concept 5.5: Nucleic acids store, transmit, and help express hereditary information Nucleic Acids (overview) DNA: They are macromolecules!! Inherited from biological parents Monomer: nucleotide When cells divide, DNA is Polymer: polynucleotide/nucleic replicated and passed to the next acid cell. Two types: Contains the blueprints for all the Deoxyribonucleic Acid, or proteins needed for cellular DNA function. Ribonucleic Acid, or RNA One long strand of DNA is made Gene expression: DNA directs up of many genes, and housed in the synthesis of RNA, which a structure called a chromosome codes for protein synthesis. Discrete unit of inheritance is called a gene. DNA → RNA → protein Concept 5.5: Nucleic acid structure Nucleic acid: Macromolecules that exist as polymers called polynucleotides Nucleotide: Monomer of a polynucleotide Basic structure (3 parts): 1. Pentose, or 5-carbon sugar 2. Nitrogenous, or nitrogen-containing base 3. 1-3 phosphate groups The beginning structure always has 3 phosphate groups, but loses 2 during polymerization A nucleotide without any phosphate groups is called a nucleoside Concept 5.5: Nucleic acid structure (nitrogenous bases – 2 types) Figure 5.23c 1. Pyrimidine: 1 six-membered ring of carbon and nitrogen (3 kinds): 1. Cytosine, C 2. Thymine, T (DNA only!!) 3. Uracil, U (RNA only!!) 2. Purine: 1 six-membered ring fused to a 5-membered ring (2 kinds): 1. Adenine, A 2. Guanine, G Differences due to the number of rings and the groups attached to them. Concept 5.5: Nucleic acid structure (pentoses – 2 types) Figure 5.23c 1. Deoxyribose: DNA only Lacks an oxygen atom on second carbon Why it is called deoxyribose 2. Ribose: RNA only Nitrogenous base + pentose = nucleoside! Add phosphate groups to become a nucleotide Concept 5.5: Polynucleotide synthesis The two ends of the polynucleotide chain Polynucleotide synthesis: are very different! Formed by a condensation reaction 5’ end → phosphate group attached to 5’ carbon Covalent bonds occur between the 3’ end → hydroxyl group attached to phosphate group of one nucleotide 3’ carbon Sequence of nitrogenous bases unique to and the pentose, or sugar of another each gene nucleotide. Linear structural order of the bases Called a phosphodiester linkage encodes for a specific amino acid sequence in proteins Creates a sugar-phosphate AKA the primary structure!! backbone Concept 5.5: Polynucleotide synthesis (Figure 5.23) Concept 5.5: DNA and RNA structure (Figure 5.24) Base pairings: DNA: Adenine (A) → Thymine, T (DNA) Double helix: Adenine (A) → Uracil, U (RNA) Two polynucleotides wound around RNA usually single-stranded, not paired often. an imaginary axis However, in the single RNA strand, The polynucleotides go in opposite Uracil (U) will always replace Thymine (T) directions (5’ → 3’ vs. 3’ → 5’) Guanine (G) → Cytosine, C (both) This is called antiparallel! Complementary strands: Example: The nitrogenous bases pair together DNA strand: 5’ TGCCTAT 3’ and connect the two strands with Other DNA strand: 3’ ACGGATA 5’ hydrogen bonds Concept 5.5: DNA and RNA structure (Figure 5.24) Summary slides (Things to pay attention to) (list subject to change): Difference between monomers, polymers and macromolecules Types of chemical reactions Names of linkages Important functional groups to structure of biological molecules Types of macromolecules Classes of biological molecules Structure and function of carbohydrates List of simple sugars (monosaccharides) List of disaccharides and the monosaccharides that make them Storage and structural polysaccharides 3 types of lipids (structure and function of each) Protein structure and function Protein folding (4 levels of structure) Structure and function of nucleic acids Resources Textbook: Campbell’s Biology, Custom 12th Edition for Valencia College, (includes Mastering Biology Access Code in package). ISBN 13: 9780137351824 (e-book)