Topic 2 Molecule of Life Student PDF

BIOLOGY 1 ASB0204 Topic 2 Molecule of Life Outline 2.1 Chemistry of Water 2.2 Organic Molecules 2.3 Carbohydrates 2.4 Lipids 2.5 Proteins 2.6 Nucleic Acids Learning Outcomes By the end of this lecture, you will be able to: 1. List down all properties of water. 2. De...

BIOLOGY 1 ASB0204 Topic 2 Molecule of Life Outline 2.1 Chemistry of Water 2.2 Organic Molecules 2.3 Carbohydrates 2.4 Lipids 2.5 Proteins 2.6 Nucleic Acids Learning Outcomes By the end of this lecture, you will be able to: 1. List down all properties of water. 2. Describe why the properties of water are important to life. Identify these things What makes them physically different?  2.3 Chemistry of Water Water is a polar molecule. The shape of a water molecule and its polarity make hydrogen bonding possible. This is an example of a structure-function relationship. Oxygen is partially negative ( ) O H H Hydrogens are partially positive ( ) Photo Credit: https://opentextbc.ca/anatomyandphysiology/chapter/2- 2-chemical-bonds/  Electron Model + A hydrogen bond is a H O H + weak attraction between - O hydrogen bond a slightly positive H H hydrogen atom and a slightly negative atom. Ball-and-stick Model O ▪ It can occur between atoms of different molecules or within the same molecule. H 104.5˚ H ▪ A single hydrogen bond is easily broken while multiple hydrogen bonds are Space-filling Model collectively quite strong. ▪ It helps to maintain the proper structure Oxygen attracts the shared electrons and is partially negative. - O and function of complex molecules such as + H H + proteins and DNA. Hydrogens are partially positive. Properties of Water Water molecules cling together because of hydrogen bonding. This association gives water many of its unique chemical properties. 1. Water has a high heat capacity. The presence of many hydrogen bonds allow water to absorb a large amount of thermal energy without a great change in temperature. The temperature of water rises and falls slowly. Allows organisms to maintain their normal internal temperatures, protected from rapid temperature changes.  Temperature and Water 800 Gas 600 Calories of Heat Energy / g 540 calories 400 200 Liquid 80 Solid calories 0 freezing occurs evaporation occurs 0 20 40 60 80 100 120 Temperature (°C) a. Calories lost when 1 g of liquid water freezes and calories required when b. Bodies of organisms cool when their heat is used to evaporate water. 1 g of liquid water evaporates. b: © Grant Taylor/Stone/Getty Images 8 Properties of Water 2. Water has a high heat of evaporization. Hydrogen bonds must be broken to evaporate water. Bodies of organisms cool when their heat is used to evaporate water. Example: sweating 3. Water is a good solvent. Water is a good solvent because of its polarity. Polar substances dissolve readily in water. Hydrophilic molecules dissolve in water. Hydrophobic molecules do not dissolve in water. A solution contains dissolved substances, or solutes.  High heat of evaporization DIY experiment. Follow these steps and do it at your home! (A) Put a teaspoon of Rub it for 1 Wet hand water on your hand minutes (B) Put a teaspoon of hand Rub it for 1 Dry hand sanitizer on your hand minutes Conclusion, _______________________________ _________________________________________  Water as a Solvent O H H H H O An ionic salt dissolves in water. Na+ Cl– H H H H O O O H H O H H 1. 2. Properties of Water 4. Water molecules are cohesive and adhesive. Cohesion is the ability of water molecules to cling to each other due to hydrogen bonding. Water flows freely Surface tension Adhesion is the ability of water molecules to cling to other polar surfaces. Due to water’s polarity Capillary action Cohesion and adhesion account for water transport in plants as well as transport in blood vessels. Water as a Transport Medium Water evaporates, pulling the water column from the roots to the leaves. H 2O Water molecules cling together and adhere to sides of vessels in stems. H 2O Water enters a plant at root cells. Properties of Water 5. Frozen water (ice) is less dense than liquid water. At temperatures below 4°C, hydrogen bonds between water molecules become more rigid but also more open. Water expands as it reaches 0°C and freezes. Ice floats on liquid water. Without this property, ice would sink and oceans freeze solid, instead of from the top down. Acts as an insulator on top of a frozen body of water. Ice is less dense than water A Pond in Winter ice layer Protists provide food for fish. River otters visit ice-covered ponds. Aquatic Freshwater insects fish take survive oxygen in air from water. pockets. Common frogs and pond turtles hibernate. Let’s think of suitable water properties for situation below. Water strider happily glide on water. Human able to get fish supply in Arctic region. Let’s think of suitable water properties for situation below. Car engine works efficiently for long distance journey. Double distilled water used to clear up any foreign materials on electrical board. Damped tissue paper being used as a medium for seed germination. Summary High heat capacity Frozen water High heat less dense than evaporization liquid water Properties of water Cohesive and Good solvent adhesive  Learning Outcomes By the end of this lecture, you will be able to: 3.2 Carbohydrates 3.1 Organic Molecules 1. Summarize the role of 1. Able to differentiate carbohydrates in a cell. biomolecules 2. Distinguish among the 2. Compare the role of forms of carbohydrates. dehydration synthesis 3. Compare the energy and hydrolytic reaction and structural uses of in organic chemistry starch, glycogen, and cellulose.  3.3 Lipids 3.4 Proteins 1. Identify the structure of lipids. 1. Differentiate protein 2. Contrast the function of monomer and polymer. fats, phospholipid, and 2. Explain how a steroids. polypeptide is constructed from amino 3.5 Nucleic Acids acids. 3. Compare four levels of 1. Distinguish between a protein structure. nucleotide and nucleic acid. 2. Compare the structure and function of DNA and RNA. What type of biomolecules that can be found in an apple? 2.2 Organic Molecules Organic molecules contain both carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms: Carbohydrates Lipids Proteins Nucleic Acids Functions of the four biomolecules in the cell are diverse. The Biomolecules of Cells Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules. Usually consist of many repeating units Each repeating unit is called a monomer. A molecule composed of monomers is called a polymer (many parts). Example: amino acids (monomer) are joined together to form a protein (polymer) Lipids are not polymers because they contain two different types of subunits. Synthesis and Degradation A dehydration reaction is a chemical reaction in which subunits are joined together by the formation of a covalent bond and water is produced during the reaction. Used to connect monomers together to make polymers Example: formation of starch (polymer) from glucose subunits (monomer) A hydrolysis reaction is a chemical reaction in which a water molecule is added to break a covalent bond. Used to break down polymers into monomers Example: digestion of starch into glucose monomers Process : Synthesis Reaction : Dehydration monomer OH + H monomer Dehydration H 2O reaction monomer monomer Reactants Product Side product Process : Degradation Reaction : Hydrolysis monomer OH H monomer hydrolysis reaction H 2O monomer monomer Reactants Product Side product Synthesis and Degradation Special molecules called enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions. An enzyme is a molecule that speeds up a chemical reaction. Enzymes are not consumed in the reaction. Enzymes are not changed by the reaction. Enzymes are catalysts. 2.3 Carbohydrates Functions: Energy source Provide building material (structural role) Contain carbon, hydrogen and oxygen atoms in a 1:2:1 ratio Varieties: monosaccharides, disaccharides, and polysaccharides Monosaccharides A monosaccharide is a single sugar molecule. It is also called a simple sugar. It has a backbone of 3 to 7 carbon atoms. Examples: Glucose (blood sugar), fructose (fruit sugar), and galactose Hexoses – six carbon atoms Ribose and deoxyribose (sugars contained in nucleotides, the monomer of DNA) Pentoses – five carbon atoms Glucose Disaccharides A disaccharide contains two monosaccharides joined together by dehydration synthesis. Examples: Lactose (milk sugar) = galactose + glucose Sucrose (table sugar) = glucose + fructose Maltose = glucose + glucose Lactose-intolerant individuals lack the enzyme lactose which breaks down lactose into galactose and glucose.  Synthesis of maltose CH2OH CH2OH CH2OH CH2OH O O O O H H dehydration reaction + O + H2O OH HO glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water monosaccharide + monosaccharide disaccharide + water Reactants Product Side product  Degradation of maltose CH2OH CH2OH CH2OH CH2OH O O O O H H + O + H2O OH HO hydrolysis reaction glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water monosaccharide + monosaccharide disaccharide + water Reactants Product Side product Polysaccharides: Energy-Storage and Structural Molecules A polysaccharide is a polymer of monosaccharides. Examples: ▪ Starch = energy storage in plants. ▪ Glycogen = energy storage in animals. ▪ Cellulose = made up the plants cell walls. ▪ Most abundant organic molecule on earth. ▪ Animals are unable to digest cellulose. ▪ Chitin = cell walls of fungi and exoskeleton of some animals. ▪ Peptidoglycan = cell walls of bacteria. ▪ Monomers contain an amino acid chain.  Amylose: nonbranched starch granule Amylopectin: branched a. Starch 250 m glycogen granule b. Glycogen 150 nm 2.4 Lipids Varied in structure Large, nonpolar molecules that are insoluble in water Functions: ▪ Long-term energy storage ▪ Structural components ▪ Heat retention ▪ Cell communication and regulation ▪ Protection Varieties: fats, oils, phospholipids, steroids, waxes Triglycerides: Long-Term Energy Storage Also called fats and oils Functions: long-term energy storage and insulation Consist of one glycerol molecule linked to three fatty acids by dehydration synthesis Triglycerides: Long-Term Energy Storage Fatty acids may be either unsaturated or saturated. Saturated – no double bonds between carbons Tend to be solid at room temperature Examples: butter, lard Unsaturated – one or more double bonds between carbons Tend to be liquid at room temperature Example: plant oils Can have chemical groups on the same (cis) or opposite (trans) side of the double bond Triglycerides: Long-Term Energy Storage Trans – a triglyceride with at least one bond in a trans configuration Synthesis of triglyceride Reactants Product Side product Degradation of triglyceride Reactants Product Side product Phospholipids: Membrane Components The structure is similar to triglycerides. It consists of one glycerol molecule linked to two fatty acids and a modified phosphate group. The fatty acids (tails) are nonpolar and hydrophobic. The modified phosphate group (head) is polar and hydrophilic. Function: forms plasma membranes of cells. Phospholipids: Membrane Components In water, phospholipids aggregate to form a lipid bilayer (double layer). Polar phosphate heads are oriented towards the water. Nonpolar fatty acid tails are oriented away from water. Nonpolar fatty acid tails form a hydrophobic core. Kinks in the tails keep the plasma membrane fluid across a range of temperatures. Steroids: Four Fused Carbon Rings They are composed of four fused carbon rings. Various functional groups attached to the carbon skeleton Functions: component of animal cell membrane, regulation Examples: cholesterol, testosterone and estrogen. Steroids: Four Fused Carbon Rings Testosterone and estrogen are sex hormones differing only in the functional groups attached to the same carbon skeleton. Cholesterol is the precursor molecule for several other steroids. OH Cholesterol can CH3 CH3 also contribute to circulatory O b. Testosterone disorders. CH3 HC CH3 (CH2)3 OH HC CH3 CH3 CH3 CH3 HO HO c.Estrogen a. Cholesterol Waxes Long-chain fatty acids connected to carbon chains containing alcohol functional groups Solid at room temperature Waterproof Resistant to degradation Function: protection Examples: earwax (contains cerumin), plant cuticle, beeswax 3.4 Proteins Proteins are polymers of amino acids linked together by peptide bonds. A peptide bond is a covalent bond between amino acids. As much as 50% of the dry weight of most cells consists of proteins. Several hundred thousand have been identified. 2.5 Proteins Two or more amino acids joined together are called peptides. Long chains of amino acids joined together are called polypeptides. A protein is a polypeptide that has folded into a particular shape, which is essential for its proper functioning. Functions of Proteins 1. Metabolism ▪ Most enzymes are proteins that act as catalysts to accelerate chemical reactions within cells. 2. Support ▪ Some proteins have a structural function, for example, keratin and collagen. 3. Transport ▪ Membrane channel and carrier proteins regulate what substances enter and exit cells. Hemoglobin protein transports oxygen to tissues and cells. Functions of Proteins 4. Defense ▪ Antibodies are proteins of our immune system that bind to antigens and prevent them from destroying cells. 5. Regulation ▪ Hormones are regulatory proteins that influence the metabolism of cells. 6. Motion ▪ Microtubules move cell components to different locations. Actin and myosin contractile proteins allow muscles to contract. Amino Acids: Protein Monomers There are 20 different common amino acids. Amino acids differ by their R or variable, groups, which range in complexity.  Synthesis of a Peptide amino group acidic group peptide bond dehydration reaction amino acid amino acid dipeptide water Reactants Product Side product  Degradation of a Peptide amino group acidic group peptide bond hydrolysis reaction amino acid amino acid dipeptide water Reactants Product Side product  Summary of Peptide Reaction amino group acidic group peptide bond dehydration reaction hydrolysis reaction amino acid amino acid water dipeptide Shapes of Proteins Proteins cannot function properly unless they fold into their proper shape. When a protein loses it proper shape, it said to be denatured. Exposure of proteins to certain chemicals, a change in pH, or high temperature can disrupt protein structure. Levels of Protein Structure Proteins can have up to four levels of structure: 1. Primary Primary level is the linear sequence of amino acids. Hundreds of thousands of different polypeptides can be built from just 20 amino acids. Changing the sequence of amino acids can produce different proteins. 2. Secondary Secondary level is characterized by the presence of alpha helices and beta (pleated) sheets held in place with hydrogen bonds. Levels of Protein Structure 3. Tertiary Tertiary level is the overall three-dimensional shape of a polypeptide. It is stabilized by the presence of hydrophobic interactions, hydrogen, ionic, and covalent bonding. 4. Quaternary Quaternary level consists of more than one polypeptide.  The Importance of Protein Folding and Protein-Folding Diseases Chaperone proteins help proteins fold into their normal shapes and may also correct misfolding of new proteins. Defects in chaperone proteins may play a role in several human diseases such as Alzheimer’s disease and cystic fibrosis. Prions are misfolded proteins that have been implicated in a group of fatal brain diseases known as TSEs. Mad cow disease is one example of a TSE. Prions are believed to cause other proteins to misfold. 2.6 Nucleic Acids Nucleic acids are polymers of nucleotides. Two varieties of nucleic acids: DNA (deoxyribonucleic acid) CH OH 2 O OH Genetic material that stores C H H C information for its own replication H C C H and for the sequence of amino OH H Deoxyribose (in DNA) acids in proteins RNA (ribonucleic acid) CH OH 2 Perform a wide range of functions C H H C O OH within cells which include protein H C C H synthesis and regulation of gene OH OH expression Ribose (in RNA)  Structure of a Nucleotide Each nucleotide is composed of three parts: A phosphate group A pentose sugar A nitrogen-containing (nitrogenous) base O nitrogen- –O phosphate P C containing P O base O– 5' O 4' S 1' 3' 2' pentose sugar  Structure of a Nucleotide There are five types of nucleotides found in nucleic acids. DNA contains adenine, guanine, cytosine, and thymine. RNA contains adenine, guanine, cytosine, and uracil. Pyrimidines Purines NH2 O O NH2 O C C CH3 C N CH HN C CH C N C N HN C C C T U N HN CH CH C CH A CH G CH HC C O N O N N N C N O N H2N N H H H H H cytosine thymine in DNA uracil in RNA adenine guanine  Structure of a Nucleotide Nucleotides are joined together by a series of dehydration synthesis reactions to form a linear molecule called a strand, which is a sequence of nucleotides. Structure of DNA and RNA The backbone of the nucleic acid strand is composed of alternating sugar- phosphate molecules. Structure of DNA and RNA RNA is predominately a single-stranded molecule, whereas DNA is a double- stranded molecule. DNA is composed of two strands held together by hydrogen bonds between the nitrogen-containing bases. The two strands twist around each other, forming to a double helix. Structure of DNA and RNA The nucleotides may be in any order within a strand but between strands: Adenine (purine) makes hydrogen bonds with thymine (pyrimidine). Cytosine (pyrimidine) makes hydrogen bonds with guanine (purine). The bonding between the nitrogen-containing bases in DNA is referred to as complementary base pairing. The number of A+G (purines) always equals the number of T+C (pyrimidines). Shape Helix Linear ATP (Adenosine Triphosphate) ATP (adenosine triphosphate) is a nucleotide composed of adenine and ribose (adenosine), and three phosphates. ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds, which are easily broken. ATP (Adenosine Triphosphate) Hydrolysis of the terminal phosphate bond yields: The molecule ADP (adenosine diphosphate) An inorganic phosphate, P Energy to do cellular work  Summary Biomolecules Nucleic Carbohydrates Lipids Proteins Acids Monomer Subunits Monomer Monomer Monosac- Glycerol Amino Nucleotides charides Fatty acids acids Large Polymer Polymer Polymer molecule Polysac- Triglyceride Polypeptide DNA charides RNA Summary Process : Synthesis Reaction : Dehydration Reactants Product Side product Monomers Polymer Water Process : Degradation Reaction : Hydrolysis Reactants Product Side product Polymer + Water Monomers - References 1. Mader, S. S., & Windelspecht, M. (2019). Biology (13th ed.). McGraw-Hill Education. 2. Solomon, E., Martin, C., Martin D. W. & Berg, L. R. (20 ). Biology (11th ed.). Cengage 76 Further Reading Eldra Solomon Charles Martin Diana W. Martin Linda R. Berg Chapter 2 Atom and Molecules: The Chemical Basis of Life Pg 38-41 Chapter 3 Chemistry of Life: Organic Compounds Pg 46-72 77 THANK YOU