Chapter 2 - Chemistry of Life PDF

CELL : CHEMISTRY OF LIFE Composition of Matter Matter – everything in the universe is composed of matter. Matter is anything that occupies space or has mass. Mass is the quantity of matter an object has. Weight is the pull of gravity on...

CELL : CHEMISTRY OF LIFE Composition of Matter Matter – everything in the universe is composed of matter. Matter is anything that occupies space or has mass. Mass is the quantity of matter an object has. Weight is the pull of gravity on an object. States of Matter States of Matter Atoms The simplest particle of an element that retains all the properties of that element. All atoms consist of 3 types of smaller particles: Proton = has a + charge Neutron = has no charge Electron = has a - charge Properties of atoms determine the structure and properties of the matter they compose. Our understanding of the structure of atoms is based on scientific models, not actual observation.  The Nucleus Central core Consists of positive charged protons and neutral neutrons Positively charged Contains most of the mass of the atom Elements Pure substances that cannot be broken down chemically into simpler kinds of matter. Made of only 1 type of atom A group of atoms of the “same” type. More than 100 elements (91 are naturally occurring)  More on Elements 96 % of the mass of an organism is composed of 4 elements (oxygen, carbon, hydrogen, and nitrogen) Each element has a unique chemical symbol: Consists of 1-2 letters First letter is always capitalized More on Compounds A compound is a pure substance made up of atoms of two or more elements. The proportion of atoms are always fixed. Chemical formulas show the kind and proportion of atoms of each element that occurs in a particular compound. Molecules Is two or more atoms held together by covalent bonds. Are the simplest part of a substance that retains all of the properties of the substance and exists in a free state. Some molecules are large and complex. CHEMICAL BONDS Ions form when atoms gain or lose electrons Ion is an atom that has gained or lost one or more electron. It forms because an atom is more stable when its outermost energy level is full. The gain or loss of electrons results in a full outermost level. An atom becomes an ion when its number of electrons change and it gains an electrical charge. Can be positively or negatively charged. Ionic Bond Some atoms become stable by losing or gaining electrons. Atoms that lose electrons are called positive ions. Atoms that gain electrons are called negative ions. Because positive and negative electrical charges attract each other ionic bonds form. Atoms share pairs of electrons in covalent bonds. Not all atoms gain or lose electrons easily. Some atoms “share” pairs of electrons. Shared pairs of electrons fill the outermost energy levels of the bonded atoms. A covalent bond is formed when atoms share a pair of electrons. This type of bond is very strong. The Water Molecule Water in a liquid state cover most of the earths surface. Water contains: 10 protons, 10 electrons, and 10 neutrons. Water is a polar molecule.  Properties of the Water Molecule Water molecule (H2O) is made up of three atoms – one oxygen and two hydrogen The oxygen atom attracts more than its “fair share” of electrons. Oxygen end “acts” negative Hydrogen end “acts” positive Causes the water to be polar Think of it as two magnets attracted to one another. Water is neutral (equal number of electrons and protons) Zero net charge  1. Polarity Polar molecule – a molecule with positive and negative charged regions In water, electrons shared unequally Oxygen is more electronegative, giving it a partial - charge Hydrogen atoms get a partial + charge This causes the – end of one water molecule to be attracted to the + end of a different water molecule A hydrogen bond forms between the + oxygen and – hydrogen on the different molecules Each water molecule can form hydrogen bonds with up to four neighbors. Hydrogen bonds are very weak, they break and reform easily But!-They are the basis for the other properties of water Fig. 3.1 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings  2. Capillary Action Capillary Action – the ability water has to flow upward against the force of gravity, due to cohesion and adhesion Cohesion (cohesive) – sticking together of two like molecules 2water molecules are cohesive due to the hydrogen bonds Adhesion (adhesive) – sticking together of two unlike molecules Ex: A water molecule being attracted to a sugar molecule (Like making Kool-aid) DEMO! Take a dry penny. Slowly add drops of water to the penny. How many drops can you add? COHESION!! DEMO! What allowed the coloring in the water to get to the top of the celery stalk? How does water get to the top of plants? Cohesion among water molecules causes them to pull one another upward against gravity Adhesion contributes too, as water adheres to the wall of the vessels, so it can travel upward  3. Surface Tension Surface tension- a measure of the force necessary to stretch or break the surface of a liquid Hydrogen bonds between water molecules at surface of water resist breaking creating an “invisible film” This allows some insects to walk/run on water DEMO! Take a dry paper clip and carefully try to lay it on the surface of the water SURFACE TENSION 4. Heat Capacity Specific Heat - amount of heat that must be absorbed or lost before it actually changes temperature Water has a high specific heat Water can absorb or release large amounts of heat with only a slight change in its own temperature. Ex: Water takes a long time to boil Heat Capacity Because of this water stabilizes air temperatures Cool water absorbs heat from warm air Ex: Coastal cities have mild weather 6. Density Density- a measure of how compact the atoms or molecules are within a substance or how much mass there is in a given space (volume) Water compared to other liquids (like syrup) is not very dense. Water is more dense as a liquid than as a solid When water freezes and becomes ice, the polarity causes hydrogen bonds to form but there is air in between Causes expansion Ice floats in water. If this didn’t happen all the icebergs would sink- water levels would rise. Ice floats on top and insulates water below- fish can live. 7. Universal Solvent Solvent- a liquid that dissolves a particle (solute) Solute- particle or liquid that gets dissolved in the solvent Ex: Salt water 🡪 Water- Solvent, Salt- Solute Water is a solvent that dissolves most solutes.  If the solute molecules are polar, like water, the positive ends of water are attracted to the negative ends of the solute. This is also why the solute is even throughout all the water For each Picture decide which property of water is being used. Properties of Water and their Connection to Life on Earth Density Specific heat Density Properties of Water and their Connection to Life on Earth Cohesion Surface Tension Surface Tension Cohesion Adhesion Cohesion Capillary Action Properties of Water and their Connection to Life on Earth Specific heat Insulation Properties of Water and their Connection to Life on Earth Solubility Specific Heat Density  Acids and Bases An acid is a substance that increases the hydrogen ion concentration in a solution. Any substance that reduces the hydrogen ion concentration in a solution is a base. Some bases reduce H+ directly by accepting hydrogen ions. Strong acids and bases complete dissociate in water. Weak acids and bases dissociate only partially and reversibly.  The pH Scale Chemists devised a measurement system called the pH scale to indicate the concentration of H+ ions in solution. The pH scale ranges from 0 to 14. At a pH of 7, the concentration of H+ ions and OH– ions is equal. Pure water has a pH of 7 Acids An acid is any compound that forms H+ ions in solution. Acidic solutions contain higher concentrations of H+ ions Have pH below 7 Strong acid have a pH between 1 to 3 Hydrochloric acid (HCl): produced by the stomach. Bases A base is a compound that produces hydroxide (OH–) ions in solution. Basic, or alkaline, solutions contain lower concentrations of H+ ions Have a pH greater than 7 Strong bases have a pH between 11 to 14 Lye (NaOH) is a strong base use in soapmaking Buffers Buffers are compounds in organisms produce to maintain homeostasis. Are weak acids or bases. React to strong acids or bases to prevent sudden changes in pH. Human body pH is between 6.5 to 7.5 to homeostasis. LEVELS OF ORGANIZATION… We will be repeating these ALL year! Yesterday: Atoms 🡪 Molecules 🡪 Macromolecules… Today we will dig into the four macromolecules that are essential for life to exist. What is a macromolecule? These are organic compounds that contain carbon, and are considered to be “giant molecules”. A process called polymerization combines smaller molecules together to form these larger macromolecules. These compounds are the building blocks of living things…in other words without them there would be no you!  The FOUR Classes of Large Biomolecules All living things are made up of four classes of large biological molecules: Carbohydrates Lipids Protein Nucleic Acids Macromolecules are large molecules composed of thousands of covalently bonded atoms Molecular structure and function are inseparable WE TYPICALLY GET BIOMOLECULES FROM FOOD… THIS IS WHY WE MUST EAT IN THE FIRST PLACE! THE BIOMOLECULES SERVE TO KEEP ORGANISMS ALIVE. 52  The FOUR Classes of Large Biomolecules Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomers Three of the four classes of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids 53  Six Major Elements associated with making up these macromolecules These 6 elements make up your body, and they are also important in creating these organic compounds. So what are these 6 major elements important to life: The Big Six -> CHONPS Carbon (C) Hydrogen (H) Oxygen (O) Nitrogen (N) Phosphorus (P) Sulfur (S)  So how are these the building blocks of living things? The macromolecules are the LARGER MOLECULES…so like a house, you need “bricks” to build/make them! Monomer – smallest unit of a large molecule (building blocks of things) Polymer – the large molecule; formed by joining monomers (the product/the thing made = this is the macromolecule!) 2 or more monomers make a polymer!  The synthesis and breakdown of polymers A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction 56  Dehydration Synthesis 57  Hydrolysis 58  The Diversity of Polymers Eachcell has thousands of different macromolecules Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species An immense variety of polymers can be built from a small set of monomers 59  #1: CARBOHYDRATES ARE SUGARS! We get 4 kilocalories per gram of carb that we eat! How does our body break down this bread? Breaks down into microscopic molecules Loaf of bread Bread crumbs Polysaccharid e Monosaccharide Disaccharide Challenge: Explain what you think is happening here. (at least 3 sentences) Loaf of bread Bread crumbs Polysaccharide Monosaccharide Disaccharide The diagram shows a picture of bread (starch). It also maps out the break down of carbohydrates from their most complex form (polysaccharide) to their least complex (monosaccharide). This process is called hydrolysis.  What are Carbohydrates? ⚫ Most common organic molecule ⚫ Function: Primary energy source our body needs ⚫ Elements present: C, H, O (1:2:1 ratio) IMPORTANT! ⚫ Monomer (building block): Monosaccharides (Glucose is most common) ⚫ Polymer: Polysaccharides (starch, Glycogen, Cellulose, Chitin) ⚫ Examples: Chocolate, Bread, Pasta, Fruits, Vegetables (ALL FROM PLANTS!!!) Sugars that make up Carbs ⚫ Single sugar: monosaccharide ⚫ Ex: glucose , fructose (in fruits) ⚫ 2 monosaccharides: disaccharide ⚫ Ex: maltose, sucrose ⚫ 3+ monosaccharides: polysaccharide ⚫ Ex: Starch, Glycogen, Cellulose, and Chitin I am a polysaccharide!  Glucose, Fructose, and Galactose (Monosaccharides) Glucose: Made during photosynthesis Main source of energy for plants and animals Fructose: Found naturally in fruits Is the sweetest of monosaccharides Galactose: Found in milk Is usually in association with glucose or fructose Disaccharide Disaccharide– two monosaccharide bonded together Table sugar (sucrose) = made up of glucose + fructose bonded together Milk sugar (lactose) = made up of glucose + galactose bonded together  Types of polysaccharides ⚫ Starch: ⚫ Used for energy storage in plants ⚫ Potatoes, pasta and rice are starches ⚫ They provide a quick form of energy for the body I am formed in the Liver! Glycogen: Used for energy storage in animals More Polysaccharides Cellulose: Providesstructural support in plants (found in the cell wall) GIVES US FIBER!!! Chitin: Found in exoskeletens of arthropods (insects, spiders) Found in cell wall of some fungi Structure of Carbohydrates Remember: Elements are C, H, and O Primarily in a Ring shape (but not always)  Take a minute to find the word that does NOT belong. Raise your hand, do not shout out! #2: LIPIDS ARE FATS We get 9 kcals per gram Of fat that we consume.  Lipids ⚫ Function: Store energy, Insulates your body, and make up the cell membrane! ⚫ Elements: C-H-O ⚫ Monomer (Building blocks): glycerol & 3 fatty acids ⚫ Polymer: Phospholipids, triglycerides ⚫ Example: Steroids, cholesterol, fats, Oils, Nuts, Waxes, and make up part of the cell membrane! 4 Classes of Organic Cmpds cont’d… 2. Lipids Used to store energy (for the long term) Important in making your cell membranes & waterproofing the certain coverings in the body Example: Cell Membranes Insulates/ protects your bodies organs (like a cushion) Examples 🡪 Fats, Oils, and Waxes  Lipids Lipids are Hydrophobic (water fearing) and do not dissolve in water! Import ant! Lipids can be: Saturated: The bonds between all the carbons are single bonds. Solid at room temperature Mainly animal fats (bacon grease, lard) Unsaturated: There is at least one double or triple bond between carbons present. Liquid at room temperature Mainly plant based fats (olive oil, peanut oil) as well as oily fish (Tuna, Sardines) Lipid Structure Remember: Elements present are C, H, O Satu rate Long strands d of Carbon Fats and Hydrogen Uns atur CALLED ated HYDROCARBONS! Fats At room temperature, the molecules At room temperature, the molecules of an of a saturated fat are packed closely unsaturated fat cannot pack together together, forming a solid. closely enough to solidify because of the kinks in their fatty acid tails. CLASSIFICATION OF LIPIDS A. SIMPLE LIPIDS (Triglycerides and Waxes) B. COMPOUND LIPIDS ( Phospholipids, Sphingolipids, Glycolipids) C. DERIVED LIPIDS ( Terpenes, Sterols,Fatty acids) SIMPLE LIPIDS are esters of fatty acids and alcohols. There are two kinds: triglycerides and waxes. 1. TRIGLYCERIDES OR NEUTRAL FATS consist of a glycerol moiety with each hydroxyl group esterified to a fatty acid. Commonly found in adipose tissue, olive, lard etc. Often seen as solid or semisolid at room temperature occur predominantly in animals, while those in liquid form originate from plants. Animal triglycerides are composed of high proportion of saturated fatty acids, form straight chain polymers in which the fatty acids are packed very closely (solid at room temperature and high melting point) Plant triglycerides are composed of high proportion of unsaturated fatty acids (low melting point and liquid at room temperature). 2. WAXES Are found in the surfaces of fruits, leaves, feathers, and animal fur. Important in nature: repelling property Composed of esters of long chain fatty acids and alcohols. Can be found in carnuba oil, lanolin, beeswax, cerumen, and head oil of the sperm whale. COMPOUND LIPIDS Contain substances other than alcohol and fatty acids. These are three kinds: phospholipids, sphingolipids, and glycolipids. 1.PHOSPHOLIPIDS Contain glycerol, fatty acids and phosphate. Fatty acids bind to glycerol by ester bonds. The phosphate group is water soluble, while the rest of the molecule is insoluble in water. Cell membrane is made up of a bilayer of phospholipids. Found mainly in animal tissues and are in the form of lecithin, cephalin,plasmalogen and lipositol. 2. SPHINGOLIPIDS Contain sphingosine as the alcohol backbone Sphingomyelin found in nerve tissue , brain and RBC 3.GLYCOLIPIDS Are lipids with a carbohydrate attached to it. Component of cell membrane. Extend from the phospholipid bilayer in the aqueous environment outside the cell. Functions: recognition sites for specific chemicals, maintain the stability of the membrane and attach cells to each other to form tissues. Examples: proteolipids, sulfolipids (testicles, liver, WM brain), gangliosides (spleen and nerve tissue) and cerebrosides (myelin sheaths of nerves). DERIVED LIPIDS Cannot be strictly classified as either simple or compound. 1.TERPENES are the primary constituents of the essential oils of plants and flowers. They are also found in plant pigments carotene and lycopene as well as in Vitamins A,E, and K. 2.STEROLS such as cholesterol,androgens, and estrogens (sex hormoes), adrenal corticosteroids, ergosterol (plant tissues, yeast & fungi), and 7-dehydrocholesterol have important roles in cellular structure, communication & metabolism. 3.FATTY ACIDS are long chain aliphatic carboxylic acid products that result from the hydrolysis of lipids. They cab be classified accdg. to the length of carbon chain, importance in the diet, number of double bonds contained.  Take a minute to find the word that does NOT belong. Raise your hand, do not shout out! BIOMOLECULES PART 2 PROTEINS AND NUCLEIC ACIDS! #3: PROTEINS BUILD US We get 4 kcals per gram Of protein that we consume. Proteins Function of proteins Transport molecules in and out of the cell Control the speed of chemical reactions Used for growth and repair Proteins make up the structure of living things… Hair, nails, skin, bones, muscle, etc are all built by protein! Proteins NITROGEN IS PRESENT, NOW! ⚫ Elements: C-H-O-N ⚫ Monomer (Building Block): amino acids (20 different ones!) ⚫ Polymer: proteins (tons) ⚫ Examples of proteins: hemoglobin in red blood cells, albumin in eggs, enzymes that control reactions in the body, and antibodies ⚫ Found in: fish, eggs, meat Protein Structure Remember: Elements are C, H, O, and N “R” groups represent one of the 20 Amino Acids! (so, each amino acid has something different in that spot) Why are amino acids important? When groups of amino acids are joined together a protein is formed There are 20 kinds of amino acids They consist of a carboxyl group (COOH) and an amino group NH2 Peptide bonds form between amino acids (polypeptide = many peptide bonds = protein!)  Take a minute to find the word that does NOT belong. Raise your hand, do not shout out! #4: NUCLEIC ACIDS These biomolecules are not necessarily from food Nucleic acids Function: Provide our genetic information Holds the instructions to make proteins. Elements: C-H-O-N-P Monomer : nucleotides A nucleotide is made up of: Sugar Phosphate Nitrogen Base: A, T, G, C, or U Polymer: DNA, RNA and ATP Energy Genetic carrier code! Recipe for proteins Nucleic Acids Contains C, H, O, N, P Monomer: NUCLEOTIDES Nucleotides consist of 3 parts: 1. 5-Carbon Sugar 2. Phosphate Group 3. Nitrogenous Base Nucleotide: Nitrogen Bases 5 types Cytosine In DNA: In RNA: C-G C-G Guanine A-T A-U Adenine Thymine (in DNA only) Uracil (in RNA only) Purines or pyrimidines  Nucleotides: 5-carbon sugar and phosphate group 2 types of sugars Ribose (in RNA only) Deoxyribose (in DNA deoxyribose ribose only) Phosphate group Contains phosphorus & oxygen Polymer: polynucleotide  Function Polypeptide: DNA (deoxyribonucleic acid) contains the genetic code stores & transmit heredity/genetic information found in the nucleus (mitochondria) Double stranded (double helix)  Function Polypeptide: RNA (ribonucleic acid) Carries info from DNA to cell Helps in protein synthesis found in ribosomes & nucleoli Single stranded Polypeptide: ATP Contains adenine, ribose sugar, 3 phosphates Stores and releases energy Structure of Nucleic Acid Take a minute to find the word that does NOT belong. Raise your hand, do not shout out!