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The Chemical Basis of Life Chapter 2 What’s Matter? Nothing…what’s matter with you? • Any substance that has mass and occupies space it matter • An element is the purest form of matter – it cannot be broken down into a simpler substance • Matter is composed of atoms, or one can say an Element is represented by a specific type of atom 92 Natural Elements Ag S Hg • Silver, Sulfur and Mercury are examples of naturally occurring elements • Others are laboratory synthesized radioactive elements - some of these decay rapidly. Technitium, a radioactive silver-gray metal was first to be synthesized. Plutonium, Promethium, Francium are other examples. Some of these man made elements (like Francium) actually do occur in nature in extremely minute amounts Tc - Technitium 87 Francium 25 Elements Needed for Life • 25 of the 92 elements are found in all life forms • The 4 most common elements make up 96% of a cell. They are: Hydrogen (H), Oxygen (O), Carbon (C), Nitrogen (N) • Others such as Phosphorus (P), Sulphur (S), Potassium (K), Calcium (Ca), etc. account for the remaining 4% • Trace elements are those required in minute quantities. Eg. Boron, Iodine, Iron, chromium, zinc, manganese, selenium, silicon, tin, vanadium, molybdenum, cobalt, copper and flourine. Goiter – Thyroid enlargement Atoms and subatomic particles Particle electron Representation Relative charge Relative mass -1 1 1800 proton +1 1D neutron o 1D • Atoms are the smallest units of matter that have the properties of the element they represent • An atom can be split into many different subatomic particles, but only three are stable enough to have been studied for many decades: Protons, Neutron and Electrons • Protons – positively charged, have a mass of about 1 dalton • Neutrons – electrically neutral, mass close to 1 dalton • Electrons – negatively charged; their mass is about 1/1800 of protons and neutrons, so it can be ignored • So the mass of an atom = number of protons + number of neutrons • The atomic number = the number of protons ATOMS • Atoms are the smallest units of matter that have all the characteristics of an element – they cannot be broken down into simpler substances without losing the properties of the element they represent • All matter solid, liquid or gas is made up of atoms • Atoms are made up of sub-atomic particles For example, an iron atom is the smallest unit of iron that has all the characteristics of the element iron. A helium atom (right) is the smallest unit of helium that has all the characteristics of the element helium. Atoms are the building blocks of everything in the universe. Sub-atomic Particles Most atoms are made up of three subatomic particles: 1. A positively charged particle called a Proton 2. A particle with no charge (neutral) called a neutron 3. A negatively charged particle called an electron Protons and neutrons are found packed together, in the center of the atom, called the nucleus. Electrons orbit around the nucleus in their own orbitals, at speeds close to that of light – they are so fast in fact, that the region around the nucleus where they are found is called the electron cloud. Protons :Atomic number • Protons are found in the nucleus • They have a positive (+) charge • Each atom of the same element is characterized by a certain number of protons in the nucleus. That number is called the atomic number. • Atomic number (number of protons) cannot change for the same element! In other words, all oxygen atoms will have 8 protons, all carbon atoms will have 6 protons • Protons have a mass of 1 amu (atomic mass unit) each Neutrons – subatomic glue • Neutrons are also found in the nucleus – they are tightly bound to the protons, and keep the protons from repelling each other • They have zero charge – they are neutral • Atoms of the same element can have different number of neutrons – these are called isotopes • Neutrons also have a mass of 1 amu each • The sum of the masses of protons and neutrons in the nucleus is called the atomic mass number Isotopes of Hydrogen Hydrogen 1 (hydrogen) Hydrogen 2 (deuterium) Hydrogen 3 (tritium) 1 proton, 0 neutrons Mass number = 1 1 proton, 1 neutron Mass number = 2 1 proton, 2 neutrons Mass number = 3 SAME ELEMENT – DIFFERENT ATOMS BECAUSE OF DIFFERENT NUMBER OF NEUTRONS. Chemical Bonds When atoms complete their valence shell by either sharing or transferring unpaired valence electrons, they tend to stay close together – this is a chemical bond Covalent Bonds Sharing of valence electrons by atoms – Extremely strong bonds a. Non-polar – electrons shared equally – hydrophobic - single, double and triple bonds b. Polar – electrons spend more time closer to the more electronegative atom - hydrophilic Electronegativity is the tendency of an atom to attract electrons. IONIC BONDS When electrons are lost or gained by atoms, they become charged atoms or ions. A negatively charged ion is an anion, a positively charged ion is a cation. Anions and cations are attracted to each other and form an ionic bond. These bonds are weaker than covalent bonds. Difference between Covalent and Ionic bonds Water In liquid water at 37 ˚ C, each water molecule has hydrogen bonds with 4 other water molecules. These weak bonds constantly break and form with other water molecules nearby – this gives water its fluidity. Water – the solvent of life • The polarity of a water molecules helps it dissolve ionic and hydrophilic substance easily Water molecules dissociate • Because oxygen is so electronegative, in water molecules all the electrons (even those of hydrogen) spend more time around the oxygen molecule • Sometimes, the oxygen molecule dissociates from one hydrogen, but keeps its electron – so the hydrogen is now a proton (H+) and the hydroxide molecule is (OH-) The pH Scale • pH stands for Potential of Hydrogen • It is a measure of the concentration of H+ in a solution • Acids have high concentrations of H+ and low OH-, whereas bases have the opposite • The pH of pure water is 7, or neutral – it has equal number of H+ and OH- ions Increasing [H+] Decreasing [OH-] [H+] and [OH-] equal Increasing [OH-] Decreasing [H+] Acids and Bases • Acids taste sour, are corrosive to metals, change litmus (a dye extracted from lichens) red, and become less acidic when mixed with bases – Acids have low pH values 0 - 6.9 • Bases feel slippery, change litmus blue, and become less basic when mixed with acids – Bases have high pH values – 7.1 - 14 Biological Macromolecules • Carbohydrates – Sugars – Starch, Glycogen – Cellulose, Chitin • Lipids – Triglycerides, Phospholipids, Steroids • Proteins • Nucleic Acids Carbohydrates • The building blocks of carbohydrates are simple sugars or monosaccharides (single sugars) and disaccharides (double sugars) • Important monosaccharides are: Glucose, Fructose and Galactose Structure of some Monosaccharides (also known as dextrose) Sugars are named for the number of carbons in the backbone Sugars end in “ose” Linear versus Ring forms Sugars tend to change into ring forms when placed in an aqueous solution. Here is an example of straight chain glucose changing into its ring form. α and β forms of glucose OH group on top OH group on the bottom When the glucose molecule takes on a ring form, it can form one of 2 isomers. The tiny difference between these two isomers of the same molecule means that the polysaccharide that they form is different. The 2 isomers, α and β forms of glucose is evident in the diagrams above. Making Disaccharides • 2 glucose molecules bond covalently to form maltose • 1 fructose and 1 glucose bond to form sucrose (table sugar) • 1 glucose and 1 galactose bond to form lactose (found in milk and dairy products) People who are lactose intolerant, do not make lactase, an intestinal enzyme that hydrolyzes lactose into its constituent monosaccharides, glucose and galactose which can then be easily absorbed into the blood, across the intestinal lining. When lactose cannot be broken down, it ferments in the gut and causes bloating, diarrhea, flatulence, etc. 70% of the world population is lactose intolerant. However, only 10% of Europeans are. Making Polysaccharides • Multiple monosaccharides form chains by forming covalent bonds through dehydration synthesis. These covalent bonds are called glycosidic linkages. • Polysaccharides can be considered either “storage polysaccharides” or “structural polysaccharides”, based on their structure and role in cells. Storage Polysaccharides • Starch Plants store their sugars as starch – a polysaccharide (pennies vs. dollars) - Starch is made up of α-Glucose -Starch is stored in chloroplasts • Glycogen Animals store their sugars as glycogen – Glycogen is also made of α-Glucose – Animals store glycogen in the liver and muscle cells Starch and glycogen – storage polysaccharides Structural Polysaccharides • Cellulose Plants have cellulose in their cell walls, which protects their cells from damage Cellulose is made from β-Glucose • Chitin Fungal cell wall contain chitin, as do the exoskeletons of arthropods such as insects, crustaceans, arachnids, etc. Chitin is made from β-Glucose Cellulose – a structural polysaccharide Most animals cannot digest cellulose (fiber). Cows, sheep, termites and many other animals rely on bacteria in their intestinal tracts to breakdown cellulose into glucose monomers for them. Bacteria are one of the few organisms that produce an enzyme called cellulase, which hydrolysis the glycosidic bonds between betaglucose monomers. This is mutualistic symbiosis. Chitin – a structural polysaccharide Starch is made up of alpha-glucose molecules In cellulose, every other beta-glucose molecule is upside down. Lipids • The lipid family consists of fats, oils, waxes, phospholipids and steroids. • All lipids are hydrophobic (completely or partially) • Lipids are an important storage macromolecule. They also are good insulators and shock absorbers. Fatty acids are the building blocks of lipids No double or triple bonds – filled with hydrogens – fatty acid is straight Contains double or triple bonds – not filled with hydrogens – fatty acid is bent Triglycerides • Are made up of 3 fatty acids covalently bound to a 3carbon alcohol called glycerol • The 3 covalent bonds are formed through dehydration synthesis – 3 H2O molecules are lost • The fatty acids can be saturated or unsaturated Triglycerides • Saturated triglycerides are found in animals – butter, lard, etc. They are solid at room temperature, because the fatty acids are straight (no double bonds)and can “pack” together • Unsaturated triglycerides are found in plants and fish – they are called oils and are liquid at room temperature – because the fatty acids are bent (double or triple bonds) and cannot “pack” together Saturated vs. unsaturated triglycerides or fats vs. oils!! Saturated: found in animals and is solid at room temperature Unsaturated: found in plants and fish; is liquid at room temperature Phospholipids • Phospholipids are 2 fatty acids and a phosphate group that are covalently bonded to a glycerol • The Fatty acids tails are hydrophobic and the phosphate head is hydrophilic • Phospholipids compose cell membranes Phospholipid Bilayers • The hydrophilic phosphate regions (Heads) interact with the water inside and outside the cell. The fatty acids of the phospholipids (Tails) interact and form a hydrophobic center of the bilayer. Steroids • Another major class of lipids is steroids, which have structures totally different from the other classes of lipids. • Lipid steroids include such well known compounds as cholesterol, sex hormones (estrogen and testosterone), birth control pills, etc. Proteins • Proteins can be categorized into several different families, depending on their role in a living organism • Amino acids are the building blocks of proteins • There are over 150 amino acids, only 20 of which are used in protein building, by all organisms An amino acid 2 is in the Zwitterion state – when a compound can exist as an anion and a cation at the same time Dipeptides, Polypeptides • Amino acids are joined end – to –end by enzymes through dehydration synthesis, to form polypeptides (releasing a water molecules as a by product) • The covalent bond that forms between the carbon of one amino acids and the nitrogen of another is called a peptide bond. Polypeptides • A long chain of covalently bonded amino acids is called a polypeptide (many peptide bonds). N-terminus C-terminus Protein structure • Once a polypeptide forms, it tends to fold into several possible structures • These structures form due to various types of bonding and chemical interactions between the amino acids in the chain Primary Structure • The first level of structure is called primary structure. • The primary structure of a peptide or protein is simply the sequence of amino acids or the polypeptide chain. • The primary structure is held together by peptide (covalent) bonds Secondary Protein Structure -Helix and -pleated sheets •Depending on the sequence of amino acids, a polypeptide chain can fold in a number of ways. •In an - helix, hydrogen bonding between every fourth amino acid maintains the structure •In -pleated sheets, the hydrogen bonding is between adjacent amino acids •Secondary structures are held together by hydrogen bonds Secondary Protein Structure -Helix and -pleated sheets •In an - helix, hydrogen bonding between every fourth amino acid maintains the structure •In -pleated sheets, the hydrogen bonding is between adjacent amino acids in parallel rows Tertiary Structure • This occurs when the protein folds into a complex 3-dimensional shape • It involves many different kinds of bonds and interactions between amino acids side chains • These proteins are usually called globular and are soluble in water • Enzymes are examples of globular proteins Tertiary Structure Quaternary Structure • When multiple tertiary structures interact to form a more complex globular protein, it is called a quaternary structure • Hemoglobin is a protein made up of 4 tertiary protein chains • The quaternary structure is usually held together by hydrogen bonds between the chains Protein Structure Summary, cont’d. Nucleic Acids • Category consists of DNA and RNA • DNA = Deoxyribonucleic Acid, RNA = Ribonucleic Acid • DNA is double stranded, contains the sugar deoxyribose and the nitrogenous bases Thymine, Adenine, Guanine and Cytosine • RNA is single stranded (usually), contains the sugar ribose and the nitrogenous bases Uracil, Adenine, Guanine and Cytosine Incorporation of Nucleotides into DNA The Nitrogenous Bases • They are Nitrogen-containing compounds that are basic in nature – but overall, DNA is mildly acidic • Divided into Purines and Pyrimidines • Purines are larger in structure than pyrimidines • Adenine and Guanine are purines • Cytosine, Thymine and Uracil are pyrimidines • A and T or A and U can form 2 Hydrogen bonds • G and C form 3 Hydrogen bonds (a stronger alliance than A-T) Guanine and Cytosine Adenine and Thymine 3’ to 5’ direction Sugar-phosphate backbone 5’ to 3’ direction Sugar-phosphate backbone DNA is antiparallel. One strand runs 5’ to 3’ and the other 3’ to 5’. This is the only configuration that will allow proper H bond formation and distances between the bases. DNA in a nutshell • 2 antiparallel strands • Sugar-Phosphate backbone held together by phosphodiester bonds • Sugar phosphate backbones on the outside • Bases stacked on the inside • Purine-pyrimidine pairing, stabilized by H bonds (G=C) and (A=T) DNA - View from the top DNA gets packaged into a chromosome Types of RNA THE END