Chemistry of LIfe - Mrs. B.Bell's Classes

Chemistry of LIfe - Mrs. B.Bell's Classes

CHEMISTRY OF LIFE Nature of matter Everything in the universe is made of matter. Matter: Anything that occupies space & has mass. Mass: the quantity of matter that an object has Mass and weight are not the same because weight is affected by gravity. If you were on the moon, you would have the same mass, but you would weight less due to lack of gravity.

Nature of Matter An Atom -is the smallest unit of matter that cannot be broken down by chemical means. Atoms typically have 1 electron for each proton and neutron, so they are neutral (no electrical charge) Matter consisting of atoms of the same type is called an element (iron, lead, hydrogen). There are 92 naturally occurring elements, 26 of which occur in humans. 3 Basic Particles of An Atom: Particle Charge Location

1. Proton Positive (+) Nucleus 2. Neutron neutral (0) Nucleus 3. Electron Cloud Subatomic Particles Negative (-) Electron The electrons are located in energy

levels located outside of the nucleus where the electrons can move (electron cloud). The attractions between the positive charges in the nucleus and the negative charges of the electrons keep the electrons in the vicinity of the nucleus (valence shells). Level Electrons possible in each level 1 2e2 8e3 18e-

Ex: Lithium has 3 electrons, it has 2 in its first shell and 1 in the second shell. Valence Electrons are the numbers of electrons present in the outermost shell. Atoms with the same number of valence electrons have similar chemical behaviors. An atom with a completed valence shell, like neon, is nonreactive. All other atoms are chemically reactive because they have incomplete valence shells. The number of protons in the nucleus is called

the atomic number. It is written in subscript to the left of the symbol representing the element (6C). The total number of protons plus neutrons is the atomic mass (weight) sometimes called mass number. The electrons are so light that they do not appreciably contribute to the weight. (1/2000 that of protons and neutrons) The atomic mass is written in superscript to the left of the element's symbol (12C). Ex: Oxygen has 8 electrons and, therefore, 8 protons. It also has 8 neutrons. What is its atomic weight (16)?

Element - is a substance made of only 1 kind of atom, and it is a pure substance. Matter consisting of atoms of the same type is called an element (iron, lead, hydrogen). There are 92 naturally occurring elements, 26 of which occur in humans. The elements are arranged according to characteristics in the periodic table of the elements. In the middle of the 19th century, a Russian chemist named Mendeleev devised the periodic table. He observed that the elements could be arranged in sequential order horizontally by their atomic weights and vertically by the number of electrons in their outer shells. In this arrangement

elements with similar properties appear at regular intervals or periods. For example: a. Column 1--_alkali metals___ For example: a. Column 1--alkali metals b. Column 7--nonmetals c. Column 8--noble gases Each element has a unique symbol, usually the first one or two letters of the name. Some of the symbols are derived form Latin or German names. Four elements that make up 96% of the

human body: 1. 2. 3. 4. Carbon Hydrogen Oxygen Nitrogen An isotope is an atom of an element that has the same number of protons but a different number of neutrons. Most isotopes are unstable and tend to spontaneously break

down to more stable forms with the release of radiation. Ex: Most carbon atoms have 6 protons and 6 neutrons for an atomic weight of 12 (12C or carbon 12). However, carbon 14 (14C) has 6 protons and 8 neutrons and is radioactive. Its rate of breakdown is used for measuring the age of carbon containing fossils--accurate to about 20,000 years. Atoms can Bond Together When there are fewer than 8 electrons in the outer shell, the atom tends to loose, share, or gain electrons. Every atom has a characteristic total number of covalent bonds

that it can form, equal to the number of unpaired electrons in the outermost shell. This bonding capacity is called the atoms valence. The valence of hydrogen is 1; carbon is 4. Ex: An atom may combine with itself. Two hydrogen atoms will combine with themselves to form the molecule H2. Ex: Atoms of one element may combine with atoms of other elements in (compounds). H2O; NaCl. Atoms can bond together: While pure sodium is a metal and chlorine is a gas, they combine to form an edible compound. This change in

characteristics when elements combine to form a compound is an example of an emergent property. A compound is a substance made of the joined atoms of = two or more different elements. Example: Na+ + Cl NaCl (table salt) A force that joins atoms is called a bond. There are 23 types of bonds: 1. Covalent bonds 2. Ionic bonds

3. Hydrogen bonds Ionic and covalent compounds are alike in that they both fill outer electron levels to stabilize the atoms. .Electrons are what interact during a chemical reaction, the nuclei do not come close enough to interact. These electrons vary in the amount of energy they posses. Potential Energy is the energy that matter stores because of its position and location. Ex: water being stored behind a dam has

potential energy that can be used to turn electric generators. Electrons have potential energy depending on their position to the nucleus. The farther electrons are from the nucleus, the more potential energy they have. An electron can change its position if it absorbs or releases energy. Depending on whether energy is absorbed or release, the electron moves up or down energy level(s). 1. Covalent Bonds are created when 2 or more atoms share electrons and form a molecule. The atoms in covalent bonds are

usually not metals. Hydrogen (atomic number: 1H) has one electron in its outer shell and readily shares electrons. Molecules are held together by covalent bonds. Example: H2O, CO2, and O2 All organic compounds are held together by covalent bonds. **Draw a Covalent Bond Molecules with an unequal

distribution of electrical charge such as water molecules are polar molecules. Water has a positive charge on one end and a negative charge on the other. Because of its uneven charge, water is a polar molecule A hydrogen bond is a weak chemical attraction between **Draw a Hydrogen Bond 2. Ionic Bonds are formed by the

electrical attraction between oppositely charged ions. Ion is a charged atom or molecule. Ions have an elec- trical charge because they contain an unequal number of electrons and protons. Ionic Bonds Cont. An atom that has lost electrons is

positively charged. An atom that has gained electrons is negatively charged. Ions or opposite charges may interact to form an ionic bond. Ionic bonding usually occurs between metallic & nonmetallic atoms Example of an ionic bond: Na+ + Cl- = NaCl In table salt (NaCl), the single electron in sodium's outer shell is pulled away to complete chlorine's outer electron shell. Chlorine has 7 electrons in its outer shell; it needs one more electron and takes it by force.

When the negatively charged electron is lost, the element then becomes positively charged and is written with a + superscript to the right of the element's symbol (Na+). The element then becomes an ion. Positively charged ions are called cations (+) Chlorine, with 7 electrons in its outer shell, strongly attracts additional electrons. When an electron is gained, the element becomes negatively charged and is written with a - superscript to the right of the element's symbol (Cl-). Negatively charged ions are called anions (-) . Hydrogen bond--formed when hydrogen is attracted to

2 other atoms, one of which is usually oxygen or nitrogen. They are very weak bonds. **Draw a Ionic Bond The chemical formula is a shorthand method for describing the chemical composition of a molecule. H20; NaCl The structural formula identifies the arrangement of atoms.

H:O:H or H-O-H. The chemical equation is a means for representing the chemical reactions between atoms & molecules. 6CO2 + 6H2O + Energy C6H12O6 + 6O2 The reactants are the molecules that participate in the reaction. They are shown to the left of the arrow. The products are the molecules formed by the reaction. They are shown to the right. There are _4__ types of basic chemical reactions

that are common to all living cells. 1. Synthesis (anabolism)--when two or more atoms or molecules combine to form new and larger molecules. N + 3H ----> NH3 (ammonia) 2. Decomposition (catabolism)--large molecules are broken down into smaller molecules or atoms. (methane) CH4 ----> C + 2H2 3. Reversible--the reaction can go either way. Often some factor like heat, pressure, or another chemical can cause the reaction to go one way or the other. Such a factor is called a

catalyst. (carbonic acid) H2CO3 <====> H2O + CO2 Water and Solutions Water is an inorganic substance which means it is not made from carbon or living things. Water is composed of 1 atom of oxygen and 2 atoms of hydrogen.

Water molecules are linked by hydrogen bonds. This causes water to heat up and cool down slowly. Water stabilizes air temperatures by absorbing heat from warmer air and releasing heat to cooler air. Water can absorb or release relatively large amounts of heat with only a slight change in its own temperature. (Specific heat) Water, which is essential for life, stores heat efficiently and binds to itself and other substances. The most abundant inorganic substance in a cell is water. The hydrogen bonds between water molecules cause the cohesion of liquid water. These hydrogen bonds weak and

are constantly forming, breaking, and reforming. Each hydrogen bond lasts for only a few trillionths of a second. Cohesion is an attraction between substances of the same kind. Because of cohesion, water and other liquids form drops and thin films. The thin films allow some insects to stand on the surface of water because water is cohesive and adhesive (surface tension) The hydrogen bonds between the water molecules resist stretching or breaking the surface. Kinetic Energy is the energy of motion. The faster a molecule moves, the more

kinetic energy it has. Heat is a measure of total quantity of kinetic energy due to molecular motion in a body of matter. Temperature measures heat in a body of matter due to the average kinetic energy of molecules. When two objects of different temperatures come together, heat passes from the warmer object to the cooler object until the two are the same temperature. (ice in a coke) The ability of water to stabilize temperature depends on its specific heat. Waters Heat Capacity:

The ability of water to stabilize temperature depends on its relatively high specific heat. The specific heat of a substance is defined as the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature 1 C. The specific heat of water is 1.00 cal/g C. Compared with most other substances, water has an unusually high specific heat Because water has such a high specific heat, it will change its temperature 1 C when it absorbs or loses a given amount of heat. (Basically, it can absorb a lot of energy (heat) without affecting its

temperature very much.) Water EXPANDS! Water also expands when it freezes, which means it is less dense at a frozen (solid) state. Because of this, ice can float. Ex: Ice berg in the Arctic or soft drink with ice cubes Evaporation occurs when molecules move fast enough to overcome the attraction of other molecules in the liquid. Evaporation of sweat in mammals or transpiration of water

from the leaves of plants prevents terrestrial organisms from over-heating. This attraction between water molecules (to itself) causes a condition known as surface tension. This property of water allows insects like the water striders to skate across the surface of a pond. Water molecules are also attracted to many other polar substances. Adhesion is an attraction between different substances. Because water stick to solids (adhesion), water has the property of capillarity.

Capillarity is the ability to spread through fine pores or to move upward through tubes (such as the stem of a plant) against the force of gravity. The attraction of water to the walls of the tube sucks the water up more strongly than gravity pulls it down. Water dissolves many substances: Due to waters polar nature (uneven charge), water makes a good solvent, pulling apart other molecules. Non-polar molecules do not dissolve well in water. When non-polar substances, such as oil,

are placed in water, the oil forms lumps or Nonpolar molecule beads in water. and water Polar Molecules and water Acids and Bases: pH is a measure of how acidic or basic (alkaline) a solution is. A change of one pH unit reflects a 10X change. The pH scale ranges from 0-14 and is used to measure pH. The pH scale ranges from 0-14 and is used to measure pH. . A pH below 7 indicates an acidic solution; a pH above 7

is basic (alkaline); a pH of 7 is neutral. This is a sliding scale and, a solution with a pH of 2 would be very acidic. Conversely, a pH of 12 would be highly alkaline When an acid and a base are mixed together, the H+ (hydrogen [hydronium] ion) of the acid unites with the OH(hydroxyl [hydroxide] ion) of the base to form water. When an acid, a base, or a salt is dissolved in water, the mixture can conduct electricity. For this reason, such a solution is called an electrolyte. The pH scale is a means for indicating the acidity or alkalinity of a solution (pH stands for % hydrogen).

Acids and Bases An acid is any substance that forms hydrogen ions (H+) in water. This solution contains more H+ (hydrogen) ions and has a pH<7. Acids dissociate into H+ (hydrogen ions) that lower the pH . Sour and corrosive Tend to burn Turn litmus paper red Examples: battery acid, sulfuric acid, stomach acid Acids and Bases A base (alkaline) is any substance that forms OH-

(hydroxide) ions and has a pH>7 Are bitter and feel slippery Turn litmus paper blue Examples: soaps, household cleaners Buffers Buffers are substances in solution (HCO3- bicarbonate ion) that can react with a strong acid or base to form a weaker acid or base and thus resist a change in pH. Buffers accept or release Hydrogen

molecules when necessary. (Buffers neutralize acids & bases.) HCl + NaHCO3 ----> H2CO3 + NaCl carbonic acid (weak acid) Control of pH is necessary for proper Buffers: Buffers act as that control; they neutralize acids or bases in order to help control pH. Buffers are very important to organisms because they are vital in the performance of

many processes. Controlling the pH of blood is essential to all life processes. Blood has a natural buffering ability in order to maintain proper pH within its narrowing range. If blood is NOT at optimum pH, the organisms life may be threatened. Bicarbonate & phosphate are 2 ions that are found in the blood and help maintain a healthy pH. When you exercise, your body produces more A pH of 7 indicates a

neutral pH between acidic and alkalinity. Ex: pure water Chemistry of cells Compounds may be classified as inorganic (lacking carbon and hydrogen bonds) or organic(containing carbon and hydrogen bonds). Inorganic compounds (salt, iron oxide): a. relatively small b. simple

c. Water functions as a solvent. d. Form ionic (electrolytic) solutions when dissolved (dissociated) in water. e. Organic compounds are characterized by several structural forms, such as isomers, functional groups, and polymers. Isomers are compounds that have the same molecular formula, but they have different structures (C2H60: ethanol and dimethyl ether). Functional groups allow for the synthesis of new molecules by replacing certain attached hydrogen atoms by other atoms or molecules (-OH, alcohol; -CH3, methyl). The carbon backbone of organic compounds is relatively non-reactive. Chemistry of cells Organic compounds contain carbon atoms

that are covalently bonded to other elements, typically hydrogen, oxygen and other carbon atoms. All organic compounds contain the element carbon. Carbon is the essential element that all life depends on. Carbon can form up to 4 covalent bonds with other molecules. Its nature allows the ability to form straight chains, branched chains, and rings.

Carbons ability to form covalent bonds is important in allowing for a wider variety of Four Classes of Organic Compounds Found in Living Things: 1. 2. 3. 4.

Carbohydrates Lipids nucleic acids proteins Without these compounds cells could not function. All of these compounds are long repeating units called polymers. Polymers are large molecules formed when many smaller molecules bond together usually in long chains. Each unit of a polymer is called a monomer (simple molecule).

Polymer Monomer Condensation reactions: a hydrogen ion (H+) and a hydroxide ion (OH-) combine to produce a water molecule. Condensation (dehydration synthesis) is the process of utilizing energy to link polymers by

removing hydrogen and hydroxyl ions. water is formed as a by-product from the combination of hydrogen and hydroxyl ions. Hydrolytic Reactions: (hydrolysis)a water molecule splits into a hydrogen ion and a hydroxide ion. Hydro=water -lysis= to split or break apart Polymers can be broken down into their 1. Carbohydrates are organic compounds made of carbon, hydrogen, and oxygen atoms in 1:2:1 ratio. All carbohydrates are made of carbon,

hydrogen, and oxygen. They are the main source of energy for living things, and they are found in most foodslike fruits, vegetables, and grains. Most energy that is used in the human body is stored as carbohydrates. = There are 3 types of carbohydrates: 1. Monosaccharides or simple sugars. They are the building blocks of carbohydrates. Examples of monosaccharides: 1. Glucose is manufactured by plants

during photosynthesis. It is the main source of energy for plants and animals. 2. Fructose is found in fruits and is sweet. These have the same molecular formulas, C6H12O6, but different structural formulas, which make them isomers. Carbohydrates Cont. 2. Disaccharides are 2 monosaccharide molecules linked. Maltose: 2 glucose molecules joined together Sucrose: glucose joined together with fructose Lactose: glucose joined together with

galactose = Carbohydrates Cont. 3. Polysaccharides are composed of many monosaccharide subunits. Polysaccharides function as storehouses of the energy contained sugars. Three examples of polysaccharides that store energy: 1. Starch which is made by plants (like potatoes). Energy is passed from potato to the person eating it

primarily by the energy stored in starch molecules. 2. Glycogen which is made by animals. Both starch and glycogen are made of hundreds of linked glucose molecules. 3. Cellulose is a polysaccharide that provides structural support for plants. Humans cannot digest cellulose (wood). Some herbivores have bacteria in their intestine that break down cellulose into a usable form. Starch Glycogen in Liver Cells Cellulose Lipids are non polar molecules that are

not soluble in water. Lipids are used to store energy (long term storage), for insulation, and as protective coatings. Lipids are composed of 3 fatty acids bonded to a glycerol molecule. Examples of lipids: fats, phospholipids, steroids, including cholesterol, and waxes. Fats Cholesterol Steroids Waxes

Lipids Cont. The monomers of lipids are fatty acids Lipids are an important part of the structure and functioning of cell membranes. Phospholipids make up the lipid bilayer of cell membranes. Contain phosphorus and often nitrogen, as well as glycerol & fatty acids

The molecule is polar in that its "head" contains phosphate and is hydrophilic, which means it is attracted to water. The "tail" of the molecule is composed of linked fatty acids; it is hydrophobic, which means water fearing. In the cell membrane, these molecules are formed in a double layer with the tails of one layer interdigitating with the tailsPhospholipid of the otherBilayer layer. This arrangement is known as a Lipids Cont. Fats are lipids that store energy. The fatty acids

contain tails that are called hydrocarbonsthis means that they are composed of hydrogen and carbon bonds only. Fats contain 9 kcalories per gram while carbohydrates and proteins contribute 4 kcalories per gram. saturated fats are found in natural food products (eggs, milk) and contain only single covalent bonds between their carbon and oxygen atoms--saturated with H+. These fats are solid at room temperature. unsaturated fats contain double covalent bonds between the carbon and oxygen atoms. These fats are liquid at room temperature. trans fats- new fats created by humans to

help with preservation. It used to be thought Lipids Cont. Waxes are highly waterproof. In plants, wax forms a protective coating on the outer surfaces, for example cuticles on the leaves. In animals, wax forms protective layers, for example ear wax. Lipids Cont. Steroids Composed of 4 interlocking rings. Cholesterol is a steroid that serves as a precursor for many hormones, like

estrogen, testosterone, and cortisol. A hormone is a chemical secreted into the blood that controls the activities of other parts of the body. 3. Nucleic Acids are in all of your cells. The building blocks of nucleic acids are nucleotides. A nucleic acid is a long chain of smaller molecules called nucleotides. A nucleotide has three parts; 1. a sugar 2. a base 3. a phosphate group

Sugar Phosphate Group Base polynucleotides are formed when nucleotides are linked together. There are two types of nucleic acids: 1. DNA Deoxyribonucleic Acid DNA consists of 2 strands of nucleotides that spiral around each other.

DNA is a molecule shaped like a spiral staircase also known as a double helix. 2. RNA Ribonucleic Acid RNA consists or a single strand of nucleotides RNA DNA Proteins are a chain of molecules called amino acids linked together like parts on a necklace. Amino acids are linked together by covalent bonds called peptide bonds. These strings

of amino acids are known as polypeptides. A protein consists of one or more polypeptide chains. Amino acids- are composed of an amino group (NH3), a carboxyl group (COO-an acid), a hydrogen atoms and one or more atoms called its R group. The __R__ group is what determines which amino acid is formed. It can be anything from hydrogen to a carbon Proteins Cont. Proteins are made of long chains of amino acids

Amino Acids are the building blocks of proteins. There are 20 different amino acids, which bond to each other by peptide bonds (covalent bonds formed between amino acids). Some proteins called enzymes regulate chemical reactions in the body but remain unchanged by the reaction. The complete hydrolysis of a protein would result in the formation of amino acids. Hydrolysis is a chemical reaction in which water is used to break down a compound. Proteins Cont. ATP-Adenosine Triphosphate ATP carries energy in cells.

ATP is a single nucleotide with 2 extra energy-storing phosphate groups. Energy and Chemical Reactions Energy is the ability to move or change matter. A chemical reaction - is a process during which chemical bonds between atoms are broken and new ones are formed, producing one or more different substances. Reactants Products (starting materials) (forms) (newly formed

substances) Activation energy-The energy needed to start a chemical reaction. Enzymes Help Biochemical reactions occur: Enzymes (proteins) are substances that increase the speed of chemical reactions. Enzymes are catalysts, which are substances that reduce the activation energy of a chemical reaction. A substance on which an enzyme acts during a chemical reaction is called a substrate. Each enzyme is specific and only acts on a particular

substances called substrates. An enzyme has deep folds on its surface, and these folds form pockets called active sites. Enzymes serve as catalysts. Catalysts-speed up chemical reactions. Enzymes cont. Lock and Key Model-an enzyme and its substrate have shapes that allow them to fit together like a lock and key After the reaction, the enzyme is released so that it can be used over and over again

Enzymes Without Enzyme With Enzyme Free Energy Free energy of activation Reactants Products Progress of the reaction 62 Factors that affect enzyme activity;

1. Temperature 2. pH 3. Enzyme Concentration If, for example, heat is added to an enzyme, the enzyme is denatured. When high fevers occur,proteins get denatured beyond the point of being able to return back to normal and death will occur. Temperature 5- 37oC Increase in

Activity Rate of Reaction 40oC denatures 0 <5oC inactive 10 20 30 40

50 60 Temp. (oC) 65 pH Narrow pH optima Rate of Reaction WHY? Disrupt Ionic bonds Structure

Effect charged residues at active site 1 2 3 4 5 6 7 8 66

Rate of Reaction Enzyme Concentration Enzyme Concentration 67

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