Chapter 2 Chemistry of Life

Biology Biology: The study of life In order to understand life your must have a basic understanding of chemistry

Matter and Energy Matter: anything that occupies spaces and has mass Everything around us is matter Element: a pure substance that cannot be broken down into other substances by chemical means ex. gold, helium, mercury

MAtter There are about 25 elements that are essential to life Four elements make up 96% of living matter Oxygen, Carbon, Hydrogen and Nitrogen Trace Elements: elements that make up less than 0.01% of your body mass Ex. Calcium Phosphorus, potassium and sulfur

MAtter

Matter Compounds: a substance containing two or more elements that are chemically combined in a fixed ratio Ex. H2O A compounds properties may differ greatly from those of its component elements Ex. NaCl

Atoms Atom: the smallest possible particle of an elements Atom of all elements are made of even smaller components called sub atomic particles Proton: a subatomic particle with a single unit of positive charge (+) Electron: a subatomic particle with a single unit of negative electrical charge (-) Neutron: a subatomic particle that has a neutral charge ( Think of it like a proton and electron combined)

atoms An atoms protons and neutrons are tightly packed together, forming a central core called the nucleus Electrons have much less mass than neutrons and protons and continually move about the outside of the nucleus at high speeds The attraction between the negatively charged electron and positively charged protons keeps the electrons close to the nucleus

atoms

ElemeNts An important difference between elements is the number of protons in their nucleus All atoms of a particular element have the same number of protons The number of protons is known as the Atomic Number Ex helium has two protons so it has an atomic number of 2

Elements Left alone atoms generally tend to hold as many protons and electrons. This creates an atom with an electrically neutral charge because the positive charge of the protons and the negative charge of the electrons cancel each other out The number of electrons is not always equal to the number of protons, because some elements tend to lose or gain electrons (these atoms are called Ions)

Isotopes Some elements have alternative forms called Isotopes Isotopes have the same number of protons in their atom but a different number of neutrons

Radioactive isotopes Radioactive Isotope: isotope in which the nucleus decays (breaks down) over time, giving off radiation in the form of matter and energy Ex. carbon-14 Radioactive isotopes have many uses in research and medicine because living cells use radioactive isotopes just as they would use the nonradioactive forms They are like spies

Electron configuration Electrons differ in the amount of energy they have and the how tightly they are held by the protons in the nucleus Based in these properties electron are classified into different energy levels The first and lowest energy level (nearest to the nucleus) can hold 2 electrons The second level holds 8 If the outermost energy level is not full the element is considered chemically reactive

Electron configuration

Ions Ionic Bond: type of chemical bond that occurs when an atom transfers an electron to another atom Ex. table salt NaCl Ions: atoms or groups of atoms that have become electrically charged as a result of gaining or losing electrons

Covalent Bonds Covalent Bond: forms when two atoms share electrons Covalent bonds are represented using the element symbols and dots that represent the atoms outermost electrons

Bonding Numbers of bonds The number of bonds an atom can form usually equals the number of additional electrons that will fill its highest energy level. Ex. a hydrogen atom can accept one additional electron so it can form only one bond Ex. an oxygen atom can accept 2 additional electrons so its can form up to 2 bonds

Molecule Molecule: two or more atoms held together by covalent bonds Molecules can be modeled in three different ways Chemical formula: tells you the number and types of atoms Structural formula: indicates how atoms in a molecule are linked by bonds Space filling model: shows three dimensional structure of the molecule

Chemical Reactions Chemical reactions: breaking of old chemical bond and the formation of new chemical bonds that result in new substances The starting materials in a chemical reaction are called the reactants The ending materials in a chemical reaction are called products

Properties of Water All living things are dependent on water Structure of Water Two hydrogen atoms attached to an oxygen atom by a covalent bond What makes oxygen unique is that the oxygen atom hogs all of the electrons This makes the oxygen more negatively charged than the hydrogen atoms Polar molecule: a molecule in which opposite ends have electric charges

Properties of Water Because the water molecule is polar the molecules are attracted to each other in a very specific way forming a hydrogen bond The negative end attracts the positive end

Properties of Water Hydrogen Bond: type of weak attraction between the hydrogen atom of one molecule and a slightly negative atom with in another molecule Hydrogen bonds are very weak These hydrogen bonds make water have some very unique properties

Properties of Water The Unique Properties of Water Cohesion: the tendency of molecules of the same kind to stick to one another Water has a much stronger cohesion than other liquids Adhesion: the type or attraction that occurs between unlike molecules ex. water sticks to glass Adhesion and cohesion are very important properties of water to life on Earth

Properties of Water Temperature Because of the hydrogen bonds water has a much greater resistance to temperature change Ex. getting water to boil Temperature: a measure of the average energy of random motion of the particles in a substance

Properties of Water Low density of ice Density is the amount of matter in a given volume In most substances the solid state is more dense than the liquid state But in water the solid form is much less dense than the liquid This is why ice floats on water

Properties of Water Water has the ability to dissolve other substances Solution: a uniform mixture of two or more substances Ex. when you dissolve salt into water Solvent: the substance that dissolves the other substance and is present in the greater amount Ex water Solute: the substance that is dissolved and is present in the lesser amount Ex. Salt

Carbon Based Molecules Remember that an atoms bonding ability is related to the number of electrons in the outermost energy level Carbon has four electrons in the outermost energy level which means that it has the ability the form up to four bonds with other atoms Carbon atoms can form bonds with one or more other carbon atoms producing many different carbons skeletons Organic Molecules: carbon based molecules Inorganic Molecules: non-carbon based molecules Hydrocarbons: organic molecules that are composed of only hydrogen and carbon In addition to hydrogen atoms oxygen and nitrogen are also common

Carbon Based Molecules

Carbon Based Molecules Functional Group: a group of atoms within a molecule that interacts in predictable ways with other molecules Hydrophilic: attracts water an example of a hydrophilic functional group is the hydroxyl group

Monomers and Polymers Monomers and Polymers Polymers: long chains or molecules that your cells link together Monomers: the smaller units that make up polymers Polymers can form long straight chains or the chains can fold over one other A living organisms has thousands of different polymers that help the organisms perform different functions These thousands of polymers are made up of only 50 different kinds of monomers

Monomers and Polymers Building and Breaking Polymers Organisms not only build polymers they also have to break them down Ex. many of the molecules in your food are polymers. Your body must breaks down these molecules in order for it to use Each time a monomer is added to a chain a water molecule is released This is called a dehydration reaction because it involves removing a water molecule De- (remove) Hydro- (water)

Building and breaking polymers Dehydration Reaction Hydrolysis Reaction Hydro-water Lysis- to break

Carbohydrates Life’s large molecules are classified into four main categories: carbohydrates, lipids, proteins and nucleic acids Carbohydrates: organic compound made up of sugar molecules. Sugars contain the elements carbon, hydrogen and oxygen in the ratio of 1 carbon: 2 hydrogen: 1 Oxygen Most sugars have a carbon skeleton with a ring shape

Carbohydrates Monosaccharides Monosaccharides contain just one sugar unit Ex Glucose, fructose and Galactose Sugar molecules are the main food supply for cellular work Very similar to how a car uses gasoline

Carbohydrates Disaccharides Double sugars made from monosaccharides by using a dehydration reaction Sucrose which consists of a glucose molecule linked to a fructose molecule

Carbohydrates Polysaccharides (complex carbohydrates) Long polymer chains made up of simple sugar monomers Ex. Starch is a polysaccharide made entirely of glucose molecules Starch is found in plant cells Starch chains branch and coil up into loop Animal cell do not contain starch they contain glycogen Glycogen is a polysaccharide that helps animals store excess sugar

Carbohydrates Some polysaccharides in plants serve as building materials Ex. Cellulose- protects cells and stiffens the plant Cellulose is also made of glucose molecules (like glycogen and starch) Most animals, including people cannot digest cellulose because they lack the molecule necessary to break the bonds between the glucose molecules in cellulose But some organisms like cows and termites can break down cellulose and use it for nutrients because they have microorganisms in their digestive tracts that are able to break down the cellulose

Carbohydrates

Carbohydrates Almost all carbohydrates are hydrophilic because there are many hydroxyl found on them This means that monosaccharides and disaccharides dissolve easily in water On the other hand cellulose and some forms of starch are such large molecules that they do not dissolve in water

Lipids Characteristics of lipids Uses of lipids Lipids are water avoiding Hydrophobic: meaning water fearing Uses of lipids They can act as a boundary that surrounds and contains the watery contents in your cell They can also store energy in your body

Lipids Fats Fat consists of a three-carbon backbone called glycerol attached to three fatty acids Fatty acids contain long hydrocarbon chains Some fats are solid at room temperature Some fats are oil and liquids at room temperature Unsaturated Fat

Lipids Saturated Fats Unsaturated Fats A fat in which all three fatty acid chains contain the maximum possible number of hydrogen atoms All the carbon atoms in the fatty acid chains form single bonds with each other, and the rest of their bonds are with hydrogen atoms. Saturated fats are solid at room temperature Unsaturated Fats Contains less than the maximum number of hydrogen atoms in one or more of its fatty acid chains, because some of its carbon atoms are double bonded to each other Usually liquids at room temperature

Lipids Steroids A lipid molecule in which the carbon skeleton forms four fused rings While all steroids have the core of four rings, they differ in the kinds of functional groups that are attached to the rings Steroids can circulate in your body as chemical signals Ex. estrogen and testosterone

Lipids Maybe the best known steroid is cholesterol It is an essential molecule found in the membranes that surround your cells It is also the starting point from which your body produces other steroids

proteins Function of Proteins Protein is a polymer constructed from a set of just 20 monomers known as amino acids Proteins are responsible for almost al of the day to day functioning of organisms Proteins form the structures that make up fur, hair, muscles and provide long term nutrient storage Proteins also have other functions including acting as signals and conveying messages from one cell to another

Proteins Amino Acids Each amino acid monomer consists of a central carbon atom bonded to four partners Three of the central carbon partners are the same in all amino acids One partner is a hydrogen atom One partner is a carboxyl group One partner is an amino group What is different in each amino acid is the side group The side group is responsible for the particular function of the amino acid

Proteins Building a Protein Cells create proteins by linking amino acids together into a chain called a Polypeptide Each link is created by a dehydration reaction between the amino group of one amino acid and the carboxyl group of the next amino acid in the chain There are an enormous variety of proteins that your body can create because there are many different orders the amino acids can go in Think of amino acids as letters in an alphabet and the polypeptides are the words that you can make from the alphabet

Proteins

Proteins Protein Shape A protein in a simple form of an amino acid linked together cannot function properly A functional protein consists of one or more polypeptides precisely twisted, folded and coiled into a unique shape An unfavorable change in temperature, pH, or some other quality of the environment can cause the protein to unravel and lose it normal shape This is called the denaturation of the protein

Activation energy To start a chemical reaction, it is first necessary to weaken chemical bonds in the reactant molecules To weaken the chemical bonds you usually need energy This energy is called activation energy because it activates the reactants and triggers a chemical reaction

Activation Energy One way to provide activation energy is to heat a mixture of molecules The hotter the molecules the more they will collide and the more likely the bonds in those molecules will break In cells however to provide the activation energy you cannot heat the cell because it will kill it You instead use what is called a Catalyst: a compound that speeds up chemical reactions The main catalyst in chemical reactions are proteins called enzymes

Enzymes Enzymes provide a way for reactions to occur at the cell’s normal temperature An enzyme does not provide the activation energy it lowers the activation energy Each type of enzyme catalyzes a specific kind of chemical reaction

Enzymes The reason that enzymes only catalyze one type of reaction is because of its shape. It is sort of like how a key fits into a lock Substrate: a specific reactant acted upon by an enzyme The substrate fits into a particular region of the enzyme called the active site

Enzymes

Nucleic Acids Polymers that are made up of monomers called nucleotides. There are two types of nucleic acids DNA and RNA Nucleotides contain three parts A sugar A phosphate group A nitrogen base