Chemistry in Biology Chapter 6 6 1 Atoms

Chemistry in Biology Chapter 6

6. 1 Atoms, Elements, and Compounds Chemistry: the study of matter Atoms: the building blocks of matter

Atoms They are soooo small but they are made up of even smaller particles: neutrons protons electrons

Atoms There is a nucleus at the center of an atom! In the nucleus you can find: protons: positive charge neutrons: no charge Outside the nucleus you find: electrons: negative charge

Atoms continued Electrons orbit around the atoms nucleus. The attraction between protons and electrons are what cause the structure of an atom. There are equal numbers of electrons and protons in an atom: the overall charge of an atom is zero

Atoms • The atomic number: the number of protons found in the nucleus of the atom (therefore, it is also the number of electrons found that orbit around the nucleus) • The atomic mass: the weight of the protons and the neutrons combined.

Elements • Element: pure substance that can’t be broken down further by chemical or physical means. • They are made up of only one type of atom • There are over 100 known elements

Elements • Each element has a unique symbol and name Groups: the vertical columns Periods: the horizontal rows

Isotopes: atoms of the same element that have different numbers of neutrons (so the atomic mass is different) Radioactive isotopes: less stable nucleus which may decay. When the nucleus breaks apart it gives off radiation Carbon-14 used to calculate the age of things (within 50, 000 years)

Compounds Compound: a pure substance formed when two or more different elements combine Each has a chemical formula Each formed from a specific combination of elements in a fixed ratio (like C 6 H 12 O 6)

compounds They are chemically and physically different than the elements that make them up for instance: H is a gas, O is a gas together they make H 20 which is liquid They can’t be broken down into simpler compounds or elements by physical means but they can by chemical means

Chemical Bonds • The force that holds substances together are chemical bonds. The first orbit can hold 2 electrons The next ring can hold 8 electrons The outermost ring can hold 2 electrons

Chemical bonds • In order for an element to be stable you must have the outer most energy level either completely full or completely empty • Otherwise it isn’t stable • Atoms become stable by either losing electrons to something else or by attracting more electrons from something • Either way, there is energy stored in the bonds that are made and when bonds are broken they release energy

Covalent Bonds Covalent Bond: the bond that forms when electrons are shared Most compounds in living organisms have covalent bonds holding them together.

Molecule: a compound in which the atoms are held together by covalent bonds

Ionic Bonds Ion: An atom that has lost or gained one or more electrons and carries an electric charge Ionic bond: an electrical attraction between two oppositely charged atoms or groups of atoms

ions • Substances formed by ionic bonds are called ionic compounds – Ions: sodium, potassium, calcium, chloride and carbonate ions 1. Help to maintain homeostasis 2. Help to transmit signals among cells to see, taste, hear, feel and smell

ions • Some atoms tend to donate or accept electrons more easily than other atoms • (and when given the opportunity to choose, will choose certain atoms over others)

Van der Waals Forces When molecules are attracted to each other based on positive and negative regions. Not as strong as covalent or ionic bonds but determined by the size of the molecule, its shape, and its ability to attract electrons Important in water molecules

6. 2 Chemical Reactants Chemical reaction: when two or more chemical substances mix together. They become new substances that are very different than the original substances.

Chemical reactions Sometimes substances change without involving a chemical reaction (so they are still made up of the same atoms but just a physical change happens)

Chemical Equations • Reactants and products – Reactants: The starting substances that go into a chemical reaction – Products: The substances formed at the end of a reaction (or as a middle step)

This is a chemical equation! This shows what goes in and what comes out.

Balanced equations Matter cannot be created or destroyed WHAT GOES IN MUST COME OUT (but it can be rearranged because the bonds can change and form something else) So, you must account for the atoms that go into a reaction and what comes out of a reaction

Balancing equations All chemical equations must show this balance of mass. This means that the number of atoms of each element ON THE REACTANT SIDE (the left side of the equation) must equal the number of atoms of the same element ON THE PRODUCT SIDE (the right side of the equation)

Balancing Equations • The coefficient (the number in front) is used to make the number of atoms on each side of the arrow equal (you do not use the subscript for this

Energy of Reactions There is a minimum amount of energy needed to make a reaction occur. This is called ACTIVATION ENERGY. The point: allowing the reactants create products

Energy Change in Chemical Reactions When the reaction releases energy (in the form of heat) the reaction is EXOTHERMIC this means there is more energy in the bonds of the reactant (the stuff on the left side of the arrow) compared to the products(the stuff on the right side of the arrow).

Energy Change in Chemical Reactions When the reaction requires more energy to happen than what is released the reaction is ENDOTHERMIC this means there is more energy in the bonds of the product (the stuff on the right side of the arrow) compared to the reactants (the stuff on the left side of the arrow).

Enzymes All living things are “chemical factories” driven by chemical reactions There has to be an input of energy in order for reactions to occur. Some reactions would occur incredibly slow if allowed to occur on their own.

Enzymes • In order to reduce the activation energy (reduce the amount of energy needed for a reaction to occur) ADDITIONAL substances are required. • This allows the reaction to happen more quickly.

Enzymes • These things are biological catalysts: – A CATALYST is a substance that lowers the activation energy needed to start a chemical reaction. – It doesn’t change what is made, or how much is made…only how fast it is made

Enzymes • A biological catalyst is an ENZYME • It is used to speed up a chemical reaction • It is usually specific to one reaction • Can be used over and over

Enzymes • An enzymes name describes what it does: – Such as: • Amylase breaks down amylose • Maltase breaks down maltose • Lactase breaks down lactose (lactose intolerance is when lactose isn’t broken down by lactase: causing bloating, gas, diarhea)

How enzymes work • The reactants that bind to the enzyme are called SUBSTRATES • Where the SUBSTRATE and the ENZYME bind together is called the ACTIVE SITE • The enzyme/active site fit together like puzzle pieces. Once together the active site changes shape.

How enzymes work • Enzymes help chemical reactions happen by breaking bonds and allowing new ones to form. • It increases the speed at which reactions occur.

6. 3 Water and Solutions • The properties of water make it well suited to maintain homeostasis in an organism HOMEOSTASIS: the body’s ability to regulate its internal condition by adjusting cellular processes

Recall the structure of water

Water is Polar Meaning- one side of the molecule has a slightly positive charge while the other side has a slightly negative charge Water molecules bond to each other with hydrogen bonds (shown above in the animation). The hydrogen is attracted to the oxygen.

More Properties of Water It is the universal solvent because many substances dissolve in it

Water is cohesive It has a strong attraction to other water molecules. Because of this it has high surface tension. This also causes droplets to form.

Water is Adhesive It forms hydrogen bonds with other molecules on other surfaces. (think of tape) This causes capillary action.

Acids and Bases Remember that water is a universal solvent because a lot of things dissolve in it. Your body is about 70% water. When a substance that contains hydrogen is dissolved in water it may release hydrogen (H+)

Acids • Substances that release hydrogen ions when dissolved in water are called ACIDS. • The more hydrogen released the more acidic the solution becomes

Bases • Substances that release hydroxide ions (OH-) when dissolved in water are called BASES. • The more hydroxide released the more basic the solution becomes

p. H Scale The measure of the concentration Of hydrogen in a solution is the p. H. The more hydrogen something Releases the more acidic it is. HOWEVER, the more acidic it Is the lower the p. H number on The p. H scale. The more hydroxide (OH-) that Is released the more basic Something is. The higher the number is on the p. H scale.

• Pure water is neutral and has a p. H value of 7. 0. • Acids have a p. H number lower than 7 • Bases have a p. H number higher than 7

p. H Scale Acids and bases are key substances in biology. All the chemical reactions in the body happen in certain ideal temperatures, environments and p. Hs Most chemical reactions occur between the p. H of 6. 5 and 7. 5

• Maintaining the proper p. H is important for chemical reactions to occur. • This is called HOMEOSTASISmaintaining the internal environment.

Buffers • BUFFERS are mixtures that can react with acids or bases to keep the Ph within a particular range.

6. 4 The building blocks of life • Carbon is an element that is in most biological molecules. • It has 4 electrons in its outermost shell (it would like 8 electrons there in order to live a happy and full life) • So it likes to make bonds with other elements

Organic Chemistry • Carbon forms covalent bonds with other elements (they share the electrons) • Anything with a carbon element in it is “organic”

Macromolecules • Macromolecules: large molecules that are formed by joining smaller organic molecules to each other. • These larger molecules are also called POLYMERS. • Polymers: molecules made from repeating units of identical or nearly identical compounds (called monomers) linked to each other by covalent bonds.

Biological Macromolecules • Carbohydrates (sugars, and starches and complex things like cellulose): – The name “carbo-” means it has carbon – The name “hydrate” means it has water (H 2 O) – So For every carbon there is a water. Looks like this: (C H 2 O)n

Carbohydrates play a key role as a source of energy Some are a source for structure (like cellulose for a cell wall in plants) Or Chitin which makes up the exoskeleton of things like shrimp.

Lipids • Lipids: molecules made mostly of carbon and hydrogen that make up fats, oils, and waxes. They are composed of fatty acids, glycerol and other components. • They are mainly used to store energy

Saturated fats Found mostly in animal fats. Associated with higher cholesterol levels (this is bad) obesity, heart disease (atherosclerosishardening of the arteries) etc…

Unsaturated fats Better for you in small amounts. Heart healthy, better skin, supposedly some help with depression and also keep your cholesterol down. Some research suggests it helps in keeping your brain healthy!

Saturated and unsaturated fats Lipids are important for the phospholipid bilayer (makes up cell membrane and lets things go in/out of the cell) Steroids: estrogen, testosterone and cholesterol (also, the bad ones)

Proteins • Protein: a compound made of small carbon compounds called amino acids. • Amino acids: small compounds that are made of carbon, nitrogen, oxygen, hydrogen, and sometimes sulfur.

Amino Acid Structure Carbon can make four bonds: One of those is with hydrogen Another with an amino group that Contains nitrogen there is a carboxyl group that has a carbon THE 4 TH BOND IS WITH A VARIANT GROUP (this changes depending On what kind of amino acid is Being made)

3 D protein structure Structure of the protein depends on what variable group is attached in the different amino acids. how the amino acids “line up” determines the primary structure of the protein

Protein Structure After the amino acid chain is formed it folds into a unique 3 D shape. This is its secondary structure.

3 D protein structure • The Tertiary (3 rd) type of structure can be either globular (like a glob) or they can form long fibers. • The Fourth level of structure is when one strand of protein combines with another strand of protein.

Protein Function • Make up about 15% of your body mass • They make up structures like muscles, skin and hair. • They also give other structure, they are used to transport things, they are used to communicate signals with in the cell and between cells, they speed up chemical reactions and control cell growth.

• This is the cell (plasma membrane). It uses, lipids, carbohydrates and proteins to help maintain homeostasis in organisms

Nucleic Acids • Nucleic Acids: store and transmit genetic information. • Made of repeating units of phosphorus, nitrogen, oxygen, carbon and hydrogen • A couple types: RNA (ribonucleic acid) and DNA (deoxyribonucleic acid)

Chapter 6 Chemistry in Biology 6. 4 The Building Blocks of Life § The number and the order in which the amino acids are joined define the protein’s primary structure. § After an amino acid chain is formed, it folds into a unique three-dimensional shape, which is the protein’s secondary structure, such as a helix or a pleat.

Chapter 6 Chemistry in Biology 6. 4 The Building Blocks of Life § Nucleic acids are complex macromolecules that store and transmit genetic information. § Nucleic acids are made of smaller repeating subunits called nucleotides, composed of carbon, nitrogen, oxygen, phosphorus, and hydrogen atoms.

Chapter 6 Chemistry in Biology Chapter Resource Menu Chapter Diagnostic Questions Formative Test Questions Chapter Assessment Questions Standardized Test Practice biologygmh. com Glencoe Biology Transparencies Image Bank Vocabulary Animation Click on a hyperlink to view the corresponding feature.

Chapter 6 Chemistry in Biology Chapter Diagnostic Questions Which of the following particles is negatively charged? A. electron B. isotope C. neutron D. proton 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Chapter Diagnostic Questions Isotopes are created by a change in the number of what particle of an atom? A. electrons B. neutrons C. protons D. ions 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Chapter Diagnostic Questions Identify the proteins that speed up the rate of chemical reactions. A. substrates B. enzymes C. ions 1. A 2. B D. reactants 3. C 4. D

Chapter 6 Chemistry in Biology 6. 1 Formative Questions What particles are in an atom’s nucleus? A. neutrons and electrons B. protons and electrons C. protons and neutrons 1. 2. 3. A B C

Chapter 6 Chemistry in Biology 6. 1 Formative Questions What causes the overall charge of an atom to be zero? A. an equal number of protons and neutrons B. an equal number of protons and electrons C. an equal number of neutrons and electrons 1. 2. 3. A B C

Chapter 6 Chemistry in Biology 6. 1 Formative Questions What type of substance is water? A. a compound B. an element C. an isotope D. a mixture 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 1 Formative Questions What provides the energy for all living processes? A. chemical bonds B. ionic compounds C. radioactive isotopes D. van der Waals forces 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 2 Formative Questions Which is a chemical reaction? A. a match burning B. salt dissolving C. water boiling D. gasoline evaporating 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 2 Formative Questions Which chemical reaction is endothermic? A. B. 1. A 2. B

Chapter 6 Chemistry in Biology 6. 2 Formative Questions How does an enzyme increase the rate of a chemical reaction? A. It acts as a reactant. B. It reduces the amount of heat produced. C. It increases the amount of product. D. It lowers the activation energy. 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 2 Formative Questions What occurs at the active site in the enzyme substrate complex? A. An exothermic chemical reaction takes place. B. Chemical bonds are broken and new bonds are formed. C. The enzyme gets used up in the reaction. D. The substrates provide energy for the enzyme. 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 3 Formative Questions Why is water able to dissolve a wide variety of solutes? A. It acts as a catalyst. B. Its p. H is neutral. C. It is a polar molecule. 1. A 2. B D. It is an ionic compound. 3. C 4. D

Chapter 6 Chemistry in Biology 6. 3 Formative Questions What type of bonds attracts water molecules to each other and to other substances? A. covalent bonds B. double bonds C. hydrogen bonds D. ionic bonds 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 3 Formative Questions Which ion, when released in water, causes a solution to be basic? A. Cl– B. OH– C. H+ D. Na+ 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 3 Formative Questions What is the name for a substance that keeps the p. H in cells within the 6. 5 to 7. 5 p. H range? A. alkali B. antacid C. buffer D. neutralizer 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 4 Formative Questions Which element do almost all biological molecules contain? A. carbon B. nitrogen C. phosphorus D. sodium 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 4 Formative Questions How many covalent bonds can carbon form with other atoms? A. 1 B. 2 C. 4 D. 8 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 4 Formative Questions What type of biological molecule is an enzyme? A. hormone B. nucleic acid C. protein D. steroid 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 4 Formative Questions What are fats, oils, and waxes composed of? A. lipids B. nucleotides C. polypeptides D. sugars 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 4 Formative Questions What are the monomers that make up proteins? A. amino acids B. fatty acids C. glycerols D. nucleotides 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology 6. 4 Formative Questions Which biological molecule transports substances between cells? A. carbohydrate B. lipid C. nucleic acid D. protein 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Chapter Assessment Questions ? Look at the following figure. Determine what the upward curve represents. A. activation energy B. reactants C. products D. enzymes 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Chapter Assessment Questions Look at the energy levels in the atom. What is the maximum number of electrons energy level two can hold? A. 2 B. 4 C. 6 D. 8 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Chapter Assessment Questions Explain why chemical equations must be balanced. Answer: Chemical reactions require balance of mass. Therefore, the number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side.

Chapter 6 Chemistry in Biology Standardized Test Practice Which is a result of van der Waals forces? A. atoms sharing electrons B. table salt dissolving in water C. ionic compounds forming crystals D. water molecules forming droplets 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Standardized Test Practice What is true of this chemical reaction? A. Energy is not needed to start the chemical reaction. B. Heat and/or light energy are released in this reaction. C. The activation energy is greater than the energy released. D. The energy of the products and the reactants is the same. 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Standardized Test Practice Which fruit contains a higher concentration of hydrogen ions? A. tomatoes B. bananas 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Standardized Test Practice What do cellulose and chitin have in common? A. They are energystoring polymers. B. They are found in the 1. cells of animals. 2. 3. C. They are structural 4. polysaccharides. D. They are composed of repeating sucrose units. A B C D

Chapter 6 Chemistry in Biology Standardized Test Practice Which polysaccharide stores energy in muscle and liver tissue? A. gluten B. glycogen C. starch 1. 2. D. sucrolose 3. 4. A B C D

Chapter 6 Chemistry in Biology Standardized Test Practice What is the function of this biological macromolecule? A. communicate signals between cells B. produce vitamins and hormones C. provide support and protection D. store and transmit genetic information 1. 2. 3. 4. A B C D

Chapter 6 Chemistry in Biology Standardized Test Practice Which is a characteristic of all lipids? A. They are saturated triglycerides. B. They do not dissolve in water. C. They are liquid at room temperature. D. They store less energy than carbohydrates. 1. 2. 3. 4. A B C D