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Mr. Carpenter’s Biology Biochemistry Name ________________ Pd ____ Chapter 2 Vocabulary Atom Element Compound Molecule Ion Cohesion Adhesion Solution Acid Base Carbohydrate Monosaccharide Lipid Protein Amino acid Nucleic acid Nucleotide ATP Energy Activation energy Enzyme Substrate Active site Chapter 2 Section 1 Notes • What is an atom?_________________________________________________ o An atom is very ____________________ ! Consists of: • ____________________ – center of the atom • Protons (p+): subatomic particles with a ____________________ (+) charge. • Neutrons (no): subatomic particles with ____________________ charge – ____________________. • Both have about the same ____________________ = 1 atomic mass unit (1 amu) ____________________ ____________________ – outside the nucleus. • Electrons (e-): subatomic particles with a ____________________ (-) charge. • Electrons move in pathways called ____________________ or ____________________. • Mass of an electron is ____________________. Key difference between atoms of different elements is the number of ____________________ and ____________________ they contain. Atoms have ____________________ numbers of protons and electrons, so atoms are electrically ____________________. o Opposites Attract The (+) charge of the ____________________ attracts and holds the negatively charged ____________________ in their orbitals. • What is an element? o A chemical ____________________ is a substance that cannot be broken down into any other substance. o The ____________________ unit of a chemical element is a particle called the ____________________. ____________________ naturally occurring elements. 20 elements have been ____________________ produced in labs. ____________________ elements total to date The ____________________ of most elements link up with each other in different arrangements and combinations – these links are called ____________________ bonds. When chemicals bond they form substances called chemical ____________________. Atoms form bonds in an attempt to become more ____________________ which means they seek to have a ____________________ out shell. • • • • Ionic Bonds o One must remember that with ____________________ bonds that elements are constantly trying to make their outer shells ____________________!!! Atoms on the left side of the periodic table tend to ____________________ or ____________________ electrons. Atoms on the right side of the periodic table tend to ____________________ or ____________________ electrons o When an atom gains or loses an electron, the result is an ____________________. A ____________________ ion has gained 1 or more electrons. A ____________________ ion has lost 1 or more electrons. o The strong attraction between ____________________ ____________________ ions is called an ionic bond. • Covalent Bonds o When electrons are ____________________ between atoms a ____________________ bond is formed. o The ____________________ electrons in the covalent bond, the more strongly the 2 atoms are joined. Types: • Single bond – share ____________________ electrons • Double bond – share ____________________ electrons • Triple bond – share ____________________ electrons Not easy to ____________________. A group of atoms united by covalent bonds typically acts as a single unit called a ____________________. A ____________________ can contain from 2 to millions of atoms! Chemical formula Shorthand ____________________ to describe a chemical compound. Indicates the ____________________ that form the compound and the ____________________ in which they combine. • • • Carbon—The Backbone of Biological Molecules • Although cells are ______________________ water, the rest consists mostly of ______________________ -based compounds. • Carbon is unparalleled in its ability to form _______________, ___________________, and diverse molecules. • ______________________, ______________________, ______________________, ______________________, and other molecules that distinguish living matter are all composed of carbon compounds. • __________________ compounds range from simple molecules to colossal ones. o Most organic compounds contain ______________________ atoms in addition to ______________________ atoms • Carbon atoms can form diverse molecules by bonding to _________ other atoms. o Electron ______________________ is the key to an atom’s characteristics. o Electron configuration determines the kinds and number of ______________________ an atom will form with other atoms. • The Formation of Bonds with Carbon o With four ______________________ electrons, carbon can form four ______________________ bonds with a variety of atoms. o This _____________________ makes large, complex molecules possible. o In molecules with multiple carbons, each carbon bonded to four other atoms has a ______________________ shape. o However, when two carbon atoms are joined by a ______________________ bond, the molecule has a ______________________ shape. o The electron configuration of carbon gives it covalent compatibility with many different ______________________. o The valences of carbon and its most frequent partners (_____________________, ______________________, and ______________________) are the “building code” that governs the architecture of living molecules • Molecular Diversity Arising from Carbon Skeleton Variation o Carbon chains form the __________________ of most organic molecules. o Carbon chains vary in ___________________ and __________________. o Carbon atoms can partner with atoms other than hydrogen; for example: Carbon dioxide: ______________________ Urea: ______________________ • Hydrocarbons o Hydrocarbons are organic molecules consisting of only ______________________ and ______________________. Many organic molecules, such as ______________________, have hydrocarbon components. Hydrocarbons can undergo reactions that release a large amount of ______________________. • Functional groups are the parts of molecules involved in chemical reactions. o Distinctive properties of organic molecules depend not only on the ____________ skeleton but also on the ______________________ components attached to it. o Certain groups of ______________________ are often attached to skeletons of organic molecules. ______________ groups are the components of organic molecules that are most commonly involved in chemical ________________. The ______________________ and ______________________ of functional groups give each molecule its unique properties The four functional groups that are most important in the chemistry of life: • Hydroxyl group - _______________________________ • Carbonyl group - _______________________________ • Amino group - _________________________________ • Phosphate group - _______________________________ Glucose Saturated Fats Unsaturated Fats Hydroxyl Carbonyl Carbonyl ATP ATP Amino Chapter 2 Section 2: Water • A water molecule (_____________), is made up of three atoms --- one _________________ and two _________________. Draw water molecule: • Water is Polar o In each water molecule, the _________________ atom attracts more than its "fair share" of _________________. The oxygen end “acts” _________________ The hydrogen end “acts” _________________ • Causes the water to be _________________ Hydrogen Bonds Exist Between Water Molecules o Formed between a highly _________________________ oxygen atom of a polar molecule and a _________________________ hydrogen atom. o One hydrogen bond is _________________, but many hydrogen bonds are _________________. What are the Properties of Water? o ____________________________________________________________ o ____________________________________________________________ o ____________________________________________________________ o ____________________________________________________________ o ____________________________________________________________ • • o Cohesion _________________between particles of the ______________ substance ( why water is attracted to itself) Results in _________________ _________________ (a measure of the strength of water’s surface) Produces a surface __________________ on water that allows insects to walk on the surface of water o Adhesion Attraction between two _________________substances. Water will make _________________bonds with other surfaces such as glass, soil, plant tissues, and cotton. __________________________________-water molecules will “_________” each other along when in a thin glass tube. Example: transpiration process which _________________and trees remove water from the soil, and paper towels ____________ up water. o High Specific Heat At sea level, pure water boils at ________ °C and freezes at ______ °C. The _________________ temperature of water _________________at higher elevations (lower atmospheric pressure). For this reason, an egg will take _________________ to boil at higher altitudes Water _________________temperature change, both for heating and cooling. • To determine ____________________________, it is the amount of heat needed to raise or lower ___ g of a substance ____° C. • Water can absorb or release large amounts of heat energy with _________________ change in actual temperature. o High Heat of Vaporization Heat of vaporization is determined by the amount of _________________ to convert 1g or a substance from a liquid to a gas. In order for water to evaporate, hydrogen bonds must be _______ Water's heat of vaporization is _________________ cal/g. In order for water to evaporate, each gram must _________________ 540 calories (temperature doesn’t change --100oC). As water evaporates, it removes a lot of _________________ with it (cooling effect). Water vapor forms a kind of global ‘‘___________________” which helps to keep the Earth _________________. Heat _________________ from the sun warmed surface of the earth is absorbed and held by the _________________. o Water Density Ice is less dense as a _________________ than as a liquid (_________________ _________________ ) Liquid water has hydrogen bonds that are constantly being _________________ and _________________ . Frozen water forms a crystal-like lattice whereby molecules are set at _________________ distances. o Homeostasis Ability to maintain a _________________ state despite changing _________________ conditions Water is important to this process because: • Makes a good _________________ • _________________ temperature change • Universal _________________ • _________________ • Ice protects against temperature _________________ (insulates frozen lakes) o Solutions & Suspensions Water is usually part of a _________________ . There are two types of mixtures: • _________________ • _________________ o Solution - _________________ compounds disperse as _________________ in water Evenly _________________ _________________ - Substance that is being dissolved _________________ - Substance into which the solute dissolves o _________________ - Substances that _________________ dissolve but separate into tiny pieces. Water keeps the pieces _________________ so they don’t settle out. o Acids, Bases and pH One water molecule in 550 million naturally dissociates into a Hydrogen Ion (___ ) and a Hydroxide Ion (___ ) Water Equation: The pH Scale - Indicates the _________________ of ______ ions • Ranges from _________________ • pH of 7 is _________________ • pH 0 up to 7 is _________________ … increased _____ • pH above 7 – 14 is _________________… increased ____ • Each pH unit represents a factor of _____ change in concentration • For Example: pH 3 is 10 x 10 x 10 (__________) stronger than a pH of 6 • Acids o Strong Acids have a pH of __________ o Produce lots of _______________ • Bases o Strong Bases have a pH of _______________ o Contain lots of OH-ions and fewer ______________ • Buffers o Weak _______________or _______________ that react with strong acids or bases to prevent sharp, sudden changes in pH (______________________). o Produced naturally by the body to maintain __________________________________ Chapter 2.3: The Compounds of Life Macromolecules Monomers, meaning ___________________ units, are ___________________ molecules. Polymers, meaning ___________________ units, are assembled by combining monomers to form ___________________ molecules. Macromolecules, meaning ___________________ molecules, are ___________________ polymers. Carbohydrates Include ___________________ and ___________________ Composed of C, H, and O. Generally contain ___________________ atoms for every O atom. ___________________ term storage of ___________________ and structural components of some cells. Monosaccharides –simple sugars (one unit). ___________________ - found in milk. ___________________ – found in fruit. ___________________ – found in the cells of every organism. They are ___________________ - All have the ___________________ formula C6H12O6, but each has a slightly different ___________________ of its atoms. Disaccharides – _____ simple sugars bonded together. ___________________ – table sugar ___________________ – milk sugar ___________________ – malt sugar The above are isomers of each other. ___________________ Polysaccharides - many ___________________ bonded together. ___________________ – storage form of energy for plants. ___________________ – storage form of energy for animals. ___________________ – structural component of plant cells. ___________________ – structural component of exoskeletons and fungi. Lipids Made from C, O and H. _____________, _____________ or ____________ compounds. Long-term ___________________ of energy. Oils and fats: Composed of fatty acid chains and a glycerol backbone. Act as ___________________ and ___________________. Waxes: Different backbone than oils and fats. Act as ___________________ materials for plants and animals. Phospholipids Composed of fatty acid chains, a glycerol backbone and a phosphate group. Forms the structural basis of ______________________________. Sterols Series of carbon rings. Important role in building ___________________ and carrying ___________________ in the body. ___________________ and steroid hormones. Proteins Polymers of amino acids (________ common amino acids). Amino acids are composed of: Central carbon atom Hydrogen atom Amino group (-NH2) Carboxyl group (-COOH) An R group The R group is what makes each amino acid ___________________. Amino acids join between the amino and carboxyl groups to form a ___________________. Chain of amino acids = ___________________. Principal components of ___________________, skin and ___________________. Help chemical reactions to proceed (___________________). Pump small molecules _______________________of cells. Nucleic Acids ___________________ carrying molecules. ___________________ and ___________________ Assembled from ___________________. Nucleotides consist of: ___________________ group ___________________ base 5-C sugar either ___________________ (DNA) or ___________________ (RNA). _____ different nucleotides in both DNA and RNA. ___________________ of the nucleotides determines the ___________________ that the nucleic acid contains. ATP ___________________ energy storage in cells Composed of ___________________ Chapter 2 Section 4: Energy and Enzymes Energy for Life Processes • • • ____________________ is the ability to move or change matter. Energy exists in many forms – including ___________, __________, _________________ energy, ___________________ energy, and _________________ energy – and it can be converted from one form to another. Energy can be _________________ or _________________ by chemical reactions. Energy in Chemical Reactions • In chemical reactions, energy is absorbed or released when _________________ _________________ are broken and new ones are formed. • _________________ is the term used to describe all of the chemical reactions that occur within an organism. Activation Energy • • • The energy needed to start a chemical reaction is called ___________________________. Activation energy is simply a _______________ “____________” that starts a chemical reaction. Even in a chemical reaction that _____________ energy, activation energy must be supplied before the reaction can _______________. Enzymes • • • • __________________ are substances that ________________ the ___________ of chemical reactions Most enzymes are ________________. Enzymes are ______________, which are substances that __________ the activation energy of a chemical reaction. An _____________ increases the speed of a chemical reaction by reducing the _____________________ of the reaction. Enzyme Specificity • • A substance on which an enzyme acts during a chemical reaction is called _______________. Enzymes act only on ______________ substrates. • • An enzyme’s __________________ determines its activity. Typically an enzyme is a large ____________ with one or more deep _________ on its surface. These folds form pockets called _______________ ___________. An enzyme acts only on a specific substrate because: Step 1: Step 2: Step 3: Factors in Enzyme Activity • • • Any factor that changes the __________ of an enzyme can affect the enzyme’s _________________. _________________ and __________________ can alter an enzyme’s effectiveness. The ______________ that are active at any one time in a cell determine what happens in that cell. Chapter 1 Section 1 1. What are the three parts of the atom? What is the charge of each part? a. Part: Charge: b. Part: Charge: c. Part: Charge: 2. How are elements represented? 3. If the element carbon (C) has 6 protons, how many electrons does it have? ______ 4. Carbon 14 is an isotope. What does it mean to be an isotope? 5. What holds atoms together in compounds? 6. What are chemical formulas used for? 7. What is a covalent bond? 8. Circle true or false. The closer the electrons are to the nucleus the more energy they contain. 9. When does an atom become stable? 10. What happens to an atom that does not have a full outer electron shell? 11. What are poles? 12. What are polar molecules? 13. What type of bond holds water molecules together? ________________________ 14. Why do ions have an electrical charge? 15. How does an ion become negatively charged? 16. How does an ion become positively charged? Chapter 2 Section 2 1. What percentage of the human body is water? __________ 2. Identify how each of the following properties of water are important to organisms: a. Storage of energy: b. Cohesion: c. Adhesion: 3. Why is it important for substances within the body to dissolve in water? 4. What enables substances to dissolve in water? Chapter 2 Section 3 1. What are organic compounds? 2. What is the function of carbohydrates? 3. Where are carbohydrates found in food? 4. Explain the structure of each of the following carbohydrates and an example of each: a. Monosaccharide: b. Disaccharide: c. Polysaccharide: 5. What are the functions of each of the following four types of lipids? a. Fats b. Phosopholipids c. Steroids 6. What are the seven different sources of proteins in the body? a. . b. . c. . d. . e. . f. . 7. .How many different amino acids exist? 8. What are the building blocks of proteins? 9. What are the building blocks of nucleic acids? 10. What are the two types of nucleic acids? a. . b. . 11. What is ATP used for? Chapter 2 Section 4 1. What are 5 different forms of energy? a. . b. . c. . d. . e. . 2. What happens when bonds are broken or formed? 3. Does cold water take or give energy? 4. What are catalysts? 5. What is the function of enzymes? 6. What 2 factors affect enzyme activity? a. . b. .