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Biochemistry Biochemistry Main Idea 1 The basic unit of matter is the atom. An element is a pure substance made of only one kind of atom. Atoms of an element that have different numbers of neutrons are called isotopes. ATOM- Building block of matter PROTON: (+) In nucleus; NEUTRON: (0) In nucleus ELECTRON: (-) In orbitals around nucleus How do we know? Early humans easily distinguished between materials that were used for making clothes, tools, or foods. They developed words to describe them. Empedocles (492 BCE) –One of 1st theories that attempted to describe things around us. He argued that all matter was composed of 4 elements: fire, air, water, & earth. But--Using the example of stone, which was commonly used for making tools, there is a problem with this explanation. No matter how many times you break a stone in 1/2 , the pieces never resemble fire, air, water, or earth. This theory was an important development in scientific thinking because it was among the 1st to suggest that some substances that looked pure, like stone, were actually made up of a combination of different "elements." Democritus (460 BCE) knew that if you took a stone and cut it in ½, each ½ had the same properties as the original. If you continued to cut the stone into smaller & smaller pieces, at some point you would reach a piece so tiny that it could no longer be divided. Democritus called these infinitesimally small pieces atoms. Democritus reasoned that each material’s atoms were unique to that material. Torricelli (1643) showed that air had weight & was capable of pushing down on a column of liquid mercury (thus inventing the barometer). This was a startling finding. If air this substance that we could not see, feel, or smell - had weight, it must be made of something physical. Bernoulli, a mathematician, proposed an answer. He developed a theory that air & other gases consist of tiny particles that are too small to be seen, & are loosely packed in an empty volume of space. The particles could not be felt because, unlike a solid stone wall that does not move, the tiny particles move aside when a human hand or body moves through them. Priestly experimented with red mercury calx in 1773. Mercury calx, a red solid stone, was coveted because when it is heated, it appears to turn into mercury, a silver liquid metal. Priestley had observed that it does not just turn into mercury, it actually breaks down into two substances: liquid mercury & a strange gas. Priestley carefully collected this gas in glass jars & studied it. He burned a candle in this gas and noted it had a remarkably vigorous flame. Also, a mouse placed in a sealed container of the gas lived for a longer period of time than a mouse placed in a sealed container of ordinary air. Priestley’s discovery revealed that substances could combine together or break apart to form new substances with different properties. Lavoisier (1778) experimented with dephlogisticated air (the air from Priestly’s earlier experiments) & theorized that the gas made some substances acidic. He renamed Priestley’s gas oxygen, from the Greek words that loosely translate as "acid maker". Lavoisier named hydrogen from the Greek words for "water maker“ because when hydrogen is mixed with oxygen water is formed. Lavoisier also burned other substances such as phosphorus & sulfur in air, & showed that they combined with air to make new materials. These new materials weighed more than the original substances, & Lavoisier showed that the weight gained by the new materials was lost from the air in which the substances were burned. From these observations, Lavoisier established the Law of Conservation of Mass, which says that mass is not lost or gained during a chemical reaction. Scientific experiments showed that some substances could combine with others to form new materials; other substances could be broken apart to form simpler ones; and a few key “elements” could not be broken down any further. John Dalton, a teacher & scientist, put together the pieces and developed the first modern atomic theory in 1803. Through his observations of morning fog and other weather patterns, Dalton realized that water could exist as a gas that mixed with air and occupied the same space as air. Solids could not occupy the same space as each other; for example, ice could not mix with air. So what could allow water to sometimes behave as a solid and sometimes as a gas? Dalton realized that all matter must be composed of tiny particles. In the gas state, those particles floated freely around and could mix with other gases, as Bernoulli had proposed. But Dalton extended this idea to apply to all matter – gases, solids and liquids. Dalton first proposed part of his atomic theory in 1803 and later refined these concepts in his classic 1808 paper A New System of Chemical Philosophy. ELEMENT- Substance that cannot be broken down into a simpler substance by ordinary chemical means Most abundant in life: Carbon (C) Hydrogen (H) Oxygen (O) Nitrogen (N) CARBON HYDROGEN IN PLASMA STATE LIQUID OXYGEN LIQUID NITROGEN Biochemistry video 1 goes here. Atoms are neutral. The outer shell of electrons = Valence Electrons Biochemistry video 2 goes here. An ionic bond forms when an electron from one atom “jumps” to another atom. COVALENT BOND- Atoms held together by sharing electrons Bonding sites: Carbon (4) Hydrogen (1) Oxygen (2) Nitrogen (3) *see formula sheets Hydrogen bond- Chemical bond in which a hydrogen atom is attracted to another atom. Here are some hydrogen bond examples: •Water molecules. When one molecule of water attracts another the two can bond together; adding more molecules results in more and more water sticking together. This bond is responsible for the crystal structure of ice, which allows it to float. •Human DNA. The hydrogen bonding that occurs between base pairs in a strand of DNA results in DNA’s familiar double helix shape. This hydrogen bond actually enables the replication of DNA strands. Oxygen Atom has 8 protons & 8 electrons Hydrogen Atom has 1 proton & 1 electron The Water Molecule: Polar Bond, Covalent Bond, Hydrogen Bond Biochemistry video 3 goes here. https://www.youtube.com/watch?v=_M9khs87xQ8 Biochemistry video 4 goes here. http://www.vevo.com/watch/right-saidfred/Im-Too-Sexy/GBBRL9290469 Biochemistry Main Idea 2 Carbon atoms have the ability to form millions of different large and complex compounds. Four groups of organic compounds found in living things are carbohydrates, lipids, nucleic acids, and proteins. COMPOUND- Chemical combination of two or more elements in definite proportions ORGANIC COMPOUND: Contain carbon with bonded hydrogen Types: Carbohydrates Lipids (Fats) Proteins Nucleic acids (DNA & RNA) *will look at in Genetics *not now* Nutrients Packet CARBOHYDRATES- The energy compounds (-ose) Sugars: Simple carb’s Glucose Fructose Starches: Complex carb’s Cellulose (plants) Glycogen (animals) LIPIDS (FATS)- The storage compounds PROTEINS- The growth compounds Contain nitrogen (N) and sometimes sulfur (S) AMINO ACIDS- Building blocks of protein * see diagrams Lab 9 Pattern Matching: Organic Molecules Black Blue Red White Lab 10 Organic Molecule Construction H O N C 1 2 3 4----Covalent Bonding Sites 1 Bonding Site 4 bonding sites #7: C2H6 Lab 11 Identifying Organic Compounds Organic Elements: Oxygen Nitrogen Hydrogen Carbon Organic Molecules: Carbohydrates Lipids Proteins Nucleic Acids Building Blocks: Monosaccharides Glycerol & Fatty Acids Amino Acids Foods: Organic Molecules are held together by chemical bonds. Hydrogen Bond- has hydrogen Covalent Bond- has shared electrons Ionic Bond- electrons move from one atom to another and form ions Polar Bond- has an uneven distribution of electrons Water has the following bonds: Hydrogen Covalent Polar Water is cohesive- attracted to itself adhesive- attracted to other things Substances made of water demonstrate capillary action because of water’s adhesive quality. They move through narrow areas against gravity. The pH scale is based on water’s ability to form multiple bonds. Lab 12 Using an Acid-Base Indicator pH: Potential of Hydrogen- measures the concentration of H+ ions in solution. The pH scale goes from 0-14. 7 is neutral. Fluids in organisms each have varying pHs’. Enzymes (special proteins) in organisms need certain pHs’ to work. If the pH is wrong, the enzyme will denature (change shape) and fail to work. If the pH of a substance is high---adding a weak acid will bring the pH closer to neutral. If the pH of a substance is low---adding a weak base will bring the pH closer to neutral. A weak acid or base can act as a buffer to help maintain homeostasis in a living organism. Biochemistry Main Idea 3 Nutrients provide activation energy necessary for chemical reactions that drive life processes. Cells use enzymes to speed up chemical reactions. Enzymes lower the activation energy needed to get a reaction started. Enzymes may be affected by pH value, temperature, and enzyme concentration. Enzymes are Proteins that Lower Activation Energy Needed to get a Reaction Started ENZYMESChange the rate of reactions in living things (-ase) SUBSTRATE- Substance that enzyme acts on SUBSTRATE ENZYME Lactose………………………………………………………………..Lactase Maltose……………………………………………………………….Maltase Proteins……………………………………………………………….Protease ENZYMES-SUBSTRATE COMPLEX- Lock - &- Key Model Lock & Key Model of Enzyme Action FACTORS INFLUENCING ENZYME ACTION pH Temperature (Concentration)Amount of Enzyme (Concentration) Amount of Substrate F Concentration Rate Of Enzyme Action Chemical Reactions Energy Releasing Reaction Energy Absorbing Reaction https://www.youtube.com/watch?v=XTUm-75-PL4 Biochemistry video 5 goes here. Biochemistry video 6 goes here. https://www.youtube.com/watch?v=ok9esggz N18 Lab 13: Enzyme- Catalase