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Chapter 2 Unit two nature of matter STUDENT Lecture Notes All life depends on chemistry. Chemistry begins with the atom. 100 million atoms in a line would equal1 cm. Atoms have protons, neutrons and electrons. Protons are_________________, neutrons are neutral charged and electrons have a negative charge. Electrons are in constant motion and are what allows for _________________ _________________. The loss of an electron makes the molecule positive. An unequal number of protons and electrons will cause the molecule to be an _______that has a positive (fewer electrons) or negative (more e- than p+) charge. Isomers are important to biochemistry. An isomer has the same atomic mass, and has the same number of molecules, but the arrangement is different. Glucose and Dextrose both have the same chemical formula of C6H12O6. The carbon chains are aligned differently. Draw and example: Radioactive isotopes have larger number of _________________in the nucleus. They have a different atomic mass. They decay (break down) into the same element or different element at a constant rate. Carbon has an atomic mass of 12 (6P+ and 6N). Carbon 14 has 6P and 8N. As it decays, it can be used to determine the age of organic matter. Elements combine and form compounds. The bonding of elements can either be ionic (give or take an electron) or covalent (share electrons). Most biological bonds are _________________. Water is a covalent bond and has some unique properties. It expands when frozen, rather than sink. Ice is less dense and water is polar (charged on different sides). Draw a water molecule and label the polar parts. The positive side (hydrogen) is attracted to negative molecules. The negative side (oxygen) is attracted to positive molecules. This ability to bond with both positive and negative molecules makes water a universal solvent. About 70% of our body is made of high quality H 2O. Cohesion -attraction between molecules of the same type. This is why insects can walk on water and water makes a bead when in a drop. Adhesion- attraction between molecules of different types. Water will stick to the sides of glass because of adhesion. It is the reason that we must read volume from the bottom of the meniscus. Roots from plants use both adhesion and cohesion to bring water to the top of a plant. Solution- mixture of two or more liquids or solids dissolved in liquids. Solute- Solid being dissolved. Solvent- liquid dissolving the solute. Acid pH _________________ Neutral pH _________________ Base pH _________________ The more H+ ions given off, the lower the pH. The more OH- ions given off (meaning very few H+ ions will be given off), the higher the pH. Buffers can _________________ changes in pH. Carbon Compounds. Carbon has 4 bonding sites and can either be a negative 4 charge when combing with positives in CH4. (Methane). Hydrogen is positive, so carbon is _________________. In CO2 (carbon dioxide), Oxygen is negative, so carbon is _________________. The diversity makes life possible. All protein fats and carbohydrates are carbon based. All life is carbon based. Since it has 4 bonding sites, it can create limitless shapes of covalent bonds. Large carbon chains are called macro (large) molecules. Carbohydrates The smallest unit of a carbohydrate is _________________ C6H1206. When you combine several simple sugars such as glucose, galactose and fructose, you form a carbohydrate chain. One glucose unit is called a _________________. Several monomers combined are called a _________________. Carbohydrates are called _________________ or polysaccharides. Poly = many, Saccharide = sugar. 4 calories/gram. Animals store excess sugars in their muscles as glycogen. Plants store it as starch. Cellulose is an isotope of glucose. Humans cannot digest it. It is in the cell wall of plants wood is cellulose. Lipids fatty fat fat not phat Lipids are _________________ in water. They mostly have carbon and hydrogen atoms. One saturated fat molecule has 98 hydrogen atoms, 54 carbon atoms and 6 oxygen atoms (pg46). Lipids have 9 calories per gram. 1. They store energy 2. line cells membranes are also found in steroids 3. Aid in protection of organs. . A saturated fat has all _________________bonds of hydrogen. Unsaturated fats have double bonds. As large as the fat molecules is, it is considered to be monomer. There are no polymer fats. (PG 46) sub unit = glycerol+ 3 fatty acids Saturated fats are worse for you because they are saturated with hydrogen. Saturated fats are solids at room temperature. (Bacon grease, animal fat) unsaturated fats are liquids at room temperature. NUCLIC ACIDS DNA & RNA These macromolecules contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. Each unit of this large molecule is called a _________________. The nucleotide has 3 parts. Sugar- ribose, Nitrogen Base ( A T G C ) and phosphorus. Several million nitrogen bases bonded together make up ___________. The arrangement of the adenine, guanine, cytosine and thymine determine your genetic makeup. AATGCCTACCATGGC CATGCGGTACCGTA These are two examples different individuals DNA sequence. PROTEIN – more variety than any other fat or carb. They contain H, C, O and Nitrogen. The smallest unit of protein is an_________________ _______. There are 20 different amino acids. This allows for the diversity of proteins. Hairs, nails and muscle are proteins. Yet they are very different in shape ant texture. All _________________ are also protein. Blood cells are protein. The proteins on the surface of cells are what cause organ transplants to be rejected. There are 4 buildings levels of proteins 1. Amino acid chain. 2. Twisting of that chain into a specific shape. 3. The chain is folded. 4. Combing two or more proteins. Prions are specialized proteins that enter the ____________and cause holes in it along with other tissue damage. Bovine Spongiform Encephalopathy is also called ________________________ Millions of chemical reactions takes place in your body every minute. These reactions are from building new molecules or breaking down molecules. List three examples of chemical reactions in your body. CO2 + H2O H2CO3 (carbonic acid) this is the way the blood carries CO2 to the lungs. H2CO3 CO2 + H2O the lungs release. When a chemical reaction takes place, either it requires energy or energy is _________________. Movement of muscles requires energy. When we eat food, when food is broken down, energy is released or stored as fat or glycogen. Activation Energy - Energy needed to get a reaction started Depending on the reaction, a certain amount of energy is required to begin the chemical reaction. Enzymes- proteins They are proteins that speed up chemical reactions, but are not absorbed or used up in the reaction. These types of enzymes are called catalysts. They can also reduce the amount of activation energy required for a reaction to take place From the below chemical reaction with carbonic acid, an enzyme called carbonic anhydrase speeds up that reaction by 10 million. CO2 + carbonic anhydrase + H2O H2CO3 + carbonic anhydrase Why would this be so important? Enzymes are like car keys, they only can fit into one ignition. Enzymes can only react with one other molecule. This specific enzyme must fit into or attach to another molecule. (pg. 52) The enzymes cellulase can only break down cellulose. Some people do not have the enzyme lactase, which breaks down lactose sugar in diary products. Lactase only works on Lactose. It will only break this molecule down. One enzyme, one molecule to bond to. Enzyme Substrate complex (lock and key) Each enzyme has a _________________shape that matches the molecule’s shape. This shape where the reaction will take place is called the__________________ ___________. The _________________is the molecule that will react with the enzyme. When the substrate attaches to the activation site, anew product is formed. This new product can be a larger molecule or two or more smaller molecules. You eat an egg for protein. The egg protein combines with digestive enzymes to break it down into the amino acids. These amino acids attach to enzymes that make human protein. Draw an example below THINGS THAT AFFECT ENZYMES Enzymes activity can be altered or regulated due to: 1. 2. 3. 4. Biochemistry Vocabulary Study Guide 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. Acid Activation Energy Adhesion Affect Enzyme Activity Amino Acid Base Carbohydrate Catalyst Cohesion Common Element in Living Things Covalent Bond Disaccharide DNA Electron Element Enzyme Enzyme Inhibitor Inorganic Molecule Ion Ionic Bond Lipid Lock and Key Monosaccharide Water Neutron Nucleotide Organic Molecule pH Scale Polar Molecule Polymer Polypeptide Polysaccharide Protein Proton Substrate 32_______Large polymer made from many monosaccharide 34_______Found in the nucleus of an atom, positive charge 27_______2 or more carbons in a molecule 2_______Amount of energy needed to get a chemical reaction started 31_______Many amino acids connected, forming a protein chain 5_______Building block of proteins 10_______Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus 15_______Found on the periodic table 33_______Large polymer or polypeptide made from amino acids 18_______less than two or no carbon atoms in a molecule 21_______Large Macromolecule made of glycerin and 3 fatty acids 6_______pH 8 or more 7_______Many sugar molecules, forming starch 25_______Found in the nucleus of an atom, neutral charge 28_______Measurement of hydrogen ion concentration from 1-14 35_______Molecule that the enzyme will react with 26_______Monomer of DNA, containing A,T,G, or C 22_______One enzyme will fit with only one substrate 29_______One side of molecule is more positive or negatively charged 1_______pH 6 or less 4_______Temperature, pH, amount of substrate, amount of enzyme 30_______Term used for any large molecule formed from monomers 19_______The loss or gain of an electron in an atom 24_______pH neutral 13_______Polymer found in the nucleus of the cell, made from many nucleotides 17_______Prevents a enzyme substrate complex from forming 11_______Sharing of electrons by two atoms 3_______Attraction of different type of molecules 9_______Attraction of same type of molecules 20_______When one atom gives or takes electrons from another atom 23_______Single sugar molecule 16_______Specialized protein that aids in metabolism 8_______Speeds up chemical reactions 14_______Spinning around an atom, negative charge 12_______Two sugar molecules