Chapter 6 Notes

Biochemistry Chemistry is the study of matter, its composition and properties. Matter is anything that has mass and takes up space.

Atoms- building blocks of matter Atoms are made of three small particles called proton, electrons, and neutrons. Protons= positive + Electrons = negative – Neutrons= neutral Atoms contain an equal number of protons and electrons, therefore the overall charge of an atom is neutral.

The first energy level holds 2 electrons. 2 nd energy level holds 8 electrons. 3 rd energy level holds 18 electrons. 4 th energy level holds 32 electrons. 5 th energy level holds 18 electrons. 6 th energy level holds 1 electron.

Elements- pure substances that cannot be broken down into other substances by physical or chemical means 6.Each element has a unique name and symbol. What are the symbols for Carbon- Oxygen- Hydrogen- Nitrogen- C O H N

The elements are arranged on the periodic table by their atomic number, which is the number of protons for that element. The periodic table of elements is organized into horizontal rows, called periods, and vertical columns, called groups. Elements in the same group have similar chemical and physical properties.

Isotope- any atom of the same element that have different number of neutrons *The number of protons and electrons remain the same. Ex. Carbon-12 has 6 neutrons, most abundant Carbon-14 has 8 neutrons, radioactive, used for “carbon dating” Changing the number of neutrons can in fact affect the stability of the nucleus, sometimes causing it to decay or break apart. When this happens, the atom gives off radiation that can be detected.

Compound- pure substance formed when two or more different elements are combined There are thousands of known compounds and more are discovered each year. Ex. Water- H ₂ O Salt/Sodium chloride- NaCl Compounds have unique properties: 1.Always formed from specific combinations of elements in fixed ratios. 2.Cannot be broken down into simpler compounds or elements by physical means(tearing or breaking), but can be broken down by chemical means.

Chemical Bonds Covalent bond-form when electrons are shared between two elements Molecule- compound in which atoms are held together by covalent bonds

Ionic bond-electrical attraction between two oppositely charged atoms called ions, elements exchange electrons Metals donate electrons Nonmetals accept electrons Ion- atom that has lost or gained an electron

WaterH ₂ O Covalent bond Sharing electrons Sodium chloride NaCl Ionic bond Exchanging electrons

van der Waals forces- attractions between molecules, not elements These forces are what holds water molecules together to form droplets and water surface. Geckos use van der Waals forces to climb surfaces due to the attraction of atoms making up tiny hair like structures on their toes and atoms making up the surface they are climbing.

6.2 Chemical Reactions Chemical reaction- process where atoms or compounds are reorganized into different substances by breaking or forming chemical bonds Chemical change Ex. Rust formingFe + O ₂  Fe ₂ O ₃ The iron and oxygen change forms to make rust/iron oxide Physical change Ex. Water freezing or boiling, changes appearance but not composition *A chemical change involves a change in the composition of the substance.

Chemical formulas describe the substances in the reaction and arrows indicate the process of change. Chemical equations Reactants- starting substances, left side of arrow Products- substances formed, right side of arrow Reactants  Products Ex. Photosynthesis equation H ₂ O + CO ₂  O ₂ + C ₆ H ₁₂ O ₆ Carbon dioxide + water  Glucose + oxygen *The arrow means yields.

The law of conservation of mass states matter cannot be created nor destroyed. All chemical reactions must balance. *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. The coefficient is the number in front of the reactant or product. The subscript is the number of atoms. The coefficient times the subscript equals the total number of atoms. 6CO ₂ + 6H ₂ O  C ₆ H ₁₂ O ₆ + 6O ₂

Activation energy- minimum amount of energy needed for reactants to form products in a chemical reaction Exothermic- releases heat energy, product energy is lower than reactants Endothermic- absorbs heat energy, product energy is higher than reactants Exothermic Endothermic

Catalyst- substance that lowers the activation energy needed to start a chemical reaction. They are not used up in a reaction, but are re- used over and over again Enzyme- special proteins that are catalysts in biological chemical reactions Substrate- reactants that bind to enzymes Active site- specific location where substrate binds to enzyme Factors such as pH, temperature, and other substances affect enzyme activity.

6.3 Water and Solutions Polar molecule have unequal distribution of charges or oppositely charged poles/ends. Polarity is the property of having two opposite poles. Water is a polar compound. Hydrogen bond- weak interaction involving hydrogen and a fluorine, oxygen, or nitrogen atom.

Why is it that water and oil do not mix? Water is a polar molecule as compared to oil The answer behind this puzzle is that oil does not dissolve in water because of the way molecules of each of these substances interact with each other. Water is a polar molecule. This means this is a molecule that likes to take sides. One side of the molecule is positively charged, while the other is negatively charged. The two atoms of oxygen cling to each other with the single hydrogen atom on the other side. Oil on the other hand is made of carbon atoms bonded to hydrogen atoms forming hydrocarbon chains, this makes them non-polar. What this means is that oil molecules are attracted to each other more than water molecules. There is a particular saying in chemistry called 'Like dissolves like' which basically means polar substances will only dissolve polar substances and so is the same for non-polar substances. Size does matter Did you know that water molecules are much smaller than other molecules? So a number of water molecules have to break their hydrogen bonds to accommodate oil molecules, which is another reason why oil doesn't easily mix with water.

Mixture- combination of two or more substances in which each substance retains its individual characteristics Homogeneous mixture- uniform composition, also called a solution Solution = Solute + Solvent Solute- substance that is dissolved Solvent- substance that the solute is dissolved into Ex. Kool-Aid, salt water, saliva

Water is the universal solvent because many substances dissolve in it. Water is adhesive (sticks to surfaces) which allows it to travel up the stem of a plant. Water is cohesive (molecules stick together) which causes water to form droplets.

Heterogeneous mixture- components remain distinct Ex. salad Suspension- heterogeneous mixture in which the particles settle out over time Ex. sand and water Colloid- heterogeneous mixture where the particles do not settle Ex. Fog, milk, blood

Acids & Bases Acid-substance that releases hydrogen ions (H+) when dissolved in water Ex. Vinegar, bananas, stomach acid Base- substance that releases hydroxide ions (OH-) when dissolved in water Ex. Sodium hydroxide, baking soda, sea water

pH & Buffers The measure of concentration of hydrogen(H+) ions in a solution is called pH. Acidic solutions have pH values lower than 7. Basic solutions have pH values higher than 7. Buffers are mixtures that can react with acids or bases to keep the pH within a particular range.

6.4 Organic Chemistry The element carbon is a component of almost all biological molecules. Carbon has four electrons in its outermost energy level. One carbon atom can form four covalent bonds with other atoms. This enables carbon atoms to bond to each other which results in a variety of important organic compounds.

Macromolecule- large molecules that are formed by joining smaller organic molecules together Polymers- molecules made from repeating units of identical compounds called monomers 4 majors types: Carbohydrates Lipids Proteins Nucleic acids

Group or Macromolecule ExampleFunctionMonomerComponents Bread  Stores energy  Structural support monosaccharide Lipids  Store energy  steroids  waterproofs coatings Fatty acid andC, H Hemoglobin  transports substances  speeds reaction structural support  hormones C,N, O,H, S Nucleic acids  Stores and communicates genetic information Phosphate N-base Ribose sugar Carbohydrates Proteins C, H, O Fats, oils, waxes triglyceride Amino acids DNA, RNA, ATP nucleotides

Carbohydrate- compound composed of carbon, hydrogen, and oxygen CH ₂ O ratio- 1 carbon: 2 hydrogen: 1 oxygen Monosaccharide- simple sugars, can be linked to form larger molecules Disaccharide- two monosaccharides linked together ex. Glucose, sucrose, lactose Polysaccharide- longer chains, more than three monosaccharides linked together ex. Glycogen

Lipids- molecules mostly made carbon and hydrogen, made of fatty acids Ex. Fats, oils, and waxes The primary function of lipids is to store energy. A triglyceride is a fat if it is solid at room temperature and an oil if it is liquid at room temperature.

Saturated fats- fatty acid chain with tails made with single bonds between carbons Unsaturated fats- fatty acid chain with tails made with at least one double bond between carbons Fats with more than one double bond in the tail are called polyunsaturated fats. Phospholipids- makes up the structure of plasma membranes Lipids are hydrophobic, which means they do not dissolve in water.

Proteins- compound made of small carbon compounds called amino acids Amino acids are made of carbon, nitrogen, oxygen, hydrogen, and sometimes sulfur Amino acids have a central carbon atom. One of the four carbons bond with a hydrogen atom. The other three are with an amino group(NH ₂ ), a carboxyl group(-COOH), and a variable group(-R)

Nucleic acid- complex molecules that store and transmit genetic information Nucleic acids are made of smaller repeating subunits called nucleotides. Nucleotides are composed of three units- a phosphate group, a nitrogenous base, and a ribose sugar Two types of nucleic acids: DNA- Deoxyribonucleic acid RNA- Ribonucleic acid