BIOCHEMISTRY 10/9/17 CHEMISTRY OF LIFE. Elements: simplest form of a substance - cannot be broken down any further without changing what it is

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1 BIOCHEMISTRY CHEMISTRY OF LIFE Elements: simplest form of a substance - cannot be broken down any further without changing what it is THE ATOM Just like cells are the basic unit of life, the ATOM is the basic unit of matter. They are very small. If placed side by side one million would stretch a distance of 1cm. The atom is made up of 3 particles. Particle Charge PROTON + NEUTRON NEUTRAL ELECTRON - 1

2 COMPOUNDS a substance formed by the chemical combination of 2 or more elements in definite proportions Ex: water, salt, glucose, carbon dioxide The cell is a COMPLEX CHEMICAL FACTORY containing some of the same elements found in the nonliving environment. Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatest percentages TWO TYPES OF COMPOUNDS Organic - Contain C, H, and O in some ratio (usually referred to as chemicals of life) Carbohydrates, Proteins, Lipids, Nucleic Acids Inorganic - usually "support" life - no specific ratio of C, H, and O Water (H 2 O), Carbon Dioxide (CO 2 ) 2

3 CHEMICAL BONDS Chemical bonds hold the atoms in a molecule together. There are 2 types of chemical bonds IONIC and COVALENT IONIC BONDS Occur when 1 or more electrons are TRANSFERRED from one atom to another. When an atom loses an electron it is a POSITIVE charge. When an atom gains an electron it is a NEGATIVE charge These newly charged atoms are now called IONS Example: NaCl (SALT) 3

4 COVALENT BONDS Occur when electrons are SHARED by atoms. These new structures that result from covalent bonds are called MOLECULES ** In general, the more chemical bonds a molecule has the more energy it contains SHARING IS CARING! MIXTURES Water is not always pure. It is often found as part of a mixture. A mixture is a material composed of TWO OR MORE ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXED Ex: salt & pepper mixed, sugar and sand can be easily separated SOLUTION Two parts: SOLUTE SUBSTANCE THAT IS BEING DISSOLVED (SUGAR / SALT) SOLVENT - the substance in which the solute dissolves Materials that do not dissolve are known as SUSPENSIONS. Blood is the most common example of a suspension. Cells & other particles remain in suspension. 4

5 FORMULA The chemical symbols and numbers that compose a compound ("recipe") Structural Formula Line drawings of the compound that shows the elements in proportion and how they are bonded Molecular Formula the ACTUAL formula for a compound C 2 H 6 O ACIDS & BASES Acids: always (almost) begin with "H" because of the excess of H+ ions (hydrogen) Ex: lemon juice (6), stomach acid (1.5), acid rain (4.5), normal rain (6) Facts about Acids Acids turn litmus paper BLUE and usually taste SOUR. You eat acids daily (coffee, vinegar, soda, spicy foods, etc ) ACIDS & BASES Bases: always (almost) end with -OH because of the excess of hydroxide ions (Oxygen & Hydrogen) EX: oven cleaner, bleach, ammonia, sea water, blood, pure water Facts about Bases Bases turn litmus BLUE. Bases usually feel SLIPPERY to touch and taste BITTER. 5

6 Neutralization Reactions When an acid reacts with a base to produce a salt and water. ph SCALE measures degree of substance alkalinity or acidity Ranges from 0 to strong acid 7 neutral 8-14 strong base The goal of the body is to maintain HOMEOSTASIS (neutrality) to do this when ph is concerned, we add weak acids & bases to prevent sharp changes in ph. These are called BUFFERS 6

7 And now for the BIOCHEMISTYR portion of things. CARBOHYDRATES Living things use carbohydrates as a key source of ENERGY! Plants use carbohydrates for structure CELLULOSE include sugars and complex carbohydrates (starches) contain the elements carbon, hydrogen, and oxygen (the hydrogen is in a 2:1 ratio to oxygen) 7

8 Monosaccharides (simple sugars) Have the formula C 6 H 12 O 6 Have a single ring structure (glucose is an example) Disaccharides (double sugars) all have the formula C 12 H 22 O 11 sucrose (table sugar) is an example What is Missing? Water (H 2 O) Where did it go? The formation between two things results in a loss of water in a process called dehydration synthesis. 8

9 Polysaccharides Formed of three or more simple sugar units Glycogen - animal starch stored in liver & muscles Cellulose - indigestible in humans - forms cell walls Starches - used as energy storage 9

10 How are complex carbohydrates formed and broken down? Dehydration Synthesis Combining simple molecules to form a more complex one with the removal of water ex. monosaccharide + monosaccharide ----> disaccharide + water (C 6 H 12 O 6 + C 6 H 12 O > C 12 H 22 O 11 + H 2 O Polysaccharides are formed from repeated dehydration syntheses of water They are the stored extra sugars known as starch 10

11 Hydrolysis Addition of WATER to a compound to SPLIT it into smaller subunits (also called chemical digestion) ex. disaccharide + H 2 O ---> monosaccharide + monosaccharide C 12 H 22 O 11 + H 2 O ---> C 6 H 12 O 6 + C 6 H 12 O 6 Lipids (Fats) Fats, oils, waxes, steroids Chiefly function in energy storage, protection, and insulation Contain carbon, hydrogen, and oxygen but the H:O is not in a 2:1 ratio Tend to be large molecules -- an example of a neutral lipid is below 11

12 Neutral lipids are formed from the union of one glycerol molecule and 3 fatty acids 3 fatty acids + glycerol ----> neutral fat (lipid) Fats -- found chiefly in animals Oils and waxes -- found chiefly in plants Oils are liquid at room temperature, waxes are solids Lipids along with proteins are key components of cell membranes Steroids are special lipids used to build many reproductive hormones and cholesterol Dehydration Synthesis Again Saturated vs Unsaturated Fats Saturated fats DO NOT have any double bonds between the carbon molecules in the fatty acid chains. Because of this, the chains can pack tight and these will be solids at room temperature. An example is butter. 12

13 Saturated vs Unsaturated Fats Unsaturated fats have double bonds between the carbon molecules in the fatty acid chains. Because of this, the chains are loosely packed and these will be liquids at room temperature. An example is olive oil. PROTEINS Contain the elements carbon, hydrogen, oxygen, and nitrogen Composed of MANY amino acid subunits It is the arrangement of the amino acid that forms the primary structure of proteins. The basic amino acid form has a carboxyl group on one end, a methyl group that only has one hydrogen in the middle, and a amino group on the other end. Attached to the methyl group is a R group. AN R GROUP IS WHAT DIFFERENTIATES ONE AMINO ACID FROM ANOTHER. THERE ARE 20 AMINO ACIDS. SOME ARE HYDROPHOBIC, HYDROPHILIC AND OTHERS ARE CHARGED 13

14 Proteins form just like lipids and carbs. They are composed of smaller subunits, in this case called amino acids, and form by dehydration synthesis. Major Protein Functions Growth and repair Energy Enzymes and hormones Buffer -- helps keep body ph constant 14

15 Dipeptide Formed from two amino acid subunits Formed by the process of Dehydration Synthesis amino acid + amino acid dipeptide + water Peptide Bond This is a special bond found between the last carbon of one amino acid and the first nitrogen of the next amino acid. Hydrolysis of a Dipeptide Breaking down of a dipeptide into amino acids Dipeptide + H 2 O ---> amino acid + amino acid 15

16 Polypeptide (protein) Composed of three or more amino acids linked by synthesis reactions Examples of proteins include insulin, hemoglobin, and enzymes. ** There are an extremely large number of different proteins. The bases for variability include differences in the number, kinds and sequences of amino acids in the proteins NUCLEIC ACIDS In all cells, aka DNA and RNA Composed of NUCLEOTIDES Store & transmit heredity/genetic information Nucleotides consist of 3 parts: 1. 5-Carbon Sugar 2. Phosphate Group 3. Nitrogenous Base Nucleotide 16

17 Nucleotides in DNA Just like amino acids, there are several different nucleotides. They are different in only the nitrogenous base. Adenine Thymine Cytosine Guanine 17

18 DNA (Deoxyribonucleic Acid) Contains the genetic code of instructions that direct a cell's behavior through the synthesis of proteins Found in the chromosomes of the nucleus (and a few other organelles) RNA (Ribonucleic Acid) Directs cellular protein synthesis Found in ribosomes & nucleoli CHEMICAL REACTIONS A process that changes one set of chemicals into another set of chemicals REACTANTS elements or compounds that enter into a chemical reaction PRODUCTS elements or compounds that are produced in a chemical reaction Chemical reactions always involve the breaking of bonds in reactants and the formation of new bonds in products. 18

19 Enzymes and Enzyme Action Catalyst: inorganic or organic substance which speeds up the rate of a chemical reaction without entering the reaction itself Enzymes: organic catalysts made of protein Most enzyme names end in -ase Begin to be destroyed above 45 degrees C. (Above this temperature all proteins begin to be destroyed) The protein is said to be DENATURED. How do enzymes work? Substrate: molecules upon which an enzyme acts The enzyme is shaped so that it can only lock up with a specific substrate molecule enzyme substrate > product "Lock and Key Theory" Each enzyme is specific for one and ONLY one substrate (one lock - one key) This theory has many weaknesses, but it explains some basic things about enzyme function. 19

20 1. The enzyme must form a temporary association with the substance or substances whose reaction rate it affects. These substances are known as substrates. 2. The association between enzyme and substrate is thought to form a close physical association between the molecules and is called the enzyme-substrate complex. 3. Upon completion of the reaction, the enzyme and product(s) separate. The enzyme molecule is now available to form additional complexes. Factors Influencing Rate of Enzyme Action 1. ph - the optimum (best) in most living things is close to 7 (neutral) 2. High or low ph levels usually slow enzyme activity A few enzymes (such as gastric protease) work best at a ph of about Temperature - strongly influences enzyme activity Optimum temperature for maximum enzyme function is usually about C. Reactions proceed slowly below optimal temperatures Above 45 C most enzymes are denatured (change in their shape so the enzyme active site no longer fits with the substrate and the enzyme can't function) 20

21 3. Concentrations of Enzyme and Substrate ** When there is a fixed amount of enzyme and an excess of substrate molecules -- the rate of reaction will increase to a point and then level off. 21

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