Biochemistry PDF

BIOCHEMISTRY CHEMISTRY OF LIFE Elements: simplest form of a substance - cannot be broken down any further without changing what it is Atom: the actual basic unit - composed of protons, neutrons, and electrons THE ATOM Just like cells are the basic unit of life,...

BIOCHEMISTRY CHEMISTRY OF LIFE Elements: simplest form of a substance - cannot be broken down any further without changing what it is Atom: the actual basic unit - composed of protons, neutrons, and electrons 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 -  Electrons are not present within the atom, instead THEY REVOLVE AROUND THE NUCELUS OF THE ATOM & FORM THE ELECTRON CLOUD Draw a helium atom. Indicate where the protons, neutrons and electrons are. NEUTRONS PROTONS - ATOMIC # = 2 (PROTONS) + + ELECTRONS - ATOMIC MASS = 4 (PROTONS & NEUTRONS) ISOTOPES atoms of the same element that HAVE A DIFFERENT NUMBER OF NEUTRONS Some isotopes are radioactive. This means that their nuclei is unstable and will break down at a CONSTANT RATE over time. There are several practical uses for radioactive isotopes: 1. CARBON DATING 2. TRACERS 3. KILL BACTERIA / CANCER CELLS 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 (H2O), Carbon Dioxide (CO2) 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) 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. 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 C2H6O 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. 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 14 0 – 5 strong acid 6-7 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  And now for the Biochemistry 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) Monosaccharides (simple sugars) all have the formula C6 H12 O6 all have a single ring structure – (glucose is an example) Disaccharides (double sugars) all have the formula C12 H22 O11 sucrose (table sugar) is an example 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  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 – (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O Polysaccharides are formed from repeated dehydration syntheses of water – They are the stored extra sugars known as starch Hydrolysis Addition of WATER to a compound to SPLIT it into smaller subunits – (also called chemical digestion) – ex. disaccharide + H2O ---> monosaccharide + monosaccharide C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6 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  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 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 ANY GROUP OF ATOMS – THIS CHANGES THE PROPERTIES OF THE PROTEIN! FUNCTIONAL GROUPS There are certain groups of atoms that are frequently attached to the organic molecules we will be studying, and these are called functional groups. These are things like hydroxyl groups which form alcohols, carbonyl groups which form aldehydes or ketones, carboxyl groups which form carboxylic acids, and amino groups which form amines. Major Protein Functions Growth and repair Energy Buffer -- helps keep body pH constant Dipeptide formed from two amino acid subunits Formed by the process of Dehydration Synthesis amino acid + amino acid ----- dipeptide + water Hydrolysis of a dipeptide Breaking down of a dipeptide into amino acids dipeptide + H2O ---> aminoacid + amino acid 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 composed of NUCLEOTIDES store & transmit heredity/genetic information Nucleotides consist of 3 parts: 1. 5-Carbon Sugar 2. Phosphate Group 3. Nitrogenous Base 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.  In a reaction, energy is either TAKEN IN (ENDOTHERMIC) or GIVEN OFF (EXOTHERMIC) Can you think of an everyday example of each type of reaction? 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 enzymes lower the energy needed to start a chemical reaction. (activation energy) begin to be destroyed above 45øC. (above this temperature all proteins begin to be destroyed) It is thought that, in order for an enzyme to affect the rate of a reaction, the following events must take place. 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. While the enzyme-substrate complex is formed, enzyme action takes place. 4. Upon completion of the reaction, the enzyme and product(s) separate. The enzyme molecule is now available to form additional complexes. 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 Factors Influencing Rate of Enzyme Action 1. pH - the optimum (best) in most living things is close to 7 (neutral) high or low pH levels usually slow enzyme activity A few enzymes (such as gastric protease) work best at a pH of about 2.0 2. Temperature - strongly influences enzyme activity optimum temperature for maximum enzyme function is usually about 35-40 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) 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.