Biochemistry

Goal of all Atoms The goal of all atoms is to have a stable outer energy level. This goal leads to the bonding of atoms. (Octet rule) Bonding can happen two ways. Sharing of valence electrons Transfer of valence electrons

Bonding 2 Types of Bonding Covalent bonding – when 1 or more electrons are SHARED between atoms Ex. Water (H2O) – Hydrogen and Oxygen each share 1 electron Ionic Bonding – when 1 or more electrons are TRANSFERRED between atoms Ex. Salt (NaCl) – Sodium looses an electron making it a +1 ion and Chlorine gains an electron making it a - 1 ion. Opposites attract and an ionic bond is formed

Chemical Bonds

Chemical and Structural Formulas Chemical Formula – each element is represented by its chemical symbol and the number of atoms is shown in subscripts. Ex. H2O, CO2, CH4, C6H12O6 Structural Formula – it show the chemical symbol of each element and how they are bonded to one another.

Structural Formula

Amino Acid Structural Formula

Chemical reactions Chemical change or chemical reactions – whenever different substances are formed a chemical change or reaction has occurred Reactants – substance that were present before the chemical reaction Products – the new substances produced by the chemical reaction

Make up of Biological Molecules ** The cell is a complex chemical factory containing some of the same elements found in the nonliving environment. - Carbon, hydrogen, oxygen, and nitrogen are present in the greatest percentages.  - Sulfur, phosphorus, magnesium, iodine, iron, calcium, sodium, chlorine, and potassium are found in smaller quantities in living things. ** Organisms consist of both organic and inorganic compounds.

- Elemental Properties H C O N S P Hydrogen Carbon Oxygen Nitrogen Electropositive Forms 1 covalent bond ethanol Hydrogen Carbon Oxygen Nitrogen Sulphur Phosphorus H C H O C Forms 4 covalent bonds acetic acid Strongly electronegative Forms 2 covalent bonds O C N H O Weakly electronegative Forms 3 covalent bonds N glycine Weakly electronegative Forms 2 covalent bonds H O S H N C C O H In oxidized form Forms 5 covalent bonds H P H C H O cysteine S H R -- O -- P -- O -- H - phosphate side group O

Common elements in a Cell The most common elements in a cell are: Hydrogen (H) 59% Oxygen (O) 24% Carbon (C) 11% Nitrogen (N) 4% Others such as phosphorus (P) and sulphur (S) 2% combined

2 TYPES OF COMPOUNDS Organic Molecules – is when carbon and hydrogen are bonded together (C-H bonds) - associated with living things and their products ex. carbohydrates, lipids, proteins, and nucleic acids CH4 (methane), C6H12O6 (Sugar), NH2RHC2OOH (Amino Acid) 2. Inorganic Molecules - lack carbon and hydrogen bonds --when carbon is present it is usually combined with oxygen ex. carbon dioxide, inorganic acids, salts, water, and bases CO2 (carbon dioxide), H2O2 (hydrogen peroxide), NaCl (Salt)

Compounds to Know: H2O = Water CH4 = Methane COOH = Carboxyl group (makes all organic acids organic acids) OH- = Hydroxyl group (excess concentration of these in solution makes solution a base) NH2 = Amino group (plays important role in making proteins)

Chemical Bonds (covalent and ionic) Chemical bonds hold the atoms in a molecule together. ** In general, the more chemical bonds a molecule has the more energy it contains.

Basic Organic Compounds in Living Things Major Categories of Organic Compounds carbohydrates (sugars and starches) lipid (fats, oils, and waxes) proteins (functional and structural) nucleic acids (RNA and DNA)

Nucleic Acid

Starch

Carbohydrates 1. Carbohydrates: contain the elements C,H,O -- made up of subunits called simple sugars or monosaccharides -- include a variety of sugars and starches, ex. glycogen and glucose 3 Types Monosaccarcharides Disaccarcharides Polysaccarcharides all sugar names end in -OSE 

Monosaccharides Monosaccharides: single or simple sugars all have the same basic molecular formula as glucose -- include glucose, fructose, and galactose (all isomers) isomer: compounds with the same molecular formula, but different structural formulas -- have different properties pentoses: 5 carbon sugars 2 important pentose sugars deoxyribose -- sugar in DNA ribose -- sugar in RNA

Fructose (monosaccharide)

Disaccharides double sugars -- consist of 2 monosaccharides joined by dehydration synthesis ex. (form maltose from two glucose molecules) Some disaccharide isomers include: sucrose (table sugar) maltose (seed sugar) lactose (milk sugar)

Sucrose (disaccharide)

Polysaccharides: more than two monosaccharides joined by dehydration synthesis -- include the starches and complex sugars Polysaccharide examples glycogen -- animal starch stored in the liver and muscles cellulose -- undigestible in humans -- forms cell walls starches -- used as energy storage

Raffinose (polysaccharide)

Carbohydrates Main Function - ENERGY: When carbohydrates are in our body, they are being broken down and used as energy. When the body doesn't need to use the carbohydrates for energy, it stores them into the liver and muscles and is called glycogen. When the liver and muscles cells cannot store anymore glycogen, it is turned into fat. When our body needs a quick boost of energy, it converts glycogen into energy. When it needs a prolonged burst of energy, it converts fat to energy.

Major Types of Reactions in Living Things 1. Dehydration Synthesis: chemical combination of two small molecules to make one larger molecule caused by the remove of water Dehydration – removing water + Synthesis – combining of two smaller things to make 1 larger thing 2. Hydrolysis: (digestion) -- addition of water to a larger molecule to form two or more smaller molecules -- opposite of dehydration synthesis hydro(water) + lysis(break apart) = break apart with water

Proteins -- The presence of nitrogen distinguishes proteins from carbohydrates and fats. Major Protein Functions 1. Growth and repair 2. Energy 3. Buffer -- helps keep body pH constant Amino acids -- the building blocks of proteins – there are 20 different amino acids 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.

Amino Acids 3 groups that make up amino acids 1.) An amine group -NH2 2.) A carboxyl group -COOH 3.) An R group

Peptide Bonds Peptide bond: single bond formed between two amino acids Dipeptide: two peptide bonds Polypeptide: 3 or more peptide bonds Repeated linking of amino acids results in a polypeptide(protein) being formed. A protein is usually composed of one or more polypeptide chains. (ex.) amino acid + amino acid --> dipeptide

Peptide Bond

Functions of Proteins Structural protein -components of cell structures and organelles(little organs inside cells) Functional protein -enzymes that catalyze(speed up) chemical reactions

Lipids Lipids (Fats) ex. fats, oils, waxes Function of Lipids -- lipids chiefly function in energy storage, protection, and insulation -- fats -- chiefly in animals -- oils and waxes -- chiefly in plants -- lipids along with proteins are key components of cell membranes -- made of the elements carbon, hydrogen, and oxygen -- each fat is formed from a dehydration synthesis rxn. of 3 fatty acids and a glycerol molecule 3 Fatty Acids + Glycerol ------> 1 Fat + 3 HOH

There are two types of Lipids saturated - contain no double bonds in hydrocarbon chain; carbons are "saturated" with the most hydrogen's possible unsaturaated - there are double bonds between some of the carbons in the hydrocarbon chain

Saturated Lipid

Unsaturated Lipid