Biochemistry The Chemistry of Life

Basic Chemistry Atom Simplest unit of matter Made up of three different “subatomic” particles

Subatomic Particles Protons Neutrons Electrons Have a positive charge (+) Have mass Located in nucleus Neutrons Are neutral, have no charge (0) Electrons Have a negative charge (-) Almost no mass Located in “energy levels” outside of nucleus

# Protons (+) = # Electrons (-) Atomic Number: Tells you the number of protons an atom has, and also the # of electrons Atoms are neutral # Protons (+) = # Electrons (-)

Atomic Mass: Add together the number of protons and neutrons in nucleus of atom Electrons hardly contribute any mass

Isotopes: Atoms of one type of element with different atomic masses Same # of protons Different # neutrons Changes the mass only, the properties are the same

Radioactive Isotopes: The nucleus of some isotopes is unstable The atom with emit radiation Radiation can be measured with tools ex. Geiger counter These isotopes can be used as useful tools in science Ex: Carbon-14 dating Radiation treatment for cancer

Elements Substance made of only one type of atom Each element has a unique atomic # Elements most commonly found in living things Carbon (C) Hydrogen (H) Oxygen (O) Nitrogen (N)

Compounds Two or more elements chemically combined Atoms held together by bonds. Once bonds form, compounds will have new, and different properties

Organic Compounds Inorganic Compounds Contains carbon and hydrogen (and often O, N) Ex: Glucose (C6H12O6), carbohydrate, lipids, proteins Inorganic Compounds Doesn’t contain carbon and hydrogen together Ex: H2O, CO2, NH3, NaCl

Why do atoms form compounds? Bonds that form between atoms give atoms a stable outer electron level. Called a “stable octet” of valence electrons (8)

Types of Chemical Bonds Ionic Bonds: One or more electrons are transferred from one atom to another. Neutral atoms become positive & negative ions Forms salts (Ex: NaCl) Ionic bond = attraction between (+) and (-) ions

Covalent Bonds: Electrons are shared between atoms Each bond represents a shared pair of electrons Can form single, double or even triple bonds

Covalent bonds form molecules Subscripts in the formula tell # of each atom Ex: H2O, NH3, CO2, CH4

Ionic Bonds: Transfer electrons Covalent Bonds: Share Electrons

Properties of Water Water is necessary for life Contains covalent bonds

Water Molecules: H2O (look like Mickey Mouse)

Water is a “Polar” molecule (like a magnet) The bonds are “polar” Oxygen attracts the electrons more than Hydrogen

Hydrogen Bonding: bonding between the (+) H of one molecule and the (-) end of another molecule. Makes water good at sticking to itself and other substances Makes water good dissolver

Cohesion: water sticks to itself Ex: Water forms “beads” on smooth surface Surface Tension allows insect to “skate”

Adhesion: water sticks to other substances Ex: Capillary action: water molecules rise up small tubes

Heat Capacity: Water has a relatively high heat capacity Ex: Lakes and oceans can absorb a lot of heat from sun without a drastic temperature change

Water as a Solvent: Dissolves most ionic and covalent substances “Universal Solvent” = many things can dissolve in it.

Solute: substance being dissolved Solvent: substance in which solute dissolves Solution: evenly disbursed mixture Suspensions: material in the water but just suspended not dissolved (ex: blood cells in blood)

pH of Solutions pH Scale: way to measure concentration of H+ ions in solution Ranges from 0 to 14 Pure water is neutral pH = 7

Litmus Paper: Used to test pH of a solution Red = acidic Blue = basic

Acids: Form H+ ions pH is <7 Ex: HCl (stomach acid), lemon juice

Bases: Produces OH- (hydroxide ions) Also called “alkaline” pH >7 Ex: Lye (NaOH) used as drain cleaner

Buffers: Maintain pH at a certain level Usually between 6.5 – 7.5 (close to neutral) Helps to maintain homeostasis in organism

Major Types of Chemical Reactions Dehydration Synthesis: (Condensation) Chemically combine two smaller molecules Water is removed “Dehydrate” = remove water “Synthesis” = to make

Hydrolysis: Break apart large molecule into smaller pieces Water is added “Hydro” = water “Lysis” = to break

Polymerization: Create a large molecule (polymer) Join up smaller “monomer” units Often a dehydration synthesis reaction Ex: Join amino acids (monomer) to make protein (polymer) Join glucose (monosaccharide) to make starch (polysaccharide)

Organic Compounds

Carbohydrates Sugars and starches FUNCTION: Used as an energy source Energy released during cellular respiration Made of carbon, hydrogen and oxygen Ex: C6H12O6, C12H22O11 Ratio of H of O is always 2:1

Basic Structure: “Ring” made of 5 carbons and 1 oxygen Rings can join up by dehydration synthesis

3 Types of Carbohydrates Monosaccharide's: 1 sugar ring Disaccharides: 2 sugar rings Polysaccharides: many sugar rings

Monosaccharide's: (Simple sugars) All have formula C6H12O6 Single ring structure End in “-ose” Ex: glucose, fructose, galactose

Disaccharides: double sugars All have formula C12H22O11 End in “-ose” Ex: sucrose, lactose, maltose

Polysaccharides: 3 or more sugar units Ex: Starch (energy storage in plants) Glycogen (how animals store sugar in liver) Cellulose (plant cell walls) Chitin (insect exoskeletons)

Combining molecules by removing water Simple sugars form into complex sugars by dehydration synthesis (condensation). Combining molecules by removing water Monosac. + Monosac.  Disac. + Water C6H12O6 + C6H12O6  C12H22O11 + H2O

and H2O

Complex sugars are broken down into simple sugars by hydrolysis. Breaking down molecules by adding water Also called chemical digestion Disac.+ Water  Monosac. + Monosac. C12H22O11 + H2O  C6H12O6 + C6H12O6

Dehydration Synthesis and Hydrolysis are OPPOSITE Reactions

**Chemical reactions are often enzyme mediated.

Lipids Fats, oils and waxes FUNCTION: Long term energy storage Insulation Protective coating around cells Cell membranes Made of carbon, hydrogen, and oxygen Ratio of H to O is not 2:1 Ex: C15H26O6 (fewer oxygens)

Animals store energy mostly as fats Plants store energy mostly as oils

Lipids Made up of: 1 glycerol molecule 3 long fatty acid chains Looks like a giant letter “E” Also called a “triglyceride”

GLYCEROL FATTY ACID CHAIN Note: 3 “OH” groups Note: CARBOXYL GROUP: “COOH” group at end of molecule

Basic Lipid Structure

Lipids are: formed by dehydration synthesis broken down by hydrolysis

Saturated vs. Unsaturated Fats all single bonds between carbon atoms Unsaturated: One or more double bonds between carbon atoms Makes fatty acid more bent

Proteins Protein Structure: Made of carbon, hydrogen, oxygen and NITROGEN Large complex polymer molecules that can have a large range of sizes, shapes and properties

Proteins FUNCTIONS: Enzymes: speed up chemical reactions Hormones: chemical messengers Antibodies: defend against disease Hemoglobin: binds oxygen to red blood cells Cell growth and repair Cell Membrane Channels

Amino Acid: basic building block of proteins

Parts of an Amino Acid Carboxylic Acid Group Amino Group “R”-Group (varies depending on amino acid)

Examples of Different Amino Acids There are 20 different amino acids All have different “R” groups

Peptide Bond: bond between amino acids Dipeptide: two amino acids joined. Polypeptide: many amino acids joined Proteins are polypeptides

Forming a Peptide Bond

and H2O

+ H2O

Amino acids join up to form proteins at ribosome The function of the protein comes from it’s specific sequence of amino acids and the shape the protein forms The “code” for the specific sequence of amino acids comes from DNA

Nucleic Acids Large complex macromolecule Stores information in “code” Composed of carbon, hydrogen, oxygen, nitrogen and phosphorus

Structure of Nucleic Acids: Made of chains of nucleotides Nucleotide: (made of 3 components) Phosphate Group Sugar Nitrogenous Base

Two Types of Nucleic Acids DNA: (Deoxyribonucleic Acid) Contain genetic information Found in nucleus Divides when cell divides RNA: (Ribonucleic Acid) Copies code from DNA Takes code to ribosomes for protein synthesis Found in nucleus and cytoplasm

Differences Between DNA & RNA Double strand of nucleotides Sugar is deoxyribose Nitrogenous Bases Adenine, Thymine, Cytosine, Guanine RNA: Single strand of nucleotides Sugar is ribose Nitrogenous bases Adenine, Uracil, Cytosine, Guanine