Biochemistry

Slide 1:Biochemistry

Slide 2:All Matter is composed of Atoms

Slide 3:The Structure of the Atom

Electrons: Negative electrical charge Protons: Positive electrical charge Neutrons: No net electrical charge

Slide 4:Molecules

Two or more atoms held together by Chemical bonds

Slide 5:Chemical Bonds

form because of the interactions between the electrons of the atoms

Slide 6:The atom�s ELECTRONEGATIVITY(ability to attract electrons)

Determines the type and strength of the Chemical bond

Slide 7:Ions

Ions are atoms that have either a positive or negative electrical charge because the electron number is NOT equal to the proton number

Slide 8:IONIC BONDS

Form between atoms when electrons are TRANSFERED from one atom to another forming ions of opposite electronic charges http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/anim/anim0904.htm

Slide 9:Covalent Bonds

Form when atoms share electrons Occur when the electronegativities between the atoms are similiar http://www.dac.neu.edu/physics/b.maheswaran/phy1121/data/ch09/anim/anim0904.htm

Slide 10:Some molecules have Single Covalent Bonds� which means the atoms share one pair (a single pair) of electrons

Slide 11:Some molecules have Double Covalent Bonds� which means the atoms share two pairs of electrons

Slide 12:Some molecules have Triple Covalent Bonds� which means the atoms share Three pairs of electrons

Slide 13:Nonpolar Covalent Bonds

Occur when the electronegativities of both atoms are identical and the electrons are shared equally

Slide 14:Polar Covalent Bonds

Occur when the electronegativities of both atoms are Different and the electrons are shared unequally Negative Pole Positive Pole

Slide 15:Hydrogen Bonds

Hydrogen bonds are weak bonds which form between molecules Hydrogen Bond

Slide 16:Bond Strengths

Ionic Bonds are weak and are easily broken in water Covalent Bonds are generally strong Hydrogen Bonds are very weak

Slide 17:The Properties of Water

1. Water is the Universal Solvent. Ionic compounds and Polar covalent molecules readily dissolve in water

Slide 18:Hydrophilic Molecules (water-loving)

Are substances that dissolve in water�. Salts, sugars, etc�.

Slide 19:Hydrophobic Molecules (water-fearing)

Are substances that do not dissolve in water� oils, waxes, etc�

Slide 20:Water Has A High Specific HeatCapacity�. The capacity of a substance to change temperature in response to a gain or loss of heat� water changes temperatures very slowly

Specific Heat - the amount of heat needed to raise 1 g of the substance 1 degree C. Why? ��� Hydrogen bonding.

Slide 21:Water Has A High Heat Of Vaporization

Heat of Vaporization: the quantity of heat a liquid must absorb for 1g of it to convert to a gaseous state.

Slide 22:Liquid Water Is Cohesive

Water sticks to water. Why? Because the polarity of water results in hydrogen bonding.

Slide 23:Liquid Water is Adhesive

Water sticks to other molecules. Why? Hydrogen bonding.

Slide 24:Water transport in trees uses Cohesion and Adhesion

Slide 25:Water Has A High Surface Tension

The surface of water is difficult to stretch or break. Why? Hydrogen bonding.

Slide 26:Water Stabilizes Temperature

Water can absorb and store a huge amount of heat from the sun. Result - climate moderation Result - organisms are able to survive temperature changes.

Evaporative Cooling

Slide 28:Result:

Water cools organisms from excessive heat buildup. Why? As water evaporates it takes the heat with it.

Slide 29:Water Expands and becomes less dense when It Freezes�.so it floats

The distance between water molecules INCREASES from the liquid to the solid form. Why? Hydrogen bonding

Water Benzene Floats Sinks

Slide 31:Result

Ice floats and forms an blanket of insulation during the winter���.Aquatic life can live under ice.

Slide 32:Water is used to make Solutions

A Solution is a Homogeneous mixture of two or more substances. Solvent + Solute Solution Sugar water, Saltwater, Pepsi

Slide 33:Solvent

The dissolving agent Present in a greater proportion Examples: Water Methane

Slide 34:Solute

The substance that is dissolved. Present in smaller quantity Examples: Salt in saltwater Sugar in sugar water

Slide 35:Solution Concentration

Usually based on Molarity Molarity - the number of moles of solute per liter of solution. A mole is = 6.021x1023

Slide 36:One Mole of each

Sulfur Sugar Copper Sulfate Mercury Oxide Copper Sodium Chloride

Slide 37:Dissociation of Water

Water can sometimes split into two ions. In pure water the concentration of each ion is 10-7 M

Slide 38:Adding certain solutes disrupts the balance between the two ions. The two ions are very reactive and can drastically affect a cell.

Slide 39:Acids

Materials that can release H+ Example: HCl HCl H+ + Cl- Hydrochloric acid, vinegar, etc�

Slide 40:Effects of Acid Rain

Slide 41:Bases

Materials that can absorb H+ Often reduce H+ by producing OH- Example: NaOH NaOH Na+ + OH- Drano, Soaps, etc��.

Slide 42:pH Scale

A logarithmic scale for showing H+ concentration in a solution. pH = - log [H+]

Slide 43:pH Scale

Acids: pH < 7 Neutral: pH 7 Bases: pH >7

Slide 44:Acids: pH <7 etc. Bases: pH >7 etc. Each pH unit is a 10x change in H+

Slide 45:Buffers

Materials that have both acid and base properties. Resist pH shifts. Cells and other biological solutions often contain buffers to prevent damage.

Slide 46:Organic Molecules

Contain carbon atoms, exceptions are carbon monoxide and carbon dioxide Carbon has 4 electrons available to form 4 chemical bonds�.therefore large molecules are easily formed using carbon as the backbone. Large carbon based molecules are usually found as long chains or rings.

Slide 47:Macromolecules

Most macromolecules are �polymers� �.molecules that consist of a single unit (monomer) repeated many times.

Slide 48:Functional Groups

Many organic molecules share similar properties because they have similar clusters of atoms, called the�.. Function Groups Each Functional Group gives the molecules a particular property, such as acidity or polarity.

Slide 49:Functional Groups

Slide 50:Four Main Types Of Macromolecules

Carbohydrates Lipids Protein Nucleic acids

Slide 51:Carbohydrates

Used for fuel, building materials, and receptors. Made of C,H,O General formula is CH2O C:O ratio is 1:1

Slide 52:Types Of Carbohydrates

Monosaccharides Disaccharides Polysaccharides

Slide 53:Monosaccharides

Mono - single Saccharide - sugar Simple sugars. Can be in linear or ring forms. Glucose, Fructose, Galactose�. all with the chemical formula C6H12O6�.. Same chemical formula, different shapes.

Slide 54:Most words ending with the letters OSE are carbohydrates. Glucose, Fructose, Galactose

Slide 55:Disaccharides

Sugar formed by joining two monosaccharides together thru the process of Dehydration Synthesis�.(removing water)�aka�. Condensation Synthesis. all with the chemical formula C12H22O11 glucose + fructose = sucrose (table sugar) + H2O glucose + galactose = lactose ( the sugar in milk) + H2O glucose + glucose = maltose + H2O

Slide 56:Condensation Synthesis or Dehydration Synthesis

The chemical reaction that joins monomers into polymers. Covalent bonds are formed by the removal of a water molecule between the monomers.

Slide 57:Hydrolysis

Reverse of condensation synthesis. Using water (Hydro), to split (Lysis) Breaks polymers into monomers by adding water

Slide 60:Examples of Disaccharides produced through Dehydration Synthesis

Maltose = glucose + glucose Lactose = glucose + galactose Sucrose = glucose + fructose

Slide 61:Polysaccharidesall with the chemical formula (CH2O)n

Many joined simple sugars. Used for storage or structure. Examples: Starch - a polymer of a-glucose molecules, principle energy storage molecules in plants Glycogen - a polymer of a-glucose molecules, principle energy storage molecules in animals, stored in the liver and muscles cells Cellulose - a polymer of b-glucose molecules, principle structural molecules in plant cell walls�. Major component of wood Chitin - a polymer of b-glucose molecules, each modified with a nitrogen group, principle structural molecule in the cell walls of fungi and the exoskeletons of the arthropods.

Slide 64:Lipids (Fats)

Diverse hydrophobic molecules which are insoluble in water (and other polar molecules) and soluble in non-polar molecules like ether and chloroform Made of C,H,O No general formula. C:O ratio is very high in C

Slide 65:Types of Lipids (Fats)

Triglycerides Phospholipids Steroids

Slide 66: Triglycerides

Three fatty acids joined to one glycerol. Joined by an �ester� linkage between the -COOH of the fatty acid and the -OH of the alcohol. Differ in which fatty acids are used. Used for energy storage, cushions for organs, insulation.

Acid Fat

Slide 68:Fats and Oils

Fats - solid at room temperature. Oils - liquid at room temperature. Saturated - solid at room temperature. Unsaturated - liquid at room temperature.

Slide 69:Saturated Fats

Saturated - no double bonds.

Slide 70:Unsaturated Fats

Unsaturated - one or more C=C bonds. Can accept more Hydrogens. Double bonds cause �kinks� in the molecule�s shape.

Slide 72:Question ?

Which has more energy, a kg of fat or a kg of starch? �. (Hint) in Fats there are more C-H bonds which provide more energy per mass. Answer� carbohydrates (starch) have 4 calories per gram, lipids have 9 calories per gram

Slide 73:Phospholipids

Similar to fats, but have only two fatty acids. The third -OH of the glycerol is joined to a phosphate group replacing a fatty acid Major component of the Plasma Membrane of all cells

Slide 74:Result

Phospholipids are amphipathic which means they have a nonpolar, hydrophobic tail, but a polar, hydrophilic head. Self-assembles into bilayers, an important part of cell membranes.

Slide 76:Steroids

Characterized by a backbone of four fused carbon rings. Differ in the functional groups attached to the rings. Examples: cholesterol sex hormones

Slide 77:Proteins

Made of C,H,O,N, and sometimes S. No general formula Polymers of amino acids

Slide 78:Uses Of Proteins

Structural Proteins: used to make skin, hair, muscles, etc� Enzymes: Control Metabolism Antibodies: Provide protection against foreign substances Transport Proteins: Transport molecules across membranes Storage: such as ovalbumin in eggs

Slide 79:Proteins

Proteins are Polypeptide chains of Amino Acids linked by peptide bonds.

Slide 80:Amino Acids

All have a Carbon with four attachments: -COOH (acid) -NH2 (amine) -R group 20 different kinds of amino acids because there are 20 different kinds of R groups Amino Group Carboxyl Group AKA: Acid Group

Slide 81:Amino Acids

Slide 82:Amino Acids

Slide 83:R groups

The properties of the R groups determine the properties of the protein.

Slide 84:Polypeptide Chains

Formed by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the second Amino Acid.

Slide 86:Levels Of Protein Structure

Organizing the polypeptide into its 3-D functional shape. Primary Secondary Tertiary Quaternary

Slide 87:Primary Structure

Order of amino acids in the polypeptide chain. Many different sequences are possible with 20 AAs.

Slide 88:Secondary Structure

3-D structure formed by hydrogen bonding between the R groups. Two main secondary structures: - a helix - pleated sheets

Slide 89:Tertiary

3D shape as bonding occurs between the R groups. Examples: Hydrophobic interactions Ionic bonding Disulfide bridges Hydrogen Bonding

Slide 90:Quaternary

When two or more polypeptides unite to form a functional protein. Example: hemoglobin

Slide 91:Is Protein Structure Important?

Slide 92:Denaturing Of A Protein

Events that cause a protein to lose structure (and function). Example: pH shifts high salt concentrations heat

Slide 94:Nucleic Acids

Stores the genetic Information Polymers of nucleotides Made of C,H,O,N and P No general formula Examples: DNA and RNA

Slide 95:Nucleotides of DNA and RNA

Nucleotides have three parts: Nitrogenous Base Pentose sugar (Deoxyribose in DNA and Ribose in RNA) Phosphate Group

Slide 96:Nitrogenous Bases

Rings of C and N Two types: Pyrimidines (single ring) Thymine, Cytosine Purines (double rings) Adenine, Guanine

Slide 97:Pentose Sugar

5-C sugar Ribose - RNA Deoxyribose � DNA

Slide 99:DNA: Deoxyribonucleic Acid

Double Helix Structure The two strands of DNA are antiparallel, oriented in opposite directions� one strand is arranged in the 3� � 5� direction while the other is arranged in the 5� � 3� direction (5� means the phosphate group is attached to the 5th carbon on the Deoxyribose molecule. Makes up genes.

Slide 100:RNA: Ribonucleic Acid

Important molecule in protein synthesis. Genetic information for a few viruses only.

Slide 101:Differences between DNA and RNA

RNA is a single strand DNA has Deoxyribose, RNA has ribose Thymine is replaced by Uracil

Slide 102:Chemical Reactions in Metabolic Processes

In order for chemical reactions to occur, the reacting molecules must first collide and then have enough energy (Activation energy) to trigger the formation of new bonds. Some reactions require catalysts. Catalysts are molecules which trigger or accelerate chemical reactions without being chemically altered themselves.

Slide 103:Metabolism

Chemical reactions which occur within living organisms are called Metabolic reactions�.. Two types of Metabolic Reactions: *Anabolic Reactions: Build molecules and store energy *Catabolic Reactions: Breakdown Molecules and release energy

Slide 104:Chemical Equilibrium

The net direction of metabolic reactions, forward or reverse, is determined by the concentration of the reactants and the products.

Slide 105:Enzymes: Globular proteins which catalyze metabolic reactions.

Enzyme: Catalyzes the Reaction Substrate: molecule acted upon Products: Resulting molecules Enzyme + Substrate Enzyme � Substrate Complex Enzyme + Products Maltase + Maltose Maltase + Maltose Complex Maltase + glucose + glucose Active Site

Slide 106:Enzymes

Most Enzymes end with the letters - ASE Enzymes are substrate specific�.. Examples: Maltase can only breakdown Maltose Sucrase can only breakdown Sucrose Amylase can only breakdown Amylose

Slide 107:Enzymes

The efficiency of Enzymes is affected by: pH shifts: pepsinogen is only activated when stomach acids lower the pH Heat: denatures enzymes

Slide 108:Cofactors

Are nonprotein molecules that assist enzymes� since they are nonproteins they are used up in the reactions. A holoenzyme is the union of a cofactor and enzyme. The enzyme is called an Apoenzyme when it�s part of a holoenzyme

Slide 109:Inorganic Cofactors

Are usually metals, like Iron (Fe+2), Magnesium (Mg+2)

Slide 110:CoEnzymes

Are organic molecules which aid in enzyme reactions��. Some vitamins are coenzymes. Since they are nonproteins they are also used up in the reactions.

Slide 111:ATPAdenosine TriPhosphate

Source of Activation energy for Metabolic Reactions

Slide 112:Allosteric Enzymes

Have two types of binding sites�. One for the substrate and one for the allosteric effector. Two types of Allosteric Effectors: 1. Allosteric Activator � binds to the enzyme and changes its shape to induces a reaction 2. Allosteric Inhibitor � binds to the enzyme and induces inactivity

Slide 113:Allosteric Enzymes

Slide 114:Competitive Inhibition

Is when an enzyme mimic occupies the active site preventing a reaction.

Slide 115:Noncompetitor Inhibitor

Prevents enzyme reactions by binding to the substrate at locations other than the active or allosteric site.

Slide 116:Cooperativity

Occurs when an enzyme becomes receptive to additional substrate molecules after one substrate molecule attaches to an active site. Example: Hemoglobin�� its binding capacity to additional oxygen molecules increases after the first oxygen fills the active site.

Slide 117:Cooperativity