the basics of chemistry for biology atoms: the units of elements bonding: covalent vs. ionic water:...

The Basics of Chemistry for Biology Atoms: The units of elements Bonding: Covalent vs. Ionic Water: Waters unique properties

The Chemistry of Life Matter (anything that takes up space) Composed of atoms Atom Smallest unit of an element that has the properties of the element 2 regions Nucleus Electron cloud

Inside the Atom: Subatomic Particles Protons: positive charged particles found in the nucleus (p + ) Neutrons: neutral particles found in the nucleus (n) Electrons: negative particles found in the electron cloud (e - ) Move around the nucleus in energy levels

Energy Levels of the Electron Cloud The number of electrons on each level is given by the formula 2n 2 where n is the level number Number/Name# of e - it can hold 1-K2 2-L8 3-M18 4-N32 5-O50 6-P72 7-Q98

Info from the Periodic Table Symbol Atomic Number (Z) = Number of p + Mass Number (A) = p + + n

Nuclides A Z X Copper Oxygen

Practice Set Symbol/Na me Atomic Number Atomic Mass NuclideProtonsNeutronsElectrons O Oxygen Au Gold Na Sodium K Potassium Cl Chlorine F Fluorine Ca Calcium

Lets Draw an Atom 1.Write the nuclide. 2.Draw the Energy levels. 3.Write the number of protons and neutrons in the nucleus. 4.Place the correct number of electrons on each energy level. 5.Leave unused energy levels empty.

Practice Drawing

Ions For a neutral atom, protons = electrons Ion: an atom with more or fewer electrons than it should normally have, causing a charge Loss of electrons forms a positive ion Cation Gain of electrons forms a negative ion Anion

Isotopes Isotopes: atoms of the same element with different masses due to different # of neutrons radioactive isotopes: unstable nuclei breakdown over time (nuclear decay)

Summary Chart Subatomic particle number to be changed How changedAtom is now a __ of the original atom Electron Gained Lost Anion (negative ion) Cation (positive ion) NeutronGained or LostIsotope

Bonding and Compounds Compound: two or more atoms bonded together due to electron exchange (give & take) or electron sharing

Metals Metals are found mainly in columns I to III They give away electrons to bond This forms positive ions: cations

Non-metals Non-metals are found mainly in columns III to VIII They can take in electrons from a metal to bond and form negative ions: anions They can share electrons with another non- metal and form molecules

Ionic Bonding Ionic Bonding: involves the giving of electrons by metals and the taking of electrons by non-metals Examples Sodium chloride Calcium chloride Sodium oxide Forms IONS

Ionic bonding

Covalent Bonding Covalent Bonding: the sharing of electrons between two non-metals Carbon dioxide Methane Nitrogen dioxide Diphosphorus pentoxide Forms MOLECULES

Covalent Bonding

Polarity Polar: electrons are not shared equally between the two non-metals in a covalent bond Non-polar: electrons are shared equally between the two non-metals in a covalent bond

Polar covalent bond

Polar/nonpolar bonds

van der Waals forces: forces of attraction between molecules Weak forces van der Waals forces

van der Waals interactions Weak interactions between molecules or parts of molecules that are brought about by localized change fluctuations Due to the fact that electrons are constantly in motion and at any given instant, ever-changing hot spots of negative or positive charge may develop

Hydrogen bonds Hydrogen atom covalently bonded to one atom is also attracted to another atom (oxygen or nitrogen) on another molecule Strong Water is best example

Cohesion Cohesion: attraction of molecules of the same substance to each other Example water molecules to other molecules in a glass

Waters Properties Polar~ opposite ends, opposite charges Cohesion~ H+ bonds holding molecules together (same substance, water to water) Adhesion~ H+ bonds holding molecules to another substance Surface tension~ measurement of the difficulty to break or stretch the surface of a liquid Specific heat~ amount of heat absorbed or lost to change temperature by 1 o C Heat of vaporization~ quantity of heat required to convert 1g from liquid to gas states Density.

Density Less dense as solid than liquid 1.Due to hydrogen bonding 2.Crystalline lattice keeps molecules at a distance

Mixtures Combination of 2 or more elements physically but not CHEMICALLY (not bonded together)

Wet Mixtures Soution zAll components are distributed evenly zParts 1.Solute: is dissolved 2.Solvent: does the dissolving Example: Kool-aid dissolved in water Suspension zComponents are distributed unevenly, just mixed together zParts 1.Supernant: liquid 2.Precipitate: solid Example: snowglobe

Acid/Base & pH Dissociation (breaking apart) of water into a hydrogen ion and a hydroxide ion Acid: increases the hydrogen concentration of a solution Base: reduces the hydrogen ion concentration of a solution pH: power of hydrogen Buffers: weak acids or bases that react with strong acids or bases to prevent changes in pH

pH Scale Acid Neutral Base 0 1 2 3 4 5 6 7 8 9 10 1112 13 14 Stronger WeakerWeakerStronger Human body prefers pH of 6.5 to 7.5

Acids vs. Bases Acid Acidic More H + than OH - Tastes sour Turns litmus paper red Found in coffee, tea, soft drinks, and fruit juices Base Alkaline More OH - than H + Tastes bitter Turns litmus paper blue Found in cleaners and soaps

Neutralization When Acids and Bases are mixed chemically, they produce salt and water. This reaction is called neutralization because the end products are not acidic nor alkaline, they are neutral!

2006-2007 The Chemistry of Life What are living creatures made of? Why do we have to eat?

96% of living organisms is made of: carbon (C) oxygen (O) hydrogen (H) nitrogen (N) Elements of Life

Molecules of Life Put C, H, O, N together in different ways to build living organisms What are bodies made of? carbohydrates sugars & starches proteins fats (lipids) nucleic acids DNA, RNA

Why do we eat? We eat to take in more of these chemicals Food for building materials to make more of us (cells) for growth for repair Food to make energy calories to make ATP ATP

What do we need to eat? Foods to give you more building blocks & more energy for building & running bodies carbohydrates proteins fats nucleic acids vitamins minerals, salts water

Water 65% of your body is H 2 O water is inorganic doesn t contain carbon Rest of you is made of carbon molecules organic molecules carbohydrates proteins fats nucleic acids Don t forget water

2006-2007 How do we make these molecules? We build them! How do we make these molecules? We build them!

How to take large molecules apart Digestion taking big molecules apart getting raw materials for synthesis & growth making energy (ATP) for synthesis, growth & everyday functions + ATP

Example of digestion starchglucose ATP Starch is digested to glucose

Building large molecules of life Chain together smaller molecules building block molecules = monomers Big molecules built from little molecules polymers

Small molecules = building blocks Bond them together = polymers Building large organic molecules

Building important polymers sugar sugar sugar sugar sugar sugar nucleotide nucleotide nucleotide nucleotide Carbohydrates = built from sugars Proteins = built from amino acids Nucleic acids (DNA) = built from nucleotides amino acid amino acid amino acid amino acid amino acid amino acid

How to build large molecules Synthesis building bigger molecules from smaller molecules building cells & bodies repair growth reproduction + ATP

How to take large molecules apart Digestion taking big molecules apart getting raw materials for synthesis & growth making energy (ATP) for synthesis, growth & everyday functions + ATP

Example of digestion starchglucose ATP Starch is digested to glucose

Example of synthesis amino acidsprotein amino acids = building block protein = polymer Proteins are synthesized by bonding amino acids

Old Food Pyramid

New Food Pyramid

The Chemistry of Life

Carbon, the Backbone Carbon is special in the world of elements because it is able to bond to 4 other atoms at the same time!

Carbon, the Backbone Since Carbon can form so many bonds, it is considered the backbone of many compounds, that is Carbon is what the other atoms are all attached to

Special Covalent Bonds 1.Single bond: one pair of electrons is shared between two atoms 2.Double bond: two pair of electrons are shared between two atoms 3.Triple bond: three pair of electrons are shared between two atoms

Who can do these special cases? C, N, O, and S can all form double bonds. Only C and N can form triple bonds!

Carbons Shapes When Carbon bonds to other Carbon atoms, the resulting bond can take one of the following shapes: 1.Straight chain (in a straight line) 2.Branched chains (like the straight chain, but with a fork in the road 3.Ring structures

Carbohydrates Biochemical molecules that are used as both sources of energy and as short term energy storage commonly called sugars and starches

Glucose C 6 H 12 O 6

Carbohydrates, I Monosaccharides CH 2 O formula; simple sugars multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldoses) ketone (ketoses) raw material for amino acids and fatty acids

Carbohydrates, II Disaccharides glycosidic linkage (covalent bond) between 2 monosaccharides; covalent bond by dehydration reaction Sucrose (table sugar) most common disaccharide

Carbohydrates, III Polysaccharides (Storage) Starch~ glucose monomers Plants: plastids Animals: glycogen Polysaccharides (Structural) Cellulose ~ most abundant organic compound; Chitin ~ exoskeletons; cell walls of fungi; surgical thread

Monomers and Polymers -mer: building blocks Monomer: one building block Polymer: many building blocks

Proteins Importance: instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known Monomer: amino acids (there are 20) ~ carboxyl (-COOH) group, amino group (NH 2 ), H atom, variable group (R). Variable group characteristics: polar (hydrophilic), nonpolar (hydrophobic), acid or base Three-dimensional shape (conformation) Polypeptides (dehydration reaction): peptide bonds~ covalent bond; carboxyl group to amino group (polar)

Primary Structure Conformation: Linear structure Molecular Biology: each type of protein has a unique primary structure of amino acids Ex: lysozyme Amino acid substitution: hemoglobin; sickle-cell anemia

Secondary Structure Conformation: coils & folds (hydrogen bonds) Alpha Helix:coiling; keratin Pleated Sheet: parallel; silk

Tertiary Structure Conformation: irregular contortions from R group bonding hydrophobic disulfide bridges hydrogen bonds ionic bonds

Quaternary Structure Conformation: 2 or more polypeptide chains aggregated into 1 macromolecule collagen (connective tissue) hemoglobin

Lipids No polymers; glycerol and fatty acid Fats, phospholipids, steroids Hydrophobic; H bonds in water exclude fats Carboxyl group = fatty acid Non-polar C-H bonds in fatty acid tails Ester linkage: 3 fatty acids to 1 glycerol (dehydration formation) Triacyglycerol (triglyceride) Saturated vs. unsaturated fats; single vs. double bonds

Lipids, II

Phospholipids 2 fatty acids instead of 3 (phosphate group) Tails hydrophobic (water fearing); heads hydrophilic (water loving) Micelle (phospholipid droplet in water) Bilayer (double layer); cell membranes

Steroids Lipids with 4 fused carbon rings Ex: cholesterol: cell membranes; precursor for other steroids (sex hormones); atherosclerosis

Nucleic Acids, I Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA->RNA->protein Polymers of nucleotides (polynucleotide): nitrogenous base pentose sugar phosphate group Nitrogenous bases: pyrimidines~cytosine, thymine, uracil purines~adenine, guanine

Nucleic Acids, II Pentoses: ribose (RNA) deoxyribose (DNA) nucleoside (base + sugar) Polynucleotide: phosphodiester linkages (covalent); phosphate + sugar

Nucleic Acids, III Inheritance based on DNA replication Double helix (Watson & Crick - 1953) H bonds~ between paired bases van der Waals~ between stacked bases A to T; C to G pairing Complementary

Give the complimentary DNA strand: AGTCTGCAAGTCTGCA

Give the complimentary RNA strand: AGTCTGCAAGTCTGCA

Biochemical Type CarbohydratesLipidsProteins Nucleic Acids MonomersMonosaccharides Sugars Fatty acids and glycerol Amino acidsnucleotides PolymersPolysaccharides Starches NONEPolypeptides, aka proteins polynucleotide Forces holding together Glycosidic linkagesEster linkages Peptide bondsBonds and van der Waals phosphodiester linkages UsesEnergy storage and structural support Energy storage, hormones, membranes Structural building materials Genetic information transfer

Biochemical Test CarbohydratesLipidsProteins Nucleic Acids Biuret's Reagent Blue turns violet in proteins, and pink with short-chain polypeptides proteins polypeptides Benedicts Solution Simple sugars heated with Benedicts turns from blue to red IodineStarches turn dark purple or black Brown Bag Test/ Sudan III stain Leaves spot on brown bag/ turns fats red

Conformation Test Lab

Lab Information In the laboratory investigation you will perform known tests using known reagents in order to obtain positive results for comparison with an unknown. Be sure to follow your lab directions exactly!

IDENTIFYING MACROMOLECULES IN FOOD LAB

Introduction Carbohydrates, proteins, and fats are all essential nutrients. We cannot manufacture these nutrients so we must obtain them from our environment.

Introduction In this lab, with the use of indicators as chemical detection tools, you will analyze a variety of foods for the presence of nutrients. Detection is based upon observing a chemical change that takes place most often a change in color.

Objective Identify the presence of major nutrients such as simple carbohydrates (glucose), complex carbohydrates (starch), protein and fat in common foods.

What is an indicator? Indicators are chemical compounds used to detect the presence of other compounds.

Background Information INDICATORMACRO- MOLECULE NEGATIVE TEST POSITIVE TEST Benedicts solution simple carbohydrate blueorange IKI solutioncomplex carbohydrate dark redblack Biuret solution proteinblueviolet, black Sudan IVlipiddark redreddish- orange

What is a Standard? An acknowledged measure of comparison for quantitative or qualitative value; a criterion.

Test for Simple Carbohydrates Benedict s solution Benedict's solution is a chemical indicator for simple sugars such as glucose: C 6 H 12 O 6. Aqua blue: negative test; yellow/green/brick red, etc.: positive test

Test for Simple Carbohydrates Benedict s solution Unlike some other indicators, Benedict s solution does not work at room temperature - it must be heated first.

Test for Complex Carbohydrates IKI solution IKI solution (Iodine Potassium Iodine) color change = blue to black

Test for Complex Carbohydrates IKI solution Iodine solution is an indicator for a molecule called starch. Starch is a huge molecule made up of hundreds of simple sugar molecules (such as glucose) connected to each other.

Test for Protein (amino acids) Biuret solution Biuret solution dark violet blue to pinkish purple

Test for Fats (lipids) Sudan IV Like lipids, the chemical Sudan IV is not soluble in water; it is, however, soluble in lipids. In this test dark red Sudan IV is added to a solution along with ethanol to dissolve any possible lipids.

Test for Fats (lipids) Sudan IV If lipids are present the Sudan IV will stain them reddish-orange (positive test).

Question Why didn t the test tube containing sucrose change colors?

Question Why didn t the test tube containing starch change colors?

Procedure Simple carbohydrate 1.Add 5ml distilled H 2 O using pipette to test tube 2.Add 1ml of food sample to test tube 3.Add 20 drops of Benedict solution 4.Place test tube in a hot water bath for 10 minutes.

Procedure Complex carbohydrate 1.Add 5ml distilled H 2 O using pipette to test tube 2.Add 1ml of food sample to test tube 3.Add 20 drops of IKI solution

Procedure Protein (amino acids) 1.Add 5ml distilled H 2 O using pipette to test tube 2.Add 1ml of food sample to test tube 3.Add 20 drops of Biuret solution

Procedure Fats (lipids) Add 5ml distilled H 2 O using pipette to test tube Add 1ml of food sample to test tube Add 20 drops of Sudan IV

LAB SAFETY and CLEAN UP WEAR safety goggles and apron at all times THOROUGHLY CLEAN lab area and equipment NO EDIBLE products in lab

Enzymes

Enzymes & Their Function

Reactions (Chemical Changes) Bonds are made or broken Energy is used or released Starting material: Reactant Ending material: Product

Enzymes Catalytic proteins: change the rate of reactions w/o being consumed Free E of activation (activation E): the E required to break bonds Substrate: enzyme reactant Active site: pocket or groove on enzyme that binds to substrate Induced fit model

Enzymes Learning objective: to examine what enzymes are and describe how they work.

Enzymes What are they? Why do we need them? Name some examples ?

Enzymes Globular proteins that catalyse chemical reactions in living organisms Properties

Enzymes Properties Specific

Enzymes Properties Specific Increase rate of the reaction

Enzymes Properties Specific Increase rate of the reaction Unchanged at the end of the reaction

Enzymes Globular proteins that catalyse chemical reactions in living organisms Properties Specific Increase rate of the reaction Unchanged at the end of the reaction Need them

Enzymes Globular proteins that catalyse chemical reactions in living organisms Properties Specific Increase rate of the reaction Unchanged at the end of the reaction Need them Reactions too slow to maintain life Cant increase temperatures/pressure in cells (fatal)

Enzymes Are Proteins The enzyme binds to the substrates by its active site The active site is a pocket formed by the folding of the protein where the substrates bind.

Active site The active site involves a small number of key residues that actually bind the substrates The rest of the protein structure is needed to maintain these residues in position

How do enzymes work?

An Example

Sucrose + H 2 O Glucose + Fructose

An Example Sucrose + H 2 O Glucose + Fructose Substrates Products

For a reaction to occur the sucrose and water would have to collide with enough energy to break and form bonds

For a reaction to occur the sucrose and water would have to collide with enough energy to break and form bonds This is the activation energy

Sucrose + H 2 OGlucose + Fructose + + SubstratesProducts

Energy Progress of reaction

Energy Progress of reaction Substrates

Energy Progress of reaction Substrates Products

Energy Progress of reaction Substrates Products High energy intermediate

Energy Progress of reaction Substrates Products High energy intermediate Activation energy

The minimum amount of energy needed to start the reaction, leading to the formation of a high energy intermediate = The Activation energy

Energy Progress of reaction Substrates Products High energy intermediate Activation energy Enzymes reduce the height of the energy barrier

Activation Energy In a natural reaction the product has a lower energy than the substrate so equilibrium will take it in the direction of the product. However there is an energy barrier to be overcome Enzymes lower the activation energy required to bring about a reaction. Ex. catalase reduces the activation energy for the reduction of H 2 0 2 86-fold

Enzyme Action What are the different models for enzyme action and which factors which control the rate of an enzyme reaction?

Lock and Key

However certain substances can bind to the enzyme at sites other than the Active site and modify its activity (inhibitors/co-factors) Idea that the enzyme is flexible

E S E S E PP

Induced Fit

How do enzymes work? Reaction Mechanism In any chemical reaction a substrate is converted into a product. In an enzyme catalysed reaction the substrate first binds to the active site of the enzyme to form the enzyme-substrate complex

Molecule Geometry Substrate molecule fits into the enzyme like a lock & key. Enzyme shape distorts or it changes other factors to make the reaction happen

Enzyme reactions enzyme + substrate enzyme-substrate complex

Enzyme reactions enzyme + substrateenzyme-substrate complex E +S ES Synthesis reaction since you are forming ONE product

Synthesis Reaction Active site es

Synthesis reaction Glucose-1-phosphate Starch

Enzyme reactions enzyme + product enzyme-substrate complex E +PES enzyme + substrateenzyme-substrate complex E +S ES Decomposition reaction since you are breaking down one thing into parts

Degradation reactions animation

Degradation reactions Starch Maltose

Catalase The enzyme catalase breaks down the waste substance hydrogen peroxide into water and oxygen. Hydrogen peroxide oxygen + water (enzyme) catalase (substrate) (products)

Degradation reaction SubstrateEnzymeProduct Hydrogen peroxide CatalaseOxygen and water StarchAmylaseMaltose MaltaseGlucose ProteinPepsinPeptides ProteaseAmino acids FatsLipaseFatty Acids and Glycerol

Enzyme activity How fast an enzyme is working Rate of Reaction

Enzyme activity How fast an enzyme is working Rate of Reaction Rate of Reaction = Amount of substrate changed (or amount product formed) in a given period of time.

Rate of Reaction Enzyme activity Variable you are looking at

Enzyme activity Four Variables

Enzyme activity Four Variables Temperature pH Enzyme Concentration Substrate Concentration

Effects on Enzyme Activity Temperature pH Cofactors: inorganic, nonprotein helpers; ex.: zinc, iron, copper Coenzymes: organic helpers; ex.: vitamins

Reaction rate factors Substrate concentration Initially rate increases with substrate concentration

Enzyme activity Temperature and pH affect the activity of an enzyme.

Rate of Reaction Temperature

Rate of Reaction Temperature 0203050104060

Rate of Reaction Temperature 0203050104060 40 o C - denatures 5- 40 o C Increase in Activity

the basics of chemistry for biology atoms: the units of elements bonding: covalent vs. ionic water:...

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