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Biochemistryhttp://www.youtube.com/watch?v=tpBAmzQ_pUE

Atoms, Ions, MoleculesLiving things consist of atoms of different elementsEverything is made of very small particlesAtoms: smallest basic unit of matterMillions of atoms could fit in the period at the end of a sentence

Atoms and ElementsAtoms consist of three smaller particlesProtons: positive chargeNeutrons: no chargeElectrons: negative chargeProtons and Neutrons make up the atomic nucleusElectrons surround this dense center

An atom has an equal number of protons and neutronsElement: one particular type of atom that cannot be broken down into simpler substances by ordinary chemical meansExamples of elements: hydrogen, oxygen, aluminum, goldAtoms of different elements have a different amount of protons

Electrons in atoms determine its propertiesElectrons move around the nucleus in energy levelsAtoms are most stable when they have a full outermost energy levelThere are about 91 elements that naturally occur on earth25 are found in organisms96 percent of human mass is made of 4 elementscarbon: Coxygen: ONitrogen: NHydrogen: HThe other 4 percent are trace elements: very small amounts but are necessary for survival

CompoundsSubstance made of atoms of different elements bonded together in a certain rationExamples: carbon dioxide: CO2, Water: H2OA compounds properties are often different from the properties of the elements that make up the compoundExample: Oxygen and Hydrogen are both gases. When combined they make water.

Determine if the following are elements or compounds:1.Carbon ______________2.Carbon Dioxide ______________3.Water ______________4.H ______________5.CO3 ______________6.SiO ______________7.O ______________8.Ca ______________IonsIons form when atoms gain or loose electronsIon: atom that has gained or lost one or more electionsGain or loss of electrons results in a full outermost energy levelAn atom becomes an ion when it gains electrical chargeIons have certain properties: because of the chargeExample: compounds consisting of only ions ionic compounds- easily dissolve in waterSome ions can be positive or negatively chargedIons usually form when electrons are transferred from one atom to anotherIonic bond: forms through the electrical force between oppositely charged ionsIonic Bonds

Covalent BondsNot all atoms easily gain or loose electronsSome share pairs of electronsCovalent bonds: form when atoms share a pair of electronsVery strong bonds

Molecule: two or more atoms held together by covalent bonds Almost all substances that make up organisms (lipids to nucleic acids to water) are held together by covalent bondsProperties of Waterhttp://www.youtube.com/watch?v=aVmU3CLxvgU

Hydrogen Bonds in WaterWater exists as a solid, liquid, and gasLess dense as a solid than a liquidWater is polarPolar molecules have a region that is slightly positive and a region that is slightly negative

Opposite charges interact to form hydrogen bondsHydrogen bonds: attraction between a slightly positive hydrogen atom and a slightly negative atom (often nitrogen or oxygen)Part of DNA

Properties of Hydrogen BondsMuch weaker then covalent bonds3 important propertiesHigh Specific Heat: water resists change in temperatureCohesion: attraction amount molecules of a substance, provides surface tensionAdhesion: attraction among molecules of different substances

Compounds dissolve in waterMany substances in the body dissolve in waterSolutions: mixture of substances that is the same throughout (homogenous mixture)Solutions are made of 2 partsSolvent: substance that is present in greater amount and dissolves another substanceSolute: substance that dissolves in a solventEXAMPLE: water and sugarWater: SolventSugar: Solute

Amount of solute dissolved in a certain amount of solvent is a solutions concentrationBlood Plasma is where many molecules dissolve: such as protein and sugarPolar molecules dissolve in water because the attraction between the water molecules and the solute molecules are greater than the attraction among the molecules of the soluteNonpolar substances (fats and oils) do not dissolve in waterthey lack a charged region and are not attracted to polar molecules

Compounds can form Acids and Basesacid: compound that releases a proton when it dissolves (H+ increases)base: compounds that remove H+ from a solutiona solutions acidity is measured on the pH scale

pH: measures a solutions acidity on a scale of 1-1414: Basic0: Acidic7: Neutral

Examples:

Stomach acid: pH 2Water: pH 7Blood: pH 7.4Bile: pH 8-9

Different organisms need different pH for survivalBuffers regulate pH in organismsBuffer: compound that can bind to an H+ ion when H+ concentration decreases

Carbon Based MoleculesInorganic vs Organic CompoundsInorganic: contain any of Earths elements but rarely contain carbon and hydrogen together. Organic: all organic compounds contain the elements carbon and hydrogen always!Label the Following as organic or inorganic:Water (H2O) ____________Methane (CH4) ______________Carbon Dioxide (CO2) ______________Salts (NaCl)_____________Sugar (C6H12O6) _____________Ozone (O3)_________________

Carbon Atoms have unique bonding propertiesCarbon is often called the building block of lifeEach carbon atom has four unpaired electrons in its outer energy levelCarbon atoms can form up to four covalent bonds with four other atoms

Carbon has three structuresStraight chainsBranched chainsRing chains

Many carbon based molecules are subunits of an entire moleculeMonomer: each subunit in the complete moleculePolymer: large molecule (macromolecule) made of many monomers bonded together

1. CarbohydratesMolecules composed of carbon, hydrogen, and oxygen, and they include sugar and starchesCan be broken down to provide a useable source of chemical energy for cellsMajor part of plant cell structure

Basic sugar formula = C6H12O6Carbon to Hydrogen ratio is always 1:2

Monosaccharides: most basic carbohydrates (Building Blocks!!)Fructose: 6-carbon sugar in fruitsGlucose: 6-carbon sugar made during photosynthesis (C6H12O6)

Disaccharide: two sugars bonded together(2 monosaccharides)Examples: Maltose and Sucrose

Polysaccharides: many glucose molecules bonded together(3 or more monosaccharaides)Examples: starches, glycogen, and celluloseStarches: stored by plantsGlycogen: stored by animalsCellulose: straight rigid structure (makes up cell wall)

What are carbohydrates used for?ENERGY!

How do monomers become polymers?Building PolymersDehydration synthesis atoms that make up water (H2O) are removed from the small molecules to bring them together

How do molecules get broken apart?Simply add water!

Hydrolysis Literally means splitting with waterWater replaces the bond holding molecules together

LipidsNonpolar molecules that include fats, oils, and cholesterol Chains of carbon atoms bonded to oxygen and hydrogen atomsCan be a source of usable energy for a cellsCan be part of a cells structureFats and oils: store large amounts of chemical energy in organismsFats and oils contain glycerol bonded to fatty acidsFatty acids: chains of carbon atoms bonded to hydrogen atoms Many lipids contain 3 fatty acids bonded to a glycerol (triglycerides)Saturated fats: animal fats: max number of hydrogen possibleUnsaturated fats: oils: not saturated with hydrogen atomsAnimal fats are solid, plant fats are liquid

3 fatty acid molecules attached to glycerol backbone.

+ =Cell membranes are made of phospholipidsConsists of a glycerol, two fatty acids, and a phosphate groupCholesterol: lipid with a ring structure

What are uses of lipids?Long term energy storageBuild cell membranesHeat insulator of organisms3. ProteinsContain Nitrogen!Polymer made of monomers called amino acidsAmino acids: molecules that contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfurOrganisms use 20 amino acids to build proteinsBody makes 12 of these amino acids, the rest is from food you eat

Amino acids are made of:Hydrogen atomAmino group (NH2)Carboxyl group (COOH)

Amino acids differ on their side groups (called R group)Amino acids form covalent bonds (called peptide bonds)Bonds form between amino group on one amino acid and carboxyl group on anotherLinked to form chains called polypeptidesProteins are one or more polypeptides

Uses of ProteinsHormonesEnzymesMaking new cellsTransport materialsHelp with immunity4. Nucleic AcidPolymers that are made of monomers called nucleotidesMade of a sugar, a phosphate group, and a baseTwo types of Nucleic Acids: DNA and RNAOnly have one functionWork together to make proteins

Chemical ReactionsBonds Break and FormChemical reactions: change substances into different substances by breaking and forming chemical bonds

Reactants, Products, Bond EnergyReactants: substances changed during a chemical reactionProducts: substances made by a chemical reaction6CO2 + C6H12O6 6CO2 + 6H2O reactants direction products

Bond energy: amount of energy that will break a bond between two atomsBonds between different types of atoms have different bond energiesEnergy is released when bonds are formed

The amount of energy that is released is equal to the amount of energy that breaks the same bondExample: energy is released when hydrogen and oxygen atoms bond to form water. The same amount of energy is needed to break apart a water molecule.

Chemical EquillibriumMany reactions in living things are reversibleWhen a reaction takes place at an equal rate in both directions, the reactant and product concentrations stay the sameEquilibrium: reached when both the reactants and products are made at the same rate

Chemical Reactions Release or Absorb EnergyAdded energy breaks chemical bondsDuring chemical reactions both energy is used and madeActivation energy: amount of energy that needs to be absorbed for a chemical reaction to start

ExothermicExothermic: chemical reaction released more energy than it absorbs

EndothermicEndothermic: Chemical reaction absorbs more energy than it releases

EnzymesCatalyst lowers activation energyCatalyst: a substance that decreases the activation energy needed to start a chemical reactionThis results in the same amount of product but requires less energyCatalysts are not considered to be either reactants or products because catalysts are not changed or used up during a reaction

Enzymes allow chemical reactions to occur under tightly controlled conditionsReactants can be found in low concentrationsEnzymes: catalysts for chemical reactions in living thingsLower the activation energy and increase rate of chemical reactionsEnzymes do not affect chemical equilibrium

Enzymes just change the amount of time neededExample: Amylase protein in saliva that breaks down starch to simple sugarsAlmost all enzymes are protein

Enzymes depends on structure to function properlypH levels and temperature can effect an enzymes functionwhen the structure changes, it can no longer function properly

Enzyme structure is important because it allows specific reactants to bindSubstrates: specific reactants that an enzyme will work withSubstrates bond temporarily at active sites.Lock and key model