BiochemistryBiochemistry

Textbook Chapter 6Textbook Chapter 6

Review Topic 2Review Topic 2

Basic ChemistryBasic Chemistry

Chemistry – the study of matter (anything Chemistry – the study of matter (anything with a mass and takes up space)with a mass and takes up space)

All of the organisms we study are made of All of the organisms we study are made of mattermatter

AtomsAtomsBuilding blocks of matterBuilding blocks of matter

Made of protons (+), Made of protons (+),

neutrons (0) & electrons (-)neutrons (0) & electrons (-)

Structure contains a nucleus (protons/neutrons) Structure contains a nucleus (protons/neutrons) and an energy field (electrons)and an energy field (electrons)

Atoms will contain equal numbers of protons Atoms will contain equal numbers of protons and electrons (so the overall charge is zero)and electrons (so the overall charge is zero)

ElementsElements

Pure substance that cannot be broken down Pure substance that cannot be broken down into other substances (physically or into other substances (physically or chemically)chemically)

Made of ONE type of atomMade of ONE type of atom

100 known elements (92 occur naturally)100 known elements (92 occur naturally)

Each element has a name and a symbolEach element has a name and a symbol

Organized in the periodic table of elementsOrganized in the periodic table of elements

Elements continued…Elements continued…

Periodic table of elementsPeriodic table of elements

Each element has an assigned symbol, name, atomic Each element has an assigned symbol, name, atomic number (# protons), atomic mass number (# protons), atomic mass

(# protons + # neutrons)(# protons + # neutrons)

Organized into horizontal rows (periods) and vertical Organized into horizontal rows (periods) and vertical columns (groups)columns (groups)

Each block is a different elementEach block is a different element

Elements with similar chemical and physical properties Elements with similar chemical and physical properties are grouped togetherare grouped together

Elements continued…Elements continued… IsotopesIsotopes

Atoms of the same element with different numbers Atoms of the same element with different numbers of neutronsof neutrons

Found by comparing the difference in protons plus Found by comparing the difference in protons plus neutrons (atomic mass)neutrons (atomic mass)

Isotopes of an element have the same chemical Isotopes of an element have the same chemical characteristics but can be less stable (radioactive)characteristics but can be less stable (radioactive)

Ex. Carbon-12 and Carbon-14Ex. Carbon-12 and Carbon-14

CompoundsCompoundsFormed when two or Formed when two or

more different elements more different elements combine (NOT a mixture!)combine (NOT a mixture!)

Use chemical formulas showing element Use chemical formulas showing element symbols and subscriptssymbols and subscripts

Compounds are chemically and physically Compounds are chemically and physically different from the elements involveddifferent from the elements involved

Cannot be broken down physically ONLY Cannot be broken down physically ONLY CHEMICALLYCHEMICALLY

Chemical BondsChemical Bonds

Forces which hold the elements in a compound Forces which hold the elements in a compound togethertogether

Involves the electrons of an atomInvolves the electrons of an atomShared between two atoms (covalent bond)Shared between two atoms (covalent bond)

Transferred between two atoms forming ions with Transferred between two atoms forming ions with opposite charges (ionic bond)opposite charges (ionic bond)

Forming bonds stores energy, breaking bonds Forming bonds stores energy, breaking bonds releases energyreleases energy

Can be single, double or tripleCan be single, double or triple

Van der Waals ForcesVan der Waals ForcesAttractive forces between molecules due to Attractive forces between molecules due to

their positive and negative regionstheir positive and negative regions

Not as strong as bondsNot as strong as bonds

Ex. GeckosEx. Geckos

Chemical ReactionsChemical Reactions

Process where compounds are Process where compounds are reorganized to form different compoundsreorganized to form different compounds

Bonds are broken and reformedBonds are broken and reformed

Not all changes are chemical reactionsNot all changes are chemical reactionsEx. Melting of ice (physical) versus rusting of Ex. Melting of ice (physical) versus rusting of

a car (chemical)a car (chemical)

Chemical EquationsChemical Equations

Reactants are the starting substancesReactants are the starting substances

Products are formedProducts are formed

Arrow represents the reaction that occurredArrow represents the reaction that occurred

Reactants Reactants Products Products

Ex. CEx. C66HH1212OO66 + O + O22 CO CO22 + H + H22OO

Matter is not created or destroyed in a chemical Matter is not created or destroyed in a chemical reaction (conservation of mass)reaction (conservation of mass)

Main IdeasMain Ideas Atoms consist of protons, neutrons and electronsAtoms consist of protons, neutrons and electrons

Elements are pure substances made up of only one kind Elements are pure substances made up of only one kind of atomof atom

Isotopes are forms of the same element that have a Isotopes are forms of the same element that have a different number of neutronsdifferent number of neutrons

Compounds are substances with unique properties that Compounds are substances with unique properties that are formed when elements combineare formed when elements combine

Elements can form covalent and ionic bondsElements can form covalent and ionic bonds

Chemical reactions cause the rearrangement of atoms Chemical reactions cause the rearrangement of atoms into different substancesinto different substances

EnzymesEnzymes Most compounds in living things cannot undergo Most compounds in living things cannot undergo

chemical reactions without energychemical reactions without energy

The minimum energy needed to start a reactions The minimum energy needed to start a reactions is called the activation energyis called the activation energy

If the activation energy is high, reactions occur If the activation energy is high, reactions occur slowerslower

In nature, a catalyst is used to lower the In nature, a catalyst is used to lower the activation energy of a reactionactivation energy of a reaction

A catalystA catalystSpeeds up a reactionSpeeds up a reaction

Does NOT make more products just makes Does NOT make more products just makes them fasterthem faster

Is not used up in the reaction and can be Is not used up in the reaction and can be reusedreused

Ex. Enzymes (biological catalysts)Ex. Enzymes (biological catalysts)

EnzymesEnzymes

Substrate – reactants which bindSubstrate – reactants which bindto the enzymeto the enzyme

Active site – location where the Active site – location where the substrate binds on the enzymesubstrate binds on the enzyme

Only substrates with the same size and shape as the Only substrates with the same size and shape as the active site will bind to the enzyme (lock & key model)active site will bind to the enzyme (lock & key model)

Once it binds, the active site changes shape, forming Once it binds, the active site changes shape, forming the enzyme-substrate complex which breaks/forms the enzyme-substrate complex which breaks/forms the bonds necessary to form the products of the the bonds necessary to form the products of the reaction which are then releasedreaction which are then released

Factors such as pH, temperature, Factors such as pH, temperature, concentration and other substances can affect concentration and other substances can affect an enzymes functionan enzymes function

Main IdeasMain Ideas

Activation energy is the energy required to Activation energy is the energy required to begin a reactionbegin a reaction

Catalysts are substances that alter Catalysts are substances that alter chemical reactions by speeding up the chemical reactions by speeding up the reactionreaction

Enzymes are biological catalystsEnzymes are biological catalysts

Properties of WaterProperties of Water

Chemical formula - HChemical formula - H22OO

Molecule is in a “bent” Molecule is in a “bent” shape shape

Electrons are shared unequally Electrons are shared unequally Oxygen (-)Oxygen (-)Hydrogen (+)Hydrogen (+)

Polarity is caused from having two oppositely Polarity is caused from having two oppositely charged ends in a molecule (ex. magnet)charged ends in a molecule (ex. magnet)

““Opposites attract” forming hydrogen Opposites attract” forming hydrogen bondsbonds

Weak interaction Weak interaction

betweenbetween molecules molecules

Forms between a Forms between a

hydrogen (H) and a hydrogen (H) and a

oxygen (O), fluorine (F),oxygen (O), fluorine (F),

or nitrogen (N) atomor nitrogen (N) atom

These unique properties of water are These unique properties of water are important for the survival and homeostasis important for the survival and homeostasis of living thingsof living things

Ex. Surface tension, capillary action, universal Ex. Surface tension, capillary action, universal solvent, floating ice, adhesion, cohesionsolvent, floating ice, adhesion, cohesion

Mixtures with WaterMixtures with Water

Mixture – combination of two or more Mixture – combination of two or more substances which retain their own individual substances which retain their own individual characteristics and propertiescharacteristics and properties

Types:Types: HomogeneousHomogeneous HeterogeneousHeterogeneous

Homogeneous mixtureHomogeneous mixtureUniform composition throughoutUniform composition throughout

Also known as a solution which Also known as a solution which

contains two partscontains two parts

Solvent – substance in which another Solvent – substance in which another substance is dissolvedsubstance is dissolved

Solute – substance being dissolvedSolute – substance being dissolved

Ex. Salt water, saliva, flavored drinks, airEx. Salt water, saliva, flavored drinks, air

Heterogeneous mixtureHeterogeneous mixtureComponents remain distinct (individual)Components remain distinct (individual)

Ex. Suspensions (sand in water, salad), Ex. Suspensions (sand in water, salad), colloid (fog, smoke, butter, mayonnaise, milk, colloid (fog, smoke, butter, mayonnaise, milk, paint, ink, blood)paint, ink, blood)

AcidsAcids

Created when a substance Created when a substance

containing hydrogen is containing hydrogen is

dissolved in waterdissolved in water

Releases hydrogen ions (HReleases hydrogen ions (H++))

The more HThe more H++ ions, the more acidic ions, the more acidic

a solution becomesa solution becomes

Ex. HCl, HSOEx. HCl, HSO44

BasesBases

Created when a substance dissolved in water Created when a substance dissolved in water releases hydroxide ions (OHreleases hydroxide ions (OH--))

The more OHThe more OH-- released, the more basic the released, the more basic the solution becomessolution becomes

Ex. NaOHEx. NaOH

pHpH The amount of ions in a solution determines the The amount of ions in a solution determines the

strength of an acid or basestrength of an acid or base

pH is a scale which measures the amount of HpH is a scale which measures the amount of H++ ions ions in a solutionin a solution

Scale from 0-14Scale from 0-14Acidic solution range from pH 0 – pH 6Acidic solution range from pH 0 – pH 6Neutral solutions at pH 7Neutral solutions at pH 7Basic solutions range from pH 8 – pH 14Basic solutions range from pH 8 – pH 14

pH can be identified by using pH indicator paperpH can be identified by using pH indicator paper

Majority of cells carry out metabolism between Majority of cells carry out metabolism between pH 6.5 and pH 7.5pH 6.5 and pH 7.5

Buffers are mixtures that can react with acids Buffers are mixtures that can react with acids or bases to keep the pH within a certain range or bases to keep the pH within a certain range (maintenance of homeostasis)(maintenance of homeostasis)

Ex. Pepto bismol, tumsEx. Pepto bismol, tums

Main IdeasMain Ideas

Water is a polar moleculeWater is a polar molecule

Solutions are homogeneous mixtures formed Solutions are homogeneous mixtures formed when a solute is dissolved in a solventwhen a solute is dissolved in a solvent

Acids are substances that release hydrogen ions Acids are substances that release hydrogen ions into solutionsinto solutions

Bases are substances that release hydroxide ions Bases are substances that release hydroxide ions into solutioninto solution

pH is a measure of the concentration of hydrogen pH is a measure of the concentration of hydrogen ions in a solutionions in a solution