chemistry chapter 2. atomic structure particleschargemass proton+11 amu neutronno charge1 amu...

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Chemistry Chemistry Chapter 2 Chapter 2

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ChemistryChemistry

Chapter 2Chapter 2

Atomic StructureAtomic Structure

ParticlesParticles ChargeCharge MassMass

ProtonProton +1+1 1 1 amuamu

NeutronNeutron no chargeno charge 1 1 amuamu

ElectronElectron - 1- 1 0 amu0 amu

Chemical BondsChemical Bonds

Ionic bonds: electrons are transferred Ionic bonds: electrons are transferred Cation + Anion –Cation + Anion –

Covalent bonds: electrons are sharedCovalent bonds: electrons are shared Polar (slight charge) Polar (slight charge)

Nonpolar (no charge)Nonpolar (no charge)

Hydrogen bonds: (weak intramolecular bonds)Hydrogen bonds: (weak intramolecular bonds)

Chemical ReactionChemical Reaction

SynthesisSynthesis DecompositionDecomposition Single DisplacementSingle Displacement Double DisplacementDouble Displacement HydrolysisHydrolysis DehydrationDehydration

A + B A + B C C C C A + B A + B AB + C AB + C AC + B AC + B AB + CD AB + CD AD + CB AD + CB HH22O + CO + C A + B A + B

A + B – HA + B – H22O O C C

Energy TransferEnergy Transfer

Endothermic / Endothermic / Endergonic – Endergonic – Absorption of energy Absorption of energy

Exothermic / Exothermic / Exergonic – Release Exergonic – Release of energyof energy

Rate of ReactionRate of Reaction

Temperature Temperature – increase in temperature leads – increase in temperature leads to an increase in kinetic energy (faster moving to an increase in kinetic energy (faster moving particles)particles)

Particle SizeParticle Size – increased surface area allows – increased surface area allows particles to collide more frequently.particles to collide more frequently.

ConcentrationConcentration – the more concentrated a – the more concentrated a solution is, the more likely the particles will solution is, the more likely the particles will collide.collide.

CatalystsCatalysts – (enzymes) – help by lowering the – (enzymes) – help by lowering the amount of energy needed for a reaction to amount of energy needed for a reaction to proceed. (not used up during the rxn)proceed. (not used up during the rxn)

Acids and BasesAcids and Bases pH scale (0 – 14) (measures the hydrogen pH scale (0 – 14) (measures the hydrogen

ions in a soln)ions in a soln) AcidAcid (sour taste; corrosive) (sour taste; corrosive)

molecule capable of releasing Hmolecule capable of releasing H++

molecule that absorbs a OHmolecule that absorbs a OH-- BaseBase (bitter taste; slippery) (bitter taste; slippery)

molecule capable of absorbing Hmolecule capable of absorbing H++

molecule that releases a OHmolecule that releases a OH--

Titration – balancing acid and baseTitration – balancing acid and base

SaltsSalts

Formation of a saltFormation of a salt HCl + NaOH –> HHCl + NaOH –> H22O O

+ NaCl+ NaCl

Salt is an ionic Salt is an ionic compound that compound that contains cations contains cations other than Hother than H++ and and anions other than anions other than OHOH--

BuffersBuffers

BufferBuffer - a substance - a substance that either releases that either releases or absorbs Hor absorbs H++ and and helps to prevent a helps to prevent a drastic change in pH. drastic change in pH.

When the buffer runs When the buffer runs out the pH will again out the pH will again begin to fall with the begin to fall with the addition of more Haddition of more H++..

CarbohydratesCarbohydrates

MonosaccharidesMonosaccharides – simple – simple sugar (single chain or sugar (single chain or ring) ex: glucose, ring) ex: glucose, galactose, fructosegalactose, fructose

DisaccharidesDisaccharides – double – double sugar ex: sucrose, sugar ex: sucrose, lactose, maltoselactose, maltose

Polysaccharides Polysaccharides – many – many sugars ex: starch, sugars ex: starch, glycogen, cellulose, glycogen, cellulose,

LipidsLipids

Fats, Oils, WaxesFats, Oils, Waxes Higher number of C – H Higher number of C – H

bonds than carbohydratesbonds than carbohydrates Used for Lubrication, Used for Lubrication,

Waterproofing, Insulation, Waterproofing, Insulation, Energy StorageEnergy Storage

Saturated vs. UnsaturatedSaturated vs. Unsaturated Phospholipids, Steroids, Phospholipids, Steroids,

TriglyceridesTriglycerides

ProteinsProteins

Composed of 20 different amino acids. (vary by Composed of 20 different amino acids. (vary by the side chain: R-group)the side chain: R-group)

What makes one protein different from another What makes one protein different from another is the amino acids making it up and the order is the amino acids making it up and the order of the amino acids.of the amino acids.

Each amino acid has an amine group (-NHEach amino acid has an amine group (-NH22))

and a carboxyl group (-COOH)and a carboxyl group (-COOH)

Protein FormationProtein Formation

Peptide bond formationPeptide bond formation: long : long chains of amino acids joined chains of amino acids joined by a dehydration reaction by a dehydration reaction

Proteins are classified based Proteins are classified based on on functionfunction..

Folding of proteins creates Folding of proteins creates different structures: primary, different structures: primary, secondary, tertiary, secondary, tertiary, quaternaryquaternary

Proteins can form bonds with Proteins can form bonds with themselves or other themselves or other proteins proteins

Protein ClassificationProtein Classification

2 ways of classifying proteins2 ways of classifying proteinsStructural ProteinStructural Protein – – fibrous proteins; fibrous proteins; composed of intertwined chains, resembles a composed of intertwined chains, resembles a rope, used for support, insoluble (ex: collagen)rope, used for support, insoluble (ex: collagen)

Functional ProteinsFunctional Proteins – – globular proteins;globular proteins; compact and spherical, water soluble, compact and spherical, water soluble, chemically active, mobile (ex: antibodies, chemically active, mobile (ex: antibodies, enzymes, and protein-based hormones)enzymes, and protein-based hormones)

Protein DenaturationProtein Denaturation

Denaturing Denaturing – heat or pH effects hydrogen – heat or pH effects hydrogen bonds in a globular protein and can bonds in a globular protein and can permanently change itpermanently change it

Denaturation destroys active sites Denaturation destroys active sites ex: hemoglobin becomes unable to bind ex: hemoglobin becomes unable to bind

and transport oxygen when blood pH is and transport oxygen when blood pH is too hightoo high

Molecular ChaperonesMolecular Chaperones

Globular proteins that prevent incorrect Globular proteins that prevent incorrect folding, help move certain ions across folding, help move certain ions across cell membranes, break down cell membranes, break down damaged/denatured proteins, etc.damaged/denatured proteins, etc.

Ex: stress proteins- produced in Ex: stress proteins- produced in response to traumatizing stimuliresponse to traumatizing stimuli

EnzymesEnzymes

Globular proteins that act as catalystsGlobular proteins that act as catalysts

They regulate and accelerate They regulate and accelerate biochemical reactionsbiochemical reactions

Each enzyme is chemically Each enzyme is chemically

specificspecific

Nucleic AcidsNucleic Acids

DNADNA Found in the nucleusFound in the nucleus Blueprint of life (CGAT)Blueprint of life (CGAT) Inheritable Inheritable

RNARNA 3 types3 types

mRNA (messenger)mRNA (messenger) tRNA (transfer)tRNA (transfer) rRNA (ribosomal)rRNA (ribosomal)

Single StrandedSingle Stranded Uracil replaces thymineUracil replaces thymine

ATPATP Adenosine triphosphateAdenosine triphosphate energyenergy