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!Chapter!2:!
Chemistry!of!Life!
Chemistry!
Matter is anything that has mass and takes up space it is made up of elements. For instance: organisms -Examples: C, H, O, N, P, S
Elements are the basic building blocks of matter that cannot be broken down by chemical means (92 of 115 !(!ununpen'um )
Atoms are the smallest units of an element that retain the element s physical and chemical properties. These bond together to form molecules
Naturally!Occurring!Elements!in!Humans!
Nutrient!Deficiencies!
4
Subatomic!par'cles!of!atoms!
Neutrons!have!a!neutral!charge! Protons!are!posi?vely!charged! Neutrons!and!protons!make!up!the!nucleus! Electrons!are!nega?vely!charged!and!orbit!around!the!nucleus!
carbon C
6p 6n
Subatomic Particles Particle
Proton
Neutron
Electron
0
1
1
0.00055
Atomic Mass Charge
1
+ 1
nitrogen N
7p 7n
8p 8n
oxygen O
hydrogen H
1p
How!many!protons,!electrons,!and!neutrons!are!in!an!atom?!
Atomic!Number!And!Atomic!Mass!
Atoms!of!elements!differ!in!their!number!of!subatomic!par?cles!
! Atomic!number!
Mass!number!! Atomic!mass!
Step!1!
Use!your!periodic!table!to!find!an!element!
http://education.jlab.org/qa/pen_number.html
Step!2! The!number!of!Protons!(+!charge)!! The!atomic!number!=!#!protons!! Kr!has!36!protons!
http://education.jlab.org/qa/pen_number.html
Step!3!
The!number!of!Electrons!(Q!charge)! Remember!atoms!have!no!overall!charge.! Atoms!must!have!an!equal!#!of!protons!and!electrons! #protons=#electrons! Kr!has!36!electrons!
Step!4!
The number of Neutrons (no charge) Mass # (atomic weight rounded to nearest whole #) Neutrons = Mass # - Protons Neutrons = 84 36 Neutrons = 48
Summary!
Number!of!Protons!=!Atomic!#! Number!of!Electrons!=!Protons!! Number!of!Neutrons!=!Mass!#!Q!Protons!
!
Problems!
1. Find!the!protons!(p+),!electrons!(eQ),!neutrons!(n)!of!Oxygen!
2. Find!the!p+,!eQ,!n!of!Xenon!(Xe)!
3. Find!the!p+,!eQ,!n!of!Zirconium!(Zr)!!
Oxygen!(O)!p+,!eQ,!n!
Number!of!Protons!=!Atomic!#! Number!of!Electrons!=!Protons!! Number!of!Neutrons!=!Mass!#!Q!Protons!
Protons!=!8! Electrons!=!8! Neutrons!=!16Q8!=!8!
Xenon!(Xe)!p+,!eQ,!n!!
! Number!of!Protons!=!Atomic!#! Number!of!Electrons!=!Protons!! Number!of!Neutrons!=!Mass!#!Q!Protons!
Protons!=!54! Electrons!=!54! Neutrons!=!131Q54!=!77!!!
Zirconium!(Zr)!p+,!eQ,!n!
Number!of!Protons!=!Atomic!#! Number!of!Electrons!=!Protons!! Number!of!Neutrons!=!Mass!#!Q!Protons!
Protons!=!40! Electrons!=!40! Neutrons!=!91Q40!=!51!
What!Is!An!Isotope?!
Radioac've!Isotopes!
Nuclei!decay!spontaneously!and!give!off!par?cles!and!energy!(halfQlife)!
Used!to!date!fossils,!trace!atoms!through!metabolic!processes,!sterilize!medical!equipment,!diagnose!medical!disorders,!and!treat!cancer!
Radioac've!Isotopes!Have!Many!Medical!Uses!
Low!Levels!
Small!amounts!of!radia?on!can!be!used!as!a!tracer!allowing!doctors!to! see !inside!of!the!body!!
! !!a)!I131!used!to!examine!thyroid!!
! !!
High!Levels!
Excessive!amounts!of!radia?on!will!damage!DNA!!and!(cancer!cell)!Can!be!used!to:!!!Kill!pathogens!!!Treat!disease!(e.g.,!cancer)!
a: Biomed Commun./Custom Medical Stock Photo; b(patient): Courtesy National Institutes of Health (NIH); b(brain scan): Mazzlota et al./Photo Researchers, Inc.
ELEMENTS a review
Made!of!individual!atoms.! Cannot!be!broken!down!into!simpler!substances.!
Listed!on!the!periodic!table.! Created!to!be!the!building!blocks!of!all!maeer.!
Molecules!&!Compounds! Molecule Two or more of the same element chemically join
together. Hydrogen (H2), Oxygen (O2), Nitrogen (N2) are not compounds
because each is composed of a single element. Compound At least two different elements chemically join
together.
Water (H2O), carbon dioxide (C02), and methane (Ch4), are compounds because each is made from more than one element
Atoms are to elements as molecules are to
compounds!!
3 Types of Bonds:
Ionic Bond Covalent Bond Hydrogen Bond
Energy!Levels!Of!Electrons!
Electrons are located in energy levels or electron shells
Periodic!Table!of!Elements!
Forma'on!of!Chemical!Bonds!
!Interac?ons!of!atoms!that!result!in!atoms!staying!close!together!temporarily!
Ionic!bonding!
Covalent!bonding!
Ionic!Bonding!
Covalent!bonds! Atoms!in!this!type!of!bond!share!electrons! Results!in!a!stable!outer!shell!
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
8p 8n
8p 8n
8p 8n
8p 8n
8p 8n
1p 1p
1p 1p
a. When an oxygen and two hydrogen atoms covalently bond, water results.
b. When two oxygen atoms covalently bond, oxygen gas results.
8p 8n
2 hydrogen 2H
oxygen O
water H2O
oxygen O oxygen O
oxygen gas O2
Covalent!Bonding!
Electronega'vity!A!Covalent!Bond!can!be!Polar!or!Nonpolar!
Electronegativity the attraction of an atom for the electrons in a covalent bond
Atoms in a molecule share electrons to varying degrees depending on the element
Nonpolar covalent bond when the sharing of
electrons between atoms is relatively equal
Polar covalent bond unequal sharing of electrons
Electronega'vity!and!the!!Periodic!Table!
Waters!Importance!To!Life!
Water!contains!unique!proper?es!that!make!it!a!life!!suppor?ng!substance!and!this!stems!from!the!structure!of!the!molecule!
Polar!molecule!
Hydrogen!bonding!
Hydrogen!Bonds!Between!H2O!Molecules!
Four!Emergent!Proper'es!Of!Water!
Proper?es!of!water!arise!from!the!aerac?on!!between!oppositely!charged!atoms!of!different!water!molecules!by!hydrogen!bonds!
Cohesive!and!adhesive!behavior!Ability!to!moderate!temperate!Expansion!upon!freezing!Versa?lity!as!a!solvent!
Cohesion!and!Adhesion!of!Water!
Cohesion!is!the!clinging!of!water!each!other!!!! Adhesion!is!the!clinging!of!water!another!substance!
Both!adhesion!and!cohesion!helps!transport!!water!and!dissolved!nutrients!against!gravity!
Cohesion!and!Adhesion!In!Plants! Transpires
Modera'on!of!Temperature!
Water!moderates!temperatures!by!absorbing!heat!from!warmer!air!and!releasing!stored!heat!to!cooler!air!with!only!slight!changes!in!its!own!temperature!
High!specific!heat!of!water!(boil!water)!High!heat!of!vaporiza?on!of!water!
Floa'ng!Of!Ice!On!Liquid!Water!
Water:!The!Solvent!Of!Life!
Water!is!the!solvent!in!aqueous!solu?ons!
Solvent!
Solute!
Acidic!And!Basic!Condi'ons!
Water!is!in!a!state!of!dynamic!equilibrium!in!which!water!molecules!dissociate!at!the!same!rate!at!which!they!are!formed!
The!pH!Scale!
Buffers!
Substances!that!minimize!changes!in!concentra?on!of!hydrogen!ion!or!hydroxide!ion!in!a!solu?on!(pH)!
!Usually!buffers!are!acidQbase!pairs!that!accept!hydrogen!ions!in!solu?on!or!donate!hydrogen!ions!
Weak Acid! Weak Base!
Carbon:!The!Backbone!Of!Life!
Cells!are!70Q95%!water,!but!living!organisms!are!made!up!of!chemicals!that!are!mostly!carbonQbased!
Organic!chemistry!is!the!study!of!compounds!that!contain!carbon!
The!Forma'on!of!Bonds!With!Carbon!
Carbon!contains!four!valence!electrons!(tetravalence)!in!a!shell!that!holds!eight!
Most!frequent!bonding!partners!include!hydrogen,!oxygen!and!nitrogen!
Molecules!Of!Life!
Dehydra'on!Synthesis!
Hydrolysis!
Nucleic!Acids!
Made!of!monomers!called!nucleo?des!Deoxyribonucleic!acid!(DNA)!
Ribonucleic!acid!(RNA)!
Nucleo'de!Structure!
Nitrogenous!Bases!
Structure!of!DNA!
Structure!of!RNA!
Proteins!
Proteins!account!for!more!than!50%!of!the!dry!mass!of!most!cells!and!the!func?ons!of!living!organisms!depends!on!proteins!(enzymes,!defense,!storage,!transport,!hormones,!receptors,!contrac?le!and!structural)!
Made!of!monomers!called!amino!acids!
Amino!Acid!Structure!
Polypep'des!
Polymers!of!amino!acids!that!range!in!length!from!a!few!to!more!than!a!thousand!amino!acids!Amino!acids!are!linked!together!by!pep?de!bounds!by!dehydra?on!synthesis!
A!protein!consists!of!one!or!more!polypep?des!
Forma'on!Of!A!Pep'de!
Protein!Structure!and!Func'on!!
A!func?onal!protein!consists!of!one!or!more!polypep?des!twisted,!folded,!and!coiled!into!a!unique!shape,!which!is!determined!by!the!sequence!of!amino!acids!
Protein!structure!determines!its!func?on! Primary!structure,!secondary!!structure,!ter?ary!structure!!and!quaternary!structure!
Primary!Structure!Of!A!Protein!
Secondary!Structure!Of!A!Protein!
Ter'ary!Structure!Of!A!Protein!!
ThreeQdimensional!shape!of!a!protein!!!
Quaternary!Structure!Of!A!Protein!!
Results!when!two!or!more!polypep?de!chains!form!one!macromolecule!
What!Determines!Protein!Structure?!!
In!addi?on!to!primary!structure,!physical!and!chemical!condi?ons!can!affect!the!structure!of!a!protein!
Altera?ons!in!pH,!salt!concentra?on,!temperature!or!other!environmental!factors!can!cause!a!protein!to!unravel!
Denatura'on!
Rela'onship!Between!Proteins!and!DNA!
Enzymes!
Cataly?c!protein!that!speeds!up!a!chemical!reac?on!by!lowering!the!ac?va?on!energy!(EA)!
Enzymes!are!substrateQspecific!
Example:!hydrolysis!of!sucrose!by!sucrase!(enzyme)!into!glucose!and!fructose!
Cataly'c!Cycle!Of!An!Enzyme!
What!are!EnzymesQHow!Do!They!Work?!
Carbohydrates!
Made!of!monomers!called!monosaccharides!or!simple!sugars!(CH2O)!
Fuel!for!cellular!work,!raw!material!for!making!other!organic!molecules!or!disaccharides!and!polysaccharides!
Monosaccharide's!
Simple!sugars!containing!3!Q7!carbons!in!their!backbone!
Disaccharides!Synthesis!
Polysaccharides!
Polymers!containing!a!few!100!to!a!few!1,000!monosaccharide's!linked!together!
Provide!sugar!for!the!cell!(storage!polysaccharides)!or!protect!the!cell!or!a!whole!organism!(structure!polysaccharides)!
Storage!Polysaccharides!
Structural!Polysaccharide:!Cellulose!
Structural!Polysaccharide:!Chi'n!
Lipids!
Large!class!of!molecules!that!have!liele!to!no!affinity!for!water!because!they!contain!mostly!hydrocarbons!
Examples!include!triglycerides,!phospholipids,!steroids,!waxes!and!some!pigments!
Fats!Or!Triglycerides!
Fa\y!Acid!Varia'on!
Phospholipids!
Plasma!Membrane!
Steroids!
Lipids!characterized!by!a!carbon!skeleton!consis?ng!of!four!fused!rings!
CHAPTER!2!Q!CHEMISTRY!OF!LIFE!REVIEW!QUESTIONS!
1.!Define!the!following!terms:!chemistry,!maeer,!mass,!weight,!element,!trace!elements,!atom,!subatomic!par?cles,!atomic!symbol,!atomic!number,!atomic!mass,!mass!number,!isotope,!radioac?ve!isotope,!halfQlife,!valence!shell,!valence!electrons,!octet!rule,!ion,!ca?on,!anion,!molecules,!compounds,!electronega?vity,!polar!covalent!bond,!nonpolar!covalent!bond,!hydrogen!bonding,!cohesion,!adhesion,!specific!heat,!heat!of!vaporiza?on,!solvent,!solute,!hydrophilic,!hydrophobic,!buffer,!organic!chemistry,!polymers,!monomers,!dehydra?on!synthesis,!hydrolysis!synthesis,!phosphodiester!bond,!polypep?de,!protein,!pep?de!bond,!alpha!helix,!betaQpleated!sheet,!glycosidic!bond,!saturated!fat,!unsaturated!fat!and!trans!fat.!2.!Name!the!four!elements!make!up!96.0%!of!the!human!body.!!3.!Describe!the!characteris?cs!(loca?on,!charge!and!mass)!of!the!three!subatomic!par?cles!that!make!up!an!atom.!How!to!calculate!each!one!by!using!the!periodic!table.!4.!Describe!the!maximum!number!of!electrons!that!can!be!located!in!the!first!shell!and!second!shell!of!an!atom.!5.!Describe!what!happens!to!electrons!during!ionic!bonding!and!provide!an!example!of!a!molecule!that!forms!this!way.!6.!Describe!what!happens!to!electrons!during!covalent!bonding!and!provide!examples!of!molecules!that!form!this!way.!!7.!Describe!how!the!structure!of!water!influences!the!behavior!of!water!molecules!(polar!molecule!and!hydrogen!bonding).!8.!Describe!the!four!emergent!proper?es!of!water!and!how!each!property!contributes!to!the!homeostasis!of!human,!plant!or!aqua?c!life.!!9.!Describe!the!pH!scale!and!understand!its!rela?onship!to!concentra?ons!in!hydrogen!and!hydroxide!ion!concentra?ons.!
10.!Describe!the!structure!of!carbon!and!its!importance!to!the!study!of!the!diversity!of!organic!molecules.!!11.!Describe!the!four!organic!macromolecules!of!life.!!12.!Describe!the!structure!of!a!nucleo?de.!13.!Compare!and!contrast!the!structure!and!func?on!of!DNA!and!RNA.!!14.!Describe!the!general!func?ons!of!proteins.!!15.!Describe!the!structure!of!an!amino!acid!and!the!importance!of!the!R!group.!16.!Describe!&!Iden?fy!the!four!levels!of!protein!structure.!!17.!Describe!denatura?on!and!the!altera?ons!that!can!occur!in!an!environment!to!make!denatura?on!happen.!!18.!Describe!the!structure!and!func?on!of!monosaccharide's.!!19.!Describe!an!example!of!disaccharides!that!was!discussed!in!lecture.!!20.!Describe!the!structure!and!func?on!of!a!triglyceride.!!21.!Describe!the!structure!and!func?on!of!a!phospholipid.!!22.!Describe!the!structure!and!func?on!of!a!steroid.!