!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!

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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.!