The Chemistry of LifeThe Chemistry of Life

Basic ChemistryBasic Chemistry

MatterMatter has mass & takes up

space

ElementsElements 25 required for life C,H,O,N – make up

96% of living things P,S,Ca,K – most of

the remaining 4%

Trace ElementsTrace Elements Required but only in

minute amounts Some required by all

living things – Fe Others required only

by certain species – Iodine only for vertebrates

Goiters caused by iodine deficiency

www.pipevet.com/photos/goiter.htm

The thyroid gland requires iodine to produce one of it’s hormones.Without iodine, the gland swells. Iodized salt provides enough iodine to prevent this condition.

AtomsAtoms

Smallest units of matter

Composed of protonsprotons (+) and neutronsneutrons in nucleus and electronselectrons (-) in orbitals

www.phschool.com

Periodic Table InformationPeriodic Table InformationAtomic NumberAtomic Number Represents # of

protons Also # of electrons in

a stable atom of an element

Atomic MassAtomic Mass Sum of protons & neutrons Electron mass is small and almost negligible

www.sparknotes.com

Unstable AtomsUnstable AtomsIonsIons Different # of

electrons Atoms with a charge More electrons &

charge is negative Less electrons &

charge is positive

IsotopesIsotopes Different # of neutrons Often radioactive Used as diagnostic tracers

EX: barium, iodine

** The number of protons does not change! This would create an entirely different element.

Diagnostic Tracers

www.nature.com/gimo/contents/pt1/full/gimo29.html

http://student.bmj.com/issues/03/10/education/358.php

BondingBondingAtoms bond in order to fill their valence shell (outer energy level)

Octet RuleOctet Rule The idea that most atoms want 8 electrons

in their outer shell and will share, steal, or give away electrons in order to fill the valence shell

Exceptions are those who have less than 6 total electrons

Covalent BondingCovalent Bonding

Valence electrons (outer shell) are shared

Form molecules

Single, double or triple bonds are possible

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Types of Covalent BondsTypes of Covalent BondsNonpolar CovalentNonpolar Covalent Electrons are shared

equally EX: O2

Polar CovalentPolar Covalent Electrons are not

shared equally The more

electronegative atom exerts a greater pull on the electrons being shared

EX: H2O

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Electrons are lost or gained from the outer shell in order to fulfill the octet rule

Ionic BondingIonic Bonding

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Hydrogen BondingHydrogen Bonding

Weak bonds formed between molecules that contain polar covalent bonds

http://trc.ucdavis.edu/biosci10v/bis10v/media/ch02/bond_types.html

Bonding animation: www.biology.arizona.edu

Molecular Molecular Structure vs. FunctionStructure vs. Function

Each molecule has a characteristic size & shape which determine its functionendorphins are brain signal molecules that

fit into specific receptors used in pain suppression & euphoria.

Morphine & heroin mimic the shape of endorphins and produce similar effects when they bind to receptors

www.charisma.org.uk/neuron-p.gif

Endorphin molecule

Morphine molecule

http://www.bio.davidson.edu/Courses/anphys/1999/Self/Ligands.htm

Earth’s Biological Earth’s Biological MediumMedium

PolarityPolarity

Slight charge on either end of the molecule due to the unequal electronegativities of hydrogen & oxygen

This leads to many other properties…

CohesionCohesion

http://www.arroyoseco.org/conservation.htmwww.biology.arizona.edu

AdhesionAdhesion

en.wikivisual.com www.ccs.k12.in.us

Surface TensionSurface Tension

http://faculty.vassar.edu/suter/1websites/bejohns/mateselection/files/female.htm

news.bbc.co.uk/.../photo_galleries/4670308.stm

www.ext.vt.edu

Specific HeatSpecific HeatAmount of heat that must be absorbed or lost for 1g of a substance to change by 1oCWater has high specific heat – it resists temperature changeThis keeps the earth

within viable temperature limits.

www.michigan.org

Evaporative CoolingEvaporative Cooling

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AP Photo/Darin Cummings

Density of IceDensity of IceSolid water is less dense than its liquid because as hydrogen bonds freeze, they force molecules further apart

In large bodies of water, a top layer of ice actually insulates the water below

4oC is when water is at its most dense

www.astrobiology.com/lter/album01/179.html

http://www.astrobiology.com/lter/album01/209.html

Universal SolventUniversal SolventWater dissolves many materials creating aqueous solutions (water is solvent, what’s being dissolved is solute)This property is the direct result of water’s polar structure HydrophilicHydrophilic – substances attracted to

water HydrophobicHydrophobic – repel water (or not

attracted)

Water & pHWater & pH

In pure water, even if dissociation occurs, the concentration of H+ and OH- ions is equalWhen acids or bases are added to water, these concentrations change quicklypH is a measure of hydrogen ion concentration on a scale between 0-14

AcidsAcidsChemical compounds that donate H+ ions as they dissociate in solution

EX: HCl H+ Cl-

The more acidic a solution,The higher the H+ concentrationThe lower the pH

Taste sourpH < 7

www.elmhurst.edu

BasesBasesCompounds that accept H+ ions and remove them from solution

Some donate OH- ions

The more basic a solution,The lower its H+ concentrationThe higher its pH value

Taste bitter

www.chemistryland.com

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BuffersBuffersSubstances that resist changes in pH

Many of these in the body since even minor changes can be life threatening EX: blood ph is 7.4 CO2 (carbonic acid when dissolved in water)

donates H+ to lower pH HCO3 (bicarbonate) binds excess H+ to raise pH

I am HI am H22OO

Organic CompoundsOrganic Compounds

Functional GroupsFunctional Groups

Parts of organic compounds most commonly involved in chemical reactions

Determine what bonds will be formed and functions of specific compounds

(Structure/Function)

Functional GroupsFunctional Groups

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

Organic CompoundsOrganic CompoundsAll the compounds found in living things that contain CARBONCARBON

These compounds are divided into 4 families:CarbohydratesLipidsProteinsNucleic Acids

1.1. CarbohydratesCarbohydrates

Their main function is to provide energyenergy

Examples of “carbs” include candy, sugar, pasta, bread, etc.

All contain hydroxyl & carbonyl groups

There are 3 groups of carbohydrates:1. Monosaccharides

2. Disaccharides

3. Polysaccharides

A.A. MonosaccharidesMonosaccharides

Mono = single or simpleSaccharide = sugarThese are simple sugarsExamples are glucose & fructoseMonosaccharides always have the formula CH2O (they are a hydrate of Carbon)EX: glucose formula is C6H12O6

Glucose StructureGlucose Structure

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

Examples of MonosaccharidesExamples of Monosaccharides

ResearchResearchers have found new evidence that soft drinks sweetened with high-fructose corn syrup (HFCS) may contribute to the development of diabetes, particularly in children. In a laboratory study of commonly consumed carbonated beverages, the scientists found that drinks containing the syrup had high levels of reactive compounds that have been shown by others to have the potential to trigger cell and tissue damage that could cause the disease, which is at epidemic levels. HFCS is a sweetener found in many foods and beverages, including non-diet soda pop, baked goods, and condiments. It is has become the sweetener of choice for many food manufacturers because it is considered more economical, sweeter and more easy to blend into beverages than table sugar. Some researchers have suggested that high-fructose corn syrup may contribute to an increased risk of diabetes as well as obesity

B. DisaccharidesB. Disaccharides

Double sugarsThese are things like sucrose, lactose, and maltoseThey are formed by removing a water to bond monosaccharides together GlycosidicGlycosidic linkage - bond formed between monosaccharides

Dehydration SynthesisDehydration Synthesis

Dehydration SynthesisDehydration Synthesis

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

Monomers Monomers Polymers Polymers

http://universe-review.ca/I11-10-reactions.jpg

C. PolysaccharidesC. Polysaccharides

Complex sugars

Breads, pastas

We break these down in order to get energy in our body. Water must be added to bust these apart –

HydrolysisHydrolysis

HydrolysisHydrolysis

www.biotopics.co.uk/as/disaccharidehydrolysis.gif

Indicators of CarbohydratesIndicators of Carbohydrates

Benedicts SolutionTurns from blue to orange in

a MONOSACCHARIDE

IodineTurns from amber to black in a

POLYSACCHARIDE

biology.unm.edu

iws.ccccd.edu

2. Lipids2. LipidsHydrophobic - little or no affinity for waterSmaller than true polymersHighly varied in form & functionTypes of lipids include

A. FatsB. PhospholipidsC. SteroidsD. Waxes & oils

A. FatsA. FatsMonomersGlycerolFatty acids

Ester linkageEster linkage - bond between fatty acids & glycerol formed by dehydration synthesis

Function in energy storage & protection

Dehydration SynthesisDehydration Synthesis of a fat- 3 waters removed between hydroxyl of glycerol and carboxyl of fatty acid to form ester linkages

io.uwinnipeg.ca/~simmons/cm1503/Image76.gif

Saturated vs. Unsaturated FatsSaturated vs. Unsaturated Fats

SaturatedSaturatedSolids @ room

tempAnimal fatsBuild up inside

vesselsNo double bonds

between carbons (saturated with hydrogens)

UnsaturatedUnsaturatedLiquids @ room

tempPlant oilsDouble bonds

between carbons (do not have max # of hydrogens

Unsaturated vs. SaturatedUnsaturated vs. Saturated

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

FATSFATS

Which of these are saturated?

B. PhospholipidsB. Phospholipids

Similar to fats but with only 2 fatty acids rather than 3

The 3rd hydroxyl group of glycerol is joined to a phosphate group

Ambivalent behavior toward waterLipid tails are hydrophobicPhosphate heads have – charge and are

hydrophilic

Major component of cellular membranes

PhospholipidsPhospholipids

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/phospc.gifwww.biologycorner.com/resources/lipidbilayer.gif

C. SteroidsC. SteroidsCarbon skeleton of 4 fused rings

Used in animal cell membranes & hormones

Extreme levels in the bloodstream may contribute to atherosclerosis

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html

3. Proteins3. ProteinsMonomers – amino acids

Contain both amino & carboxyl groups

Sophisticated in both structure & function

Used in support, storage, transport, signaling, immunity, metabolism

Account for more than 50% of dry weight of cells

PeptidesPeptidesPeptidesPeptides Individual amino

acids OR sequence of 2 or

more amino acids created by dehydration synthesis

Peptide bondPeptide bond – between amino acids

ghs.gresham.k12.or.us

ProteinsProteins

One or more polypeptides folded and coiled into specific conformations

www.biosci.ohio-state.edu

Levels of Protein StructureLevels of Protein StructurePrimary Structure (1Primary Structure (1oo))Unique sequence of amino acidsEX: Hemoglobin – normal vs. sickledEX: Insulin

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG

Secondary Structure (2Secondary Structure (2oo)) Initial coiling and folding patterns that result

from hydrogen bondsEX: alpha helix – coils (alpha keratin in hair)EX: pleated sheet – folds (silk proteins of

insects & spiders

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG

Tertiary Structure (3Tertiary Structure (3oo)) – secondary coiling and folding

Quaternary Structure (4Quaternary Structure (4oo)) – overall protein structure that comes from the way all the polypeptide subunits are situated

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG

Protein StructureProtein Structure

Conformation & structure of proteins can be affected by pH, salt concentration, temperature and other environmental factors.

If the shape of a protein is changed, it is DENATURED and becomes inactive.

EnzymesEnzymesProteins that lower the amount of activation lower the amount of activation energy neededenergy needed to start reactions

CatalystsCatalysts that speed up reactions without being consumed or changed by the reaction

Has a specific active sitespecific active site that fits a specific substrate

Rate at which they work depends on things like temperature, pH, amount of substrate and temperature, pH, amount of substrate and amount of enzyme presentamount of enzyme present

Metabolism, Energy & Metabolism, Energy & EnzymesEnzymes

Chapter 6

MetabolismMetabolism

The total amount of an organism’s chemical processes and reactions

Metabolism = catabolic + anabolic Metabolism = catabolic + anabolic reactionsreactions

Catabolic ReactionsCatabolic Reactions

Chemical reactions that break down molecules

Release energy

EX: cellular respiration where glucose is broken down and ATP is released

Anabolic ReactionsAnabolic Reactions

Reactions that build complex molecules from simpler ones

Requires energy input

EX: synthesis of proteins from amino acids

Energy TransformationsEnergy Transformations

11stst Law of Thermodynamics Law of ThermodynamicsEnergy can be transferred and

transformed, but it can be neither created nor destroyed ~ Conservation of Energy

22ndnd Law of Thermodynamics Law of ThermodynamicsEvery energy transfer makes the universe

more disordered (Entropy)EX: heat is energy in its most random state

Free EnergyFree Energy

Portion of a system’s energy that can perform work when temperature is uniform throughout the system

“free” because its available for work

Represented by G

Energy ReactionsEnergy ReactionsExergonic ReactionExergonic ReactionHas a release of free energy - ΔGCatabolic reactions are also exergonic

EX: cellular respiration

Endergonic ReactionEndergonic ReactionAbsorbs free energy +ΔGAnabolic reactions are also endergonic

EX: photosynthesis

Cellular WorkCellular Work3 main kinds of work done by a cell

1.1. MechanicalMechanicalMovement

EX: muscle contraction; cilia beating

2.2. TransportTransportPumping of substances across membranes

3.3. ChemicalChemicalPushing of endergonic reactions that d not occur spontaneously

EX: dehydration synthesis

ATPATP

Adenosine TriPhosphateAdenosine TriPhosphate Energy molecule used to power cellular work Adenine, ribose sugar & 3 phosphate groups Hydrolysis of the last phosphate group causes the

release of free energy Renewable molecule regenerated by the addition

of a phosphate group to ADP (phosphorylation)

ATP Animation

biology.clc.uc.edu www.theory-of-evolution.net

www.biochem.arizona.edu

InhibitionInhibition

Competitive InhibitionCompetitive InhibitionWhen another molecule competes directly

for the active site of an enzyme and blocks it so the substrate cannot attach

Noncompetitive InhibitionNoncompetitive InhibitionWhen a molecule attaches to the enzyme

somewhere other than the active siteThis changes the shape of the active site

preventing attachment to the substrate

4. Nucleic Acids4. Nucleic AcidsStore & transmit hereditary informationEX: DNA & RNAMonomers are nucleotidesEach nucleotide contains a sugar,

phosphate group and nitrogen base (A, T, G, C)

Sugars – DNA has deoxyribose sugarsRNA has ribose sugars

http://www.csb.yale.edu/userguides/graphics/ribbons/help/dna_rgb.html