CHAPTER 2CHAPTER 2THE CHEMICAL CONTEXT OF LIFE

ESLRS:ESLRS:Core LearningCore LearningCritical ThinkingCritical ThinkingCommunicationCommunicationCommunityCommunity

STANDARDS:Investigation & Experimentation: 1 a,b,c,d,jChemistry: 1 a,d,e; 2 a-h; 5 a-d; more…Cell Biology: 1 b, f, g, & h

Figure 2.0 Bombardier beetleFigure 2.0 Bombardier beetle

This bomardier beetle illustrates the interdisciplinary nature of scientific research... Focus today is CHEMISTRY

Matter- anything that takes up space and has mass.

Element- substance that cannot be broken down to other substances by chemical reactions.

92 elements exist in natureLIFE REQUIRES 25C, H, N, O - 96%P, S, Ca, K - 4%

and trace elements

Table 2.1 Naturally Occurring Elements in the Human BodyTable 2.1 Naturally Occurring Elements in the Human Body

What kinds of molecules will an What kinds of molecules will an animal, plant, or bacterium take animal, plant, or bacterium take up as necessary building blocks up as necessary building blocks and excrete as waste products?and excrete as waste products?

What elements are these What elements are these molecules made of?molecules made of?

DISCUSS.DISCUSS.

Water- solvent of lifeWater- solvent of life

CarbohydratesCarbohydratesLipidsLipidsProteinsProteinsNucleic AcidsNucleic Acids

Carbon, Hydrogen, Nitrogen, Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, SulfurOxygen, Phosphorus, Sulfur

Which elements are most Which elements are most essential for life? essential for life?

96%:CarbonHydrogenOxygenNitrogen

The other 4%?PhosphorusSulfur CalciumPotassium

I. Elements essential to lifeI. Elements essential to life

C carbonH hydrogenN nitrogenO oxygenP phosphorusS sulfur

Ca calciumK potassium

And trace elements…

I iodine Fe iron

specific to the species

Enlarged thyroid gland

Figure 2.4 GoiterFigure 2.4 Goiter

Goiter-Caused byiodinedeficiency.

Swollen thyroid gland.

Hormones thyroxine and triiodotyronine (T3)contain Iodine.

Figure 2.3 Nitrogen deficiencyFigure 2.3 Nitrogen deficiency

A. STRUCTURE OF ATOMSA. STRUCTURE OF ATOMS

Proton- positive chargeNeutron- no charge

Electron- negative charge

Atomic structure determines the behavior of an atom.

ATOM = the entire stadiumNUCLEUS = pencil eraser on the pitcher’s moundELECTRONS = gnats buzzing around stadium

Figure 2.11 Electron orbitalsFigure 2.11 Electron orbitals

Electron Orbitals are the three-dimensional space where an electron is found 90% of the time.No more than 2 electrons can occupy the same orbital.You don’t need to remember this 1s, 2s, 2p etc. stuff for AP Bio

Figure 2.10 Electron configurations of the first 18 elementsFigure 2.10 Electron configurations of the first 18 elements

2 electrons fit in the first energy shellOuter shells can hold up to 8 electronsThis is the “octet rule”

Atoms with unpaired electrons are reactive.

Valence electrons are the outermost electrons- they determine the bonding behavior of the atom.

What are the valences of the What are the valences of the “essential” elements?“essential” elements?

HONK!

Hydrogen - 1Oxygen - 2Nitrogen - 3Carbon - 4

This tells you how many bonds each needs to make.

PHOTON is a packet of radiation from the sun.Electrons exist at fixed levels of potential energy calledelectron shells. Outer shells have more energy. Electronscan shift energy level by absorbing or releasing energy.

Ex.Photons of lightcan causea quantum leap- electrons jump shells

Heat is released when the electrons fall back to the lower energy level.

Isotopes have the same # of P & EIsotopes have the same # of P & E but a different # of neutrons. but a different # of neutrons.

In nature, an element occurs as a In nature, an element occurs as a mixture of its isotopes.mixture of its isotopes.

Radioactive isotopesRadioactive isotopes Are unstable. The nucleus decays spontaneously, giving off particles

and energy. When the decay changes the # of PROTONS, it

transforms the element. Half-life is the length of time required for half of a given

number of initial number of atoms of that isotope to be transformed to the decay element.

a) CAN BE USED TO DATE FOSSILS Radioactive Carbon 14 decays to Nitrogen 14 through

beta decay half-life = 5730 years so used in archaeology to determine the age of carbonaceous materials up to 60,000 years old.

Uranium-238 decays to Lead…half-life = 4.5 billion years… used to date OLD OLD fossils, like 1st cells.

b) CAN BE USED TO TRACE ATOMS b) CAN BE USED TO TRACE ATOMS THROUGH METABOLISMTHROUGH METABOLISMRadioactive tracers are important

diagnostic tools in medicine.Used to follow atoms through

metabolism, the chemical processes of an organism ◦ex. Old “breath” test for ulcers caused by

Heliobacter pylori used C14 labeled urea- which will be converted to ammonia and radioactive carbon dioxide.

◦ex: kidney disorders can be detected by measuring the radioactivity of urine w/ a scintillation counter.

◦ex. Metabolic activity (brain activity) can be observed using a PET scanner.

TheCalvinCycle

UsedC14

Figure 2.6 Using radioactive isotopes to study cell chemistryFigure 2.6 Using radioactive isotopes to study cell chemistry

Phosphorus 32has a half-life of 14 daysPart of DNA nucleotidesUsed in biotech research.

Figure 2.8 The Tokaimura nuclear accidentFigure 2.8 The Tokaimura nuclear accident

Radiation from decaying isotopes damages cellular molecules. Mutates DNA causing cancer, birth defects, death.

Danger: Nuclear Power Plant disasters.

II. the glue of life: chemical bondsII. the glue of life: chemical bonds Unless the atom is a noble gas, it will react

with other atoms. Chemical bonds are interactions between

atoms that allow them to complete their valence shells.

Ionic and Covalent bonds are strong. Ionic bonds are weak in the presence of

water. Hydrogen bonds are weak- but plentiful. Van der Waals interactions are extremely weak and only occur when molecules are

close together.

Figure 2.14 Electron transfer and ionic bondingFigure 2.14 Electron transfer and ionic bonding

Ionic bonds happen when one electron is transferred to Another atom making a + and - ion. Opposites attract.

“electrostatic attraction”Ionic bond = Ionic attraction

cation anionIons are charged atoms. Unequal Protons & Electrons.

Figure 2.15 A sodium chloride crystalFigure 2.15 A sodium chloride crystal

Ioniccompound

A Molecule is a collection of two or more atoms bonded together.

Ex. Oxygen O=O Water H-O-H Salt Na+Cl-

A compound is a substance consisting of two or more Elements combined in a fixed ratio.

Sodium- a metal

Chlorine- poisonous gas

Sodium Chloride-edible compound

Notice the EMERGENT PROPERTY of “flavor enhancement”… the compound formed has different qualities than the elements below in a level of organization of matter!

Sodium- a metal

Chlorine- poisonous gas

Sodium Chloride-edible compound

Figure 2.12 Covalent bonding in four moleculesFigure 2.12 Covalent bonding in four molecules

Covalent Bonds =When atoms shareelectrons.

The goal is toget the valenceshells full.

Hydrogen - 1 bondOxygen- 2 bondsNitrogen- 3 bondsCarbon- 4 bonds

Figure 2.12x MethaneFigure 2.12x Methane

Methane

CH4

Carbon &Hydrogen Share the electronsEvenly.

NONPOLAR COVALENTBOND

Smells bad.Contributes to global warming.

HARRIS RANCH

Figure 2.13 Polar covalent bonds in a water moleculeFigure 2.13 Polar covalent bonds in a water molecule

Water is a polar covalent molecule. The oxygen is moreelectronegative than hydrogen… the shared electrons spend more time around the Oxygen nucleus than the Hydrogen resulting in “partial” negative and positive charge.

POLAR COVALENT BOND = unequal sharing of electrons

ElectronegativityElectronegativity

Is the attraction of a particular kind of atom for the electrons of a covalent bond.

Carbon & Hydrogen are =‘ly electronegative.◦So molecules that are composed only of these

elements are nonpolar- they have no charge.OXYGEN & NITROGEN are EXTREMELY

ELECTRONEGATIVE◦So molecules that have these elements in them are

polar where the N or O is bonded.◦Will you remember this?◦NO!!!!! I mean yes.

Hydrogen bonds Hydrogen bonds form when a partially positive hydrogen atom covalently bonded to one electronegative atom is also bonded to a partially negative electronegative atom on another molecule.

Bond from the +Hydrogen of onePolar moleculeBonding to the - part of the other.

These are weak bondsDrawn as a dotted line.

Water molecules H bondedWater molecules H bonded

Water

DNA- DNA- hydrogen hydrogen bonds hold bonds hold the two the two strands strands togethertogether(via nitrogen (via nitrogen containing containing bases).bases).

Van der Waals interactions Van der Waals interactions (negative and positive “hot spots”) (negative and positive “hot spots”) are weak and only occur when are weak and only occur when molecules are very close together.molecules are very close together.

Ex. #1Immune SystemAntigen-AntibodySpecificity

Notice how all of theseBonds function in variousBiological phenomena:

Figure 2.18 Molecular shape and brain chemistryFigure 2.18 Molecular shape and brain chemistry

Ex. #2NeurotransmitterStimulatingNext neuron

Figure 2.19 A molecular mimicFigure 2.19 A molecular mimic

Endorphin = endo + morphine

Both block pain receptors from sending signal

Man made

CHAPTER 3CHAPTER 3Water and the Fitness of the Environment

Figure 3.0 EarthFigure 3.0 Earth

Figure 3.x1 WaterFigure 3.x1 Water

The polarity of water results in The polarity of water results in hydrogen bondinghydrogen bonding

Hydrogen bonding of waterresults in these Emergent Properties

1. Versatility as a solvent2. Cohesive behavior3. Ability to stabilize temperature4. Expansion upon freezing

Water is the “universal solvent”… it Water is the “universal solvent”… it dissolves better than most things… dissolves better than most things… but not everything- it is the solvent but not everything- it is the solvent of life. of life.

Solute+ Solvent Solution

Water can form hydration shells around ions & breakIonic bonds.

Note- the Cl- is surrounded by the + hydrogen parts of water & the Na+ is surroundedby the - oxygen parts of water.

Water, as the universal solvent, Water, as the universal solvent, supports chemical reactions that supports chemical reactions that occur within cells.occur within cells.

Figure 3.8 A water-soluble proteinFigure 3.8 A water-soluble protein

Cohesion is an Cohesion is an attractive force betweenattractive force betweenlike substances.like substances.

Surface tension, caused by the cohesion of water molecules, allows a water strider to exploit the habitat of surface water to find food, mates, or escape predators.

Surface tension is a measure of how difficultit is to stretch or breakthe surface of a liquid.

The basilisk can “run on water” to escape larger predatorswho will sink….

Figure 3.2 Water transport in plantsFigure 3.2 Water transport in plants

Transpiration- result of cohesion and adhesion. It is A “water chain” being pulled up from the roots to the leaves.Adhesion is the attraction of the water molecules to anothertype of molecule… in this case the dead cells of the xylem.

Benefit to plants = don’t need to use ATP to move water…

Water will change its Water will change its temperature less than other temperature less than other materials when it gains or loses a materials when it gains or loses a given amount of heat. given amount of heat.

Where would yourather be on a hot day…In the desert or at the beach?

Which boils faster… a pot of alcohol or a pot of water?

Water has an unusually high specific heat.

Heat Capacity or Specific Heat is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by one degree C.

Heat must be absorbed to breakhydrogen bonds (so it takes along time to boil water) and heat is released when hydrogen bonds form (it takes longer to cool and to freeze water.)

This makes it a great moderator of temperature.

Heat must be absorbed to break all Heat must be absorbed to break all four hydrogen bonds before the four hydrogen bonds before the molecule transitions to the gas phasemolecule transitions to the gas phase..

SWEATING =EVAPORATIVECOOLING

Evaporative cooling occurs when liquids evaporate. they absorb heat to be converted from liquid to gas & leave the remaining liquid cooler.

Because heat must be absorbed to breakhydrogen bonds to allow the water to evaporate.

Water’s high heat of vaporizationmoderates earth’s climate and organism’s temperatures.

Figure 3.6x2 Ice floats and frozen benzene sinksFigure 3.6x2 Ice floats and frozen benzene sinks

Water is one of the few Water is one of the few substances that is less dense assubstances that is less dense asA solid. ICE FLOATS.A solid. ICE FLOATS.

Figure 3.5x1 Ice, water, and steam

Figure 3.6 Floating ice and the fitness of the environmentFigure 3.6 Floating ice and the fitness of the environment

Since oceans and lakes don’t freeze solid. Organisms in aquatic environments don’t losetheir habitat during winter.

Hydrophilic = water loving ex. Polar substances will bond with water…

are attracted to water.Ex. Sugar dissolves in water and is easily

transported through it to cells and organelles w/in cells that use it.

Hydrophobic = water hating ex. Nonpolar substances will NOT have

attraction to water… actually repel water.Ex. The phospholipid molecule is used

(many of them) to create the cell membrane.

Living systems depend on Living systems depend on properties of water that result properties of water that result from its polarity and hydrogen from its polarity and hydrogen bonding. Explain this statement bonding. Explain this statement and provide multiple examples.and provide multiple examples.

Unnumbered Figure (page 47) Chemical reaction: hydrogen bond shiftUnnumbered Figure (page 47) Chemical reaction: hydrogen bond shift

acid base

Figure 3.9 The pH of some aqueous solutionsFigure 3.9 The pH of some aqueous solutions

An acid increases thehydrogen ionconcentrationof a solution.

A baselowers thehydrogen ionconcentrationof a solution.

Hydrogenacceptor

Hydrogendonator

pH is a logScale, 10x

Figure 3.10x1 Pulp millFigure 3.10x1 Pulp mill

Figure 3.10x2 Acid rain damage to statuary, 1908 & 1968Figure 3.10x2 Acid rain damage to statuary, 1908 & 1968

Figure 3.10 The effects of acid precipitation on a forestFigure 3.10 The effects of acid precipitation on a forest

BUFFERSBUFFERS Are substances that minimize

changes in the concentrations of H+ and OH- in a solution.

Carbonic Acid is the buffer in human blood that keeps it at a pH of 7.4. (CO2 + H20)

It disassociates to form Bicarbonate and releases a H+ when pH levels exceed 7.4 (becomes basic)

The reversible reaction occurs when blood becomes too acidic. Excess H+ bonds with bicarbonate to form Carbonic Acid.

Oxygen as an Electron acceptor.Oxygen as an Electron acceptor. In cell respiration reactions occur in the

mitochondria to make ATP by metabolizing organic molecules (like glucose).

Oxygen, a highly electronegative molecule, is crucial to the process.

It attracts and bonds to itself: Hydrogen ions and electrons, to form water.

Without oxygen “attracting” electrons the whole system wouldn’t work.

When you die from asphyxiation, it is because you run out of ATP- since Cell Resp. stops.