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Chapter 2Chapter 2

The Chemical The Chemical Context of LifeContext of Life

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Why are we Why are we studying studying

chemistry?chemistry?Biology has chemistry at its foundationBiology has chemistry at its foundation

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The BasicsThe BasicsEverything is made of matterEverything is made of matter

Matter is made of atomsMatter is made of atoms

Atoms are made of:Atoms are made of:protonsprotons ++ mass of 1mass of 1 nucleusnucleus

neutronsneutrons 00 mass of 1mass of 1 nucleus nucleus

electronselectrons - - mass <<1mass <<1 orbits orbits

Different kinds of atoms = elementsDifferent kinds of atoms = elements

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The World of The World of ElementsElements

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Elements of LifeThe names of the elements are abbreviated. Often, the abbreviation makes perfect sense (C for carbon) and sometimes it does not (Na for sodium).

There is an abundance of elements on earth and in living systems (over 100 on the Periodic Table) but

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Life requires ~25 chemical Life requires ~25 chemical elementselements

About 25 elements are essential for lifeAbout 25 elements are essential for lifeFour elements make up 96% of living Four elements make up 96% of living matter: matter: • • carbon (C)carbon (C) • hydrogen (H)• hydrogen (H)

• • oxygen (O)oxygen (O) • nitrogen (N)• nitrogen (N)

Four elements make up most of remaining Four elements make up most of remaining 4%: 4%: • • phosphorus (P)phosphorus (P) • calcium (Ca)• calcium (Ca)

• • sulfur (S)sulfur (S) • potassium (K)• potassium (K)

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Models of atomsModels of atoms

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Atomic structure determines Atomic structure determines behaviorbehavior

The number of protons in an atom The number of protons in an atom determines the elementdetermines the element

# of protons = atomic number# of protons = atomic number

this also tells you # of electronsthis also tells you # of electrons

All atoms of an element have same All atoms of an element have same chemical propertieschemical properties

all behave the sameall behave the same

properties don’t changeproperties don’t change

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IsotopesIsotopesDifferent number of neutrons (heavier)Different number of neutrons (heavier)

Some are unstableSome are unstablenuclear reactions / decaynuclear reactions / decay

Split off neutrons &/or protonsSplit off neutrons &/or protonsradioactivityradioactivity

Biological toolBiological tool

Biological hazardBiological hazard

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Effect of electronsEffect of electronschemical behavior chemical behavior of an atom of an atom depends on its depends on its electron electron arrangementarrangementdepends on the depends on the number of number of electrons in its electrons in its outermost shell, outermost shell, the the valence shellvalence shell

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Bonding Properties

How does this atom behave?

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Effect of electronschemical behavior of an atom depends on number of electrons in its outermost shell

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Bonding Properties

How does this atom behave? How does this atom behave?

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Elements & their valence Elements & their valence shellsshells

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Elements in the same row have the same number of shells

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Elements & their valence Elements & their valence shellsshells

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Elements in the same column have the same valence & similar chemical properties

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Elements & their valence Elements & their valence shellsshells

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Moving from left to right, each element has a sequential addition of electrons (and protons)

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Chemical Chemical reactivityreactivityAtoms tend toAtoms tend to

Complete a partially filled outer (valence) Complete a partially filled outer (valence) electron shellelectron shell

oror

Empty a partially filled outer (valence) Empty a partially filled outer (valence) electron shellelectron shell

This tendency drives chemical reactionsThis tendency drives chemical reactions

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Ionic bondsIonic bonds

IonsIons are produced when atoms can obtain a are produced when atoms can obtain a stable number of electrons by giving up or stable number of electrons by giving up or gaining electrons.gaining electrons.

For example Na (sodium) can donate an For example Na (sodium) can donate an electron to Cl (chlorine) generating Na+ and electron to Cl (chlorine) generating Na+ and Cl-. The ion pair is held together by strong Cl-. The ion pair is held together by strong electrostatic attractions called electrostatic attractions called ionic bondsionic bonds

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Covalent bondsCovalent bondsTwo atoms need an electronTwo atoms need an electron

Share a pair of electronsShare a pair of electrons

StrongStrong bond bondboth atoms holding onto the electronsboth atoms holding onto the electrons

Forms moleculesForms molecules

example:example:water = takes energy to separatewater = takes energy to separate

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Double covalent Double covalent bondsbonds

Two atoms can share more than one Two atoms can share more than one pair of electronspair of electrons

double bonds (2 pairs of electrons)double bonds (2 pairs of electrons)

triple bonds (3 pairs of electrons)triple bonds (3 pairs of electrons)

Very strongVery strong bonds bonds

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Multiple covalent Multiple covalent bondsbonds1 atom can form covalent bonds with two 1 atom can form covalent bonds with two

or more other atomsor more other atomsforms larger moleculesforms larger moleculesex. ex. carboncarbon

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Polar covalent Polar covalent bonds aka bonds aka Hydrogen Hydrogen bondingbondingPair of electrons not shared equally by Pair of electrons not shared equally by

2 atoms2 atoms

Water = O + HWater = O + H

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oxygen has stronger “attraction” for the shared electrons than hydrogen

oxygen has higher electronegativity

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Polar covalent Polar covalent bondsbonds

2 hydrogens in the water molecule form 2 hydrogens in the water molecule form an angle an angle

Water molecule isWater molecule is polarpolaroxygen end is –oxygen end is –hydrogen end is +hydrogen end is +electrostatic attractionelectrostatic attraction

Leads to many Leads to many interesting properties interesting properties of water….of water….

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Hydrogen bondsHydrogen bondsPositive H atom in Positive H atom in 1 water molecule is 1 water molecule is attracted to negative O attracted to negative O in anotherin another

Can occur wherever an Can occur wherever an -OH exists in a larger -OH exists in a larger moleculemolecule

WeakWeak bonds bonds

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Hydrogen Bonds

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Van der Waals interactions

(how geckos walk on the ceiling)very weak, transient connections that are the result of asymmetrical distribution of electrons within a molecule

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Just as a summary to what each bond looks like…

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Bonding by Analogy: Dog - Bone Bonds

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Ionic Bonds: One big greedy thief dog!Ionic bonding can be best imagined as one big greedy dog steeling the other dog's bone.  If the bone represents the

electron that is up for grabs, then when the big dog gains an electron he becomes negatively charged and the little dog

who lost the electron becomes positively charged. 

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Covalent Bonds: Dogs of equal strength.

Covalent bonds can be thought of as two or more dogs with equal attraction to the bones.  Since the dogs (atoms) are identical, then the dogs share the pairs of available bones

evenly.  Since one dog does not have more of the bone than the other dog, the charge is evenly distributed among both

dogs. The bond is not “polar” because the dogs share equally.

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Polar Covalent Bonds: Unevenly matched but willing to share.

These bonds can be thought of as two or more dogs that have different desire for bones.  The bigger dog has more strength to

possess a larger portion of the bones.  Sharing still takes place but is an uneven sharing.  In the case of the atoms, the electrons spend

more time on the end of the molecule near the atom with the greater electronegativity (desire for the electron) making it seem more

negative and the other end of the molecule seem more positive.

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Reductionist view of Reductionist view of biologybiology

Matter is made of atomsMatter is made of atoms

Life requires ~25 chemical elementsLife requires ~25 chemical elements

Atomic structure determines behavior of an Atomic structure determines behavior of an elementelement

Atoms combine by chemical bonding to form Atoms combine by chemical bonding to form moleculesmolecules

Weak chemical bonds play important roles in Weak chemical bonds play important roles in chemistry of lifechemistry of life

A molecule’s biological function is related to its A molecule’s biological function is related to its shapeshape

Chemical reactions make & break chemical bondsChemical reactions make & break chemical bonds2011-20122011-2012

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Any Questions??Any Questions??

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