Chapter 2 – the chemistry of lifeChapter 2 – the chemistry of life

Why is it important to have an Why is it important to have an understanding of chemistry to study understanding of chemistry to study anatomy?anatomy?– All biological functions can be explained All biological functions can be explained

chemicallychemically What are the components of life?What are the components of life?

– MatterMatter– EnergyEnergy

Nature of Matter: Atomic StructureNature of Matter: Atomic Structure

– NucleusNucleus——very small size compared to the entire atom, very small size compared to the entire atom, composed of composed of a)a) protonsprotons (p (p++):): have a positive electrical charge, have a positive electrical charge, have some mass, and have some mass, and b)b) neutronsneutrons (n (n00):): have no electrical charge, have the have no electrical charge, have the same mass as a proton.same mass as a proton.

– Electrons Electrons (e(e--):): thesethese orbit the nucleus, they have a orbit the nucleus, they have a negative electrical charge which is equal and opposite negative electrical charge which is equal and opposite the charge of a proton, they have a negligible mass.the charge of a proton, they have a negligible mass.

– Atoms are usually Atoms are usually electrically neutralelectrically neutral—number—number of of electrons = number of protons.electrons = number of protons.

Nature of Matter: Atomic StructureNature of Matter: Atomic Structure

How can we tell one atom from another? What is the How can we tell one atom from another? What is the distinction?distinction?– Atomic NumberAtomic Number — — the number of protons in an atom.the number of protons in an atom.– Atomic Mass (weight)Atomic Mass (weight) – mass of atom, which would include # of – mass of atom, which would include # of

protons + # of neutronsprotons + # of neutrons Other Definitions Other Definitions

– ElementElement – matter composed of atoms of only one kind. – matter composed of atoms of only one kind.» The number of protons in the nucleus of any given atom is always The number of protons in the nucleus of any given atom is always

the same AND each element has a different number of protons in its the same AND each element has a different number of protons in its nucleus nucleus

– MoleculesMolecules:: A combination of atoms where electrons in the A combination of atoms where electrons in the outermost orbital are either transferred or shared.outermost orbital are either transferred or shared.

– CompoundCompound:: A molecule that has two or more kinds of atoms. A molecule that has two or more kinds of atoms.– Chemical FormulaChemical Formula:: C C66HH1212OO66

http://wine1.sb.fsu.edu/chm1045/tables/period/PT_large.jpg

other 7%

oxygen 65%

carbon 18%

other 8%

oxygen 50%

silicon26%

aluminum 8%

calcium 3%

iron 5%

Earth’s crust Human body

hydrogen10%

Table. 2.2Table. 2.2

Nature of Matter: Key Components of the AtomNature of Matter: Key Components of the Atom

– Size -Size - nucleus is much smaller than surrounding orbital and atoms nucleus is much smaller than surrounding orbital and atoms are really, really tiny.are really, really tiny.

– Identity –Identity – # of protons determines identity of atom. Neutrons only # of protons determines identity of atom. Neutrons only provide additional mass.provide additional mass.

– Charge -Charge - is determined by comparing the number of electrons to is determined by comparing the number of electrons to number of protons. If they are equal, then atom is electrically number of protons. If they are equal, then atom is electrically neutral. If they are not, then atom is existing in an ionic state. neutral. If they are not, then atom is existing in an ionic state.

– ReactivityReactivity – – is determined by the valence electrons in the is determined by the valence electrons in the outermost shell. The number of valence electrons really does make outermost shell. The number of valence electrons really does make a difference in the way an atom will behave around other atoms. a difference in the way an atom will behave around other atoms. Some are stable; others are very reactive.Some are stable; others are very reactive.

– Lowest Energy State –Lowest Energy State – all matter (atoms being the smallest all matter (atoms being the smallest particles of matter) always seek there lowest energy state, so they particles of matter) always seek there lowest energy state, so they prefer to be neutral and they prefer to have their outermost energy prefer to be neutral and they prefer to have their outermost energy shell full!shell full!

– Isotopes –Isotopes – Most atoms exist in various isotopic forms. How can Most atoms exist in various isotopic forms. How can you tell? If number of neutrons is different from number of you tell? If number of neutrons is different from number of protons, atom is in an isotopic state. # of neutrons = atomic mass protons, atom is in an isotopic state. # of neutrons = atomic mass (weight) – atomic number.(weight) – atomic number.

Radioactive IsotopesRadioactive Isotopes

Medical DiagnosisMedical Diagnosis Cancer TherapyCancer Therapy Other Biological UsesOther Biological Uses

– Radiometric DatingRadiometric Dating– Radioactive LabelingRadioactive Labeling

Chemical BondingChemical Bonding

The goal of atoms is to find their The goal of atoms is to find their lowest energy lowest energy statestate!!

Types of bondsTypes of bonds– Ionic BondingIonic Bonding – – one atom loses an electron and one one atom loses an electron and one

gains an electron.gains an electron.

– Covalent Bonding Covalent Bonding – two atoms share a pair of – two atoms share a pair of electrons, sometimes equally/sometimes unequally. electrons, sometimes equally/sometimes unequally.

» Single Covalent Bond Single Covalent Bond (one pair of electrons)(one pair of electrons)

» Double Covalent Bond Double Covalent Bond (two pairs)(two pairs)

» Triple Covalent Bond Triple Covalent Bond (three pairs)(three pairs)

Carbon

Hydrogen

Sodium

unstable, very reactive stable, unreactive

e- e- e-

e- e-

e- e-

e- e-

e-

e- e-

e-e-e-

e-

e- e-

e-

e-

e-

e-

e-

e-

e-

e- e- e-

e-

e-

e-

e-

e-

e- e-

e-

e-

e-

e-e-

e-e-

e-e-

e-

e-

e- e-

Helium

Neon

Argon

e-

e-

Sodium atom (Na) Chlorine atom (Cl)

Chlorine ion (Cl-)

electrontransfer

IonicCompound(Na+ + Cl-)

Salt crystals

Polar vs. Non-polar Covalent BondsPolar vs. Non-polar Covalent Bonds Nonpolar Covalent BondsNonpolar Covalent Bonds

– Neither nucleus exerts more attractive pull on shared Neither nucleus exerts more attractive pull on shared electrons (equal electronegativity and equal sharing, electrons (equal electronegativity and equal sharing, like joint custody).like joint custody).

Polar Covalent BondsPolar Covalent Bonds

– HH22O is most common example in the bodyO is most common example in the body

– Oxygen has a greater atomic number than hydrogen.Oxygen has a greater atomic number than hydrogen.

– Oxygen’s nucleus attracts the shared electrons with a Oxygen’s nucleus attracts the shared electrons with a greater electronegativity than hydrogen in a water greater electronegativity than hydrogen in a water molecule.molecule.

– Unequal sharing results in polar charges on different Unequal sharing results in polar charges on different parts of the molecule.parts of the molecule.

Hydrogen bond

O

O O

O

O

O

OH

H

H

H

H

H

H

H

HH

H

HH

H

HH

–

+

+

+

+

+

+

+

+

+

+

––

–

–

–

–

–

–

–

– O

Dissociation and ElectrolytesDissociation and Electrolytes

Functional Groups (Handout)Functional Groups (Handout) These are small groups of atoms that when attached to larger organic These are small groups of atoms that when attached to larger organic

molecules will give those molecules predictable properties such as molecules will give those molecules predictable properties such as hydrophilic hydrophilic (polar) (polar) or hydrophobic or hydrophobic (non-polar(non-polar)/)/acid or base.acid or base.

a)a) HydroxylHydroxyl (R-OH): When attached to a hydrocarbon chain, it creates an (R-OH): When attached to a hydrocarbon chain, it creates an alcohol. This group is found all over sugars. Because it contains a polar alcohol. This group is found all over sugars. Because it contains a polar covalent bond, the Hydrogen atom is polar positive (+) and makes that part covalent bond, the Hydrogen atom is polar positive (+) and makes that part

of the molecule hydrophilic andof the molecule hydrophilic and capable of forming H-bonds.capable of forming H-bonds.

b)b) CarbonylCarbonyl (>C=O): It contains a polar covalent bond and the oxygen is (>C=O): It contains a polar covalent bond and the oxygen is therefore polar negative (-) which makes that part of the molecule therefore polar negative (-) which makes that part of the molecule hydrophilic and capable of forming H-bonds. There are two types of hydrophilic and capable of forming H-bonds. There are two types of carbonyl:carbonyl:

1) 1) AldehydeAldehyde: when the group is found at the : when the group is found at the end end of a chain, and theof a chain, and the

2) 2) KetoneKetone: when the group is found in the middle of a chain.: when the group is found in the middle of a chain.

Functional Groups, ContinuedFunctional Groups, Continued

c)c) CarboxylCarboxyl (R-COOH): This group loses the H off of the hydroxyl group (R-COOH): This group loses the H off of the hydroxyl group which forms both a negative charged Oxygen (- ion) and a Hydrogen ion which forms both a negative charged Oxygen (- ion) and a Hydrogen ion (H+) is released into solution. This makes the molecule to which it is (H+) is released into solution. This makes the molecule to which it is attached an acid. The polar charges and the ionic charges cause this part attached an acid. The polar charges and the ionic charges cause this part of a molecule to be highly hydrophilic.of a molecule to be highly hydrophilic.

d)d) AminoAmino (>NH2): This group tends to pick up H+ ions from the solution (>NH2): This group tends to pick up H+ ions from the solution and causes the pH to rise. Therefore this group makes the molecule a and causes the pH to rise. Therefore this group makes the molecule a base. The group becomes ionically charged (+) and this makes this part base. The group becomes ionically charged (+) and this makes this part of the molecule highly hydrophilic.of the molecule highly hydrophilic.

e)e) PhosphatePhosphate (R-PO4): This group releases H+ into solution making the (R-PO4): This group releases H+ into solution making the molecule to which it is attached both acidic and hydrophilic.molecule to which it is attached both acidic and hydrophilic.

f)f) MethylMethyl (R-CH3): The nonpolar covalent bonds in this group make the (R-CH3): The nonpolar covalent bonds in this group make the part of the molecule to which it is attached hydrophobic.part of the molecule to which it is attached hydrophobic.

ACIDIC

NEUTRAL

BASIC

100

10-1

10-2

10-3

10-4

10-5

10-6

10-7

10-8

10-9

10-10

10-11

10-12

10-13

10-14

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

battery acidhydrochloric acid

lemon juice, gastric

(stomach) juice

cola, beer, wine, vinegar

tomatoes

black coffee

urine

pure water

human bloodseawater

baking soda

Great Salt Lake

lye

household ammonia

household bleach

oven cleaner

Chemical reactionsChemical reactions

Types of chemical reactions:Types of chemical reactions:

1.1. Synthesis reactionsSynthesis reactions

2.2. Decomposition reactionsDecomposition reactions

3.3. Exchange reactions – single or double Exchange reactions – single or double replacementreplacement

All metabolic pathways require energy at some All metabolic pathways require energy at some point! – ATP/ADPpoint! – ATP/ADP

Most biological reactions are Most biological reactions are reversiblereversible as well! as well!

Fig. 2.20Fig. 2.20

Chemical reactions, cont’dChemical reactions, cont’d

Reversible reactions - equilibriumReversible reactions - equilibriumIn the body, reactants and products tend to react with one In the body, reactants and products tend to react with one

another back and forth until equilibrium is reached - another back and forth until equilibrium is reached - homeostasishomeostasis

Reaction Rates – what affects rate of rxn?Reaction Rates – what affects rate of rxn?– Concentration of reactantsConcentration of reactants– TemperatureTemperature– Enzymes (catalyst)Enzymes (catalyst)

biochemistrybiochemistry

Inorganic MoleculesInorganic Molecules – Molecules that do not – Molecules that do not contain carboncontain carbon

1.1. WaterWater – inorganic – inorganica.a. High Specific Heat, meaning water resists High Specific Heat, meaning water resists

temperature changes which helps in maintaining body temperature changes which helps in maintaining body temperature. temperature.

b.b. High Heat of Vaporization – Evaporative CoolingHigh Heat of Vaporization – Evaporative Coolingc.c. Effective lubricant – surface of the eyeEffective lubricant – surface of the eyed.d. Necessary reactant in chemical reactions – digestionNecessary reactant in chemical reactions – digestione.e. Universal Solvent – works for transport of nutrients Universal Solvent – works for transport of nutrients

throughout bodythroughout body

Biochemistry, cont’dBiochemistry, cont’d

Macromolecules of Life (organic)Macromolecules of Life (organic) – Molecules – Molecules that contain carbon (Table 2.3 – page 31)that contain carbon (Table 2.3 – page 31)

CarbohydratesCarbohydrates – mono, di and polysaccharides– mono, di and polysaccharides LipidsLipids – fats, fatty acids, glycerol, – fats, fatty acids, glycerol,

triaglycerols/triglycerides – saturated and triaglycerols/triglycerides – saturated and unsaturated fatsunsaturated fats

ProteinsProteins – amino acids – amino acids– Enzymes – activation energyEnzymes – activation energy

Nucleic acidsNucleic acids – DNA, RNA – DNA, RNA

Fig. 2.11Fig. 2.11

Fig. 2.12Fig. 2.12

Fig. 2.13Fig. 2.13

Fig. 2.14Fig. 2.14

O

CH3

HO

CH3

OH

testosterone

CH3

OH

estrogen

HO

CH3

CH3

CH3

CH3

CH2

CH2

CH2

CH3

HC

HC

cholesterol

Fig. 2.16aFig. 2.16a

Fig. 2.16bFig. 2.16b

Fig. 2.19bFig. 2.19b

The detailed structure of an animal cell’s plasma membrane, in cross sectionThe detailed structure of an animal cell’s plasma membrane, in cross section

Enzyme ActionEnzyme Action

Three-Dimensional Shape: Important in Three-Dimensional Shape: Important in BiologyBiology

– Compounds have very definite spatial Compounds have very definite spatial configurations.configurations.

– Shape determines how molecules can bind one Shape determines how molecules can bind one another, a critical step in many activities. This another, a critical step in many activities. This is especially true where enzymes are concerned.is especially true where enzymes are concerned.

– Throughout biology we see a complementarity Throughout biology we see a complementarity of structure to function. This is easily seen of structure to function. This is easily seen throughout all of biology.throughout all of biology.

Activation Energy & EnzymesActivation Energy & Enzymes