Chapter 2

AP Biology AP Biology BASIC CHEMISTRY (Review)BASIC CHEMISTRY (Review)

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Structure and function of all living things are governed by the laws of chemistryUnderstanding the basic principles of chemistry will give you a better understanding of all living things and how they function!

“We are all connected; To each other, biologically. To the earth, chemically. To the rest of the universe atomically.” ― Neil deGrasse Tyson

QUESTION: What examples can you give of how chemistry is involved in biology?

• Photosynthesis– Is an example of a

chemical reaction

CHEMISTRY- The science of the composition, structure, properties, and reactions of matter

CHEM REVIEW• Matter- • Mass- • Is MASS the same thing as WEIGHT?

– - The pull of gravity on an object is what gives an object its "weight"

– - A bowling ball having the same mass on Earth and the moon would weigh less on the moon than it does on Earth due to a gravitational pull present on the Moon.

– How much do you weigh on other planets??? Find out here: http://www.exploratorium.edu/ronh/weight/

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States of MatterStates of Matter• SOLID: molecules are tightly linked; little movement and

definite shape• LIQUID: molecules are less tightly linked; moves more freely

than solids; conforms to container• GAS: molecules are usually not attracted to one another;

move very fast; fills the entire volume of a container

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Biology application:How does this affect diffusion across a membrane? Homeostasis in cells?

ElementsElements• Pure substances that

cannot be broken down into simpler substances

• Periodic Table• created in 1869 by

Mendeleev • categorizes elements

and shows trends • 118 elements, 92

occurring naturally5

•Noble or "inert" gases on far right•Alkali metals on far left (minus H)•Atomic radii increase from left to right and decrease from top to bottom

Biologists love CHONPS CHONPS most of all!

• 96% of all living matter: Sulfur, Phosphorus, Oxygen, Nitrogen, Carbon and Hydrogen (CHONPS).

• From these six elements, you can make almost any combination of organic molecules!– Carbs– Lipids– Nucleic acids– Amino acids, proteins

• Living organisms still need 14 other elements, but in smaller amounts.

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Trace elements: Are required by an organism in only minute quantities

Make up the remaining 4% of living matter

Table 2.1

(a) Nitrogen deficiency (b) Iodine deficiency

• The effects of essential element deficiencies

Figure 2.3

Coenzymes/Cofactors

• Cofactors (ions) Cu, Fe, Zn, Mg

• Coenzymes: vitamins

• http://education-portal.com/

academy/lesson/coenzymes-

cofactors-prosthetic-groups-

function-and-

interactions.html#lesson

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AtomsAtoms• Simplest part of an element that retains all properties of that element• Too small to see so we make up models to help us understand the structure

of atoms and predict how they will act• Nucleus- • Electrons (-) orbit around nucleus; very fast• Farther an E- is from the nucleus- More ENERGY!• Atomic Mass- • Atomic Number- • # of electrons = # of protons (and usually neutrons, too)• - Electrons balance out + charge of protons and have very little mass

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Isotopes• We can determine the number of neutrons by using the mass number which

is the sum of the protons and neutrons.• The number of protons is fixed, but the number of neutrons can vary within

the same element. • Thus, the same element may have different atomic masses. Atoms of the

same element that have different atomic masses are called isotopes:Hydrogen: 1p, 1e-

Deuterium: 1p, 1n, 1e- Tritium: 1p, 2n, 1e-

= 1 amu, 2 amu, 3 amu (respectively)

• Some combinations of protons and neutrons are stable, but other combinations are internally unstable and break down spontaneously.

• When this happens, the atom releases various subatomic particles and radiation. These isotopes are called radioactive isotopes.

Isotopes• Radiation can be harmful by

damaging cells and DNA and/or causing cancer

• Some Radioactive isotopes are useful in dating old objects, imaging body organs and tissues through x-rays and killing cancer cells

2.1 From atoms to molecules

larynx

thyroid gland

trachea

b.

a.

a: © Biomed Commun./Custom Medical Stock Photo; b(patient): Courtesy National Institutes of Health (NIH); b(brain scan): © Mazzlota et al./Photo Researchers, Inc.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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Radioisotope Dating– Ex: Radioactive 14C (in Organic Matter) changes into 14N (1/2 of

14C will change into 14N in 5,730 yrs) – Assuming that organic matter always begins with the same

amount of 14C. – Goal is to compare the 14C radioactivity of the fossil to that of a

modern sample of organic matter. The amount of radiation left in the fossil can be converted to the age of the fossil.

– Other similar methods are used to date rocks that are thought to be billions of years old.

ex: Starting with 8g of 14C, down to 1g; how much time has elapsed?answer: 8 4 2 1 = 5730 + 5730 + 5730 = 17,190 yrs

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Parent Daughter Change in…

Carbon-14 Nitrogen-14 5730 years

Uranium-235 Lead-206 4,470 million yrs

Potassium-40 Argon-40 1,208 million yrs

Thorium-232 Lead-208 14,010 million yrs

Rubidium-87 Strontium-87 48,800 million yrs

Commonly used radioisotopes for dating:

CompoundsCompounds• Most elements do not exist by themselves in nature

but rather like to combine with other elements• A molecule is formed when two or more atoms join

together chemically. • A compound is a molecule that contains at least two

different elements. All compounds are molecules but not all molecules are compounds.– Chemical properties of compounds are different than the

elements alone (2 gases = liquid. Ex: Na + Cl = table salt)

• “Chemical rxn’s”- chemical bonds can be broken, atoms can be rearranged, and new chemical bonds are formed!

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BondingBonding• Most bonding takes place because atoms are

most chemically stable when their outermost energy levels are filled

• “The Octet Rule”

Valence electrons• Outer shell electrons are called the valence

electrons and are the ones involved in all the bonding and chemical reactions of each atom.

• Knowing the valence of an electron will give you a better idea of it’s bonding properties

• To find out how many valence electrons an atom has, you can do a shell diagram (2, 8, 8, 18) or a dot diagram (shows only valence)

• http://www.green-planet-solar-energy.com/electron-dot-structure.html

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BondingBonding• Most bonding takes place because atoms are

most chemically stable when their outermost energy levels are filled

Types of Chemical Bonds• Covalent bonds:

– Strong bonds– Shared electrons, simulate a full outer orbital

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Nonpolar covalent bonds• The atoms have similar electronegativities

– Share the electron equallyExamples of this are the DIATOMIC molecules

H, O, N, Cl, Br, I, F

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Hydrogen (H2). Two hydrogen atoms can form a single bond.

Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

H H

O O

Figure 2.11 A, B

Polar covalent bonds:

• Electrons are shared, but not evenly shared

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This creates further potential for hydrogen bonds to form between molecules

The Significance of Weak Chemical Bonds

• Several types of weak chemical bonds are important in living systems

• Weak chemical bonds– Reinforce the shapes of large molecules– Help molecules adhere to each other– Hydrogen bonds are such bonds

Hydrogen BondsHydrogen Bonds

• Relatively weak, singly, but rather strong collectively

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Van der Waals Interactions• Van der Waals interactions

– Occur when transiently positive and negative regions of molecules attract each other

• Weak bonds help determine molecular shape– For example, the folding of a protein– Determines how biological molecules recognize and

respond to one another with specificity

Molecular Shape often determines function

Ionic BondsIonic Bonds

• Strong bonds• Create ions• Create electrical charges: when + and – charges

attract, ionic bonds are created• OXIDATION: Na becomes (Na+) = loses e-• REDUCTION: Cl becomes (Cl-)= gains an e-

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EnergyEnergy• Basic definition?• Laws of Thermodynamics. • Energy can neither be created or destroyed but it can be

changed from form to form• Many energy forms are important in biology:

– chemical energy – thermal energy– radiant energy– electrical energy– mechanical energy

• Amount of energy in the universe remains the same over time– Energy = usable energy + dissipates (ex: heat)

• Free energy ΔG: energy in a system that is available for work. – For example, in a cell, it is the energy available to fuel cell

processes (growth, cell division, metabolism, etc)25

Energy and Chemical ReactionsEnergy and Chemical Reactions• Exergonic rxn’s = release energy (products have less

chemical energy than reactants) - ΔGex: AB + CD AC + DB + energy

• Endergonic rxn’s = absorb energy (products have more chemical energy than reactants) + ΔG

ex: AB + CD + energy AC + DB

• Activation energy: energy added to reactants to "jumpstart" the rxn

• Catalysts: reduce the amount of activation energy that is needed to start the rxn. See Figure 2-7 in your book.

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The energetics of chemical reactions

• Think about rolling a boulder up a hill…it takes energy input, right? And the boulder at the top of the hill now has that energy stored in it (potential). So the product ends up having MORE energy than the reactant.

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• Think about a boulder rolling down a hill…it has lots of energy. And the boulder at the bottom of the hill now has less (potential) energy. So the product ends up having LESS energy than the reactant.

Quiz

• Which of these biological processes is (overall) endergonic? Exergonic? –ΔG ? +ΔG ?

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The role of catalysts

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SolutionsSolutions

• Water is extremely important to all living things, so the chemistry of living things often involves the study of solutions!

• Solution: mixture in which substances are uniformly distributed in another substance– Solutions can be mixtures of liquids, solids, or gases

• Solute: • Solvent:• Concentration [ ]: measurement of the amount of solute dissolved in a

fixed amount of solvent• Saturated? • Aqueous solutions:

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Acids and BasesAcids and BasesDissociation: force between H2O molecules is so

strong that the O- atom from one H2O molecule can pull off the H+ atom from another molecule

• Water dissociates into H+ and OH- equally (hydrogen and hydroxide)

• A Hydronium ion (H3O+)can form when a free H+ ion can react with another H2O molecule

• Acidity and Alkalinity is a measure of the relative amount of OH- and H+ ions in a solution!

• Pure water has equal OH- and H+ ions in solution; pH of 7.0

• Acidic solutions have H+ > OH- ions– pH is below 7.0– sour

• Basic (alkaline) solutions have H+ < OH- ions– pH is above 7.0– slippery and bitter 31

H2O H+ + OH-

Acids and BasesAcids and Bases

• “Acidity” and “Alkalinity” is a measure of the relative amount of OH- and H3O+ ions in a solution!

• The acidity or alkalinity (base) is known as pH (from the French term Pouvoir Hydrogene meaning "hydrogen power").

• pH= measure of how many H3O+ (or H+) ions are in a solution

• The more hydrogen ions present, the higher the hydrogen ion concentration, and the more acidic the solution.

pH = - log base ten of [H+]

If pH = 6 then the concentration of H+ per liter is 10-6 in a solution.

pH of 4 is then 100x more acidic than a pH of 6 (10-4 compared to 10-6)

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BuffersBuffers

• …are chemical substances that neutralize small amounts of either an acid or a base

• Most chemical rxn’s in living organisms are controlled by pH, therefore...

• Buffers are very important for maintenance of homeostasis.

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Bicarbonate Buffer in Human Blood

– If blood pH drops below 7.0 (acidosis), it could be fatal– If blood pH goes above 7.7 (alkalosis), it could be fatal

• If our blood did not contain a buffering system (bicarbonate ion), we would not be able to drink and eat acidic/basic foods!

• Great chem review: http://scidiv.bcc.ctc.edu/rkr/Biology101/lectures/pdfs/Chemistry101.pdf 34