BIOCHEMISTRYThe Chemical Context of Life

INQUIRY: What creates “devil’s gardens” in the rain forest?

• Devil's gardens are large stands of trees in the Amazonian rainforest that consist almost entirely of a single species.

• Which ant? Myrmelachista schumanni

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Which tree? Duroia hirsuta

INQUIRY: Care to formulate a hypothesis, or two, or three?

Who tends this garden?

Duroiatree

Devil’s garden

Cedrelasapling

Inside,unprotected Inside,

protected

Insectbarrier

Outside,protected

Outside,unprotected

EXPERIMENT

INQUIRY: Care to test a hypothesis, or two?

Working under Deborah Gordon and with Michael Greene, graduate student Megan Frederickson sought the cause of “devil’s gardens”. Field experiments were performed in Peru.

Duroiatree

Devil’s garden

Cedrelasapling

Inside,unprotected Inside,

protected

Insectbarrier

Outside,protected

Outside,unprotected

EXPERIMENT

INQUIRY: Care to test a hypothesis, or two?

Two saplings of a local nonhost tree species, Cedrela odorata, were planted inside each of 10 devil’s gardens.

• At the base of one, a sticky insect barrier was applied.

• The other was left unprotected. WHY?

Duroiatree

Devil’s garden

Cedrelasapling

Inside,unprotected Inside,

protected

Insectbarrier

Outside,protected

Outside,unprotected

EXPERIMENT

INQUIRY: Care to test a hypothesis, or two?

Next, two more Cedrela saplings were introduced about 50 meters outside each garden, one with and one without the sticky insect barriers.

Duroiatree

Devil’s garden

Cedrelasapling

Inside,unprotected Inside,

protected

Insectbarrier

Outside,protected

Outside,unprotected

EXPERIMENT

INQUIRY: Care to collect some data?!

The researchers observed ant activity on the Cedrela leaves and measured areas of dead leaf tissue after one day. They also chemicallyanalyzed contents of the ants’ poison glands.

INQUIRY: What do we conclude? !

Ants of the species Myrmelachista schumanni kill nonhost trees by injecting the leaves with formic acid, thus creating hospitable habitats (Devi's gardens) for the ant colony.

RESULTS

INQUIRY: Care to analyze some data?!

The ants made the injections from the tips of their abdomen into leaves of unprotected saplings in their gardens.

Within one day, these leaves developed dead areas (examine the graph again!).

RESULTS

Inside,unprotected

Inside,protected

Outside,unprotected

Outside,protected

Cedrela saplings, inside and outside devil’s gardens

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12

8

4

0Dea

d le

af ti

ssue

(cm

2 )af

ter o

ne d

ay

INQUIRY: Care to analyze some data?!

"Here we show that the ant, Myrmelachista schumanni, which nests in D. hirsuta stems, creates devil's gardens by poisoning all plants except its hosts with formic acid.

By killing other plants, M. schumanni provides its colonies with abundant nest sites—a long-lasting benefit, as colonies can live for 800 years."

INQUIRY: The formal conclusion from the authors of the study.

Matter consists of chemical elements in pure form and in combinations called compounds.

• Element: a substance that cannot be broken down into other substances by chemical reactions.

• There are 92 naturally occurring elements

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Matter consists of chemical elements in pure form and in combinations called compounds.

• Compound: consists of 2 or more different elements combined in a fixed ratio.

• A compound has characteristics different from its element.

• Na (soft metal, explodes in water) + Cl (poisonous gas) NaCl (a seasoning we sprinkle on food without fear!)

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The Elements of LifeC. HOPKINS CaFe

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• About 20–25% of the 92 elements are essential to life

• Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

• Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur

• Trace elements are those required by an organism in minute quantities

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An element’s properties depend on the structure of its atoms

• An atom is the smallest unit of matter that still retains the properties of an element.

• Atoms are composed of subatomic particles• Relevant subatomic particles include

– Neutrons (no electrical charge)– Protons (positive charge)– Electrons (negative charge)– p+ and n0 reside in a very dense nucleus– e− reside in the electron cloud

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Cloud of negativecharge (2 electrons)

Electrons

Nucleus

(a) (b)

One of these diagrams is fraught with danger!

More annoying Atomic Structure Vocabulary

Atomic Number and Atomic Mass• Atoms of the various elements differ in number of

subatomic particles• An element’s atomic number is the number of protons

in its nucleus• An element’s mass number is the sum of protons +

neutrons in the nucleus • Atomic mass, the atom’s total mass, can be

approximated by the mass number but is actually represented by an AVERAGE molecular mass based on the abundance of various isotopes.

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Speaking of Isotopes…

• All atoms of an element have the same number of protons but may differ in number of neutrons

• Isotopes are two atoms of an element that differ in number of neutrons

• Radioactive isotopes decay spontaneously, giving off particles and energy

• Some applications of radioactive isotopes in biological research are

– Dating fossils (C-14)– Tracing atoms through metabolic processes (I-131)– Diagnosing medical disorders

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Question 1

Which of the following is the criterion upon which the modern periodic table is organized?

A. Number of protons B. Number of neutronsC. Atomic mass numberD. All of the above

Question 2

Why might scientists be interested in the "atomic mass" of an atom?

A. It tells how it will behave in a chemical reaction.B. It lets us know the valence of the atom if we know

the atomic number.C. If we know the atomic number, we can determine the

number of neutrons.D. We can use it to know if the atom is radioactive or

not.

On to the electron cloud…

• The Energy Levels of Electrons

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• Energy is the capacity to cause change, perhaps by doing work.

• Potential energy is the energy that matter has because of its location or structure, there are many kinds…not just gravitational PE!

• The electrons of an atom differ in their amounts of potential energy

• An electron’s state of potential energy is called its energy level, or electron shell*

* “Shell” is fraught with misconception—but biologists often use this description. “Energy level” is a much better phrase since the region is not “hard” like a shell.

Electrons farther from the nucleus have more potential energy

• A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can come to rest only on each step, not between steps.

• It’s a quantized event!

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Energy must be absorbed in order to promote an electron to a higher E-level

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What’s the big deal?

Electron Distribution and Chemical Properties

• The chemical behavior of an atom is determined by the distribution of electrons in electron energy levels and sublevels

• The periodic table of the elements shows the electron distribution for each element—think of it as a giant BINGO card

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This diagram focuses on the “shells” which can be misleading!

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First shell

Second shell

Third shell

Hydrogen1H

Lithium3Li

Sodium11Na

Beryllium4Be

Magnesium12Mg

Boron5B

Aluminum13Al

Carbon6C

Silicon14Si

Nitrogen7N

Phosphorus15P

Oxygen8O

Sulfur16S

Fluorine9F

Chlorine17Cl

Neon10Ne

Argon18Ar

Helium2He

2He

4.00Mass number

Atomic number

Element symbolElectrondistributiondiagram

Stuff you probably already know!

• Valence electrons are those in the outermost energy level (or sublevel) , or valence sublevel

• The chemical behavior of an atom is mostly determined by the valence electrons

• Elements with a full valence shell are chemically inert

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Neon, with two filledShells (10 electrons)

First shell

Second shell

(a) Electron distribution diagram

Out with the old model…

Question 3

Whether an atom will be able to interact with other atoms can be determined by

A. Looking at the ratio of protons to neutrons in the nucleus.

B. Whether it has an even or odd number of electrons.

C. Determining the stability of the electrons in their valence orbitals around the nucleus.

D. Identifying the atom as a metal or non-metal.

…in with a better one—electron orbitals

• An orbital is the three-dimensional space where an electron is found 90+% of the time

• Each electron energy level consists of a specific number of orbitals

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First E-level Second E-level

1s orbital 2s orbital Three 2p orbitals

(b) Separate electron orbitals

x y

z

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(c) Superimposed electron orbitals

1s, 2s, and2p orbitals

Heard of s, p, d and f?

The formation and function of molecules depend on chemical bonding between atoms

• Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

• These interactions usually result in atoms staying close together, held by attractions called chemical bonds

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Covalent Bonds

• A covalent bond is the sharing of a pair of valence electrons by two atoms

• In a covalent bond, the shared electrons count as part of each atom’s valence shell

• A covalent bond is formed between shared pairs of electrons:

1 pair—a single bond

2 pairs—a double bond

3 pairs—a triple bond37

Hydrogen atoms (2 H) Hydrogen atoms (2 H)

Hydrogen atoms (2 H)

Hydrogen molecule (H2)

Covalent Bonds: To share or not to share, that is the question!

• The notation used to represent atoms and bonding is called a structural formula

– For example, H—H

• This can be abbreviated further with a molecular formula

– For example, H2

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(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

Name andMolecularFormula

ElectronDistribution

Diagram

Lewis DotStructure and

StructuralFormula

Space-FillingModel

(d) Methane (CH4)

Electronegativity

• Atoms in a molecule attract electrons to varying degrees

• Electronegativity is an atom’s attraction for the electrons in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself

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Not all sharing is created EQUAL!

• In a nonpolar covalent bond, the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

• Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule

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H H

H2Oδ+ δ+

δ–

O

Not all sharing is created EQUAL!• In a nonpolar covalent bond,

the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electrons equally

• Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule

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H H

H2Oδ+ δ+

δ–

O

Net dipole moment

Not all molecules with polar bonds are polar!

• In a nonpolar covalent bond, the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electrons equally

• Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule

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Question 4

Which of the following statements best describes the difference between an element and a molecule?

A. An element is composed of atoms; a molecule is not.B. An element is composed of only one kind of atom;

molecules can be composed of more than one kind of atom.

C. Elements always have lower atomic weights than molecules.

D. Elements exist in nature only as parts of molecules.

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Question 5

For a covalent bond to be polar, the two atoms that form the bond must have

A. different atomic weights.B. the same number of electrons.C. different electronegativities.D. similar electronegativities.

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Ionic Bonds: A case study involving greed!

• Atoms sometimes strip electrons from their bonding partners

• An example is the transfer of an electron from sodium to chlorine

• After the transfer of an electron, both atoms have charges

• A charged atom (or molecule) is called an ion

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Ionic Bonds: A case study involving greed!

• A cation is a positively charged ion• An anion is a negatively charged ion• An ionic bond is an attraction between an anion and

a cation• Compounds formed by ionic bonds are called ionic

compounds, or salts• Salts, such as sodium chloride (table salt), are often

found in nature as crystals

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Question 6

Why are covalent bonds more prevalent among biological molecules than ionic bonds? A. Ionic bonds only occur between metals and non-metals,

and therefore aren't usually present in biological systems.

B. You can have double covalent bonds, but not double ionic bonds, so covalent bonds provide more variety consistent with the structural demands required in biological systems.

C. Biological conditions are often aqueous, and the water would cause ionic bonds to dissociate.

D. Ions only form under extreme conditions not compatible with the cell's environment.

Here’s where the trouble starts…• There is a rift between biology and chemistry text books.

• The biology book often speaks of “weak bonds” when they really mean intermolecular forces (forces of electrostatic attraction “between molecules”) which are not at all the same as sharing a pair of electrons within a molecule

• IMFs are intermolecular whereas chemical bonds are intramolecular

• Inter—means between molecules (think interstate highway, one between states, connecting states)

• Intra—means within the molecule (actual chemical bonds)

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Here’s where the trouble continues…• Furthermore, the biology books often speak of van der

Waals interactions which “lumps” all of the different IMFs together

• Older chemistry books spoke of van der Waals but specifically meant London Dispersion forces.

More on that coming up…

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There are many types of IMFs London dispersion forces (LDFs)—every molecule has

these since every molecule has moving valence electrons. Essentially the electrons are in constant motion and not always evenly distributed (think traffic jam).

If the electrons pile up on one portion of the three dimensional molecule, then we get a temporary concentration of negating charge, creating a temporary negative pole, if you will, since the electrons are not dispersed evenly we now refer to the molecule as a temporary dipole.

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LDFs increase with increasing numbers of electrons on a given molecule

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The larger the molecule, the more likely this will happen since the valence electrons are farther from the mother nucleus, thus less tightly held! What wasn’t polar at all is now “sort of” polar, thus +/- attractions now exist.

Temporary Dipole has formed

“Peer pressure”

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The dotted lines represent attractive forces. This is also happening in all THREE DIMENSIONS!

What’s the big deal?

• Molecules that were not originally attracted to one another, now find each other quite attractive, thus more energy is required to separate them!

• In other words, molecules become “sticky” or adhere to one another.

• Collectively, such interactions can be strong, as between the molecules of a gecko’s toe hairs and the surface of a wall. He’s not really defying gravity!

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Induced Dipole- Induced Dipole IMFs a.k.a. LDFs, or Dispersion Forces

• Induced-Dipole, Induced-Dipole is just another name for what we just described as LDFs. (Don’t you just love grown-ups that can’t agree on terminology??)

• A spontaneous traffic jam of electrons created a slight (-) charge on the end of the molecule with the most electrons leaving the other end slightly (+)

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Dipole - Induced Dipole IMFs

• In Dipole-Induced Dipole, there is a permanent dipole (electronegativity difference is enough to make a permanent (+) and (-) end of the molecule) that induces a nonpolar molecule to become a dipole.

• Now the two are more attracted to each other than they were before the induction occurred.

• Ever induced behavior in another human? Got siblings??

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Dipole – Dipole IMFs

• In Dipole-induced dipole, there is a permanent dipole (electronegativity difference is enough to make a permanent (+) and (-) end of the molecule that induces a nonpolar molecule to become a dipole.

• Now the two are more attracted to each other than they were before the induction occurred.

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Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs

• A hydrogen bond is not the same as a bonded hydrogen!

• It’s a special case of Dipole-Dipole IMFs

• A bonded hydrogen is within a water molecule

• A hydrogen bond is between molecules!

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Hydrogen bonds (IMFs)

Bonded Hydrogens

(actual chemical bonds consisting of a shared

pair of electrons)

Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs

• Hydrogen bonding occurs when the H of one molecule is attracted to a highly electronegative molecule on an adjacent molecule.

• THE CATCH: For an H to be a candidate for hydrogen bonding, it must itself be attached to a highly electronegative element such as F, O or N (think “phone”…call me!)

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Hydrogen “bonds” (IMFs)

Bonded Hydrogens

(actual chemical bonds consisting of a shared

pair of electrons)

Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs

• Hydrogen bonding is an IMF that makes molecules more attracted to each other, thus more tightly held to each other, thus more energy is required to separate them!

• Higher MP, BP, heat of vaporization, etc. occur as a result.

• Also, enhanced solubility of substances such as ammonia.

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Question 7

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Which of the following is true?I. Hydrogen bonds are a special case of dipole-dipole

IMFs. II. Ionic substances dissolve in water.III. Polar substances dissolve in water.

A) I only C) I and III onlyB) III only D) I, II and III

Time to think in 3-D!

• A molecule’s shape is very important to its function

• A molecule’s shape is determined by the positions of its atoms’ valence orbitals

• In a covalent bond, the sand p orbitals may hybridize, creating specific molecular shapes

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Why is Linus Pauling famous??• He developed the electronegativity scale.

• In the 1930’s Linus Pauling introduced the concept of hybridization to explain chemical bond formation. Hybridization is the mixing of atomic orbitals in an atom to generate a set of new atomic orbitals called hybrid orbitals.

• Mixing an s orbital with one of the p orbitals generates two equivalent sp hybrid orbitals. Note that the number of hybrid orbitals is equal to the number of atomic orbitals that are hybridized. The set of two sp hybrid orbitals has a linear arrangement. The angle between the orbitals is 180˚.

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Step 1: 1-s and 3-p atomic orbitals blend to make 4 sp3 molecular orbitals

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Water & Methane are both sp3 hybridized

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Question 8

Consider the Lewis structures shown below. Explain why each is or is not a valid structure.

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The puzzle pieces have to fit!

• Biological molecules recognize and interact with each other with a specificity based on molecular shape

• Molecules with similar shapes can have similar biological effects

• Long ago you accepted that the 4 DNA bases pair A-T and G-C, but WHY??

• Why can’t the A pair with the C?

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The puzzle pieces have to fit!

• Why does a molecule have shape in the first place?• That has to do with IMFs holding things in “place” defining

its 3-D shape. The big people word for “shape” is “conformation”.

• In the case of A-T vs. G-C, it’s all about lining up that IMF called “hydrogen bonding”; 2 sites for A-T and 3 for G-C

Ever heard of “a runner’s high”?

• Our body manufactures endorphins which are made by the pituitary gland and bind to the receptors in the brain that relieve pain and produce euphoria during times of stress, such as intense exercise.

• Opiates such as morphine and heroin are structured similarly, thus can bind with the receptors . These “bindings” are actually those electrostatic attractions we call IMFs.

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The boxed regions are shaped similarly!

Natural endorphin

Morphine

CarbonHydrogen

NitrogenSulfurOxygen

(a) Structures of endorphin and morphine

Pain killer!

• The brain receptors “bind” with either with similar results.

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(b) Binding to endorphin receptors

Brain cell

MorphineNaturalendorphin

Endorphinreceptors

Chemical Reactions Make and/or Break Chemical Bonds

Lets get two things straight before going further…1. Energy must be added to a system to BREAK a

chemical bond.

2. Energy is released when chemical bonds are MADE.

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Chemical Reactions Make and/or Break Chemical Bonds

• Chemical reactions are the making and breaking of chemical bonds

• The starting molecules of a chemical reaction are called reactants

• The final molecules of a chemical reaction are called products

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Chemical Reactions Make and/or Break Chemical Bonds

• Chemical reactions are the making and breaking of chemical bonds

• The starting molecules of a chemical reaction are called reactants

• The final molecules of a chemical reaction are called products

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Photosynthesis is a mighty important chemical reaction!

• Photosynthesis is an important chemical reaction

• Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen

6 CO2 + 6 H2O → C6H12O6 + 6 O2

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Chemical Equilibrium

• All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction

• Chemical equilibrium is reached when the rate of the forward reactions is equal to the rate of the reverse reaction

• Chemical equilibrium does NOT mean “equal” amounts of reactants and products are present, but rather that their concentrations have stabilized in a constant ratio!

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Created by:

René McCormickNational Math and ScienceDallas, TX