+SBI4U

BIOCHEMISTRY

Ms. Manning

Atoms, Bonding & Molecular Polarity

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“. . . Everything that living things can do can be understood in terms of the jigglings and wigglings of atoms.”

Richard P. Feynman, 1963

Sperm approaching an egg

Atoms, Bonding, and Molecular Polarity

6 types of atoms make up 99% of all living organisms

Element Symbol Atomic #% of human body weight

Oxygen O 8 65.0

Carbon C 6 18.5

Hydrogen H 1 9.5

Nitrogen N 7 3.3

Calcium Ca 20 1.5

Phosphorus P 15 1.0

Potassium K 19 0.4

Sulfur S 16 0.3

Sodium Na 11 0.2

Chlorine Cl 17 0.2

Magnesium Mg 12 0.1

Naturally Occurring Elements in the Human Body

+MATTERMATTER

All MATTER is made up of tiny little particles called ATOMS.

Just like cells are the basic unit of life…

Atoms are the basic unit of matter.

+MATTERMATTER

Atoms are the basic unit of matter

An atom is made up of a central nucleus which contains protons and neutrons.

The nucleus is surrounded by a cloud of electrons, which are orbiting around the nucleus.

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6

CCarbon12.011 Mass Number = protons + neutrons

The element carbon - 6th element in the periodic table

Symbol

Atomic Number = # of protons = # electrons

Bohr model of a hydrogen and oxygen atom

Shells

Nucleus

Protons

Neutrons

Subatomic Particles

Nonradioactive carbon-12 Nonradioactive carbon-13 Radioactive carbon-14

6 electrons6 protons6 neutrons

6 electrons6 protons8 neutrons

6 electrons6 protons7 neutrons

Isotopes are atoms of the same element that vary in the number of neutrons.

Because they have the same number of electrons, all isotopes of an element have the same chemical properties.

Why are electrons so important?• The chemical behavior of an atom is determined by its electron configuration – that is, the distribution of electrons in the atom’s electron shells.

•The chemical behaviour of an atom depends mostly on the number of electrons in its outermost shell. (= valence electron/shell)

•All atoms with incomplete valence shells are chemically reactive.

Octet Rule = atoms tend to gain, lose or share electrons so as to have 8 electrons

C would like to N would like toO would like toH would like to

Gain 4 electronsGain 3 electronsGain 2 electronsGain 1 electron

Atoms bond to form compounds

• Compounds are made up of at least 2 different kinds of atoms (e.g., H2O)

• Bonds are formed by the sharing or transfer of electrons2 Types of Chemical Bonds

Ionic Bonds

Covalent bonds

Ionic Bonds – occur when one atom donates or gives up one or more electrons

Ionic Compound ( Na+Cl-) Salt crystals

Opposite charges

attract to form ionic

bonds

Reaction between Na and Cl to form ionic sodium chloride

(salt)

Covalent Bonds – involve a sharing of a pair of valence electrons between atoms.

Figure. 1.5, p.10

Single covalent bond

Double covalent bond

Four single covalent bonds

Two single covalent bonds

Covalent bond between H2 and O to form one molecule of water

(H2O)

2 Types of Covalent Bonds

Polar Covalent Non-polar covalent

Equal sharing of electrons

Unequal sharing of electrons

All bonding types aredetermined by the atoms

ELECTRONEGATIVITY

E.g., H2

O2

E.g., H2O

Electronegativity

• the measure of the relative abilities of bonding atoms to attract electrons (Pauling Scale)Electronegativity = Stronger pull of shared electrons

The periodic table has electronegativity values.

•We can determine the nature of a bond based on ΔEN (electronegativity difference).

Electronegativity

• In a non-polar covalent bond, there is relatively no electronegative difference. Electrons are shared equally. E.g., O2 oxygen

atoms have the same elecronegativity

• In a polar covalent bond, there is an electronegative difference. Electrons are shared unequally. E.g., H2O oxygen atom is more

electronegative than the hydrogen atoms

Calculating the Electronegative Difference

ΔEN = higher EN – lower EN

NBr3: ΔEN = 3.0 –2.8 = 0.2 (for all 3 bonds).

• Basically: a ΔEN…

below 0.5 = covalent (equal é sharing)

0.5 -1.7 = polar covalent (unequal é sharing)

above 1.7 = ionic (loss/gain of é)

Calculate electronegativity(ΔEN):

Determine the ΔEN and bond type for:HClBr2

CrOCH4

H2OKCl

The boy is not equally sharing with anyone else but rather taking all the food for

himself.

Polar Covalent Bond Analogy

Non-Polar Covalent Bond Analogy

The children are equally sharing the drink between themselves.

Ionic Bond Analogy

Parents giving up their money to keep stable when their children beg to gain

cash

Water is a polar molecule because oxygen is more electronegative than hydrogen, and therefore electrons are pulled closer to oxygen.

Shared electrons spend more time near the the oxygen nucleus

As a result, the oxygen atom gains a slightly negative charge and the hydrogen atoms become slightly positive

• Polar Molecules (like water) have an unequal distribution of charge.

• Since water is polar, it can attract other water molecules.

• The attraction betweenwater molecules are called hydrogen bonds.

Hydrogen bonds are weak forces between molecules

Electronegativity and Physical Properties

Electronegativity can help to explain properties of compounds like those in the lab.

Lets look at HCl: partial charges keep molecules together.

The situation is similar in NaCl, but the attraction is even greater

(ΔEN = 2.1 vs. 0.9 for HCl.

Which would have a higher melting/boiling point?

Electronegativity and Physical Properties

Solubility of Substances in Water

Cl-

Water

Cl-

Na+

Water

Na+

Due to water’s polarity, it is a great solvent. A solvent is a substance in which a solute dissolves. A solute is what is being dissolved. What is happening in the example below?

Water is great at dissolving both ionic (+,-) compounds and polar (partialpositively, partial negatively charged molecules) molecules.

Solubility of Substances in WaterHydrophilic (means water-loving) compounds interact with water by dissolving in it.

E.g., Anions (chloride ions) in salt attracted to + poles of water (causes sodium cation to dissociate)

Hydrophobic (means water-hating) compounds do not interact with water because they cannot form hydrogen bonds

E.g., Non-polar compounds are insoluble in water

Oil – non-polar compound of carbon and hydrogen

Choice Board Task: Atoms, Bonding and Molecular Polarity

Task:

Demonstrate your understanding of the relationship between electronegativity, bonding, and the polarity of molecules.

Success Criteria: • Incorporate, at least, the following terms in your product:

• Include examples and/or diagrams where appropriate.• Ensure that your product is self-explanatory (provide

explanations for visual elements where appropriate)• Prepare to present to a group of your peers• References (APA)

Electron(s) Atom(s) Protons Neutrons

MoleculesValence shell or

valence electron

Covalent bond Ionic bond

Cation AnionElectronegativit

yNon-polar

covalent bond

Polar covalent bond

Hydrogen bondElectronegative

differenceReactivity or

reactive

Hydrophilic HydrophobicSoluble/Solubility

Insoluble

Isotope CompoundIntra- and inter-

molecular forces

Polar molecule

Choice Board

LOGICAL-MATHEMATICAL

Create a flow chart or matrix

Be sure to study the criteria carefully before you select and as you

proceed.

BODILY-KINESTHETICConstruct a model, or

representation (include a written explanation)

VISUAL SPATIALDesign a graphic

organizer (e.g., concept map with

connecting phrases between words )

WILD CARD

INTERPERSONAL Write a short story that incorporates characters

and a plot.

MUSICAL-RHYTHMICCreate a rap, jingle or

song

INTERPERSONAL Develop a role play, an oral presentation, or a

YouTube video

VERBAL LINGUISTICCreate a poem, poster or print advertisement

Choose a mode to express your understanding:

+Credits

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