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Biochemistry Basics. Section 1.1. Subatomic Particles and the Atom. Protons (+ charge) and neutrons (neutral) found in the nucleus Electrons (- charge) Surround the nucleus in a “cloud” or orbital Orbital the 3D space where an electron is found 90% of the time

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subatomic particles and the atom
Subatomic Particles and the Atom
  • Protons (+ charge) and neutrons (neutral)
    • found in the nucleus
  • Electrons (- charge)
    • Surround the nucleus in a “cloud” or orbital
  • Orbital
    • the 3D space where an electron is found 90% of the time
    • Each orbital can fit only 2 electrons
bonding covalent bonds

Hydrogen atoms (2 H)

In each hydrogen

atom, the single electron

is held in its orbital by

its attraction to the

proton in the nucleus.

+

+

2

3

1

When two hydrogen

atoms approach each

other, the electron of

each atom is also

attracted to the proton

in the other nucleus.

+

+

The two electrons

become shared in a

covalent bond,

forming an H2

molecule.

+

+

Hydrogen

molecule (H2)

Bonding – Covalent Bonds
  • Atoms bond through interaction of their valence (outer orbital) electrons
  • Covalent bond
    • electrons are shared between atoms and the valence orbitals overlap
slide5

Name

(molecular

formula)

Electron-

shell

diagram

Space-

filling

model

Structural

formula

Water (H2O).

Two hydrogen

atoms and one

oxygen atom are

joined by covalent

bonds to produce a

molecule of water.

H

O

H

Methane (CH4).

Four hydrogen

atoms can satisfy

the valence of

one carbon

atom, forming

methane.

H

H

H

C

H

ionic bonds
Ionic Bonds
  • In some cases, atoms strip electrons away from their bonding partners
  • Ionic bond – electrons are transferred from one atom to the other, resulting in a negative ion (anion) and a positive ion (cation), which are electrostatically attracted to each other
slide7

Each resulting ion has a completed

valence shell. An ionic bond can form

between the oppositely charged ions.

The lone valence electron of a sodium

atom is transferred to join the 7 valence

electrons of a chlorine atom.

+

Cl

Na

Na

Cl

Cl–

Chloride ion

(an anion)

Na+

Sodium on

(a cation)

Na

Sodium atom

(an uncharged

atom)

Cl

Chlorine atom

(an uncharged

atom)

Sodium chloride (NaCl)

slide8

Covalent bonds are stronger than ionic bonds

  • Covalent and Ionic bonds are intramolecular forces of attraction because they are within molecules
polarity
Polarity
  • Electronegativity
    • Is the attraction of an atom for electrons
  • The more electronegative an atom
    • The more strongly it pulls electrons toward itself
  • The smaller the atom
    • the more electronegative
slide10

to determine the type of bond between two atoms, calculate the difference between their electronegativity values

=0 covalent strong electrons shared equally

electrons

0 < x < 1.7 polar covalent partially shared

>= 1.7 ionic weak electrons not (extreme polarity) shared

  • the greater their difference in electronegativity, the greater the polarity of that substance
slide11
Polar Covalent Bond – electrons are shared unequally between atoms of different electronegativity; electrons are closer to the atom with the higher value

Because oxygen (O) is more electronegative than hydrogen (H),

shared electrons are pulled more toward oxygen.

This results in a

partial negative

charge on the

oxygen and a

partial positive

charge on

the hydrogens.

d–

O

H

H

d+

d+

H2O

intermolecular forces
Intermolecular Forces
  • intermolecular forces of attraction exist between molecules
  • London forces
    • form when the electrons of one molecule are attracted to the positive nuclei of neighbouring molecules; holds large nonpolar molecules together; very weak
slide13

H

Water

(H2O)

O

A hydrogen

bond results

from the

attraction

between the

partial positive

charge on the

hydrogen atom

of water and

the partial

negative charge

on the nitrogen

atom of

ammonia.

H

 +

 –

Ammonia

(NH3)

N

H

H

d+

+

H

Figure 2.15

  • hydrogen bonds
    • form when the slightly negative O or N that is bonded to a slightly positive H is attracted to the slightly positive H of a neighbouring molecule; strongest

 +

 –

slide14

dipole-dipole forces

    • form when the slightly negative end of a polar molecule is attracted to the slightly positive end of a neighbouring polar molecule; stronger
    • Occurs because electrons are in constant motion and may accumulate by chance on one part of the molecule. The result is “hot spots” of positive and negative charge.
water

–

Hydrogenbonds

+

H

–

+

H

+

–

 –

+

Figure 3.2

Water
  • highly polar because of asymmetrical shape and polar covalent bond
  • The polarity of water molecules results in hydrogen boding
like dissolves like
“Like Dissolves Like”
  • ionic compounds dissolve in water because the ions separate
slide17

However, molecules do not need to be ionic to dissolve in water

  • Smaller polar covalent molecules (eg: sugars, alcohols) can dissolve in water, but large nonpolar molecules (eg: oils) do not
  • small nonpolar molecules (eg: O2, CO2) are slightly soluble and need soluble protein molecules to carry them (eg: hemoglobin transports oxygen through the blood)
slide18

hydrophilic – “water-loving;” dissolves in water

    • e.g. polar or ionic molecules, carbohydrates, salts
  • hydrophobic – “water-fearing;” does not dissolve in water
    • e.g. non-polar molecules, lipids
acids and bases
Acids and Bases
  • acid – donates H+ to water; pH 0-7
  • base –donates OH- to water (or H3O); pH 7-14
  • neutralization reaction – the reaction of an acid and a base to produce water and a salt (ionic compound)
strong and weak acids bases
Strong and Weak Acids/Bases
  • strong acids and bases – ionize completely when dissolved in water
    • HCl(aq) (100% H3O+(aq))
    • NaOH(aq) (100% OH-(aq))
  • weak acids and bases – ionize only partially when dissolved in water
    • CH3COOH(aq) (1.3%  H3O+(aq))
    • NH3(aq) (10%  OH-(aq))
buffers
Buffers
  • The internal pH of most living cells must remain close to pH 7
  • Buffers
    • Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution
    • Can donate H+ ions or remove H+ ions when required
    • E.g. carbonic acid creates bicarbonate ions (base) and hydrogen ions (acid) (reversible reaction)
to do
To Do
  • Section 1.1 Questions
    • Pg. 23 #1, 2, 4, 6-8, 12, 14, 15