Biochemistry Basics

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Biochemistry Basics

• Section 1.1

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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 only fit only 2 electrons

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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

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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
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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

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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)
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• Covalent bonds are stronger than ionic bonds
• Covalent and Ionic bonds are intramolecular
  forces of attraction because they are within
  molecules

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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

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• to determine the type of bond between two atoms,
  calculate the difference between their
  electronegativity values
• 0 covalent strong electrons
  shared equally
• electrons
• 0 lt x lt 1.7 polar covalent
  partially shared
• gt 1.7 ionic
  weak electrons not
  (extreme polarity)
  shared
• the greater their difference in
  electronegativity, the greater the polarity of
  that substance

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• 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
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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

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• 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

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• 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.

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Water

• highly polar because of asymmetrical shape and
  polar covalent bond
• The polarity of water molecules results in
  hydrogen boding

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Like Dissolves Like

• ionic compounds dissolve in water because the
  ions separate

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

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• 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

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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)

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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))

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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)

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Functional Groups

• Functional groups
• Are reactive clusters of atoms attached to the
  carbon backbone of organic molecules

Group Chemical Formula Structural Formula Found In
hydroxyl OH alcohols (eg ethanol)
carboxyl COOH acids (eg vinegar)
amino NH2 bases (eg ammonia)
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sulfhydryl SH rubber
phosphate PO4 ATP
Carbonyl (aldehydes) (keytones) COH CO aldehydes (eg formaldehyde) ketones (eg acetone)
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To Do

• Section 1.1 Questions
• Pg. 23 1, 2, 4, 6-8, 12, 14, 15