The Chemistry of the Cell

1
The Chemistry of the Cell

• Reading Becker, ch. 2, pp. 17-26

2
Carbon is the most important atom in biological
molecules.

• Vast majority of biological molecules are
  carbon-containing
• An understanding of basic organic chemistry is
  important for understanding cell biology

3
The Importance of Carbon Molecules composed of
atoms that are linked to one another through
covalent bonds In covalent bonds, neighboring
atoms share electrons in order to fill their
outermost electron orbital
4
Stability of Carbon-Containing Molecules

• It takes a lot of bond energy to break covalent
  bonds
• Bond energy amount of energy required to break
  1 mole of bonds (6 x 1023)
• measured in cal/mol, where 1 cal is the amount
  of energy needed to raise the temperature of 1 g
  of water 1ºC.

5
Stability of Carbon-Containing Molecules

• Single bonds are the easiest to break
• i.e., they have the lowest bond energy
• C-N 70 kcal/mol
• C-C 83 kcal/mol
• C-O 84 kcal/mol
• C-H 99 kcal/mol

6
Stability of Carbon-Containing Molecules

• Double bonds require more energy to break
• C C 146 kcal/mol
• Triple bonds require the most energy to break
• C C 212 kcal/mol

7
Stability of Carbon-Containing Molecules
Notice that covalent bonds are much more stable
than non-covalent bonds
8
Stability of Carbon-Containing Molecules
Energy of light is inversely proportional to the
wavelength E 28,600 kcal-nm/einstein
l 28,600 amount of energy/1 mol of
photons, and l is the wavelength in nm Notice
that visible light poses no threat to covalent
bonds. UV light does!
9
Diversity of Carbon-Containing Molecules

• The principal atoms found in biological molecules
  are C, H, O, N, and less frequently S and P
• The way in which these atoms are arranged within
  a molecule greatly affects the functioning of
  these molecules.

10
Hydrocarbons

• Comprised entirely of C and H atoms as part of
  chains or ring structures
• Insoluble in water

11
Common Functional Groups

• Functional groups on carbon-containing molecules
  confer water solubility and chemical reactivity
  to the molecules in which they are found

12
Common Functional Groups

• Carboxyl and phosphoryl groups ionized at
  near-neutral pH of most cells to give them a
  negative charge.
• Amino groups protonated to give them a positive
  charge.
• Hydroxyl, sulfhydryl, carbonyl, and aldehyde
  groups are uncharged, but still polar.

13
Stereoisomers

• C has a tetrahedral geometry
• i.e., it can form bonds with as many as 4 groups
• If a C atom forms bonds with 4 different groups,
  it is called an asymmetric carbon
• Molecules with asymmetric carbons can exist in
  different geometries or conformations

14
Stereoisomers
Stereoisomers have the same chemical formula,
but their structures are mirror images of one
another (like your hands).
15
Stereoisomers
How many asymmetric Cs are present in alanine?
The number of stereoisomers for a molecule with
asymmetric Cs is 2n, where n is the number of
asymmetric Cs. Therefore, there are 2
stereoisomers of alanine.
16
Stereoisomers
The 2 stereoisomers of alanine
17
Stereoisomers
How many asymmetric Cs are present in
glucose? How many stereoisomers of glucose are
there?
18
Water is indispensable for life as we know it.

• Water makes up 75-85 of a cells weight
• Most cells exist in an aqueous extracellular
  environment
• Water is required for normal functioning of the
  cell

19
Water Molecules are Polar

• Polarity uneven distribution of charge within a
  molecule
• In H2O, the O is electronegative i.e., it draws
  electrons toward it

20
Hydrogen-Bonding Between H2O Molecules
Polarity of H2O molecules allows for
electrostatic interactions between the O of one
molecule and a H on a neighboring
molecule Hydrogen bonds weak relative
to covalent bonds Responsible for high surface
tension, high boiling point, high specific
heat, and high heat of vaporization
21
Importance of H-bonding in H2O for Cell Biology

• High specific heat (1 cal/g)
• Specific heat amount of heat a substance must
  absorb per gram to raise its temperature 1ºC.
• H2O can absorb a lot of heat, due to rapid
  breaking and reforming of H bonds buffers
  the heat
• released from cellular reactions and keeps
  cells from overheating
• High heat of vaporization
• Heat of vaporization amount of energy
  required to convert 1 g of liquid into vapor.
• Sweating and panting as ways to cool an
  organism. Energy required to vaporize water is
  drawn from the organism.

22
Importance of the Polarity of H2O for Cell Biology

• Enables H2O to serve as an excellent solvent
• Solution Fluid solvent solute
• Polarity allows for ready formation of
  electrostatic actions between H2O molecules and
  solute molecules or ions

23
Solubility of Substances in H2O

• Hydrophilic molecules dissolve readily in H2O
• e.g. Salts (such as NaCl)
• Ionized molecules (such as those with
  carboxyl, phosphoryl, or amino functional
  groups)
• Positively or negatively charged molecules
  (such as those with hydroxyl, carbonyl, or
  aldehyde functional groups)

24
H2O molecules disrupt electrostatic interactions
between ions in salts, forming spheres of
hydration around each ion.
25
Solubility of Substances in H2O

• Hydrophobic molecules insoluble in H2O
• Contain no polar regions will not interact
  electrostatically with H2O molecules
• Tend to coalesce with one another excluded by
  H2O

26
Selectively Permeable Membranes

• Cells cannot function as closed systems must be
  exchange with the extracellular environment
• Exchange is not free, but is controlled
• Cell membrane defines the boundaries of the cell
  and controls entry and exit of molecules and ions
• Membrane is selectively permeable, allowing some
  things to pass but not others

27
Components of Cell Membranes

• Amphipathic Lipids and Membrane Proteins
• hydrophilic at one end, hydrophobic at the
  other

28
Membrane Lipids
Membrane is a bilayer, with hydrophobic interior
that serves as major barrier to permeability Charg
ed or polar molecules are largely prevented from
crossing
29
Membrane Proteins
Membrane proteins are intermediaries between the
intra- and extracellular spaces Functions Tran
sport proteins Enzymes Receptors Ion channels
30
Permeability

• Non-polar molecules pass through membrane easily
• Polar or charged molecules do not unless they are
  very small (mwlt100)
• Examples of small molecules that can pass
• Small, non-polar O2, CO2
• Small, polar urea, ethanol, H2O
• Examples of small molecules that can not pass (on
  their own)
• Ions Na, K, Ca