The Chemistry of Life

1
The Chemistry of Life
2
Chemical composition of living systems

• Water
• Protein
• Complex carbohydrate
• Nucleic acids (DNA and RNA)
• Lipids
• Miscellaneous (mixtures of small molecules,
  minerals, metals, gasses)
• To understand how it works you have to know what
  it is made of!
• (reductionism)

3
Lipids, Proteins, CHOs, NAs

• Cellular lipids are easier to separate and to
  analyze by standard chemical techniques.
  Heterogenous collection but molecules are smaller
  in size.
• Proteins, CHOs, NAs are huge and complex by
  routine chemical standards
• macromolecules

4
Cellular macromolecules are polymers

• Reductionist approach to analysis
• Mild breakdown of macromolecules (hydrolysis)
  reveals existence of subunits. (proteins-amino
  acids, CHOs-simple sugars, NAs nucleotides)
• Macromolecules are polymers
• Chains of smaller subunits (monomers) linked
  together

5

• The properties of living systems depend upon the
  characteristics of the monomers and the way they
  are attached together
• Cell
• Organelle
• Macromolecule (polymer)
• Monomer
• Small molecules, arrangements of atoms
• Atom
• Subatomic particle

6
Atoms

• Submicroscopic units of matter
• Smallest unit of all physical material
• Substance composed of only one type of atom is
  called an element

7
Structure of Atoms

• Proton
• In nucleus
• Positive charge
• Neutron
• In nucleus
• No charge
• Electron
• Surround nucleus
• Negative charge

8
Atomic Mass

• Combined mass of protons neutrons
• Electron mass is too small to matter

Atomic Mass 14
9
Elements

• Made of a single kind of atom
• Type determined by its number of protons

7 Protons Nitrogen
10
Atoms Isotopes

• Isotopes-different forms of elements/atoms
• Same number of protons, different number of
  neutrons
• Differ in atomic mass

• Atoms
• protons electrons
• Electrically neutral

11
Radioiodine

• Iodine-element with atomic number 53
• Most common (stable) isotope has 74 neutrons.
• Radioisotope less common and stable-78 neutrons
• 131I
• Radiation therapy for thyroid cancer, imaging

12
Electrons

• Shells correspond to energy levels
• Energy increases away from the nucleus
• Electron arrangement influences chemical bonding

13
Molecules

• Two or more atoms attached together by a chemical
  bond
• Same elements or different elements
• Substance composed of molecules that contain more
  than one type of atom is called a compound

14
Compounds are held together by chemical bonds

• Methods of combining and forming permanent
  chemical bonds
• Sharing electrons (covalent bonding)
• Loss gain of electrons (ionic or electrostatic
  bonding)
• In biological systems-temporary combinations are
  highly important
• Chemical bonds determine properties of molecules
  and of living systems

15
Factors that Influence Patterns of Chemical
Bonding

• Tendency of electrons to occur in pairs in an
  orbital
• Tendency of substances to balance charges
  (opposites attract)
• 3. Tendency of outer electron shell to be full
  (Octet Rule)

16
Electrostatic Bonds

• One atom donates electron to other atom to
  satisfy the octet rule for both

17
Disambiguation!!!

• Electrostatic bonds are not important in BIOL
  105.
• Charge interaction (/-) is important.
• A redox reaction is a special type of electron
  transfer used for energy transfer and involving
  two electrons at a time

18
Covalent Bonds

• Atoms share outer electrons

19
(No Transcript)
20

• Molecular oxygen is O2
• (equal sharing)
• Covalent bonding can occur between a variety of
  atoms.
• Water is H2O (unequal sharing)

21
Covalent Bond Strength

• Can be weaker or stronger-depending on atoms
  involved and number of electrons shared
• Single bond, Double bond,Triple bond 1, 2 or 3
  shared pairs
• Sharing may be unequal (polar)
• Covalent bonding is flexible!

22
Covalent Bonding in Carbon

• Can form four covalent bonds
• Can bond to more than one type of atom (including
  itself)
• Single, double, triple bonds
• Single bonds of moderate strength
• Basis for many biological molecules
• organic chemistry

23
Some covalent bonds involving carbon
24
Energy and Covalent Bonds

• Bonds may be used as places to store energy (not
  the only place)
• Breaking these bonds releases energy which may be
  used (or wasted!)
• Allows organisms to store use energy in
  chemical form
• May be converted or transduced to other forms

25
Water

• Most abundant molecule in your body
• Vital to life
• Properties of life determined by properties of
  water

Frog Eggs in Water Environment
26
Molecular Structure of a Water Molecule

• Hydrogens electrons usually near Oxygen
• Molecule has polarity (polar molecule)

27
Polarity of Water

• Allows it to attract other molecules

• Allows temporary sharing of hydrogen nuclei
  (protons), aka hydrogen bonding

28
Hydrogen bonds

• Weak, non-covalent bonds
• Short-range
• Directional
• Sharing a hydrogen nucleus (one proton)
• Very useful for living systems

29
H bonds are versatile

• May involve substances other than water

30
Four key biological impacts of H bonds

• H bonds influence heat capacity
• H bonds influence solubility
• H bonds determine acid-base balance (i.e. pH)
• H bonds influence properties of macromolecules to
  attach to other substances

31
H bonds influence heat capacity

• It is hard to heat up water due to H bonding
• Modulates temperature in living bodies
• As water absorbs heat, hydrogen bonds break
• Evaporation of water is a great way to lose heat

32
H bonds influence solubility

• Water is a powerful solvent
• Ions break away in presence of water
• Polar substances generally dissolve well in
  water-nonpolar ones do not
• This influences the way a cell is built and works

33
How Salt Dissolves in Water
Hydration shell aka sphere of hydration
34
Water and non-polar molecules

• Nonpolar molecules
• Do not form hydrogen bonds
• Not dissolved in water (no hydration shell)
• Cholesterol is very non polar

35
H bonds determine acid-base balance

• Water can accept or give up a proton in a
  chemical reaction called the ionization
• of water

H2O ? OH- H3O
36
Hydronium and hydroxide concentrations

• There is enough hydronium and hydroxide in pure
  water to measure easily
• The concentrations are equal at 1 x 10-7 M
• Hydronium and hydroxide exactly balance
• Pure water is neutral

37
The pH scale measures the concentration of acid
in a solution

• Neutral pH (pure water is 7.0)
• Acid substances produce higher levels of
  hydronium and pH below 7.0
• Basic aka alkaline substances produce higher
  levels of hydroxide and pH above 7.0
• The practical range of pH measurement is 0-14.
• Determined by taking negative value of exponents
  of its hydronium ion concentration

38
pH and living systems

• Cells optimized for pH around 7.0
• Use buffer systems to maintain (carbonic
  acid/bicarbonate in blood)
• Must contend with pH changes in the environment
• Can take advantage of pH to control systems