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UNIT 1:  CELLULAR FUNCTIONS

  The Chemistry of Life

The structure of a particular molecule determines its function.  A small change in the shape of a molecule could mean an important difference in its shape and a vast difference in its function.  It is important that we learn about the chemical nature basic biological molecules, since it is these simple molecules that make up all living systems.  

A.  The Chemical Basis of Cells

ATOMS AND MOLECULES

·         biochemistry studies the chemical reactions that take place in living systems

·         the same compounds and processes take place in humans as they do in bacteria

·         the basic unit of matter is the atom

·         six types of atoms make up 99% of all living systems – they are carbon, hydrogen, nitrogen, oxygen, phosphorus, an sulfur

·         atoms bond with one another to form compounds

·         bonds between atoms can be covalent - formed by the sharing of electrons between two atoms, or ionic – electrostatic attractions established by the losing and gaining of electrons of each atom involved (Figure 1.3, p. 7)

·         most biological molecules contain covalent bonds (Figure 1.2, p. 6)

·         covalent bonds my be single, double, or triple

·         in a triple covalent bond, for example, three electron pairs are shared (i.e. six electrons are involved)

·         atoms that lose electrons become positive in charge -- captions

·         atoms that gain electrons become negative in charge – anions

·         the electrons shared in covalent bonds may be shared unequally – they may spend more time toward one particular atom over another within the molecule

·         if this is the case, then the molecule is said to be polar – it has a slightly negative charge on one end and a slightly positive charge on another

·         this polarity gives the molecule particular properties that dictate the kinds of substances it will dissolve in and the kinds it won’t

·         all substances in cells can be categorized as either organic or inorganic

·         organic compounds contain carbon – a unique element that can form strong, stable, covalent bonds with other atoms

·         examples of organic compounds are carbohydrates, proteins, lipids, and nucleic acids

·         inorganic compounds are not an integral part of the structure of living systems

·         they usually exist in the form of ions

·         the exceptions to this are water (H₂O) and carbon dioxide (CO₂)

·         in chemistry, molecular formulas are used to show the number of atoms of each type that make up a compound

·         in order to show how each atom is arranged in a molecule, structural formulas are used

·         these show how the atoms making up the molecule are bonded to one another (Figure 1.5, p. 8)

·         in biological systems, molecules are often very large

·         cells are able to make large molecules by joining smaller sub-unit molecules together into long chains known as polymers

·         the units that make up polymers are called monomers

·         an example is glucose – the monomer unit in the polymer glycogen (Figure 1.7, p. 8)

·         the reactions that take place inside cells are called metabolic reactions

·         the two kinds of metabolic reactions are anabolism – the reactions that build up compounds, and catabolism – the reactions that break down compounds into simple units

WATER AND ITS SPECIAL PROPERTIES

·         water is the most abundant molecule in living systems

·         because water has a particular 3-d shape and molecular structure, it possesses unique properties

·         in order to view a 3-d model of water, look up the site www.pearsond.ca/biology11

·         the shared electrons in the intramolecular bonds of water are not shared equally

·         since the oxygen is more electronegative than the hydrogen within the water molecule, the shared electron pairs spend more time around the oxygen than the hydrogen

·         this makes the hydrogen ends of the molecule positive and the oxygen end negative

·         the result is that water is polar

·         the intermolecular bonds formed between water molecules are called hydrogen bonds or H-bonds

·         H-bonds are forces of attraction between a hydrogen of one molecule, with a highly electronegative element of another molecule

·         H-bonds hold water molecules together (Figure 1.10, p. 10)

·         because of water’s unique polarity, and H-bonds, it tends to possess extraordinary properties, which in turn, allow it to be one of the most important biological molecules

·         some of its unique properties are as follows:

1.  water has a high surface tension    - the H-bonds hold water molecules together, giving its surface    

                                                           a trampoline

                                                        - for example, toothpicks can float on water

2.   water is cohesive     – it sticks together

                                    – if you pull on one water molecule, it will bring another water molecule with it

                                      because of the H-bonding between each water molecule

3.  water is adhesive      - it sticks onto other substances

                                    - its polarity allows it to attract other polar substances

4.  water has a high specific heat capacity     - water can absorb quite a bit of energy before its 

                                                                      temperature increases significantly

                                                                    - it can also release a lot of energy before its temperature

                                                                      decreases significantly

5.  water is denser as a liquid at 4°C than as a solid    - when water is a solid, it expands since it 

                                                                                  possesses a maximum number of H-bonds, 

                                                                                  which hold the water molecules further apart from 

                                                                                  each other, making it less dense

                                                                                - as it warms up, the H-bonds break, and the 

                                                                                  water molecules move  closer to each other, 

                                                                                  with results in a more dense condition

                                                                                - that is why ice remains at the top of frozen lakes

                                                                                  during the winter, and the liquid is below it – not 

                                                                                  the other way around

6.  water is a universal solvent   - most compounds dissolve in water (Figure 1.11, p. 10)

7.  water dissociates readily into ions (see p. 11)

ACIDS AND BASES

·         an acid is defined as a proton (H⁺) donor

·         a base is defined as a proton acceptor

·         acids have a characteristic bitter taste, they are highly corrosive, they turn blue litmus paper red, they possess a pH value of less than 7, and they react with metals to form hydrogen gas

·         bases have a characteristic bitter taste, they are highly corrosive, they turn red litmus paper blue, they possess a pH value of more than 7, and they are commonly found in soaps and detergents

·         most living systems operate at a pH value of close to 7 (neutral)

·         the pH scale is a way that chemists measure the degree of acidity or alkalinity of substances (Figure 1.12, p. 11)

·         human blood should be in between a range of 7.35 and 7.45 in order for all metabolic processes to take place properly

·         typical strong acids are hydrochloric acid -- HCl (aq), nitric acid – HNO₃ (aq), and sulfuric acid – H₂SO₄ (aq)

·         a typical strong base is sodium hydroxide – NaOH (aq)

·         strong acids have a great ability to donate protons

·         strong bases have a great ability to accept protons

Homework:  p. 13, 1-8