Download Chapter 2 Chemistry

K. Muma
Bio 6
Chapter 2
Chemistry
Study Objectives:
1. Define the terms matter, elements, and atoms
2. Differentiate between ionic, covalent, and hydrogen bonds
3. Differentiate between polar and non-polar molecules: how do they interact?
4. Describe the unique properties of water and their importance to the human body
5. Distinguish between inorganic and organic compounds
6. Describe acids and bases, and explain the concept of the pH scale
7. Explain the importance of buffer systems and how they work
8. Describe the building blocks, structure, and functions of carbohydrates:
monosaccharide, disaccharides, and polysaccharides
9. Describe the building blocks, structure, and functions of lipids: neutral fats,
phospholipids, steroids, and eicosanoids
10. Describe the building blocks, structure, and functions of proteins: fibrous and
globular
11. Explain how acidity and high temperature affect the functioning of globular proteins
12. Describe the building blocks, structure, and functions of nucleic acids: DNA and
RNA
Chapter 2 Outline
Molecular Interaction / Biochemistry
I.
Matter - anything that occupies space and has mass
a. Elements are substances that cannot be broken down into other substances
b. Atoms - the smallest unit of matter that still retains the properties
i. Structure of atoms - composed of subatomic particles
1. Protons - that are positively charged and are found in the
nucleus (center) of an atom
2. Neutrons - are neutral or have no charge; are also found in
the nucleus
3. Electrons - are negatively charged and exist in the
orbits/shells around the nucleus.
a. Maximum number of electrons per shell = 2 in the
first shell; 8 in the other shells
b. Number of electrons on the outer shell determines
the atoms chemical behavior
c. Chemical Bonds
i. Ionic Bonds - formed between oppositely charged ions
1. When an atom loses or gains electrons, it becomes
electrically charged
2. Ions are charged atoms
ii. Covalent Bonds - form when electrons are shared between atoms
1. non-polar covalent bonds – electrons shared equally
2. polar covalent bonds – electrons are NOT shared equally
iii. Hydrogen bonds – interaction between a hydrogen atom bound to
an electromagnetic atom and another electromagnetic atom.
1. The polarity of water results in hydrogen bonds between
neighboring water molecules
2. Gives water some unique vital properties:
a. High heat capacity - requires a lot of energy to
increase in temperature, and releases a lot of energy
when it cool
b. High heat of vaporization - as water evaporates it
takes large amounts of heat with it
c. Good solvent properties –dissolves chemicals,
making it a good medium for transporting
biological molecules
i. Solution - is a liquid consisting of two or
more substances evenly mixed
1. Solvent: is the dissolving agent
2. Solute: is the substance being
dissolved
ii. Hydrophilic – water soluble (likes water)
1. Polar molecules
iii. Hydrophobic – does not dissolve in water
(water fearing)
1. Non – polar molecules
iv. Amphiphilic – molecules that is both
hydrophilic and phobic
1. Polar and non-polar ends
d. Chemical reactivity
i. Hydrolysis – water breaks bond apart
ii. Dehydration – removing water to form
bonds
e. Cohesion - stickiness of water molecules
f. Cushioning
II.
Acid and Base Concepts
a. Acid – a chemical compound that donates H+ ions to solutions
i. HCl  H+
+
Cl-
b. Base - a compound that accepts H+ ions and removes them from solution
i. NaOH  Na+ +
OH-
c. pH scale - measures concentration of hydrogen ions
i. Logarithmic scale – each pH unit is a tenfold change in H+
concentration
1. pH 7 = neutral
2. pH below 7 = acidic
3. pH above 7 = basic
d. Buffers - substances that resist pH change
i. They accept H+ ions from the solution when they are in excess
ii. They donate H+ ions to the solution when they are depleted
III.
Biochemistry
a. Organic molecules – large molecules containing carbon
(macromolecules)
i. Have a unique three-dimensional shape that defines its function in
an organism
ii. The molecules of your body recognize one another based on their
shapes
iii. Most macromolecules are polymers. Polymers are made by
stringing together many smaller molecules called monomers
(subunits)
b. Four types of macromolecules found in cells
i. Carbohydrates - includes sugars and starches
1. Contain carbon, hydrogen, and oxygen (1:2:1 ratio)
2. Monomer = monosaccharide
3. Classified according to size:
a. Monosaccharides – one sugar, referred to as simple
sugars
b. Disaccharide - a double sugar
c. Polysaccharides - complex carbohydrates formed
by long chains of monosaccharides
i. Starch, cellulose (plants), glycogen
(animals)
ii. Lipids
1. Carbon and hydrogen outnumber oxygen
2. Lipids are hydrophobic
3. Functions:
a. Energy storage
b. Cushioning
c. Insulation
4. Types of lipids:
a. Neutral fats – mostly triglycerides
i. A combination of glycerol and three fatty
acids
ii. Found in fat deposits (adipose tissue)
iii. Source of stored energy and insulation
iv. Cushions organs
v. Unsaturated fatty acids - have less than the
maximum number of hydrogen bonded to
the carbons
1. Examples: Most plant oils;
vegetable or corn oil
vi. Saturated fatty acids - have the maximum
number of hydrogen bonded to the carbons
1. Example: Most animal fats
vii.
What is trans fat then???
b. Phospholipids – composed of phosphate head
(hydrophilic) and two lipid tails (hydrophobic)
i. Forms cell membranes and the myelin
sheaths of neurons
c. Eicosanoids – a 20 carbon fatty acid with a 5 or 6
carbon ring
i. Examples: prostaglandins, leukotrienes,
thromboxanes
d. Steroids - the carbon skeleton is bent to form four
fused rings
i. Cholesterol is the “base steroid” from which
your body produces other steroids
ii. Example: testosterone, estrogen, cortisol,
bile salts
iii. Protein - a polymer constructed from chains of amino acid
monomers
1. Contains C, H, O, N, and sometimes S
2. Monomer = Amino Acids
a. There is 20 different amino acids
b. The arrangement and combination of amino acids
makes each protein different
c. Amino acids are held together by peptide bonds
3. Types of Proteins
a. Fibrous proteins
i. Provides for construction materials for body
tissues
ii. Important role in structure
iii. Examples: collagen, elastic fibers, myosin
and actin
b. Globular Proteins
i. Relies on complex folded structure to
function
ii. Plays a vital role in cell function
iii. Act as enzymes, hormones, transport
proteins or antibodies
iv. Protein Shape - protein’s shape is sensitive
to the surrounding environment
1. Primary structure – order of amino
acids
2. Secondary structure -polypeptide
folded into a helix or a sheet
3. Tertiary structure- sheets and helices
folded into a 3-D globule
4. Quaternary structure - several
tertiary units put together
5. A slight change in the primary
structure of a protein affects its
ability to function
a. Example: sickle cell anemia
6. Denaturation - unfavorable
temperature and pH changes can
cause a protein to unravel and lose
its shape
iv. Nucleic Acids - information storage molecules
1. Monomer = nucleotides
a. 5 carbon sugar
b. Phosphate group
c. Nucleic base
2. Types of Nucleic Acids
a. Deoxyribonucleic Acid
i. Composed of 4 types of nucleotides
1. Purines – Adenine (A) and Guanine
(G)
2. Pyrimidines – Thymine (T) and
Cytosine (C)
ii. Organized by complimentary base pairing to
form a double stranded helix
1. A = T
2. C = G
iii. The nucleotides of the two stands are joined
by hydrogen bonds
iv. Contains a sugar-phosphate backbone
b. Ribonucleic acid
i. RNA is different from DNA in that:
1. Its sugar is ribose instead of
deoxyribose
2. It has the base uracil (U) instead of
thymine (T)
3. It’s single stranded
c. Some other nucleotides:
i. ATP used for cellular work
ii. NAD and FAD, used as electron carriers in
cellular respiration
iii. GTP, cyclic AMP, ADP in cell signaling
Post-Lecture Practice
1. List at least four vital properties of water and describe why this is important to the
human body.
2. Draw two or three water molecules interacting with each other by accurately depicting
where the hydrogen bonds would take place in your illustration.
3. Bicarbonate ions, HCO3- is an important ion in the body. It reacts in the following
way:
HCO3- + H+  H2CO3
a. Are bicarbonate ions acids or bases? _________________
b. Why?
4. HNO3 reacts in the following way when dissolved in water:
HNO3  H+ + NO3a. Is HNO3 an acid or a base? ___________
b. Why?
5. How much more H+ is in a solution that has a pH of 3 when compared to a pH of 6?
6. How much OH- is in a solution with a pH of 11 when compared to a pH of 7?
Organic Molecules
Name
Monomers (subunits) List examples of:
Monosaccharide
Carbohydrates
Disaccharide
Polysaccharide
Neutral Fats
Lipids
Phospholipids
Steroids
Eicosanoids
biological function
Name
Monomers (subunits) List examples of:
Fibrous
Proteins
Globular
DNA
Nucleic acids
RNA
biological function