Biology - Molecules and Cells

 Terms and Concepts 

SECTION 1

CHAPTER 4 - Organics Introduction

Carbon and hydrogen are the featured elements by definition in organic chemistry, but they are not the only players.  But before getting to the others, some discussion about carbon's capabilities is necessary.  For anyone who needs to "see" these examples, most of the links lead to images of the molecule structures.

Simple hydrocarbons include methane, CH₄, ethane, C₂H₆ (each carbon has a bond with the other, leaving 6 of the total 8 for hydrogens), and propane, C₃H₈.  As the number of carbons grow, the arrangement of how the carbons connect and the positions of the parts can vary, producing isomers:  molecules with the same basic formula that are put together differently.   Stereoisomers are molecules that can differ in the rotation of single bonds, often forming "mirror images" of each other.  This type of change is also called chirality when the difference is a single "twist" one way or the other.

Complex hydrocarbons with the same atomic constituents can vary even with all of the atoms bound to the same neighbors, because the bonds themselves can be turned differently - these molecules would differ in three-dimensional arrangement or conformation.  Also, similar molecules can differ in how carbons attach to each other - when double bonds exist in a molecule, it is called unsaturated (there is room on at least one carbon for more hydrogens), and if only single bonds exist between the carbons, the molecule is saturated, it has no more room for hydrogens on the carbons.

Beyond "HONC," there are other elements that are important constituents in living systems, but in much lower amounts.  Phosphorus, for example, is a critical part of Adenosine Triphosphate (ATP), the fuel molecule that supplies energy to cell functions;  Sulfur is often used to covalently cross-connect parts of proteins more strongly than hydrogen bonds can;  many metals function as associates of important protein systems;  ions have already been mentioned as being important. 

Simple hydrocarbon molecules.
 

Different structures with the same atoms.
 

Different stereoisomers.
 

How chirality affects odor molecules.
 

Molecules with different conformations react differently (Powerpoint).

ATP molecule.

There are several atom combinations that show up again and again in molecules and affect the chemistry of the molecules.  These functional groups are part of the "language" of biological chemistry, and it can be very useful to have most of them committed to memory. 

All of these groups tend to be polar, and it is often the polarity characteristics that help determine their chemistry:

ALCOHOL, -OH.

ALDEHYDE, -C=O on an end carbon.

KETONE, -C=O on an internal carbon.

ACETYL GROUP, end grouping with a ketone just inside an end methyl group (-CH₃).

METHYL GROUP, -CH₃ that can be added or removed to activate large molecules.

CARBOXYLS, ACID GROUPS, -COOH.  These will generally give up the hydrogen on the end as an ion, adding such H+ ions to solution, which is why it's an acid.

AMINES / AMINO GROUPS, -NH₂.  These tend to pick up hydrogen ions from solution, making the solution basic.

THIOLS (MERCAPTANS), -SH.  When found inside large molecules, loses hydrogens and covalently bonds to other sulfurs, forming covalent internal bridge-like connections that can help to hold a molecule in a stable form.

PHOSPHATES, -PO_X.   Varies in form according to pH.  Commonly moved onto and off molecules as an energy carrier.

Again, this terminology is used so commonly that it should be part of your basic vocabulary.

The list is this long and longer.

Alcohol group chemistry.

Aldehyde and ketone group chemistry.

How acetyl-group additions affect cell chemistry.

Methyl group chemistry.

How methyl groups affect cell chemistry.

More on methyl applications.

Carboxyl group chemistry.

Amine group chemistry.

Thiol group chemistry.

Phosphate group chemistry.

Terms and Concepts

In the order they were covered.

   Hydrocarbons - Simple  
Methane  
Ethane  
Propane  
Isomers  
Hydrocarbons - Complex  
Conformation  
Unsaturated vs Saturated  
Phosphorus Role  
Adenosine Triphosphate (ATP)  
Sulfur Role  
Metal Roles  
Functional Groups  
Alcohol Group  
Aldehyde Group  
Ketone Group  
Carboxyl Group  
Amine Group  
Thiol (Mercaptan) Group  
Phosphate Group