Notes

Chapter 3         The Chemical Basis of Life II:  Organic Molecules

Organic molecules-

Carbon-containing molecules.  (NOT CO2 and CO)

*They are named this because they were found in living organisms.

Macromolecules-

Large complex compounds

Organic Chemistry-

The science of carbon-containing molecules.

Vitalism-

The belief that organic molecules can only be made by living organisms because they are vital to life.

*This was proven incorrect by Friedrich Wohler.(p43-44)

Hydrocarbons-

Molecules with predominantly or entirely hydrogen-carbon bonds.

Functional groups-

Groups of atoms with characteristic chemical features and properties.(p.44)

Isomers-

Two structures with an identical molecular formula but a different structure and characteristic.

Structural isomers-

Structures with the same atoms, but different bonding arrangements.

Sterioisomers-

Identical bonding, but different spatial positioning.

A)Cis-trans isomers=(Figure 3.4 p. 45)-

Cis isomer=

Identical atoms are on the same side of the double bond.

Trans isomer=

identical atoms are on the opposite side of the double bond.

B)Enantiomer-

Exist as a pair of molecules that are mirror images of each other.

(left-handed and right-handed.)

Enzymes-

Proteins that catalyze(speed up) reactions.

Monomers-

The unit that is repeated in a chain.

Polymers-

The chain made of repeating units.

Condensation reaction-

The process in which two or more molecules combine to form a larger one.

Dehydration reaction-

A condensation reaction in which water is removed from the starting molecules.

Hydrolysis reaction-

The process in which a polymer is broken down into monomers.

Carbohydrates-

Molecules composed of carbon, hydrogen, and oxygen.(usually a CnH2nOn ratio)

Ex. Glucose C6H12O6

Divisions of sugar.(p.47-48)

Monosaccharides-

The simplest sugar.  (Molecules made of only one simple sugar.)

Disaccharides-

Molecule made of two simple sugars.

Polysaccharide- 

Molecules made of three or more simple sugars.

Cellulose-

Molecule used in plants to form structure.

*specific enzymes allow plants to break down starch, but not cellulose.

Chitin-

Other polysaccharide that plays a structural role.

*External skeleton of insects, arthropods, and cell walls of fungi.

Glycosaminoglycans-

Large polysaccharides that play a structural role in animals.

*found in cartilage

3.4 LIPIDS

Lipids-

Hydrophobic molecules composed of mainly hydrogen and carbon.

Triglycerides or triacylglycerols- 

Molecules formed as three fatty acids bind to glycerol. (p.49)

Saturated fatty acids-

Lipids with only single covalent bonds.

Unsaturated fatty acids-

Lipids with one double covalent bond.

*Liquid at room temperature and are called oils.

Polyunsaturated fatty acids-

Lipids with more than one double covalent bonds.

*Solid at room temperature and are called fats.

Cis-fatty acids=

Fatty acids that are bent and are usually considered healthier for people.

Trans-fatty acids=

Fatty acids that have been altered to be more linear and are associated with health issues in people.

*These have a higher melting point, longer shelf life, and better baking qualities.

Phospholipids-

A molecule in which the third hydroxyl group of the glycerol is linked to a phosphate group instead of a fatty acid.

*Phospholipids form bilayers in water.(similar to cell membranes.)

Steroids-

A lipid containing four interconnected rings of carbon atoms; functions as hormone in animals and plants.

*Cholesterol can be converted to steroids.

*The estrogen differs from testosterone   by one methyl group, a hydroxyl group instead of a ketone, and an additional double bond.

Waxes= 

Complex lipids that prevent water loss.

3.5 Proteins

Proteins=

Polymers found in all cells and play critical roles in nearly all life processes.

*Proteins account for 50 % of organic matter in the typical animal.

Amino Acid=

Building block of protein.

Structure of proteins(Remember A,B,C, and R)

A-Amino group=NH3+1 in neutral solutions.

B-Base carbon=C-H

C-Carboxyl group=CO2-1  *Some books list this as COOH

R-A side chain of various carbons.

Group question-p.54 List the and the respective R group.

Peptide bond-

The bond formed between the carboxyl group and the Amino group.

Polypeptide=

The molecule formed as many peptide bonds are formed.

Hierarchy of protein structures

1. Primary structure=The linear sequence of amino acids structure.

2. Secondary Structure=Certain sequence of amino acids in which the hydrogen bonds cause the region to fold into a spiral(alpha helix) or sheet(Beta pleated sheet).

3. Tertiary structure=Secondary structures and random coiled regions fold into a 3-dimentional shape.

4. Quaternary=Two or more polypeptides may bind to each other to form functional protein.

*Quaternary proteins are also known as multimeric proteins(Meaning multiple parts)

Protein subunits=

The individual polypeptides.

Protein structure is influenced by several factors

1. Hydrogen bonds=

These are weak bonds between various parts of the molecule, but the sheer number result in a very strong force.

*These bonds are critical in secondary structures and important in the tertiary and quaternary structure.

2. Ionic bonds and other polar interactions=

Some of the amino acid side chains are positively and negatively charged.  These areas may attract to each other or to polar side chains.

* These bonds are important in the tertiary and quaternary structure.

3. Hydrophobic effect=

Some side chains are hydrophobic, therefore when the protein folds this region of the protein is generally found inside away from water contact.

* These bonds play a major roll in the tertiary and quaternary structure.

       4.   Van der Waals forces=

Atoms within the same molecule have weak attraction towards each other if they are at an  

               optimal distance.  *If they are too close the electrons repel each other.  (Based on Van der Waals radii.)

*These forces are particularly important in the tertiary structure.

5. Disulfide bridges=

The side chains of the cysteine contains a sulfhydryl group(-SH), which can react with another SH group and form a covalent S-S bond.

*These covalent bonds help stabilize the tertiary structure.

**The first four bonds are extremely important in proteins interacting with one another.

Protein-protein interactions=

the reference that the surface of one protein must bind to the surface of another protein.

*The binding sites are usually very specific.*

*Sometimes the induced-fit model is the accepted model*

This means more than one enzyme can bind to the same site.

Genomes and Proteomes Connection

Domains(motifs or modules)=

Specific modular designs that have distinct structures and functions.

*When the same domain is found in different organisms, the 3D shape is the same and the function is the same.

Example on p.61

The STAT protein. (Signal Transducer and Activator of Transciption)-This regulates how certain genes are turned on and off.

Nucleic Acids

Nucleic Acids-

These molecules are extremely important for the storage, expression, and transmission of genetic information; yet they only account for 2 % of the organism’s weight.

DNA(Deoxyribonucleic Acid)-

Molecules responsible for storing genetic information which is coded in monomers.

*Double helix.

RNA(Ribonucleic Acid)-

Molecules responsible for decoding the information in DNA.

*Single strand. mRNA, tRNA, and rRNA

Nucleotide=

The monomer found in DNA and RNA.  

These monomers are made of three components:

A) A phosphate group

B) A pentose(five carbon sugar)-Either Ribose or Deoxyribsoe

C) A single or double ring of carbon and nitrogen. (This is referred to as nitrogenous base.) 

Pyramidines-Single ringed nitrogenous bases

Thymine (T)---Only found in DNA

Cytosine(C) 

Uracil (U)---Only found in RNA

Purines-Double ringed nitrogenous bases

Adenine (A)

Guanine (G)

p.62