NOTES FOR BIOLOGY 1001

SECTION 005

Spring 2005

DR. STEVEN POMARICO, INSTRUCTOR

PART 1C

CHAPTER 3

CARBON COUMPOUNDS IN CELLS

>>>>>>>>Aside from water, most biologically related molecules contain carbon.

---Organic compounds are made of molecules containing carbon.

                   Exceptions: All carbon molecules, graphite, diamonds, coal

                                       Carbon dioxide

                                       Carbon monoxide

                   Only living organisms can create organic molecules.

Carbon atoms are the most versatile building blocks of molecules

         Carbon has a valence of 4.

         Can bind to 2, 3, or 4 other atoms.

Some of the simplest (and most variable) organic molecules are hydrocarbons.

---Hydrocarbons are molecules which consist of hydrogen atoms covalently bonded to carbon.

>>>Another factor which leads to the versatility of organic molecules is the attachment of functional groups (See fig. 3.5)

---Functional groups are small characteristic groups of atoms which are frequently bonded to the carbon skeleton of organic molecules.

         Functional groups:

                   -Have specific chemical and physical properties.

                   -Are regions of organic molecules which are frequently chemically                              reactive.

                   -Behave consistently from one organic molecule to another.

                   -Can determine the chemical properties of the organic molecule in                              which they are located.

There are seven general functional groups found in organic molecules:

                   1) Hydroxyl (-OH)

                   2) Methyl (-CH₃)

                   3) Carbonyl (-C=O)

                   4) Carboxyl (-COOH)

                   5) Amino (-NH₂)

                   6) Phosphate (-PO₄)

                   7) Sulfhydral (-SH)

1) Hydroxyl (-OH)

---Hydroxyl group is a functional group of a hydrogen atom bonded to an oxygen atom which is bonded to a carbon atom (of the carbon skeleton).

         -Is a polar group

         -Involved in condensation (dehydration) and hydrolysis reactions

2) Methyl (-CH₃)

---Methyl group is a functional group which consists of three hydrogen atoms bonded to a carbon atom.

         -Is a non-polar group.

         -Makes the molecule more hydrophobic

3) Carbonyl (-C=O)

---Carbonyl group is a functional group in which a carbon atom is double bonded to an oxygen atom.

aldehyde or ketone.

4)Carboxyl (-COOH)

---Carboxyl group is a functional group in which a carbon atom is double bonded to an oxygen atom (like a carbonyl) and is also single bonded to the oxygen atom of a hydroxyl group.

         -Since this group can donate a proton, it is an acid

         -Involved in peptide bonds

5)Amino (-NH₂)

---Amino groups are functional groups in which two hydrogen atoms are bonded to a nitrogen atom which is bonded to a carbon atom (of the carbon skeleton).

         -Acts as a weak base (similar to ammonia)

         -Involved in peptide bonds

6)Phosphate (-PO₄ ^-3)

---Phosphate group is a functional group which is the dissociated form of phosphoric acid (H₃PO₄)

         -Acts as an acid because of the ability to donate protons.

         -Links nucleotides

         -Important in cellular energy storage and energy transfer. 

                                       Example: ATP

7) Sulfhydral (-SH)

---Sulfhydral group is a functional group found in certain amino acids which is important in stabilizing the structure of proteins.

>>>SYNTHESIZING ORGANIC MOLECULES: A MODULAR APPROACH

Biological molecules are often put together in subunits, or modules, called monomers.

         ---the simple molecules condensed into more complex ones

         ---monomers into polymers

>polymers are chains of similar building blocks or monomers.

Five categories of reactions:

1) Functional group transfer

2) Electron transfer

3) Rearrangement

4) Condensation

5) Cleavage (or hydrolysis)

>>>Biological molecules (monomer) are joined together or broken apart by adding or removing water

The reaction which forms a polymer from monomers is a condensation reaction (or dehydration synthesis )

–Condensation reaction is a reaction in which the covalent linkage of the monomers is accompanied by the “removal” of a water molecule.

         -One monomer loses a hydroxyl group (-OH), and the other monomer loses                    a hydrogen (-H).

---Hydrolysis is the breaking of the covalent bond between two monomers by the addition of water.

         -One monomer gains a hydroxyl group (-OH), and the other monomer gains                     a hydrogen (-H).

>>>THE PRINCIPLE TYPES OF BIOLOGICAL MOLECULES

>>>>Carbohydrates are used as fuels and building material

---Carbohydrates are organic molecules made of sugars and their polymers.

         -Carbohydrates are classified by the number of simple sugars.

         -Monomers are simple sugars called monosaccharides.

---Monosaccharide are simple sugars in which carbon, hydrogen, and oxygen occur in the ratio of CH₂O.

         -Major source in nutrients for cells.

         -Glucose is the most common

         -Can be produced by photosynthetic organism from CO₂, H₂O, and light.

>Monosaccharides can be joined to form disaccharides and polysaccharides

>>>>>Disaccharides

---Disaccharides are molecules which consist of two monosaccharides joined by a glycosidic linkage.

         -Glycosidic linkage is a covalent bond formed by a dehydration synthesis                                        between two sugar monomers.

Examples of disaccharides:

>>>>>Polysaccharides

---Polysaccharides are macromolecules that are polymers of a few hundred or thousand monosaccharides.

         -Formed by enzyme-mediated condensation reactions.

         -Biological functions

                   Energy storage(starch and glycogen)

                   Structural support (cellulose and chitin)

Storage polysaccharide

         -Stored sugars can be hydrolyzed as needed.

---Starch (See fig 3.9) is a glucose polymer that is used as a storage polysaccharide in plants.

---Glycogen is a glucose polymer that is used as a storage polysaccharide in animals.

         -Stored in the muscle and liver of vertebrates

Structural polysaccharide

         -Structural polysaccharides include cellulose and chitin

---Cellulose (See fig 3.9) is a linear unbranched polymer of glucose

         -plant cell walls

         -differs from starch in the type of linkage

         -different linkage gives different three-dimensional structure.

         -cellulose reinforces plant cell walls. Hydrogen bonds hold the cellulose                    strands together

         -cellulose cannot be digested by most animals because they lack the                    enzyme that can hydrolyze the linkage in cellulose.

---Chitin is a structural polysaccharide that is a polymer of an amino sugar.

         -forms the exoskeleton of arthropods (insects, crawfish, etc.)

         -found in the cell walls of some fungi.

>>>>Lipids are mostly nonpolar hydrophobic molecules composed mainly of carbon and hydrogen

---Lipids are a diverse group of organic molecules that are insoluble in water, but will dissolve in nonpolar solvents (e.g., ether, chloroform, benzene).            

         -Important lipids are grouped into 4 types:

                             1) fats (and oils) and fatty acids

                             2) phospholipids

                             3) sterols

                             4) waxes

>>>>Fats (and oils) and fatty acids

                   Characteristics

                             -composed of carbon, hydrogen and oxygen

                             -contain 1 or more fatty acids

                             -usually no ring structure

---Fats and oils are macromolecules constructed from fatty acids and glycerol.

---Fatty acids (FA) are hydrocarbon chains with a carboxyl group at one end (See fig 3.12).

         -The hydrocarbon chain, or tail, is hydrophobic and not water soluble.         -The tail has a long carbon skeleton usually with an even number (16-18) of                carbon atoms.       

         -The carboxyl group, or head, has the properties of a carboxylic acid.

---Glycerol is a three-carbon sugar.

The FA group is linked through the head to the glycerol and each hydroxyl group on the glycerol can form a linkage with a fatty acid.

---Triglyceride is a fat composed of three fatty acids bonded to one glycerol by ester linkages. (See fig 3.13)

Function of fats and oils:

         -Energy storage. One gram stores twice as much energy in its chemical                              bonds as a gram of polysaccharide.

         -Because of the higher energy per gram, energy storage is more compact with                       fats and oils than with carbohydrates.

The main difference between fats and oils is in the fatty acids

         Saturated fatty acids versus unsaturated fatty acids (See fig 3.12)

>>>>>Phospholipids (See fig 3.14)

---Phospholipids are compounds with molecular building blocks of glycerol, two fatty acids, a phosphate group and usually a small chemical group attached to the phosphate group.

         -Differs from a fat in the third carbon of the glycerol is attached to a                      negatively charged phosphate.

         -Phosphate group with a small chemical group attached is hydrophilic head          -Hydrocarbon chains of the fatty acids are hydrophobic tails.

         -Phospholipid molecules cluster in water with hydrophobic tails turned in.

>>>>>Sterols (See fig 3.15) are lipids which have four fused carbon rings with various functional groups attached.

         -Cholesterol is an important sterol

                   -found in cellular membranes

                   -acts as a precursor to many steroid hormones

                                       Male and female sex hormones

>>>>>Waxes are similar to fats and oils except the fatty acids are linked to large, long chain alcohols instead of glycerol.

         Waxes are found in plants where waterproofing is needed and are used to                              build structures (i.e., beehives)

>>>>>Proteins are the molecular tools for most cellular functions.

---Proteins are polymers of amino acids arranged in a specific linear sequence and are linked by peptide bonds.

         -Range in length from a few monomers to more than a thousand.

         -Each protein has a unique linear sequence of amino acids

         -Proteins are abundant, making up 50% (or more) of some cells dry weight.

         -Proteins have a variety of important functions.

                   Structural

                   Catalysts (enzymes)

                   Storage of material (amino acids) or energy

                   Transport (e.g., hemoglobin)

                   Movement (contractile proteins) 

                   Hormones (chemical messengers)

                   Immuno-defense (antibodies)

                   Defense (venoms)

---Amino acids (See fig. 3.16) are monomer building blocks of a protein. Most consist of a central carbon with four functional groups:

         1. A hydrogen atom

         2. A carboxyl group 

         3. An amino group

         4. A variable “R” group which is the side chain and is specific for each                    amino acid. The physical and chemical properties of the side chain                    determine the properties of the amino acid.

>>>Amino acids are joined into chains by dehydration synthesis

---Peptide bonds (See fig. 3.18) are covalent bonds formed by a dehydration synthesis that links the carbonyl group of one amino acid to the amino group of another amino acid.

         When two amino acids are joined the molecule formed is called a peptide and 3 or more amino acids joined form a polypepide chain.

>>>>>Four levels of protein structure

1)Primary structure

2)Secondary structure

3)Tertiary structure

4)Quaternary structure (when a protein has more than one polypeptide chain)

>>>>>Primary structure

---Primary structure is the sequence of amino acids in a protein. (See fig 3.18)

         -Determined by the genes.

         -Different for each different protein

         -Determines all the remaining structures

>>>>Secondary structure

---Secondary structure is a regular repeating coiling and folding of a protein’s polypeptide backbone.

         -Contributes to a protein’s overall conformation.

         -Stabilized by hydrogen bonding between peptide linkages in the protein                    backbone

         -The major types of secondary structure are helixes

                             and pleated sheets (See fig 3.19)

>>>>>Tertiary structure

---Tertiary structure is the irregular contortion of a protein backbone due to bonding or interactions between side chains (R groups). This third level of structure is may form a structurally stable portion (domain) of the larger protein.

Interactions of amino acid side chains

         -Covalent linkage

                   Disulfide bridges

         -Weak interaction

                   Hydrogen bonding

                   Ionic bonds

                   Hydrophobic interactions

>>>>>Quaternary structure

---Quaternary structure is the structure that results from the interaction among several polypeptides (subunits) in a single protein.

A protein function is dependant on the correct structure at each level.

>>>>>Denaturation

Physical or chemical conditions that disrupt the tertiary and quaternary structure of a protein can cause the unfolding or denaturation of the protein.

This change in structure of the protein usually also changes the function.

Some proteins can refold (renature) but others cannot.

>>>>>Protein structure (at all levels) is related to function.

A change (even a small one) in the structure of a protein can drastically change (or destroy) the function of the protein.

>>>>>Nucleic Acids: Information storage and transmission.

The primary structure of proteins is determined by the genes that code for the proteins. Genes are the units of heredity and are made of nucleic acid (DNA).

---Nucleic acids are polymers of nucleotides linked together by dehydration synthesis reactions.

---Nucleotides and are composed of a sugar, a phosphate group, and a base.

The sugar is a 5-carbon sugar in a ring conformation.

In RNA the sugar is ribose, whereas in DNA the sugar is a derivative of ribose called, deoxyribose.

The sugar and phosphate groups form a linkage which makes up the nucleic acid backbone.

Variation in DNA and RNA comes from the order of the nucleotides (i.e., DNA sequence)

In addition to their role in DNA and RNA, nucleotides also form energy carrier molecules like adenosine triphosphate (ATP), messengers (cAMP)  and enzyme helpers know as coenzymes.