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(Source: Dr. Nilsson's old lecture notes, and Mader, S.S. 2010. Biology. Ed. 10. Used for educational purpose.Permission given in 2001 by McGraw-Hills then sales representative, Don Grainger, to use the picture online on lecture notes.)

Organic Chemistry ("carbon chemistry")

Male and female peacocks

Testosterone (male hormone) ------------------- Estrogen (Estradiol) female hormone

--- Carbon ---

Organic molecules are molecules that contain both carbon and hydrogen atoms. This chapter reviews organic chemistry, which by tradition pertains to living things, even though many types of organic molecules can now be synthesized in the laboratory.

The national bird of India is being pushed to the brink of extinction.

This is a very important chapter in order to understand later discussions about CELL DIVISION, PROTEIN SYNTHESIS, GENETICS, and EVOLUTION -- and in General Biology II also ECOLOGY.

The Carbon Atom

Source: http://www.rsc.org/periodic-table

The carbon atom is unique.

1. Carbon can bind 4 other molecules

Functional Groups

2. Carbon can form long chains (the "skeleton" of organic molecules). These chains are often called macromolecules -- long molecules made of different buildingblocks. As long chains they are also called polymers.

C-C-C-C-C-C (C6H12O6).

This "skeleton" can vary a great deal
-- variation important for living organisms

-- Variations in carbon skeletons:

i. Length
ii. Branching (branched or unbranched)
iii. Bonding (double bonds -- vary in location)
iv. Rings (carbon skeleton arranged in rings)
v. Other elements (bonded to the skeleton) -- FUNCTIONAL GROUPS (R-groups)

Def. Functional group (R-group): A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.

Carbon can bond with as many as four different atoms, including itself to form chains and rings (see figure above), which allows for great diversity of shapes. In a cell when small molecules form larger macromolecules the reaction is called a synthesis or a dehydration reaction, because water is formed and removed. To break down molecules to smaller molecules the opposite reaction is called hydrolysis, where water is added. The chemical property of an organic molecule changes when the shape changes and when it binds to other molecules -- called functional groups. This is used by the medical industry in order to discover and manufacture different molecules with medical properties, e.g., different antibiotics to stay ahead of bacteria becoming resistant to treatment.

To illustrate another effect of functional groups look at the figure above with peacocks. Testosterone and estrogen are almost identical sex hormones. Notice the difference on the left side of the molecule. With a slight simplification the only difference is ONE hydrogen atom. (Testosterone has one hydrogen atom less than estrogen.) That ONE difference makes you male or female!!!

Dehydration vs. Hydrolysis

To understand organic macromolecules it is necessary to know the buildingblocks -- monomers.

The macromolecules are put together with monomers to form polymers with dyhydration reactions (synthesis) -- removal of water. The organic molecules are split with hydrolysis reactions (digestion) -- addition of water.

--- Carbohydrates ---

Monosaccharides, disaccharides, and polysaccharides are all carbohydrates. Carbohydrates are almost universally used as an intermediate energy source in living things -- in the form of glucose, but they also play structural roles in many organisms. The term carbohydrates includes single sugar molecules and chains of sugars -- i.e., both the monomers (buildingblocks) such as glucose, and the polymers, such as starch, glycogen, cellulose, and chitin. The cell walls of bacteria contain another type of carbohydrate known as peptidoglycan.


Starch in plants and glycogen in animals, are energy storage compounds (from where glucose is obtained), but cellulose in plant and chitin in crabs and related animals (like insects and spiders), and in fungi, have structural roles (e.g., wood in tree trunks is cellulose).





--- Monosaccharides ("sugars" often glucose)


a. Source of energy (to keep us alive)
b. Provide structural support (building material)


Monosaccharides (Simple Sugars)

-- Building blocks: One single carbon chain or ring

Example: 6C (six carbon atoms) -- glucose, fructose, galactose -- HEXOSES

--- same molecular formula, C6H12O6 (different structural formulas)
--- wh. dissolved in water (
as when inside cells) they circle up in a ring form.


Example: 5 C (five carbon atoms) -- ribose, deoxyribose -- PENTOSES

--- building block in RNA, and DNA

RIBOSE --- molecular formula, C5H10O5
--- molecular formula, C5H10O4


-- Building blocks: 2 monosaccharides

Example: sucrose, lactose, and maltose
-- same molecular formula, C

SUCROSE: table sugar (Glucose + Fructose)
LACTOSE: milk sugar (Glucose + Galactose)
MALTOSE: malt sugar (Glucose + Glucose)


-- Building blocks: many glucose units "linked" (in ring forms).

GLYCOGEN: Animal polysaccharide
--- energy storage (carbohydrate storage molecule in animals)
--- usually in the liver & the muscles

STARCH: Plant polysaccharide (glucose subunits -- same side up)
--- energy storage (carbohydrate storage molecule in plants)
--- usually in roots & seeds

CELLULOSE: Plant polysaccharide
--- structural material (= of plants -- in cell walls) :
--- cannot be digested by most animals
--- fibers (addition to our diet, we cannot digest):

1. Building blocks (monomers) of carbohydrates:

a. Nucleotides
b. Glucose
c. Aminoacids
d. Glycerol + 3 fatty acids chains
e. Phosphate group + Glycerol + 2 fatty acids

2. Which of the following is considered a carbohydrate source?

a. Cooking oil
b. Rice
c. Eggs
d. Butter
e. Water

--- Lipids ---

Lipids are insoluble in water, and includes fats and oils (triglycerides -- with three fatty acid tails), phospholipids (an important component of our cell membranes -- with two fatty acid tails), steroids (with ring structures -- see the figure on top of this page), and waxes (e.g., waxy coating of fruits, bees wax, and ear wax).

Fat (triglycerides)


Classification of Lipids, examples and overview.


--- Variable combinations of C-H chains (e.g., fat (triglyceride): Glycerol + 3 fatty acids chains)


a. can be stored in adipose tissue (= fat tissue)
b. give high amount of energy
c. heat insulator
d. cushion
e. waterproofing (inability to dissolve in water)
f. component in cell membranes
g. vitamin D



--- Building blocks: Glycerol + 3 fatty acids


--- Building blocks: Phosphate group + Glycerol + 2 fatty acids

– major component in cell membranes


--- Building blocks: 4 carbon rings (but no fatty acids)

-- cholesterol Necessary for prod. of vitamin D (react w. UV light), and various steroid hormones.

Sources of Cholesterol:

1. Diet (food)

2. Synthesis (by the cells)

---Vitamin D
-- some hormones (e.g., estrogens, testosterone)

Male and female peacocks

Source: Simon, Eric J. Biology: The Core. Pearson. Boston. 333 pp. Used for educational purposes.


--- Building blocks: varies

bee wax, ear wax

3. Building blocks (monomers) of fats:

a. Nucleotides
b. Glucose
c. Aminoacids
d. Glycerol + 3 fatty acids chains
e. Phosphate group + Glycerol + 2 fatty acids

4. Building blocks (monomers) of phospholipids:

a. Nucleotides
b. Glucose
c. Aminoacids
d. Glycerol + 3 fatty acids chains
e. Phosphate group + Glycerol + 2 fatty acids

--- Proteins ---

Proteins carry out many functions in cells and organisms, and contain polymers of amino acids. Long chains of amino acids form polypeptides, joined by peptide bonds. There are 20 different kinds of amino acids in cells.


--- Amino Acids


a. speed up chemical reactions (enzymes)
b. deliver signals (hormones)
c. transport agent (blood cells)
d. immunity (antibodies)
e. structural material


Structural proteins

i. in cell membranes (egg white albumin)
ii. muscle cells fibers ("meat")
iii. in blood cells (e.g. antibodies, hemoglobin)
iv. spider silk

Regulatory proteins

i. enzymes (lactase – help digest milk, pepsin – in stomach)
ii. some hormones (insulin)

def. Hemoglobin
def. Insulin

Protein architecture

Levels of protein structure

A polypeptide has up to four levels of structure: primary structure (amino acid sequence), secondary structure (helices or pleated sheets) held in place by hydrogen bonding between amino acids, tertiary structure (final 3-dimentional folding). Proteins that contain more than one polypeptide have a quaternary structure.

Levels of protein organization (structures)

--- Sequence of Amino Acids

2. SECONDARY STRUCTURE (superimposed on the primary structure)
--- the AA chain is coiled or pleated because of hydrogen bonds

3. TERTIARY STRUCTURE (superimposed on the secondary structure)
--- the coiled or pleated structure is folded
--- held in place by hydrogen bonds (weak)

--- If two or more polypeptide chains

--- the single folded chain in many proteins is aggregated with other chains
e.g., Collagen (3 chains twisted), Hemoglobin (4 chains)

Source: https://www.youtube.com/watch?v=lijQ3a8yUYQ#t=18

5. Building blocks (monomers) of proteins:

a. Nucleotides
b. Glucose
c. Aminoacids
d. Glycerol + 3 fatty acids chains
e. Phosphate group + Glycerol + 2 fatty acids

--- Nucleic Acids ---


--- Nucleotides (Phosphate, 5C sugar [Pentose], Base (Nitrogen base))


i. DNA - store information – genetic blueprint, our hereditary material

ii. RNA - transfer information from DNA so it can be used

ii. ATP - special molecule; energy molecule of the cell



Deoxyribonucleic acid, DNA, is the genetic molecule of the body. DNA contains two kinds of building blocks (monomers) called nucleotides, arranged like a spiral staircase. Each nucleotide contains three parts:

Double stranded molecule composed of:

(1) a phosphate group
(2) a sugar (5C - pentose) molecule (Deoxyribose)
(3) and a nitrogen containing base (Adenine, Guanine, Cytosine, or Thymine).

The sugar-phosphate bond form the "double backbone" of the molecule -- the "hand rails of staircase".

DNA is the genetic material that stores information for its own replication and for the order of amino acids in proteins in a specific species. The genetic key in DNA is in the "steps" of the stairway -- the nitrogen containing bases. These bases link up using hydrogen bonds in a very specific way: Adenine will bond only with Thymine -- A to T, Cytosine only bonds with Guanine -- C to G. This is called complementary base pairing and will be discussed again later in PROTEIN SYNTHESIS and GENETICS.

These basic pairings never change, but the order of the pairs along each strand varies slightly from one species to the next. The order of the bases functions as natures "instructions" to build all living things, and will be discussed further in EVOLUTION. DNA, with the help of mRNA, specifies protein synthesis.
This will be discussed further in the genetic chapter (if you wish to move aheard with a short introductiion-- vew the video below).

DNA structure

Source: https://www.youtube.com/watch?v=qy8dk5iS1f0


Ribonucleic acid, RNA, is another type of nucleic acid used in the cell to "assist" DNA in the production of proteins. The molecule is similar to DNA, but has noted differences.

There are three kinds of RNA molecules, messenger RNA -- mRNA, transfer RNA -- tRNA, and ribosomal RNA -- rRNA, which will be discussed further in PROTEIN SYNTHESIS. DNA and RNA have slightly different building blocks, in RNA thymine is replaced with Uracil -- U, and the sugar deoxyribose is replaced with ribose. In addition, RNA is a single stranded molecule (DNA is double), and much shorter than DNA.

SINGLE stranded molecule composed of:

(1) a phosphate group
(2) a sugar (5C - pentose) molecule (Ribose)
(3) and a nitrogen containing base (Adenine, Guanine, Cytosine, or Uracil).


a. DNA – Deoxyribonucleic Acid

-- LONG, DOUBLE stranded molecule
-- Building blocks: Nucleotides with the following composition

Phosphate group
Nitrogen base (Adenine, Thymine, Guanine, & Cytosine)

b. RNA - Ribonucleic Acid

-- SHORT, SINGLE stranded molecule
-- Building blocks: Nucleotides with the following composition

Phosphate group
Nitrogen base (Adenine, Uracil, Guanine, & Cytosine)

More in the genetic chapter...

6. Building blocks (monomers) of nucleic acids:

a. Nucleotides
b. Glucose
c. Aminoacids
d. Glycerol + 3 fatty acids chains
e. Phosphate group + Glycerol + 2 fatty acids


ATP -- ADENOSINE TRIPHOSPHATE, is the "energy molecule of every cell in our body" -- sometimes referred to as the "energy currency" of our body. It is a molecule composed of adenosin (adenine and ribose). Triphosphate stands for the three phosphate groups that are attached together and to ribose (a pentose "5-carbon" sugar). ATP is a high-energy molecule because the last two phosphate bonds can be easily broken to form energy that can be used by the cell for energy requiring processes -- making (synthesizing) or breaking down (metabolizing) things.

- - - ATP: ADENOSINE TRIPHOSPHATE (Khan Academy You Tube) - - -

COMMENT ON THE YOUTUBE: "Absolutely great! I learn more in one of these videos that I do in hours of class! Lifesaver."

If you have problems understanding the concept "ATP" here is an excellent YouTube video from Khan Academy, which will help you understand -- even though some of the information is beyond what is required for this class.

ATP: Adenosine Triphosphate

Source: https://www.youtube.com/watch?v=YQfWiDlFEcA

(1) a 3 phosphate groups
(2) a sugar (5C - pentose) molecule (Ribose)
(3) and a nitrogen containing base (Adenine).

Biology Molecules. Bozeman.

Source: https://www.youtube.com/watch?v=PYH63o10iTE

- - - DNA - - -

COMMENTs ON THE YOUTUBE: So much knowledge packed into such a short video. This is why Khan Academy is such a great place to learn. --- and --- my professor DID use this in his lesson but he was drinking diet coke, not coffee...

DNA. khanacademy.

- - - Connecting the Concepts - - -

This chapter dealt with the chemistry of carbon. The food we eat and the wood we burn are organic substances. Fossil fuel (coal and oil) formed over 300 million years ago from plant and animal life in the past that, by chance, did not fully decompose are also organic. When burned, these items release carbon dioxide into the atmosphere just as we do when we breathe. The chemistry of carbon is the chemistry of life. The groups of macromolecules discussed in this chapter -- carbohydrates, lipids, proteins, and nucleic acids -- are assembled into structures that make up cells, which will be discussed in the next chapter.

(Source: Dr. Nilsson's old lecture notes, and Mader, S.S. 2010. Biology. Ed. 10. Used for educational purpose.Permission given in 2001 by McGraw-Hills then sales representative, Don Grainger, to use the picture online on lecture notes.)


Figure Drawings: Organic Molecules

The figure on the screen is illustrating the the structural formula of cholesterol. Draw the figure on the paper.

Source: http://www.nutrientsreview.com/lipids/cholesterol.html (used for educational purposes)