Biology 30 – Unit 1The Chemical Basis of Life

• All matter is composed of ATOMS. Matter composed of one kind of atom (ex. Carbon) is called an ELEMENT.

• Any atom is composed of a NUCLEUS made up of Protons (+ charge) and Neutrons (0 charge) surrounded by Electrons (- charge)

• The PERIODIC TABLE was developed to systematically group the Elements into Groups and Periods.

• Groups are vertical and Periods are horizontal. • There are 92 naturally occurring elements and

the elements are listed by increasing Atomic Number.

• The Atomic Number is the number of Protons in the nucleus of the atom. Hydrogen (1) has 1 proton, Helium (2) has 2 protons…

Chemical Bonds and Reactions

• For the purposes of this class, we will look at the 3 main types of chemical bonds.

• IONIC Bonds – Ionic Bonds are formed when atoms gain or lose electrons.

• The second type of bond is the COVALENT bond. This is formed when atoms share electrons.

• 3rd type of bonding important to biological functions is Hydrogen Bonding.

Hydrogen bonding continued

Hydrogen bonding occurs between 2 polar molecules (Polar Molecules have a positive (+) end and a Negative (-) end). When the positive end of the molecule is attracted to the negative end of the other molecule. NOTE: Hydrogen bonding is weaker than ionic bonding.Examples of hydrogen bonding are H2O and Alcohols

Chemical Reactions

• For this class, we will look at the 2 main types of chemical reactions: Endothermic and Exothermic.

• Endothermic – energy is required from the environment in order for the process to proceed. Photosynthesis is an example.

• Exothermic – energy is released into the environment by the reaction. Digestion is an example.

Biochemical Reactions

There are 2 main types of biochemical reactions:• Synthesis reactions – different molecules are

combined together to form larger, more complex molecules. An example would be the synthesis of proteins from Amino Acids.

• Decomposition reactions – A decomposition reaction is the opposite of a synthesis reaction in that larger molecules are broken down into smaller “chunks”. An example would be the decomposition of polysaccharides into monosaccharaides.

Another way to look at biochemical reactions

• Synthesis:Alanine+Guanine+Lysine+ENERGY A Protein(Protein synthesis takes place in ribosomes)

Biochemical Reactions continued

Decomposition:Sucrose + H2O Glucose + Fructose + ENERGY

Sucrose is a disaccharide (di means 2) and breaks down into 2 simple monosaccharides – Glucose and Fructose. Both of these “simple” sugars are used by the body as a form of energy.

Pt.II - Carbon based molecules important to life.

In the second part of Unit 1, we will look at the types of molecules important for bodily functions and reproduction. These molecules are:• Proteins• Lipids• Carbohydrate• RNA • DNA

Some background information about organic molecules

Organic molecules (those wacky molecules used by all living things) all have Carbon, Hydrogen, and Oxygen as common elements. Carbon and Hydrogen are the most common, with Oxygen bringing up the rear. Phosphorous is another important element found in Amino Acids, DNA (aka Deoxyribonucleic Acid), and RNA (aka Ribonucleic Acid).

Proteins Fats and Carbs (Oh my!)

We will start with the simplest family of molecules – Carbohydrates – first. We ingest mono, di, and poly saccharides as part of our diets. The simplest monosaccharide we eat (and love) is GLUCOSE . This is a simple diagram of Glucose:

Carbs continued

You can, for simplicity, also write that pesky little

glucose as C6H12O6

Glucose is used by all living organisms to obtain energy during the process of Cellular Respiration2 other important monosaccharides are Fructose (found in many foods) and Galactose (found in dairy products)

The breakdown of Carbohydrates initially takes place in the mouth (buccal cavity) where the ground up carbs are mixed with amylase laced saliva. Amylase is an ENZYME and is secreted by your salivary glands in your mouth. Question: How can you tell amylase is working when you chew bread??P.S. Humans manufacture glucose through Gluconeogenesis (Gluco-neo-genesis) in the liver.

Lipids

The 2nd family of molecules we will look are the most delicious (mmmm Butter) and these are Lipids. Lipids are FATS, OILS, and WAXES that are soluble in alcohol but not in water. They are primarily composed of Carbon and Hydrogen with lesser amounts of Oxygen in the mix.

Lipids continued

Cholesterol is a chemical compound that the body requires as a building block for cell membranes and for hormones like estrogen and testosterone.It travels through the blood stream attached to a protein molecule and comes in 2 different versions LDL (“Bad” Cholesterol) and HDL (“Good” Cholesterol).

Lipids

~ 80% of Cholesterol is produced by the liver, with the remaining amount from diet. The problem with too much Low Density Cholesterol in the bloodstream is it tends to be “sticky” and will stick to the walls of blood vessels and will form plaques – causing atherosclerosis . Plaques can also rupture, causing blood clots that may, in turn, break free and cause strokes or heart attacks.

Lipids

Waxes are another important group of lipids as they are found in cell membranes and make up parts of fatty acids.Oil is produced by specialized glands in animals (sebaceous glands in humans, as an example) and is used to protect external body surfaces from water, rust, meteors and small children.

Proteins ’R Us and RNA

The 3rd and 4th groups of molecules we will look at are Proteins and RNA . Proteins are composed of strings of Amino Acids that are manufactured in cellular organelles called Ribosomes by RNA.RNA is a single stranded “string” made up of 4 bases Adenine (A) and Guanine (G) (these are Purines) and Uracil (U) and Cytosine (C ) (these are Pyrimidines )

Proteins and RNA

Proteins and RNA

Adenine and Uracil pair and Cytosine and Guanine pair together. The production of proteins takes place like this:1) DNA in the nucleus of the cell (in Eukaryotes) makes

RNA. 2) The RNA leaves the nucleus and travels to the ribosome3) The RNA then codes for a string of Amino Acids4) The string of Amino Acids form polypeptides and are

released into the cytoplasm of the cell5) NOTE: We will look at this in more detail in Unit 2

DNA – We are our genes

DNA is a lovely double stranded molecule that resides in the nucleus of animal cells and in the cytoplasm of bacteria.

DNA

• DNA is the “stuff of life”. It is found in every living organism on this planet (with the exception of those wacky viruses)

• Its structure is described as a double-helix (imagine if you took a ladder and twisted it)

• It has, as its rungs, the complementary pairs of A & T, and C & G. Note this are essentially the same base pairs that we saw in RNA with the exception of T (Thymine) instead of U (Uracil)

DNA

• The outer backbone of the molecule is composed of a Phosphate group (PO4) and a sugar. It looks like this:

• Thymine (T) is shown. The sugar is pink and the PO4 group is on the outside.

DNA

• The molecule has a 5’ (5 prime) end and a 3’ (3 prime) end for each strand.

• This is important to remember because during DNA replication the process starts at the 5 prime end and proceeds to the 3 prime end of each strand.

• It is more energy efficient and stable for the replication to proceed from 5’ to 3’.

DNA

A simple diagram to illustrate this point

DNA replication

1. – The hydrogen bonds between the base pairs must be broken. This happens in areas rich in A-T pairs as there are only 2 bonds between these pairs (as opposed to 3 bonds between C-G).

2. Helicase is the enzyme that makes the unraveling possible. The location where the splitting starts is called the “replication fork”.

Replication continued

3. The next, very important step, is the binding of RNA Primase at the initiation point.

4. RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3'-5' strand due to the hydrogen bonds between the bases.

5. The RNA nucleotides are the “primers” for the process of DNA replication.

Replication continued

6. The strand with the 5’ to 3’ orientation is called the leading strand and DNA polymerase adds bases in a continuous manner.

7. The 3’ to 5’ strand is called the lagging strand and replication is much more difficult as the DNA polymerase can only work in the 5’ to 3’ direction.

Replication continued

8. The solution to this sticky little problem is the creation of Okazaki Fragments. These fragments are created further away from the replication fork and are “stitched” together by DNA ligase.

9. This is called discontinuous replication.10.Two daughter DNA molecules are formed by

the replication process.