Honors Biology

Module 5The Chemistry of Life Part 2

October 22, 2015

Class Challenge

Questions on Homework

Quiz

In Figure 5.2 on Page 137 shows the difference between Diffusion and Osmosis.

Draw two beakers, one for diffusion and the other osmosis. Include the membrane, solvent and solute.

This figure represents the end stage for Osmosis

--The dividing center line is solid ( ___ ), not dashed (- - -).  A solid line  indicates a semipermeable membrane.  (partly permeable)--Only a solvent can pass thru a semipermeable membrane, so the solvent is attracted to the side of the membrane that has a higher concentration of a solute. 

In diffusion, both the solute that is in the high concentration area and the solvent can pass freely back and forth through the fully permeable membrane, so the water level would stay the same on both sides, but still the concentration of solute would get evened out in the solvent.    

Organic Chemistry

An organic molecule is one that contains only carbon and any of the following:hydrogen, oxygen, nitrogen, sulfur, and/or phosphorous.If you memorized these last week from Table 5.1, you will easily recognize these six elements. 

Look in your textbook on p. 142 for examples of organic molecules and some that are not, and why.  Memorize these.

Photosynthesis is an example of biosynthesis since photosynthesis takes smaller molecules (water and carbon dioxide) and makes a larger one (glucose).

6CO2 +  6H2O  → C6H12O6 + 6O2

Carbohydrates

Carbohydrates contain only carbon, hydrogen, and oxygen. 

You can see the 'carbo' in the name, for carbon. 

And hydrogen and oxygen make water, thus 'hydrate' in the word carbohydrate.

You may know that carbohydrates give you energy, and you've learned that glucose is a simple sugar.

Look at a molecule of glucose:

C6H12O6

You can see there are 6 atoms of carbon, 12 of hydrogen, and 6 of oxygen.

There are twice as many hydrogen atoms as there are oxygen. 

This is the same ratio as one molecule of water, H2O.

When a molecule of glucose is drawn in structural formula, it shows which atoms are linked to which.

When the atoms are linked in a straight line, we call it a chain structure. (on the left below)

The chain structure of the glucose molecule below has a line of Carbon atoms, called a carbon chain. 

But many atoms have more than one structural formula.

The most commonly accepted form of glucose is the ring structure.

These diagrams are not drawn exactly like the ones in the textbook, but if you look closely and compare to those in your textbook, you can see these indeed do represent glucose.

In the ring structure on the right below ↓,

CH2OH consists of the same atoms as drawn in your textbook, and the same as the chain structure here on the left, where C links to 2 H's, and to OH.

You will remember in your textbook, in the chain formation, one oxygen atom had 2 lines linking to a carbon atom. 

Here in the chain formation on the left, the solitary oxygen atom does have 2 links.If you look carefully and find that same oxygen atom in the ring formation on the right, you will again see the oxygen has 2 links linking to carbon.

ETA: You will notice that the Oxygen is always connected to the Carbon.  That is why in the chain structure here, HO is written instead of OH. 

The chain structure is vertical, so HO must be written this way so that the O is connected to the C.

Glucose

http://youtu.be/eeUCWpoVPw0

Isomers  (Carbohydrates, cont.) Isomers are two different molecules that have the

exact same chemical formula. 

They are different molecules because of their different structural formulas.

Glucose and Fructose are isomers.  They have the same atoms (C6H12O6), but in their structural formula, their atoms are linked together slightly differently. 

This is the reason they taste different.  

CarbohydratesGlucose and fructose are monosaccharides, also

called simple sugars.  You may know that the prefix mono- means one.

Disaccharides are carbohydrates made up of two monosaccharides.  You may remember that Carbon-Dioxide (CO2) has one atom of carbon and two atoms of oxygen.  Di- means two.

Polysaccharides are made up of more than two monosaccharides.  Poly- means many.

Table sugar is not glucose (a monosaccharide), but is a disaccharide called sucrose.

Sucrose is formed when glucose and fructose (which are isomers) chemically react in a dehydration reaction.

Figure 5.4

When something is dehydrated, water is removed.  So from the combined molecules of glucose and fructose, H2O is removed, and the result is sucrose (a dehydration reaction) -- C12H22O11  

C6H12O6  +  C6H12O6  → C12H22O11 + H2ORemember, sucrose is a disaccharide because it

was formed from two monosaccharides in the process of dehydration.

When several monosaccharides link together, it is called a polysaccharide. 

Polysaccharides aren't usually sweet.  An example is starch, and is found in most plants. 

When a plant has extra monosaccharides, it will store them as polysaccharides by having many dehydration reactions that link the monosaccharides together.

Kind of like when your Mom has a lot of a apples, she may dehydrate some to use in baking later, except in a dehydration reaction, not only do the monosaccharides lose water, they are actually combined into polysaccharides.

If the apples are now polysaccharides because they have lost water, what will the plant do to turn them back into monosaccharides? 

The opposite of dehydration is hydration.  The plant breaks down disaccharides or polysaccharides back into their monosaccharide components by adding water. 

This is called hydrolysis.  (Think of the word hydrate.)

When humans and animals have excess carbohydrates, their bodies make a starch called glycogen.

So the reverse of the dehydration of fructose and glucose to form sucrose, would be hydrolysis of sucrose to make glucose and fructose. 

This chemical reaction is achieved by honeybees when they make honey.

Organic Acids and Bases

• Acids usually taste sour, while bases tend to taste bitter.  Fruit juice contains acid, and many cleaning products contain bases.

• If acids and bases react together, they usually form water and another class of molecule called "salts." 

• Table salt is one example.

• Organic acids contain a certain pattern of atoms bonded together:  Oxygen has a double bond with Carbon, indicated by 2 lines, and the Carbon has a bond with OH.  (O=C-OH)This pattern is called an acid group. →

(In the chain structure of glucose on p. 143 (top of page), you see a double bond of C with O, but that same C does not bond directly with OH, that molecule does not contain an acid group, and therefore is not an organic acid.)

When you see this grouping within a molecule, you will know the molecule is an organic acid.

This special grouping is NOT a molecule by itself; it is a grouping that can be IN a molecule.

This molecule has an acid group in it, so the whole molecule is an organic acid.

O=C - OH

Organic bases have a group of atoms in common called the amine group, but in this chapter, organic bases are just mentioned and not discussed. 

If you have a pool, you know that you must use pool strips to check the pH of the water to keep it from turning green! 

Keeping the pH balanced is necessary for clean water.

The pH of substances other than water can also be measured.

The pH scale runs from 0-14.  For solutions measuring lower pH than 7, the lower the pH, the more acid.

For solutions having a pH higher than 7, the higher the pH, the more like a base the solution becomes. 

These are said to be alkaline.

Look at the chart on p. 147 to see which substances are acids or bases, and which are neutral.

Lipids

Lipids (or fats) link to glycerol in a dehydration reaction. 

One glycerol molecule and 3 fatty acid molecules have a dehydration reaction to make 1 lipid molecule and 3 water molecules.

Lipids cannot be dissolved in water.  An example is cooking oil. 

Lipids are said to be hydrophobic. 

This does not mean it is afraid of water, haha, but that is a good way to remember it.  =)

Animals can convert excess carbohydrates into glycogen, but lipids can actually store twice as much energy for when food is scarce. 

Saturated fats are called "saturated" because they have all the hydrogens it can take.  It is "saturated" with hydrogen.

These saturated fats have no double bonds between carbons.

Unsaturated fats have at least one double bond between carbon atoms.

Lipids

https://youtu.be/VGHD9e3yRIU

Proteins and Enzymes Proteins come in many different shapes and sizes

and are very complex.  Their basic building blocks are amino acids. 

When amino acids link up using a dehydration reaction, a peptide bond forms.

The structural formula for a protein very complex. 

An average amino acid has about 20-40 atoms, and the most simple protein has 124 amino acids.  But an average protein has several thousand amino acids!

The Ribonuclease Protein--Simple or Not?

• http://youtu.be/WL4TizC5qG4

Enzymes are a special class of proteins that act as catalysts. 

For animals, these catalysts speed up the breaking down process of polysaccharides and disaccharides.

Most enzymes do their job based on the shape that the enzyme molecule has. 

Cellular Metabolism, Enzymes

http://youtu.be/cbZsXjgPDLQ

Remember, lactose is a disaccharide.  If the particular enzyme in someone's body that is specifically designed  for the lactose disaccharide is unable to work properly, a person will not be able to digest the lactose that is in milk. 

There are medicines to help this.

• Why is it when you are making a Jell-O mold they caution you not to add pineapple.

• Fresh Pineapple contains an enzyme that stops the reaction which causes Jell-O not to gel. As is the case with most enzymes, this enzyme is very fragile. In Experiment 5.3, you are asked to add heat to the pulpy part of the pineapple and then the jell-o did congeal. The heat destroyed the enzyme.

Most food enzymes are very fragile, so that any food processing destroys them.

That is why it is important to eat foods that are closest to their natural state as possible so that your body will digest these enzymes.

For some people though, when they eat pineapple their gums bleed. The pineapple enzymes break down the tissues in their gums.

Deoxyribonucleic Acid - DNA In Figure 5.10 as you read the text, learning the parts of a

DNA strand. DNA, or deoxyribonucleic acid, is formed in a double chain. These two chains are made up of three basic parts:

1. Deoxyribose (a simple sugar that contains 5 carbons) 2. A phosphate group (an arrangement of 3 things: 

phosphorous, hydrogen, and oxygen atoms - see the picture on the right of Figure 5.10 in your textbook)

3. A nucleotide base

The nucleotide's base can be one of four different types:  adenine, thymine, guanine, or cytosine. 

Notice which pairs are consistently linked together in this image.  

The phosphate groups link to the deoxyribose units, which is what the outer "rails" of the DNA strand is made of.   

DNA Structure

http://youtu.be/qy8dk5iS1f0

DNA Double Helix Structure

http://youtu.be/VegLVn_1oCE

What is DNA

http://youtu.be/q6PP-C4udkA

Experiment 5.C: The pH Scale See Figure 5.6 on page 147Litmus paper :Substance pH Reading Acid/Base?1. Vinegar2. Milk3. Ammonia4. Water5. Salt Water6. Unknown lower pH than 7, the lower the pH, the more acid.pH higher than 7, the higher the pH, the more like a base (alkaline)