Biochemistry Notes



Biochemistry Notes

I. Carbohydrates

A. Includes sugars, starches, and cellulose (most abundant organic compound in the

world).

B. Carbohydrates are used for energy storage and structure in living organisms.

C. Monosaccharides (CH2O)

1. All monosaccharides are either aldehydes or ketones.

2. Made up of chains of three to nine carbons. The monosaccharides are identified by the number of carbons in the chain (triose-3, pentose-5).

3. Used for quick energy or as the monomers of polysaccharides.

4. Pentose sugars are found in nucleic acids (DNA, RNA).

D. Disaccharides (CnH2n-2On-1)

1. Disaccharides are formed by joining two monosaccharides by dehydration

synthesis. They are broken apart into monosaccharides by hydrolysis.

2. Used as transport sugars in organisms.

3. Examples are sucrose, lactose, and maltose.

E. Polysaccharides (CnH2n-2On-1)n

1. Polysaccharides are formed by joining many monosaccharides through

dehydration synthesis.

2. Used to store energy or to provide structure for an organism.

3. Examples are glycogen, starch, cellulose, and chitin.

II. Lipids

A. Lipids do not dissolve in water because they are nonpolar, they contain mostly

carbon and hydrogen atoms, very few oxygen atoms. Carbon and hydrogen have very little difference in electronegativity thus have little polarity.

B. Lipids are found in cell membranes, are used in transporting messages in

organisms, and are used as energy storage in organisms. A gram of lipid contains

twice as much energy as a gram of carbohydrate because lipids have more energy rich carbon-hydrogen bonds.

C. Triglycerols (Triglycerides)

1. Triglycerols are composed of three fatty acid chains joined to a glycerol

by dehydration synthesis.

2. Saturated triglycerols (saturated fat found mainly in anmals) have only single

bonds between their carbon atoms in the fatty acid chains. Saturated triglycerols exist as solids at room temperature. Unsaturated triglycerols (oils found mainly in plants) have at least one double bond in their carbon chains.

Unsaturated triglycerols exist as liquids at room temperature.

3. Triglycerols have a great ability to store energy due to their long carbon-

hydrogen chains.

D. Phospholipids

1. One fatty acid group in a triglycerol is replaced by a phosphate group.

Phosphate has a negative charge which makes the phosphate side of the

phospholipid polar, the fatty acids are nonpolar. These compounds have a

polar and nonpolar end.

2. Phospholipids are the major component of biological membranes. They

automatically align themselves with the hydrophobic tail to the inside away

from the water environment. The hydrophilic head goes to the outside toward

the water. The automatic alignment based on polarity saves the cell a tremendous amount of energy.

E. Waxes – Water proof coatings used by organisms.

F. Steroids

1. Steroids are lipids that have a structure that contains four contiguous carbon rings.

2. Cholesterol, testosterone, and estrogen are examples of steroids.

III. Proteins

A. The major structural component of animals, protests, and monerans. They make up over 50% of the dry weight of animals. Examples of materials composed of proteins are hair, fingernails, silk, antibodies, hemoglobin, muscles, and enzymes.

B. Proteins are composed of the elements carbon, hydrogen, oxygen, nitrogen, and sulfur.

C. The monomers of proteins are amino acids. Twenty different amino acids make up all the proteins of the human body.

D. The structure of protein is determined by four levels of structure.

1. The primary structure is the sequence of amino acids that make up a protein. The primary structure is directly determined by DNA.

2. The secondary structure has the amino acid chain start to bond within itself. Amino acids form hydrogen bonds and form an alpha helix or a beta pleated sheet.

3. The tertiary structure is determined by additional bonding which refines the three-dimensional shape. The secondary structure can either form an alpha-helix or a beta pleated sheet.

4. The quaternary structure is found in some proteins when two or more polypeptide chains combine together to form the finished protein.

IV. Enzymes

A. Enzymes are protein molecules that act as catalysts. Enzymes are found in all living things, there would be no life without them.

B. Enzymes reduce the energy needed to get a chemical reaction started (activation energy). Enzymes are not changed or used up in a reaction. By reducing activation energy, enzymes greatly increase the speed at which chemical reactions can take place. For example, at room temperature and without an enzyme, cat urea is broken down into ammonia and carbon dioxide at a rate of 30,000 molecules in three million years. With the enzyme, the reaction rate is increased to 30,000 molecules per second.

C. The substrate is the substance that the enzyme works on. Enzymes are very specific, they work on only one substance.

D. The names of almost all enzymes end in “ase.” The base word is the name of the compound the enzyme works on.

E. Enzymes have a very specific shape that will allow a compound with a corresponding shape to fit (substrate). This specific fit between enzyme and substrate is known as the lock and key model. The substrate fits into the enzyme much like a key fits into a lock.

F. There are some enzymes that need additional ions or nonprotein molecules to bond with the substrate. The ions are known as cofactors (Fe+2, Ca+2, Mg+2) and nonprotein molecules are known as coenzymes (vitamins).

G. Increasing the amount of substrate usually speeds up the reaction. Enzymes seldom work to their potential, more substrate allows them to work at a faster speed.

H. Inhibitors are substances that slow down or stop the activity of enzymes.

1. Competitive inhibitors have a shape similar to the substrate. They bond to the active site instead of the enzyme. Competitive inhibitors do not damage the enzyme and can be overcome by adding large amounts of substrate.

2. Noncompetitive inhibitors inactive crucial groups in the enzyme’s active site. They charge the enzyme and thus can not be overcome. Cyanide is an example, it bonds to the iron in prosthetic groups of cytochromes preventing them from accepting electrons in respiration.

I. Allosteric enzymes have two or more binding sites. They exist in two or more shapes, one active and one inactive. The regulatory site, which is separate from the active site, changes the shape of the active site when a regulator compound bonds at the regulatory site. Allosteric enzymes can be turned off when they are not needed. Blood clotting is an example is an example of a pathway that contains allosteric enzymes and can be turned off.

J. Temperature greatly effects the activity of an enzyme. Very high temperatures (above 105 °C) cause the weak tertiary bonds to break destroying the shape of the enzyme inactivating it. Low temperatures cause the enzyme and substrate to slow down, which reduces the chance for the two coming together. Changes in pH will stop the activity of an enzyme.

V. Vitamins

A. Vitamins are coenzymes, they are involved in enzymatic reactions in the body. They are required in small amounts and each vitamin may be involved in several reactions.

B. Fat-soluble vitamins can be stored in fatty tissues of the body do not need to be consumed daily. They can become toxic is taken in high concentrations (vitamins A, D, E, K).

C. Water-soluble vitamins can not be stored in the body so need to be consumed daily so they are available for chemical reactions (vitamin C and all the B vitamins).

VI. Minerals

A. Elements needed by the body in small quantities for good health. Some are needed for body compounds (iron in hemoglobin) or needed as ions for reactions to occur (Ca+2 in nerve stimulus transfer).

B. Macrominerals like potassium, calcium, and sulfur are needed in milligram accounts each day, microminerals are needed in microgram amounts each day.

Biochemistry Questions

1) In many recent articles it is stated that eating foods high in fat will cause you to gain weight. Is this belief true? Why does the body store energy in the form of lipids rather than some other type of compound, for instance carbohydrates?

2) Many athletes and body builders take protein supplements. Are these supplements an advantage? Are they harmful?

3) Explain the process in which allosteric enzymes are regulated. How does this regulation process differ from other enzymes?

4) Most body builders and many world-class athletes take “steroids.” What are they? How can steroids be beneficial to these athletes? Explain what physiological changes take place with steroid use.

5) Explain, in detail, the dehydration synthesis of a glucose and fructose molecule to form sucrose. Why do you feel thirsty when you eat sweets?

6) Draw the structural formula of a triglyceride and explain how it forms. What are triglycerides used for and why? What is the difference between fats and oils? How is vegetable oil changed to solid margarine?

7) How do phospholipids differ from triglycerides? How does the structure of a phospholipid make it a great component of biological membranes?

8) Explain the process, using a diagram, where amino acids are combined to make proteins. Proteins are said to have three different structures, how do they differ?

9) How do enzymes speed up chemical reactions? Explain why high temperatures or strong acids can stop the activity of enzymes.

10) Why do you need vitamins? Which vitamins should you get in your diet everyday? Which vitamins will make you sick if you get too much of them? What accounts for the difference in daily requirements?

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