1. Chapter 20 Biochemistry by Christopher Hamaker
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2. Introduction to Biochemistry
There are 30 elements that are essential for life.
The study of the chemistry of living things is called biochemistry.
Biological compounds are often large and complex with molar masses greater than 1,000,000 g/mol.
These large molecules are polymers of smaller molecules.
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3. Biological Compounds
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4. Proteins
Proteins are naturally occurring polymers composed of many amino acids.
An amino acid has both an amine and a carboxylic acid functional group.
Amino acids are linked together by amide bonds, which are referred to as peptide linkages.
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5. Carbohydrates
A carbohydrate is either a simple sugar or a polymer composed of many simple sugars.
A carbohydrate usually contains either an aldehyde or ketone functional group and several alcohol groups.
Starch is a carbohydrate polymer composed of glucose units linked together by glycoside linkages.
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6. Lipids
A lipid is a water-insoluble compound usually composed of an alcohol and one or more carboxylic acid molecules.
Fats and oils are esters of glycerol, an alcohol that has three –OH groups.
As a result, each molecule of a fat or an oil contains three ester groups from three carboxylic acid molecules joined to one glycerol molecule.
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7. Nucleic Acids
A nucleic acid is a biochemical polymer composed of a very large number of individual units.
Each unit in the nucleic acid contains a sugar molecule attached to an organic nitrogen-containing molecule and an attached phosphate group.
The units are attached together by phosphate linkages.
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8. Amino Acids Proteins are composed of amino acids.
An amino acid has an amine (–NH2) and a carboxyl group (–COOH) attached to a carbon atom with a side chain (R–) attached to the a-carbon.
There are 20 naturally occurring amino acids in human proteins. Each one has a different side chain (R–).
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9. The 20 Natural Amino Acids
Neutral Amino Acids
Acidic Amino Acids
Basic Amino Acids
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10. Primary Structure of Proteins
Proteins are polypeptides composed of hundreds or thousands of amino acid units (amide bonds).
The primary structure of a protein is the sequence of amino acids. Individual amino acids are represented by the ovals in the figure below.
The replacement of one amino acid by another in the primary structure of a protein can completely alter its biological activity.
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11. Secondary Structure of Proteins
When the peptide chain twists and bends, proteins acquire a secondary structure.
There are two primary types of secondary structure: a-helix and pleated sheet.
An a-helix is analogous to that in a coiled telephone cord.
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12. Pleated Sheet
In a pleated sheet, the chains run antiparallel to each other. It looks like a sheet of paper folded in an accordion shape.
Secondary structures in proteins are a result of hydrogen bonds.
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13. Tertiary Structure of Proteins
The overall three-dimensional structure of a protein is referred to as its tertiary structure.
The tertiary structure of a protein may be long and extended, or compact and folded.
The tertiary structure of a protein is held together by intermolecular forces.
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14. Enzymes An enzyme is a protein that acts as a biological catalyst.
Enzymes are incredibly selective for specific molecules.
An enzyme can speed up a biochemical reaction so that the rate is a million times faster than it would be in the absence of the enzyme.
Many reactions catalyzed by enzymes would be too slow without the enzyme to sustain life.
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15. Enzyme Mechanisms
The location where the reaction occurs on the enzyme is called the active site.
The molecule that reacts is the substrate.
We can use the lock-and-key model to describe enzyme mechanisms.
In the model, the key is the enzyme and the lock is the substrate.
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16. Enzyme Reactions An enzyme reaction takes place in two steps.
First, the substrate (S) binds to the active site on the enzyme (E).
Step 1: E + S → ES
Second, the enzyme releases two or more products (P1 and P2).
Step 2: ES → E + P1 + P2
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17. Enzyme Reactions, Continued
The active site of an enzyme has a shape specifically designed to bind its substrate.
Once the reaction has occurred, the active site is free to bind to another substrate molecule and repeat the reaction.
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18. The Enzyme Ptyalin
The enzyme ptyalin is in human saliva and catalyzes the breaking down of starch molecules into sugar units.
The reaction would take about two years to occur without the enzyme.
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19. Carbohydrates
The word carbohydrate means “hydrates of carbon,” and many have the empirical formula CH2O.
Carbohydrate names usually end in the suffix ose.
Carbohydrates have an aldehyde or ketone functional group and several hydroxyl groups.
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20. Simple Sugars
A simple sugar molecule typically has three to six carbons, an aldehyde or ketone group, and a few hydroxyl groups.
A monosaccharide with an aldehyde group is an aldose, and one with a ketone group is a ketose.
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21. Aqueous Structures of Sugars
In aqueous solution, sugar molecules usually exist in ring structures.
Glucose forms a cyclic structure by joining a hydroxyl group to an aldehyde group.
The resulting ring structure has five carbon atoms and one oxygen atom.
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22. Disaccharides
A disaccharide is two monosaccharide molecules joined together.
In the formation of a disaccharide, two simple sugars split out water and are joined together by a special –O– bond called a glycoside linkage.
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23. Polysaccharides
A polysaccharide is a polymer of many monosaccharide linkages joined by glycoside linkages.
Starch and cellulose are both polysaccharides composed only of glucose units, but with slightly different three-dimentional structures.
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24. Lipids
Unlike most other biological compounds, lipids are not water soluble.
Lipids include:
Fats and oils
Waxes
Steroids
Water-insoluble vitamins A, D, E, and K
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25. Fatty Acids
A fatty acid is a carboxylic acid with a long hydrocarbon chain.
Fatty acids can be saturated or unsaturated.
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26. Triglycerides (Triglycerols)
A triglyceride is a lipid formed from glycerol, a trihydroxy alcohol, and three fatty acids.
When three fatty acids react with glycerol, a triglyceride is formed with three ether linkages.
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27. Fats
In triglycerides obtained from animals, the fatty acids are mostly saturated and have few double bonds.
A semisolid lipid obtained from an animal source is a fat.
The following structure is an example of a saturated triglyceride from animal fat.
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28. Oils A liquid lipid obtained from a plant source is an oil.
Triglycerides obtained from plants have mostly unsaturated fatty acid chains.
The following structure is an example of an unsaturated triglyceride from a vegetable oil.
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29. Nucleic Acids
Nucleic acids are biochemical compounds found in every living cell.
Nucleic acids contain the genetic information responsible for the reproduction of a species.
There are two basic types of nucleic acids:
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
A nucleic acid is a polymer composed of many repeating units, each of which is called a nucleotide.
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30. Nitrogen Bases There are five nitrogen bases.
Three are found in both DNA and RNA, one is found only in DNA, and one is found only in RNA.
Their structures are shown below:
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31. DNA and RNA
DNA and RNA are polymers of individual nucleotides. A segment is shown here.
A DNA molecule is actually two strands of DNA wound together in a spiral structure called a double helix.
The double strand is held together by hydrogen bonds between nitrogen pairs.
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32. DNA Double Helix
An adenine (A) on one strand always hydrogen bonds to a thymine (T) on the other strand.
Also, a cytosine (C) on one strand always hydrogen bonds to a guanine (G) on the other strand.
These interactions give DNA its characteristic structure.
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33. Chapter Summary There are four major types of biological molecules:
A protein is composed of amino acids.
A carbohydrate is composed of simple sugar molecules.
A lipid is a water-insoluble biological molecule.
A nucleic acid is a polymer composed of a sugar molecule, a nitrogen base, and a phosphoric acid.
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34. Chapter Summary, Continued
An enzyme is a catalyst for biological reactions.
Enzymes work by a lock-and-key mechanism, where only a specific substrate fits into the enzyme to react.
Reactions catalyzed by enzymes can be completed in a matter of seconds, whereas the reaction would normally take many years.
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35. Chapter Summary, Continued
A triglyceride is an ester of glycerol and three different fatty acids.
A fat is a triglyceride from an animal source. An oil is a triglyceride from a plant source.
A nucleic acid is a molecule that carries genetic information.
DNA and RNA are the two basic types of nucleic acids.
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