Exercise 2-2: Biochemistry

There are two major types of chemistry: organic chemistry, the chemistry of organisms, and inorganic chemistry which is the chemistry of the nonliving world. As biologists we will focus mainly on organic but we must not forget our nonliving world. In organic chemistry we will talk about organic molecules which are molecules that contain both carbon and hydrogen atoms. These molecules then make up the organic compounds that make life possible. These organic compounds are carbohydrates, lipids, proteins, and nucleic acids.

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Carbon

Why is carbon so special? Carbon is a really small atom. It only has six electrons; two in the first electron shell and only four in its outer shell; carbon must therefore almost always bond with another atom or atoms in order to stay happy. Most of the time it only bonds to CHNOPS. Because C needs four electrons to complete its outer shell, it can bond with up to four different atoms!! This is very important!! It can even share electrons with other C atoms. This is a very stable bond. It often results in chains of C. Hydrocarbons are chains of carbon atoms bonded to only hydrogen atoms. When placed in water they turn back on themselves to form carbon rings.

Carbon can also form double and triple bonds with other carbon atoms. The more bonds the stronger.

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Functional Groups

Organic molecules are made of carbon chains also known as skeletons or backbones. They are so named because just as your skeleton gives you structure and therefore function so does a carbon chain; and just like animals are recognized by their appendages, so are organic molecules. These “appendages” of organic molecules are known as functional groups. A functional group is a specific combination of atoms that are bonded together that always react the same way regardless of the carbon skeleton. These functional groups determine the polarity of the carbon chain. Molecules of only H & C are non-polar and hydrophobic, meaning water fearing. When a functional group is added the carbon chain then becomes polar and hydrophilic, meaning water loving. Isomers are molecules that have identical molecular formulas but different arrangement of atoms.

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Glucose and Fructose both have a chemical formula of C6H 12O6. The only difference is the O atom is bonded

to a different C atom at a different place in the molecule.

Dehydration and Hydrolysis Reactions

Polymers are many subunits linked together. These subunits are also called monomers. In the case of biomolecules, how are these monomers joined to make polymers and vice versa? There are two processes: dehydration reaction, which is the removal of OH and H which then come together to make H2Owhich joins the two monomers; hydrolysis reaction, which is the addition of H 2O to the polymer which then splits into OH and H and breaks the polymer into its monomers.

**The four main polymers discussed are: carbohydrates, lipids, proteins, and nucleic acids.**

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Carbohydrates

Carbohydrates play an important role in the structural role in many different organisms and also they are a major energy source. They have a carbon to hydrogen to oxygen ratio of 1:2:1. They include single sugar molecules and also chains of sugars. The monomers are called monosaccharides. Monosaccharide means single sugar. They can have a C backbone of 3-7 C atoms. A disaccharide contains two monosaccharide’s that have joined during a dehydration reaction. Polysaccharides are polymers of monosaccharides. They are used for short term energy storage. Plants store glucose as starch. Animals store glucose as glycogen. Polysaccharides also serve a role in the structure of molecules. It is known as cellulose in plants, chitin in animals, and peptidoglycan in bacteria.

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Lipids

Lipids are the second type of organic molecules. They are insoluble in water because they lack a polar group and are therefore hydrophobic. There are four groups of lipids: fats & oils, waxes, phospholipids, and steroids.

Fats & oils are used primarily for long term energy storage. They are composed of two types of unit molecules: three fatty acids and one glycerol. When combined they are known as triglycerides. The fatty acids can be either saturated or unsaturated. A saturated fat is a carbon chain with all the hydrogen’s it can hold (no double bonded carbon atoms). An unsaturated fat is a carbon chain not bonded to all the hydrogen atoms it can hold (has double bonded carbon atom). This makes a “kink” in the fatty acid. This “kink” is very important in living things as we will find out later on.

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Phospholipids are like fats except that in the place of the third fatty acid there is a phosphate group. The phosphate group is polar and is repelled from the other two fatty acid “tails”. These phospholipids make up the bulk of the plasma membrane. They arrange themselves in a double layer known as the phospholipid bilayer.

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Steroids are a skeleton of 4 carbon rings. Examples of these include cholesterol, testosterone, and estrogen. Waxes are a long fatty acid bonds and a long chain of alcohol. They are solid at room temperature, serve a protective function, are waterproof, and resistant to degradation.

Proteins

Proteins serve a vital role in organisms of all sorts. They provide support for example keratin makes up hair and nails. They help in metabolism by speeding up or starting reactions in the cell. They provide transport like hemoglobin which transports oxygen. They provide defense; antibodies are proteins. They help regulate things in the body; hormones, specifically insulin are proteins. They also help in motion. They monomers for amino acids are called amino acids. Amino acids are composed of four parts: a carbon bonded to single hydrogen, an amino group, an acid group, and “R”.

There are 20 amino acids found in cells. They all contain the four basic parts and each has unique properties that are determined by “R”. A covalent bond between two amino acids is called a peptide. A polypeptide is a chain of amino acids joined by peptide bonds.

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Peptide

Polypeptides not only differ in the number of amino acids but also in the sequence of them. There are four structures to a protein: primary, secondary, tertiary, and quaternary. The primary structure is just the sequence of amino acids. The secondary structure is the coiling and folding of the amino acids. The tertiary structure forms the final 3-D shape of the protein and the quaternary structure is more than one polypeptide coming together.

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When a protein loses its normal configuration and/or loses its ability to perform it is called denaturation. This is when normal bonding patterns are changed and its cause by high temperature and pH.

Nucleic Acids

Nucleic acids are polymers of nucleotides with very specific functions in cells. DNA, RNA, and ATP are three nucleic acids important in biology. Nucleotides are made up of three components: a phosphate molecule, pentose sugar, and a nitrogenous base specific to the nucleic acid it is a part of. The sugar in DNA is deoxyribose and ribose in RNA. The nucleotides are divided into two categories: pyrimidines and purines. Pyrimidines are made of a single carbon ring and purines are made of two carbon rings.

The five different nucleotides are adenine, guanine, cytosine, thymine, and uricil. Cytosine, thymine, and uricil are all pyrimidines and adenine and guanine are purines. Purines always bond with pyrimidines. DNA consists of adenine, thymine, cytosine, and guanine. RNA consists of adenine, uricil, cytosine, and guanine. In DNA adenine always bonds with thymine and cytosine always bonds with guanine. In RNA adenine always bonds with uricil and cytosine always bonds with guanine. This is known as complimentary base pairing.

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ATP or adenosine triphosphate is an energy related nucleotide. It is made of adenine, ribose, and 3 phosphate groups. When it is broken down into adenine diphosphate it releases energy. It takes energy to form ATP from ADP.

4 Classes of Organic Molecules

1. Name two differences in inorganic and organic molecules.a. b.

2. What makes carbon so special that it plays a critical role in organic molecules?a. b. c. d.

3. Fill in the blanks in the chart below.

4. Give an example for each of the following.

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________________

_______

a. Monosaccharideb. Disaccharidec. Polysaccharide

5. Name the monomers for each of the following.a. Carbohydratesb. Lipidsc. Proteinsd. Nucleic acids

6. What is important about double bonded carbon atoms in lipids?7. What is a phospholipid and where would you find one?8. What are the differences in the structures of proteins?9. Describe the structure of an amino acid.10. What are the differences in DNA and RNA?11. What are the purines?12. What are the pyrimidines?

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