BIOMOLECULES & BIOCHEMISTRY

BIOMOLECULES & BIOCHEMISTRY In recent years, it has become increasingly evident that an understanding of biology requires a thorough understanding of chemistry. More and more biological research is devoted to understanding the chemistry of biomolecules. Biomolecules include the proteins, carbohydrates, lipids, nucleic acids, and the building blocks of which they are made. Understanding the relationship between structure and function is critical to understanding biology at the organismal level. Similarly, understanding the structure of biomolecules and how that structure relates to their function is critical to understanding biology at the molecular level. OBJECTIVES Learn the structure and chemical characteristics of the most common functional groups found in biomolecules Understand the relationship between the redox state, the chemical structure and energy content. Learn the chemistry and recognize the structures of the building blocks of proteins, carbohydrates, lipids, and nucleic acids. Perform and Understand condensation and hydrolysis reactions using models of monomers found in protein, carbohydrates, and lipids. Perform and Interpret biochemical assays for proteins and carbohydrates. PART 1: COMMON FUNCTIONAL GROUPS FOUND IN BIOMOLECULES There are eight common functional groups found in biomolecules. In today s lab we will explore six of them. Use the molecular model kits provided to build the molecules on page 2. These molecules contain 5 of the 6 functional groups that will be disucssed in lab. Count how many of each atom and each bond you will need. Collect these pieces on a tray. PLEASE, TAKE ONLY THE AMOUNT OF MATERIALS YOU NEED. Key to pieces: Carbon - Black Hydrogen - White Oxygen - Red Nitrogen - Blue Phosphorus - Brown Single bonds - short gray rods Double bond - long flexible rods (use 2) 06Feb17 12:18 pm Biomolecules & Biochemistry - 1

NOTE: Sections 1a - 1d (pg 2-3) apply to the molecules enclosed by the box only. The Amino group will be covered in Section 3 1a. The C H Functional Group This functional group, commonly called a hydrocarbon, is made of a single carbon atom covalently bonded to a single hydrogen atom. A single pair of electrons is shared between the carbon and the hydrogen. Chemical bonds represent stored energy. When a bond is broken, the stored energy is released. In order to make the bond, energy must be provided. Count the number of C H groups in each molecule. Which molecule has the most C H groups? Which has the least?. Arrange the molecules in order of decreasing number of C H groups. 06Feb17 12:18 pm Biomolecules & Biochemistry - 2

1b. The -OH Functional Group This functional group, commonly called a hydroxyl or alcohol, is made of a single oxygen atom covalently bonded to a hydrogen atom. A single pair of electrons is shared between the oxygen and the hydrogen. Due to the high electron affinity of the oxygen atom, this functional group has polar characteristics. The oxygen has a partial negative charge while the hydrogen has a partial positive charge. As a result of the charge separation, this group tends to form hydrogen bonds. When the group is bonded to a carbon atom (the bond is between the carbon and the oxygen), the hydrogen retains its partial positive charge while the partial charge on the oxygen becomes less localized. The hydrogen atom is acidic in nature and will be released into solution as a proton under the proper conditions. W hen the group is ionized in this way, the oxygen is left with a full negative charge. Which molecules have -OH groups? 1c. The -C=O Functional Group This functional group, commonly called a carbonyl, is made of a single carbon atom covalently bonded to a single oxygen atom. The bond is a double covalent bond. The two atoms share two pairs of electrons, hence the name double bond. To differentiate the atoms in this group from others in the molecule to which it is attached, the oxygen is referred to as the carbonyl oxygen and the carbon as the carbonyl carbon. The carbonyl group can have polar characteristics. The oxygen can have a partial negative charge again due to its high electron affinity. The partial positive charge is not localized on any single atom. As a result of this characteristic, the carbonyl oxygen can form hydrogen bonds. This is especially important in forming the secondary structures of proteins, a topic to be covered at a later date. Which molecules have -C=O groups? 1d. The -C=O Functional Group OH This functional group, commonly called a carboxyl or carboxylic acid, is made of a carbonyl group with a hydroxyl group bonded to the carbonyl carbon. This group possesses the characteristics of the two groups of which it is made. It can form H-bonds with other molecules through the hydroxyl and carbonyl oxygen. The hydroxyl group is acidic. Which molecules have carboxyl groups? 06Feb17 12:18 pm Biomolecules & Biochemistry - 3

PART 2: OXIDATION, REDUCTION, AND THE ENERGY CONTAINED IN MOLECULES You should still have the molecules arranged in the order specified in Part 1a. If not, rearrange the molecules from most to least number of C H functional groups. We will begin by reviewing the definitions of OXIDATION and REDUCTION and their relationship to energy. Oxidation is defined as the loss of electrons. Reduction is defined as the gain of electrons. The process of oxidation results in an overall loss of energy while reduction results in a gain of energy. In other words, a molecule that has undergone oxidation contains less energy than it did prior to the oxidizing event. Similarly, a molecule that has undergone reduction contains more energy than it did prior to the reducing event. In biomolecules, oxidation is most often accomplished by replacing the hydrogen in C H groups with a hydroxyl group ( OH). The C OH can be further oxidized by removing the hydrogen attached to the oxygen and a hydrogen attached to the carbon. These two single bonds are replaced with a double bond between the carbon and the oxygen. In general, the degree of oxidation (or reduction) of an atom can be determined by counting the number of hydrogens directly bonded to an atom (in this example, the atom is a carbon atom). In the reaction example above, the carbon contained in the molecule on the left (reactant) is more reduced than the carbon in the molecule on the right (the product)(1 hydrogen bonded to the carbon vs. none). So the diagramed reaction is described as an oxidation. The reverse reaction would be described as a reduction. Returning to the molecules you have made, they are in descending order based on the number of C--H groups. Based on the discussion above, you can now see that they are also in descending order based on energy and degree of reduction. Draw in the structure of each molecule under its name. (see pg. 2) Highest Energy Most Reduced Least Oxidized Lowest Energy Least Reduced Most Oxidized Methane Methanol Methyl Aldehyde Methanoic Acid Carbon Dioxide You are responsible for the names of all the molecules and identifying their relative level of oxidation, reduction, and/or energy 06Feb17 12:18 pm Biomolecules & Biochemistry - 4

PART 3 - PROTEINS Proteins are strings of covalently bonded amino acids. They primarily serve as structural components and enzymes. The functional structure of proteins is dependent on their amino acid sequence. Interactions between amino acids produce complex three-dimensional molecules. In this exercise you will examine the structure of amino acids and the covalent bond that links them together. You will also examine a common biochemical assay for proteins. 3a. Amino Acid Structure There are twenty essential amino acids. Each amino acid has the same chemical backbone. Amino acids differ chemically due to their side chains (referred to as functional or "R" groups). These functional groups can be polar (hydrophilic), non-polar (hydrophobic), acidic, or basic. Examine the structures of the amino acids on the next page. Get enough molecular model pieces to construct both amino acids. Referring to the diagrams: Part a - Amino Group Part b - Carboxylic Acid Group Part c - Functional or "R" Group Examine the models by taking note of the following points and answering some questions. 1. Note that the name "amino acid" comes from the amino group and the [carboxylic] acid group. 06Feb17 12:18 pm Biomolecules & Biochemistry - 5

2. Note that all amino acids have the same "amino - carbon - acid" backbone. As a result, all amino acids have both basic (due to the amino group) and acidic characteristics. The amino group is basic since it can accept a proton (becoming NH 3 + ) under the proper conditions. The acid group can donate a proton (becoming COO - ) under the proper conditions. Molecules with regions that are acidic and other regions that are basic are termed: AMPHOTERIC In addition, amphoteric molecules like amino acids will carry a double charge at certain ph s. For example, at physiological ph s The amino group of amino acids will be positively (+) charged The acid group of amino acids will be negatively (-) charged. 3. In addition to the acidic/basic qualities of the backbone, many amino acids have acidic or basic R-groups. These can also be charged at certain ph s. 4. Note the differences in the functional or R-groups. Of the molecules you constructed, which R-groups would have polar characteristics? Non-polar characteristics? 06Feb17 12:18 pm Biomolecules & Biochemistry - 6

3b. Linking Amino Acids Together to Make Peptides and Proteins - The Peptide Bond Amino acids are joined together to form peptides (longer chains are referred to as proteins). This is accomplished through a general reaction called DEHYDRATION or CONDENSATION. The reaction involves the removal of water, hence the name. When joining amino acids, the amino group contributes a hydrogen while the acid group contributes an alcohol group (-OH). The reaction is mediated by a specific enzyme. The reaction is diagramed below. Perform a dehydration reaction on your two amino acid models. The bond that forms between the amino nitrogen and the carbonyl carbon is called a PEPTIDE BOND. The reaction can be reversed by adding water to the peptide bond. This reaction is called HYDROLYSIS. It is also enzyme-mediated. Use your model to reverse the reaction. 06Feb17 12:18 pm Biomolecules & Biochemistry - 7

3c. The Biuret Test - An Assay for Protein Biochemical assays test for the presence of certain types of molecules. The assay usually tests for a specific functional group known to be part of the molecule. Assays can be qualitative, testing for presence or absence, or quantitative, providing a numerical value to the amount of material present. Qualitative tests can be sensitive enough to give some indication as to the amount of the material present (e.g., none vs. a small, medium, or large amount). Such distinctions are subjective. They may depend on how long the assay was allowed to proceed or the conditions under which the assay was conducted. The Biuret Test is a qualitative test for proteins. It specifically tests for the presence of two CONH groups joined together by a carbon atom. This is the peptide linkage. Biuret's reagent is blue in color. It turns pink to purple in the presence of peptide linkages. A pink color indicates less protein than a purple color. Procedure for Performing Biuret Test You will test five unknown materials marked A through E for the presence of protein. 1. Secure 5 test tubes and a test tube rack. Mark each tube with two lines, one 3 cm from the bottom of the tube and one 4cm from the bottom. Mark each tube with one letter, A - E. 2. Add unknown material (A-E) to the corresponding tube up to the 3cm line. 06Feb17 12:18 pm Biomolecules & Biochemistry - 8

3. Add CuSO 4 (Biuret's Reagent) up to the 4cm line. 4. Observe the color change. Record the results below. Unknown A B C D E Color QUESTIONS: 1. The unknown materials are Water, Starch, Glucose, Egg Albumin (a source of pure protein), and a Nutrient Supplement (containing carbohydrate and protein). Based on your test results try to identify the unknowns. If you aren't sure, list all the possibilities for each unknown. Unknown A: Unknown B: Unknown C: Unknown D: Unknown E: 2. Which unknowns did not contain any protein? How do you know this? 06Feb17 12:18 pm Biomolecules & Biochemistry - 9

PART 4 - CARBOHYDRATES Carbohydrates are large macromolecules made by linking simple sugars (MONOSACCHARIDES). Carbohydrates are often referred to as POLYSACCHARIDES since they are made of strings of monosaccharides. Monosaccharides can also be joined in pairs to form disaccharides. Common disaccharides are: Sucrose (table sugar) and Lactose (milk sugar). Carbohydrates have a variety of uses. Their primary function is energy storage. Examples of carbohydrates used as energy sources are glycogen and starch. Both of these molecules are polymers of glucose. Carbohydrates serve structural role in plants. Cellulose, the primary constituent of plant cell walls, is also a polymer of glucose. Certain monosaccharides (ribose and deoxyribose) are structural components of the nucleic acids, DNA and RNA, and the energy transfer molecule, ATP. 4a. The Structure of Monosaccharides Monosaccharides are usually represented as rings containing 5 or 6 carbon molecules. The ring structures are highly variable. You will examine two common monosaccharides, glucose and fructose. Both are six carbon sugars. Glucose has 5 carbons in its ring and 1 outside the ring. Fructose has 4 carbons in its ring and 2 outside. NOTE: In the above diagrams the vertex of any lines represents a carbon atom. Glucose with carbon atoms shown is diagramed here. 06Feb17 12:18 pm Biomolecules & Biochemistry - 10

Retrieve the ready-made glucose and fructose models from the table at the front of the lab. DO NOT DISASSEMBLE THESE MOLECULES. YOU MAY ONLY MAKE THOSE CHANGES SPECIFIED IN THE LAB INSTRUCTIONS. ALWAYS RETURN THE MOLECULES THE WAY YOU FOUND THEM. Now examine the molecules using the instructions that follow. 1. Orient the molecular model of each sugar with the flat drawing on the preceeding page. Notice that the hydrogen and hydroxyl groups are not in the same plane as the ring of carbon molecules. The 3-Dimensional orientations of these groups are important to the function of the sugar. Changing the orientation of any group changes the chemical nature of the molecule. 2. Count the number of carbons, hydrogens, and oxygens in each molecule. Record the information in the table below. Atom GLUCOSE FRUCTOSE Carbon Hydrogen Oxygen What is the ratio of Carbon to Hydrogen to Oxygen in both molecules? All Carbohydrates have this same ratio of one carbon molecule to one water molecule - C n (H 2 O) n. The name "Carbohydrate" literally means hydrated (water-soaked ) carbon. For each atom of carbon in a carbohydrate there is one molecule of water. 4b. Linking Monosaccharides to Make Disaccharides and Polysaccharides As with amino acids, monosaccharides are joined together by a DEHYDRATION REACTION. The resulting bond is called a GLYCOSIDIC BOND. It is sometimes referred to as an OXYGEN BRIDGE. The position of the hydrogen and hydroxyl groups involved in the bond vary with the types of sugars being joined and the orientation of the sugars. For example, glycogen, starch, and cellulose are all made of polymers of glucose. Glycogen and starch are both storage forms of glucose, the latter found only in plants while the former is found only in animals. Cellulose is the main structural component of plant cell walls. The only structural difference between these functionally different molecules is the orientation bonds between the glucose molecules. Again as with amino acids, the separation of joined monosaccharides is achieved using a HYDROLYSIS REACTION. Using the models, perform a DEHYDRATION reaction as diagrammed below. Then reverse the process by performing a HYDROLYSIS reaction. 06Feb17 12:18 pm Biomolecules & Biochemistry - 11

Glucose and Fructose aligned for Dehydration Reaction + H 2 O Glucose and Fructose joined by Glycosidic bond (Oxygen bridge) to form Sucrose 06Feb17 12:18 pm Biomolecules & Biochemistry - 12

4c. Biochemical Assays for Monosaccharides and Polysaccharides The Benedict's test is a qualitative assay for certain monosaccharides. The Benedict's test will show a positive result in the presence of any monosaccharide that is also a reducing sugar. Reducing sugars readily contribute electrons causing reduction. Reducing sugars become oxidized in the process. In the Benedict's test, copp er (II), Cu 2+,is used as an electron acceptor. It is reduced to copper (I), Cu 1+, in the presence of a reducing agent. The reduction of copper (II) to copper (I) is monitored by a color change. Copper (II) is blue. The solution will change from blue to green to yellowgreen to orange to reddish-orange (rust) as the copper (II) is converted to copper (I). The amount of color change is dependent on both the amount of reducing sugar present and the amount of time the assay is allowed to proceed. The Iodine test is a qualitative assay for the presence of the polysaccharide starch. Iodine, in the presence of starch, will turn a solution bluish-black. The more starch, the darker the color. Procedures for Performing the Benedict's Test You will test five unknowns for the presence of reducing sugars. 1. Secure 5 test tubes and a test tube rack. Mark each tube with one of the unknown letters (A,B,C,D,E). 2. Add 2ml of Benedict's solution to each tube.. 3. Add 1ml of unknown material to the corresponding tube. MIX THOROUGHLY 4. Place the tubes in one of the boiling water baths provided. THE TUBES ARE TO BE LEFT IN THE WATER BATH FOR EXACTLY 3 MINUTES. 5. Record the color of each tube in the table below. Use the following key to assign a qualitative value to each result. Blue: Brownish/Green: + Brownish/Orange: ++ Red/Orange: +++ Unknown Color Value A B C D E 6. Which unknown is a reducing sugar? 06Feb17 12:18 pm Biomolecules & Biochemistry - 13

Procedures for Performing the Iodine Test You will test five unknowns for the presence of starch. 1. Secure 1 ceramic spot plate. 2. Add 1 drop of each unknown to a separate depression in the spot plate. 3. Add 1 drop of iodine (in the dropper bottle labeled Lugol s) to each unknown sample and record the results below Unknown A B C D E Color 3. Which unknown(s) gave a positive Iodine Test result? 4. Based on your results from the 3 assays (Biuret, Benedict's and Iodine) identify each unknown. Unknowns: Water, Starch, Egg Albumin, Glucose, Nutrient Supplement Unknown A B C D E 06Feb17 12:18 pm Biomolecules & Biochemistry - 14

PART 5 - LIPIDS Lipids, or fats, are hydrophobic molecules with a variety of structures and functions. Triglycerides, waxes, and steroids are all examples of lipids. We will look at triglycerides and their relatives in this portion of the lab exercise. 5a. The Structure of Triglycerides and their Relatives Triglycerides are composed of a GLYCEROL backbone with three FATTY ACIDS attached through an ester linkage. An ester linkage is diagrammed below. Retrieve the 3 FATTY ACIDS that were assembled in last week s lab. AS WITH THE OTHER PRE-ASSEMBLED MOLECULES, MAKE ONLY THOSE CHANGES SPECIFIED IN THE LAB INSTRUCTIONS. ALWAYS RETURN THE MOLECULES THE WAY YOU FOUND THEM. 1. Use the diagram on the next page to construct a GLYCEROL molecule. 2. Fatty acids can be attached to glycerol via dehydration reactions. Glycerol with 1 fatty acid attached is called a MONOGLYCERIDE, with 2 fatty acids, a DIGLYCERIDE, and with 3 fatty acids, a TRIGLYCERIDE. Fatty acids can be SATURATED or UNSATURATED. In saturated fatty acids each carbon is bound to 4 other elements via single bonds. In unsaturated fatty acids, some carbons are bound to adjacent carbons by double bonds. Fatty acids with one double bond are called MONOUNSATURATED. If two or more double bonds are present, the fatty acid is called POLYUNSATURATED. Examine a saturated and unsaturated fatty acid chain. Other than presence of a double bonded carbon, what is different about them? 06Feb17 12:18 pm Biomolecules & Biochemistry - 15

3. Orient the glycerol (molecule on the left) and 3 fatty acids (molecules on the right) as diagramed below. 4. Perform 3 dehydration reactions, as diagramed below, to make a triglyceride. Note that each dehydration reaction forms an ester linkage between the glycerol and the fatty acid. 5. Would you characterize this molecule as hydrophobic or hydrophilic? Why? (Hint: the carbonyl oxygen is not partially charged in this bonding pattern) 6. Perform a hydrolysis reaction to remove the first fatty acid. You should now have the molecule diagrammed to the right. This is a diglyceride. 06Feb17 12:18 pm Biomolecules & Biochemistry - 16

7. Perform a dehydration reaction to attach the phosphocholine m olecule where fatty acid #1 was attached to the glycerol. (see diagram below) 8. The molecule you have just created is called a PHOSPHOLIPID. Its technical name is PHOSPHOTIDYLCHOLINE. Note that the phosphate group and the choline group are charged. The phosphate has a negative charge while the choline has a positive charge. 9. Can you characterize this molecule as exclusively hydrophobic or hydrophilic? Why? 10. Which portions of the molecule are hydrophobic? hydrophilic? 11. Which portions of the molecule will combine with water? Which parts will not? 12. Molecules with hydrophobic and hydrophilic regions are called AMPHIPATHIC. Phospholipids will spontaneously form bilayers when placed in a water. They form the matrix of cell membranes a topic to be discussed later. 06Feb17 12:18 pm Biomolecules & Biochemistry - 17

PART 6 - NUCLEIC ACIDS Nucleic acids serve numerous functions within the living cell. In addition to their familiar roll as information-carrying molecules, nucleic acids also serve as energy carriers, phosphate-group donors and modifiers of protein structure and function. The nucleic acid building block is the nucleotide. Nucleotides are composed of a phosphate, a five-carbon sugar (ribose or deoxyribose), and one of 5 nitrogen bases. The general structure is diagramed below. In the above molecule the sugar is deoxyribose. This is a variation of the 5- carbon sugar ribose. The difference is the replacement of an alcohol group on the 2' carbon with a hydrogen. The phosphate group is attached to the 5' carbon which is outside the ring structure. The nitrogen base is attached to the 1' carbon. T here are 5 different nitrogen bases as listed in the figure. Nucleic acids take the form of single nucleotides, nucleoside triphosphates and extended nucleotide polymers attached 5' to 3'. Nucleosides are nucleotides without the phosphate group. Two important nucleoside triphosphates are ATP (Adenosine TriPhosphate) and GTP (Guanosine TriPhosphate). ATP is diagramed below 06Feb17 12:18 pm Biomolecules & Biochemistry - 18

Both ATP and GTP can act as phosphate-group and energy donors. The terminal phosphate group is removed via a hydrolysis reaction, converting the nucleoside triphosphate to a nucleoside diphosphate (ATP ADP + P i where P i = an inorganic phosphate group). P i is also indicated as a capital P enclosed in a circle. The terminal phosphate bond is considered a high-energy bond and, upon hydrolysis, can provide 7-11 Kcal/mole of energy to drive chemical reactions with a +ÄG. In addition the phosphate group can act as a structural modifier changing the functional state of proteins. This structural modifier role is also evident in the role of the entire GTP molecule in regulating so-called G-proteins which are involved in cell signaling. Nucleic Acid polymers are used to store and transfer information throughout the cell. Nucleotides are joined via their 5' phosphate groups and 3' alcohol groups. A small polymer is diagramed at the right. This polarity (direction) of the diagramed strand is 5' to 3'. Polymers can also be 3' to 5'. DNA molecules are composed of two polynucleotide stands of opposite polarity (i.e., one strand is 5' to 3' and the other strand is 3' to 5'). Nucleic acids can be single strands of nucleotides as in the diagram to the right or they can be composed of two strands of nucleotides. When two nucleotide strands are involved, they interact to form a helical structure resembling a twisted ladder. The phosphates and sugars form the backbone while the nitrogen bases form the rungs. Find the DNA model in the lab. Referring to the model, the sugar/phosphate backbone is represented by the ribbon (phosphates) and the small squares marked with a "D" (for deoxyribose). The nitrogen bases are represented by the colored rectangles marked with the first letter of one of the four bases found in DNA (Uracil is only found in RNA). The two strands are held together by hydrogen bonds between the nitrogen bases. The bases pair very specifically due to their hydrogen bonding groups. Adenine hydrogen bonds only with Thymine and Cytosine only hydrogen bonds with Guanine. Find the nitrogen based models (Adenine, Guanine, Thymine and Cytosine). A diagram is provided below. Note that the A-T pair has two H- bonds while the G-C pair has three. 06Feb17 12:18 pm Biomolecules & Biochemistry - 19

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are central to a cell's ability to store, transfer, duplicate, and use genetic information. These processes are accomplished by template synthesis. Template synthesis uses an existing strand as a guide to produce a duplicate molecule. The two strands of a DNA molecule are not exact copies, rather they are said to be COMPLEMENTARY since base pairing depends on each base pairing with its complementary base (e.g., A/T C/G). DNA's primary function is storage of information, while RNA is used in the transfer of information into a functional form and to regulate the expression of genetic information. DNA and RNA are measured not by physical length but by the number of nitrogen bases in the polymer. Single stranded molecules are measures in bases. For example the diagram on the previous page is 4 bases in length. Double stranded molecules are measured in base pairs (bp), the number of A-T and C-G pairs in the molecule. The production of exact copies of DNA (Replication) is critical to the survival of cells and organisms. This process is accomplished with a series of enzymes that separate the two strands of the DNA helix and produce exact copies of each strand using the existing stands as templates. The result is a helix that is a duplicate of the original helix. Each helix contains one strand of DNA from the original molecule and one newly synthesized DNA strand. This method of replication is termed SEMI- CONSERVATIVE since each new molecule conserves one strand from the original molecule. Transfer and conversion of the information stored in DNA is accomplished via two processes: Transcription and Translation. Transcription involves the conversion of a section of DNA code into single-stranded RNA code for transport out of the nucleus. The RNA code can function as transcribed. These functional RNA molecules come in a variety of forms that are generally referred to as ncrnas. The nc stands for noncoding because the RNA does not code for a Protein. The rest of the RNA transcripts are in the form of mrna. The m stands for messenger. Translation of mrnas is carried out by a cellular organelle called the RIBOSOME. The Ribosome converts that RNA code into an amino-acid sequence, a protein. In the next several exercises you will, on paper, accomplish the tasks of replication, transcription, and translation. (A Key is provided at the end of the lab exercise) 1. REPLICATION - Write out the complementary sequence for the sequence given below. What is the size (in bp) of the resulting double-stranded molecule? T T C G G C C C C A G G T A T 06Feb17 12:18 pm Biomolecules & Biochemistry - 20

2. TRANSCRIPTION - Write out the complementary RNA sequence for both strands of DNA in problem #1. Begin by copying the DNA sequences in the space provided. Remember, RNA does not contain Thymine. It is replaced by Uracil. So each "A" in DNA is paired with a "U" in the RNA transcript. Thymine in DNA is still paired with Adenine in RNA. The G/C pairings also remain the same. DNA: RNA: DNA: RNA: 06Feb17 12:18 pm Biomolecules & Biochemistry - 21

3. TRANSLATION. Assume that the RNAs you made above are mrnas and translate them using the Genetic Code (Use your textbook or other reference book to find a copy of the genetic code). The genetic code matches 3-letter RNA words (called CODONS) into amino acids. Using the code, translate both RNA transcripts from the previous exercise (#2 on the preceding page) into amino acid sequences. It is helpful to circle the codons before translating. Begin at the left end of each RNA transcript and circle 3 letter codons until you reach the end of the transcript. Use the code to translate the RNA codons into amino acids. As a point of reference, the average protein is 400 amino acids long. Therefore, the RNA transcript would be 1200 nucleotides in length. RNA: AMINO ACID: RNA: AMINO ACID: KEY TO NUCLEIC ACID EXERCISES: Original sequence is in BOLD: T T C G G C C C C A G G T A T A A G C C G G G G T C C A T A Size = 15bp T T C G G C C C C A G G T A T RNA: A A G C C G G G G U C C A U A A A G C C G G G G T C C A T A RNA: U U C G G C C C C A G G U A U A A G C C G G G G U C C A U A Amino Acids: Lys Pro Gly Ser Ile U U C G G C C C C A G G U A U Amino Acids: Phe Gly Pro Arg Tyr 06Feb17 12:18 pm Biomolecules & Biochemistry - 22