Protein Workshop: Amino Acids & Their Role in Structure and Function, Study notes of Biochemistry

Download Protein Workshop: Amino Acids & Their Role in Structure and Function and more Study notes Biochemistry in PDF only on Docsity! 1 Name _________________ Proteins: Workshop I Amino Acids - The Building Blocks of Proteins Chem 306 Overview - Proteins are large biological molecules that perform many different functions. (Table I). Proteins are made of molecular building blocks called amino acids. We will investigate the structure of amino acids and how they affect the structure of a protein. We will also investigate the affect of structure on the function of a protein. Why learn about proteins? Of the three classes of biomolecules - lipids, carbohydrates, and proteins – proteins have some of the most varied structure and function. For example, even a single amino acid can have a function in the body – the amino acid glutamate is the most abundant excitatory neurotransmitter in the mammalian nervous system. Scaling up things a bit consider the hormone insulin contains over 700 atoms, 51 amino acids, and has a molecular mass of 5700 amu. Some virus proteins are still larger, having molecular weights of over 40 million amu! Many disease processes and clues about disease in the body relates to proteins and protein structure. Table I – Types of Proteins and Their Functions Type Function Examples Structure Shape / Support Collagen – provides structure to tendons & cartilage Enzymes Catalysis Enzymes aid in biochemical reactions (Amylase begins digestion of carbohydrates by hydrolysis.) Hormones Regulate body functions by carrying messages to receptors Insulin – facilitates use of glucose for energy generation Storage Make essential substances available when needed Myoglobin – stores oxygen in muscles Contraction Do mechanical work Actin & myosin – govern muscle movement Protection (Immunity) Defend body against foreign matter Immunoglobulin – aids destruction of invading bacteria Transport Carry substances through body Hemoglobin - transports O2 in blood Membrane proteins - perform active transport Part I – Amino Acids A. General Structure The building blocks of proteins are α-amino acids, small molecules that contain a carboxylic acid and an amino group. The amino group is connected to the carbon next to the carboxyl group, the α carbon. 2 There structure of most amino acids differ only in the side chain (R group). Table II contains the structures of all the 20 amino acides required by the human body to make proteins. The R group for valine is a methyl group, -CH3. Circle the R groups for six amino acids on Table II. Nine of the 20 amino acids in Table II are “essential amino acids” and cannot be made by the body. These “essential amino acids” (His, Leu, Isl, Lys, Met, Phe, Thr , Try, Val) must be obtained in the diet. a. Circle the R group in the amino acids below. Name each amino acid and write the three-letter abbreviation for each. +H3N CHC CH2 O- O +H3N CHC O- O CH2 CH2 C O- O +H3N CHC O- O CHCH3 CH2 CH3 b. Serotonin is a neurotransmitter made from an amino acid. The sites of serotonin synthesis in the body are the central nervous system and the gastrointestinal tract. Serotinin is believed to play an important role in a variety of functions including the modulation of anger, aggression, body temperature, mood, sleep, sexuality, and appetite. Which amino acid is most likely the starting material for the synthesis of serotonin? Is it an essential amino acid? serotonin c. Dopamine, a neurotransmitter and hormone, has many functions in the brain including the reward pathway. It is commonly associated with the pleasure system of the brain, providing feelings of enjoyment and reinforcement to motivate a person proactively to perform certain activities. Dopamine, like serotonin, is synthesized from a single amino acid. Which essential amino acid is most likely the starting material for the synthesis of dopamine? Dopamine 5 NH2 O OH d. Proteins can be classified in several ways – by structure, function, etc. One classification method divides proteins into globular and fibrous categories. Globular proteins, such as enzymes and hormones, are water soluble. Fibrous proteins, such as the structural proteins found in skin and hair, and blood vessels, are water insoluble. Which of the following amino acids would most likely be found on the external surface of a globular protein? Which would be found in the internal regions of a globular protein? Explain your answer. Asp Phe Ser Leu Arg C. Ionic/Acid-Base Properties Amino acids contain both a carboxylic acid and a basic amino group. The acidic group, -COOH, can donate a proton to the basic group, -NH2 to form a dipolar ion known as a zwitterion. a. The un-ionized structure for alanine is shown below. Draw the zwitterion for alanine. What is the overall charge of the zwitterion form of alanine? b. Zwitterions have many physical properties that we associate with inorganic salts. Circle the property that best describes a pure amino acid. Appearance Crystalline Powder Melting Point High Low Solubility in Water High Low Amino acids are always partially ionized. The charge depends on the side chain (-R group) and the environment (pH of the solution). In acidic solution (low pH) zwitterions accept H+ ions on their carboxylate groups, -COO-. Draw the structure of alanine in acidic solution. What is the overall charge of alanine in acid? Alanine at Low pH (Overall Charge = ) 6 In basic solution (high pH), amino acid zwitterions lose H+ from their amine groups, -NH3 +. Draw the structure of alanine in basic solution. What is the charge on alanine in base? Alanine at High pH (Overall Charge = ) The pH at which the net positive and negative charges in a sample of an amino acid are evenly balanced is the amino acid/s isoelectric point or pI. Alanine at Its pI (Overall Charge = ) c. Draw the structure for valine under the following conditions: Low pH pI high pH d. At a pH below the pI of an amino acid, the overall charge of that amino acid is __________. At a pH above the pI for an amino acid, the overall charge of that amino acid is ____________. 7 Amino acids with acidic or basic side chains have substantially lower or higher pI values than amino acids with neutral side chains. For example, the two amino acids with acidic side chains, aspartic acid and glutamic acid have pI values close to 3. A higher concentration of H+ is required to obtain the overall charge of zero for a sample of these amino acids. e. Draw the structure of glutamic acid” at pH 7.4. Why are aspartic acid and glutamic acid usually referred to as aspartate and glutamate at physiological pH (7.4)? f. Draw the structure of the given amino acid as it would commonly exist under each of the following conditions. State whether the given pH is above or below the amino acid pI. Valine in the small intestine at pH 8. Tyrosine in the stomach at pH 1.5 Lysine in blood plasma at pH 7.4