We are now in an age of exceptional opportunities for the application of our great understanding of Biochemistry to problems in medicine, dentistry, agriculture, forensics, anthropology, environmental science, nutrition, physiology, genetics, and immunology; practically all of the primary specialties on the life sciences.
1: Properties of the Twenty Common Amino AcidsAmino acids are exactly what they say they are! They are compounds containing an amino group, -NH2, and a carboxylic acid group, -COOH. The biologically important amino acids have the amino group attached to the carbon atom next door to the -COOH group. They are known as 2-amino acids. They are also known (slightly confusingly) as alpha-amino acids. 1.1: Nomenclature of Amino acidsThere are 20 common amino acids. They are composed of C, H, O, N and S atoms. They are structurally and chemically different, and also differ in size and volume. Some are branched structures, some are linear, some have ring structures. One of the 20 common amino acids is actually an imino acid. 1.2: Structure of Amino AcidsAmino acid monomers are chemically linked to form linear polymers known as proteins. 1.3: Properties of Amino AcidsProperties of Amino Acids 1.3.1. Charged Nature of Amino AcidProteins are probably the most important class of biochemical molecules, although of course lipids and carbohydrates are also essential for life. Proteins are the basis for the major structural components of animal and human tissue. Proteins are natural polymer molecules consisting of amino acid units. The number of amino acids in proteins may range from two to several thousand. 1.3.2. Stereochemistry of Amino AcidsWith the exception of glycine, all the 19 other common amino acids have a uniquely different functional group on the central tetrahedral alpha carbon. 1.4.1 Acid-base Chemistry of Amino AcidsAmino acids by themselves have amino (pKa ~9.0-10.5) and carboxyl groups (pKa ~2.0-2.4) that can be titrated. At neutral pH, the amino group is protonated, and the carboxyl group is deprotonated. The side chains of acid and basic amino acids, and some polar amino acids can also be titrated. 1.4.2. Acid-Base Reactions of Amino AcidsThis page looks at what happens to amino acids as you change the pH by adding either acids or alkalis to their solutions. For simplicity, the page only looks at amino acids which contain a single -NH2 group and a single -COOH group. 2: Proteins Structure: from Amino Acid Sequence to Three Dimensional StructureProteins are the most abundant organic molecules in living cells, constituting more than 50% of the mass once water is removed. It is estimated that the human body contains well over a million different kinds of protein, and even a single-cell organism contains thousands. Each of these is a polymer of amino acids which has a highly specific composition, a unique molecular weight (usually in the range from 6000 to 1 000 000) and its own sequence of different amino acids along the polymer chain. 2.1: The Structure of ProteinsThis page explains how amino acids combine to make proteins and what is meant by the primary, secondary, tertiary and quaternary structures of proteins. 2.2: Protein SequencingProtein sequencing by Edman degradation, developed by Pehr Edman, is the method of sequencing amino acids in a peptide by sequentially removing one residue at a time from the amino end of a peptide. 2.3: Protein Structural DeterminationMass spectrometry (MS) analysis of proteins measures the mass-to-charge ratio of ions to identify and quantify molecules in simple and complex mixtures. 2.4: Protein Folding and PrionsProteins have several layers of structure, each of which is important in the process of protein folding. The first most basic level of this structure is the sequence of amino acids themselves. The sequencing is important because it will determine the types of interactions seen in the protein as it is folding. 2.5: Denaturation of proteinsEach protein has its own unique sequence of amino acids and the interactions between these amino acids create a specify shape. This shape determines the protein’s function. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the internal interactions between the protein’s amino acids can be altered, which alter the shape of the protein. Although the protein’s primary structure does not change, the protein’s shape may change so much that it becomes dysfunctional. 2.6: Amino Acids and Proteins (Exercises)These are homework exercises to accompany Chapter 1 of the University of Arkansas Little Rock's LibreText for CHEM 4320 - Biochemistry 1. 3: Methods of Protein Purification and CharacterizationProtein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms. it is vital for the characterization of the function, structure and interactions of the protein of interest. 3.1: Protein PurificationA successful protein purification procedure can be nothing short of amazing. Whether you are starting off with a recombinant protein which is produced in E. coli, or trying to isolate a protein from some mammalian tissue, you are typically starting with gram quantities of a complex mixture of protein, nucleic acids, polysaccharide, etc. from which you may have to extract milligram (or microgram!) quantities of desired protein at high purity, and hopefully with high yield. 3.2: Cell DisruptionCell disruption is a method or process for releasing biological molecules from inside a cell. There are several ways to break open cells. Whatever method is employed, the crude lysates obtained contain all of the molecules in the cell, and thus, must be further processed to separate the molecules into smaller subsets, or fractions. 3.3:Cell Fractionation and CentrifugationFractionation of samples typically starts with centrifugation. Using a centrifuge, one can remove cell debris, and fractionate organelles, and cytoplasm. For example, nuclei, being relatively large, can be spun down at fairly low speeds. Once nuclei have been sedimented, the remaining solution, or supernatant, can be centrifuged at higher speeds to obtain the smaller organelles, like mitochondria. Each of these fractions will contain a subset of the molecules in the cell. 3.4: ChromatographyChromatography is the most discriminating analytical technique used to separate mixture of a proteins on the basis of size, affinity or ionic interaction. 3.4.1. Affinity ChromatographyAffinity chromatography is a method of separating biochemical mixture based on a highly specific interaction between antigen and antibody, enzyme and substrate, receptor and ligand, or protein and nucleic acid. 3.4.2. Gel Exclusion ChromatographyGel exclusion chromatography is a low resolution isolation method. This involves the use of beads that have tiny “tunnels" in them that each have a precise size. The size is referred to as an “exclusion limit," which means that molecules above a certain molecular weight will not fit into the tunnels. Molecules with sizes larger than the exclusion limit do not enter the tunnels and pass through the column relatively quickly by making their way between the beads. 3.4.3. Ion Exchange ChromatographyProteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will bind to a column of beads containing carboxylate groups, whereas a negatively charged protein will not. A positively charged protein bound to such a column can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer because sodium ions compete with positively charged groups on the protein for binding. 3.5: ElectrophoresisElectrophoresis is used in laboratories to separate macromolecules based on size. The technique applies a negative charge so proteins move towards a positive charge. Electrophoresis is used extensively in DNA, RNA and protein analysis. 3.5.1: BlottingBands of DNA in an electrophoretic gel form only if most of the DNA molecules are of the same size. In other situations, such as after restriction digestion of chromosomal (genomic) DNA, there will be a large number of variable size fragments and it will appear as a continuous smear of DNA. In such conditions, blotting techniques are useful. 4: Overview of Hemoglobin and MyoglobinHemoglobin and myoglobin are two of the most important proteins in the body. Their functions vary slightly, but they are vital for oxygen transport. 4.1: Myoglobin, Hemoglobin, and their LigandsHemoglobin and myoglobin have played important roles in the history of Biochemistry. They were the first proteins for which three -dimensional structures were determined by X-ray crystallography. Since then, these two proteins have been a valuable source of knowledge for many other proteins. 4.2: Oxygen Transport by the Proteins Myoglobin and HemoglobinCooperativity Enhances Oxygen Delivery by Hemoglobin. Because of cooperativity between O2-binding sites, hemoglobin delivers more O2 to tissues than would a noncooperative protein (pO2, partial pressure of oxygen.) 4.3: ExercisesAlmost all biochemistry textbooks start their description of the biological functions of proteins using the myoglobin and hemoglobin as exemplars. These are very rational approaches since they have become model systems to describe the binding of simple ligands, like dioxygen (O2), CO2, and H+, and how the structure of the protein determines and is influenced by binding of ligands. 5: Michaelis-Menten Enzyme Kinetics, Inhibitors, pH optima; Bi-Substrate ReactionsEnzymes are protein catalysts, they influence the kinetics but not the thermodynamics of a reaction. 5.1: Catalytic Efficiency of EnzymesEnzymes are important for a variety of reasons, because they are involved in many vital biochemical reactions. Increasing the reaction rate of a chemical reaction allows the reaction to become more efficient, and hence more products are generated at a faster rate. These products then become involved in some other biological pathway that initiates certain functions of the human body. This is known as the catalytic efficiency of enzymes. 5.2: Enzyme ParametersScientists spend a considerable amount of time characterizing enzymes. To understand how they do this and what the characterizations tell us, we must first understand a few parameters. 5.3: Michaelis-Menten KineticsTwo 20th century scientists, Leonor Michaelis and Maud Leonora Menten, proposed the model known as Michaelis-Menten Kinetics to account for enzymatic dynamics. The model serves to explain how an enzyme can cause kinetic rate enhancement of a reaction and explains how reaction rates depends on the concentration of enzyme and substrate. 5.4: Enzyme InhibitionAn enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. Not all molecules that bind to enzymes are inhibitors; enzyme activators bind to enzymes and increase their enzymatic activity, while enzyme substrates bind and are converted to products in the normal catalytic cycle of the enzyme. 5.5: Temperature, pH, and enzyme concentration on the rate of a reactionThis section will explore the effect of temperature, pH, and enzyme concentration on the rate of a reaction. 5.6: Multi-Substrate Sequential MechanismsSequential reactions are one of the classes involved in multiple substrate reactions. In these types of reactions, all the substrates involved are bound to the enzyme before catalysis of the reaction takes place to release the products. Sequential reactions can be either ordered or random. 5.7: Double displacement reactionPing-pong mechanism, also called a double-displacement reaction, is characterized by the change of the enzyme into an intermediate form when the first substrate to product reaction occurs. It is important to note the term "intermediate" indicating that this form is only temporary. A key characteristic of the ping-pong mechanism is that one product is formed and released before the second substrate binds. 6: Classification and Catalytic Strategies of EnzymesEnzymes allow cells to run chemical reactions at rates from a million to even a trillion times faster than the same reactions would run under similar conditions without enzymes. Finally, and perhaps most importantly for life, enzymes can be regulated. 6.1: Serine proteasesThe serine proteases are a family of enzymes that cut certain peptide bonds in other proteins. This activity depends on a set of amino acid residues in the active site of the enzyme — one of which is always a serine (thus accounting for their name). In mammals, serine proteases perform many important functions, especially in digestion, blood clotting, and the complement system. 6.2: Transititon State Analogs and Catalytic AntibodiesTransition state analogs are very important in understanding the kinetics and inner workings of enzyme catalysis. Since the analog is a structure intermediate, it plays a part on a researched reaction, then determination of the actual structure and actual transformation of the original substrate is actually possible. 6.3: Restriction EndonucleaseThe discovery of restriction enzymes, or restriction endonuclease (REs), was pivotal to the development of molecular cloning. REs occur naturally in bacteria, where they specifically recognize short stretches of nucleotides in DNA and catalyze double-strand breaks at or near the recognition site (also known as a restriction site). 7: Regulation of Enzyme ActivityIn living cells, there are hundreds of different enzymes working together in a coordinated manner, and since cells neither synthesize nor break down more material than is required for normal metabolism and growth, precise enzyme regulation is required for turning metabolic reactions on and off. There is tremendous diversity in the mechanisms bacteria use to regulate enzyme synthesis and enzyme activity. 7.1: Control of Metabolism Through Enzyme RegulationCells regulate their biochemical processes by inhibiting or activating enzymes. 7.2: Amino Acids, Proteins, and Enzymes (Summary)To ensure that you understand the material in this chapter, you should review the meanings of the bold terms in the following summary and ask yourself how they relate to the topics in the chapter. 8: Carbohydrate Structures, Stereochemistry, and GlycosidesCarbohydrates, also known as sugars, are found in all living organisms. They are essential to the very source of life (ex. Ribose sugars in DNA and RNA) or sustaining life itself (ex. Metabolic conversion of carbohydrates into usable biochemical energy, ATP). Another important role of carbohydrates is structural (ex. Cellulose in plants). 8.1: Carbohydrates FundamentalsThe chemistry of carbohydrates most closely resembles that of alcohol, aldehyde, and ketone functional groups. As a result, the modern definition of a CARBOHYDRATE is that the compounds are polyhydroxy aldehydes or ketones. The chemistry of carbohydrates is complicated by the fact that there is a functional group (alcohol) on almost every carbon. 8.2: MonosaccharidesThe most useful carbohydrate classification scheme divides the carbohydrates into groups according to the number of individual simple sugar units. Monosaccharides contain a single unit; disaccharides contain two sugar units; and polysaccharides contain many sugar units as in polymers - most contain glucose as the monosaccharide unit. 8.3: DisaccharidesThe disaccharides differ from one another in their monosaccharide constituents and in the specific type of glycosidic linkage connecting them. There are three common disaccharides: maltose, lactose, and sucrose. All three are white crystalline solids at room temperature and are soluble in water. 8.4: OligosaccharidesAn oligosaccharide is a carbohydrate whose molecule, upon hydrolysis, yields two to ten Monosaccharid molecules. Oligosaccharides are classified into subclasses based on the number of monosaccharide molecules that form when one molecule of the oligosaccharide is hydrolyzed. 8.5: PolysaccharidesThe most useful carbohydrate classification scheme divides the carbohydrates into groups according to the number of individual simple sugar units. Monosaccharides contain a single unit; disaccharides contain two sugar units; and polysaccharides contain many sugar units as in polymers - most contain glucose as the monosaccharide unit. 10: Pyruvate Dehydrogenase Links Glycolysis to Krebs CycleThe fate of pyruvate depends on the species and the presence or absence of oxygen. If oxygen is present to drive subsequent reaction, pyruvate enters the mitochondria, where the citric acid cycle (also known as the Krebs Cycle) (Stage 2) and electron transport chain (Stage 3) break it down and oxidize it completely to CO2 and H2O . The energy released builds many more ATP molecules, though of course some is lost as heat. 10.1: The Krebs Cycle (Citric Acid Cycle)The fate of pyruvate depends on the species and the presence or absence of oxygen. If oxygen is present to drive subsequent reaction, pyruvate enters the mitochondria, where the citric acid cycle (also known as the Krebs Cycle) (Stage 2) and electron transport chain (Stage 3) break it down and oxidize it completely to CO2 and H2O . The energy released builds many more ATP molecules, though of course some is lost as heat. Let's explore the details of how mitochondria use oxygen to make more AT 11: Electron Transport Chain and Oxidative PhosphorylationCellular respiration must be regulated in order to provide balanced amounts of energy in the form of ATP. The cell also must generate a number of intermediate compounds that are used in the anabolism and catabolism of macromolecules. Without controls, metabolic reactions would quickly come to a stand still as the forward and backward reactions reached a state of equilibrium. In short, the cell needs to control its metabolism. 12: The Flow of Genetic Information: from DNA to RNA and ProteinsGenetic information is stored in the sequence of bases along a nucleic acid chain. The bases have an additional special property: they form specific pairs with one another that are stabilized by hydrogen bonds. The base pairing results in the formation of a double helix, a helical structure consisting of two strands. These base pairs provide a mechanism for copying the genetic information in an existing nucleic acid chain to form a new chain. 12.1: The Structure of DNAThe building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group. The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T). 12.2: DNA ReplicationDNA is the genetically active component of the chromosomes of a cell and contains all the information necessary to control synthesis of the proteins, enzymes, and other molecules which are needed as that cell grows, carries on metabolism, and eventually reproduces. Thus when a cell divides, its DNA must pass on genetic information to both daughter cells. It must somehow be able to divide into duplicate copies. This process is called replication. 12.3: DNA RepairIt is evident that if DNA is the master copy of instructions for an organism, then it is important not to make mistakes when copying the DNA to pass on to new cells. Although proofreading by DNA polymerase greatly increases the accuracy of replication, there are additional mechanisms in cells to further ensure that newly replicated DNA is a faithful copy of the original, and also to repair damage to DNA during the normal life of a cell. 12.4: RNARibonucleic acid (RNA), is quite similar to DNA. However, whereas DNA molecules are typically long and double stranded, RNA molecules are much shorter and are typically single stranded. RNA molecules perform a variety of roles in the cell but are mainly involved in the process of protein synthesis (translation) and its regulation. 12.4.1 Types of RNARibonucleic acid (RNA) is typically single stranded and contains ribose as its pentose sugar and the pyrimidine uracil instead of thymine. An RNA strand can undergo significant intramolecular base pairing to take on a three-dimensional structure. 12.4.2. RNA - TranscriptionIn both prokaryotes and eukaryotes, the second function of DNA (the first was replication) is to provide the information needed to construct the proteins necessary so that the cell can perform all of its functions. To do this, the DNA is “read” or transcribed into an mRNA molecule. The mRNA then provides the code to form a protein by a process called translation. 12.4.3. Regulation of TranscriptionThe basic mechanism by which transcription is regulated depends on highly specific interactions between transcription regulating proteins and regulatory sequences on DNA. 12.5: The Genetic CodeThe genetic code consists of the sequence of nitrogen bases in a polynucleotide chain of DNA or RNA. The bases are adenine (A), cytosine (C), guanine (G), and thymine (T) (or uracil, U, in RNA). The four bases make up the “letters” of the genetic code. The letters are combined in groups of three to form code “words,” called codons. Each codon stands for (encodes) one amino acid unless it codes for a start or stop signal. There are 20 common amino acids in proteins. With four bases forming three- 12.6: TranslationTranslation is the process by which information in mRNAs is used to direct the synthesis of proteins. In eukaryotic cells, this process is carried out in the cytoplasm of the cell, by large RNA-protein machines called ribosomes. Ribosomes contain ribosomal RNAs (rRNAs) and proteins. The proteins and rRNAs are organized into two subunits, a large and a small. 12.7: ExercisesHaving genes in common accounts for the resemblance of a mother and her daughters. Genes must be expressed to exert an effect, and proteins regulate such expression. 13: Integrated chapter (HIV)Human immunodeficiency virus (HIV) is a retrovirus, which is a class of viruses that carry genetic information in RNA.There are two types of HIV, HIV-1 and HIV-2, with HIV-1 being the most predominant. Both types of HIV damage a person’s body by destroying specific blood cells, called CD4+ T cells, which are crucial to helping the body fight diseases in the immune system. 13.1: Envelope glycoprotein GP120In order to infect a human cell, an envelope glycoprotein found on the surface of HIV called Gp120 must adsorbs to both a CD4+ molecule and then a chemokine receptor found on the surface of only certain types of human cells. 13.2: HIV-1 protease (PR)HIV-1 protease has been studied intensely using various inhibitors. Since the main target of these inhibitors is to bind to the Asp-25 of the catalytic triad, each inhibitor would vary in its mechanism to accomplish this. 13.3: HIV vaccineThere is currently no cure for HIV infection or AIDS. However, the development of new antiretroviral drugs to treat HIV infections has changed HIV infections from a fatal to a chronic disease. 9: Glycolysis and GluconeogenesisThis section is concerned mainly with the pathway by which glucose is metabolized by the process known as glycolysis. Initially, the storage fuels or foodstuffs (fats, carbohydrates, and proteins) are hydrolyzed into smaller components (fatty acids and glycerol, glucose and other simple sugars, and amino acids). In the next stage, these simple fuels are degraded further to two-carbon fragments. 9.1: Glycolysis - Reaction and RegulationGlycolysis begins with the six carbon ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. The first part of the glycolysis pathway traps the glucose molecule in the cell and uses energy to modify it so that the six-carbon sugar molecule can be split evenly into the two three-carbon molecules. The second part extracts energy from the molecules and stores it in the form of ATP. 9.2 Gluconeogenesis: Reaction and regulationGluconeogenesis is the metabolic process by which organisms produce sugars (namely glucose) for catabolic reactions from non-carbohydrate precursors. Glucose is the only energy source used by the brain (with the exception of ketone bodies during times of fasting), erythrocytes, and kidney medulla. In mammals this process occurs in the liver and kidneys.