Biochemistry Lecture 1 PDF

OVERVIEW OF BIOCHEMISTRY What Is Biochemistry? Biochemistry is the study of the chemistry of living things. This includes organic molecules and their chemical reactions. Most people consider biochemistry to be synonymous with molecular biology. What Types of Molecules Do Biochemists Study? The p...

OVERVIEW OF BIOCHEMISTRY What Is Biochemistry? Biochemistry is the study of the chemistry of living things. This includes organic molecules and their chemical reactions. Most people consider biochemistry to be synonymous with molecular biology. What Types of Molecules Do Biochemists Study? The principal types of biological molecules or biomolecules are: carbohydrates - or carbs, are sugar molecules. Along with proteins and fats, carbohydrates are one of three main nutrients found in foods and drinks. Your body breaks down carbohydrates into glucose. Glucose, or blood sugar, is the main source of energy for your body's cells, tissues, and organs. lipids - are fatty, waxy, or oily compounds that are soluble in organic solvents and insoluble in polar solvents such as water. Lipids include: Fats and oils (triglycerides) Phospholipids. proteins - are polypeptide structures consisting of one or more long chains of amino acid residues. They carry out a wide variety of organism functions, including DNA replication, transporting molecules, catalyzing metabolic reactions, and providing structural support to cells. nucleic acids - are large biomolecules that play essential roles in all cells and viruses. A major function of nucleic acids involves the storage and expression of genomic information. Deoxyribonucleic acid, or DNA, encodes the information cells need to make proteins Many of these molecules are complex molecules called polymers, which are made up of monomer subunits. Biochemical molecules are based on carbon. What Is Biochemistry Used for? Biochemistry is used to learn about the biological processes which take place in cells and organisms. Biochemistry may be used to study the properties of biological molecules, for a variety of purposes. For example, a biochemist may study the characteristics of the keratin in hair so that shampoo may be developed that enhances curliness or softness. Biochemists find uses for biomolecules. For example, a biochemist may use a certain lipid as a food additive. Alternatively, a biochemist might find a substitute for a usual biomolecule. For example, biochemists help to develop artificial sweeteners. Biochemists can help cells to produce new products. Gene therapy is within the realm of biochemistry. The development of biological machinery falls within the realm of biochemistry. What Does a Biochemist Do? Many biochemists work in chemistry labs. Some biochemists may focus on modeling, which would lead them to work with computers. Some biochemists work in the field, studying a biochemical system in an organism. Biochemists typically are associated with other scientists and engineers. Some biochemists are associated with universities and they may teach in addition to conducting research. Usually, their research allows them to have a normal work schedule, based in one location, with a good salary and benefits. What Disciplines Are Related to Biochemistry? Biochemistry is closely related to other biological sciences that deal with molecules. There is considerable overlap between these disciplines: Molecular Genetics Pharmacology Molecular Biology Chemical Biology 1 Characteristics of Living Systems 1. Living organisms are complicated and highly organized composed of many cells cells are highly structured into organelles; macromolecules within organelles take part in many chemical reactions 2. Biological structures serve functional purposes Structures are specific The levels of organization observed by organelles and macromolecules allows them to perform specific functions 3. Energy transfomations occur within living systems Solar energy is transformed into ATP (adenosine triphosphate) and NADPH (nicotinamide adenine dinucleotide phosphate) which are special biomolecules which provide energy to the cell Activities of the cell which require energy include biosynthesis, movement and osmotic work against a concentration gradient 4. Living systems are highly efficient at self-replication. This is due to DNA (deoxyribonucleic acid) molecules which are able to reproduce into duplicate DNA strands from an original DNA strand. What elements are biomolecules composed of? Biomolecules are composed mainly of six nonmetallic elements: carbon, oxygen, hydrogen, nitrogen, phosphorous, and sulfur These atoms make up >97% of the weight of most organisms These elements can form stable covalent bonds Points to note: Water is a major component of cells Carbon is more abundant in living organisms than it is in the rest of the universe Periodic Table showing the elements present in biomolecules Important elements found in living cells are shown in color The six abundant elements are in red (CHNOPS) Five essential ions are in purple Trace elements are in dark blue (more common) and light blue (less common) 2 Principles of Biochemistry: Cell Structure Cells (basic structural units of living organisms) are highly organized and constant source of energy is required to maintain the ordered state. All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids. Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life. Instructions for growth, reproduction and developments for each organism is encoded in their DNA. HYDROCARBONS and FUNCTIONAL GROUPS HYDROCARBONS Compounds containing only carbon and hydrogen – Saturated hydrocarbons contain only single bonds and are sp3 hybridized. (aliphatic) – Unsaturated hydrocarbons contain at least one double or triple bond. (aliphatic) – Aromatic hydrocarbons: very stable unsaturated compounds such as benzene: C 6H6. A = propane B = cyclohexane C = acetylene D = benzene Alkanes and Cycloalkanes ✓ Alkanes = acyclic (not cyclic) saturated hydrocarbons ✓ Cycloalkanes = cyclic saturated hydrocarbons. ✓ Molecular formula: gives number and kind of atoms ✓ Structural formula: gives how bonding between different atoms. ✓ Often called Paraffins ✓ General formula CnH2n+2 where n = 1 … E.g. n = 1  CH4; n = 2  C2H6, etc. ✓ Straight chain (normal) alkanes = carbon atoms connected to each other to form a chain of carbon atoms: Branched Chain Alkanes; Constitutional Isomers ✓ Branched chain alkanes such as isobutane are hydrocarbons with carbons not always arranged in a straight chain. 3  ✓ Butane and Isobutane have the same molecular formula, but different structure. ✓ Constitutional (Structural) Isomer – compounds with the same molecular formula but different structural formula. Butane and Isobutane (2-methyl propane) are structural Isomers. Hydrocarbons where the carbons form a ring or cyclic structure; General formula: CnH2n. Alkenes and Alkynes ✓ Unsaturated (contains one or more double or triple bonds) hydrocarbons ✓ Double and triple bonds are more reactive than single bonds which makes unsaturated hydrocarbons more reactive than saturated hydrocarbons. ✓ Alkenes (CnH2n) are also called olefins and contain carbon – carbon double bonds. – All atoms around the double bond are in a plane – Molecules containing a double bond can have geometric isomer when there are the same groups on each side of the molecule but they are located in slightly different positions. E.g. 2 - butene exists as cis and trans isomers Alkynes are compounds containing triple bonds. Naming Alkanes Straight-Chain Alkanes (see Table 24.1) Branched chain has substituents on the molecule; does not form a single simple straight chain. Name branched-chain alkanes using the format: Prefix-Parent-Suffix – Prefix specifies position and number of various substituents – Parent tells how many carbons atoms are present on the longest continuous chain. – Suffix tells to what family the molecule belongs (alkanes: -ane; alkenes: -ene, etc) CH3CH2CHCH3 CH3 Branched Chain Alkane Determine the longest chain; use the name of that chain as the parent name; be careful to look for the longest chain. 4  – The name of the chain below would be hexane not butane. CH3CH2CHCH3 CH2CH2CH3 3-methylhexane Number carbons starting from end nearest substituent. Name and locate each substituent group (-ane becomes –yl ending) With two or more substituents list them in alphabetical order; use di-, tri- etc. for identical substituents. H3C H3C CH2CH3 CH C H3C CH2CH3 3-ethyl-2,3dimethylpentane Names and Properties of the Straight Chain Alkanes Functional Group Definition: A commonly occurring group of atoms with a specific bonding arrangement, within a molecule that is responsible for characteristic reactions/properties of the group. Functional groups are a characteristic feature of organic molecules that behave in a predictable way. composed of an atom or group of atoms. groups that replace a hydrogen atom in the corresponding alkane. a way to classify families of organic compounds. 5 Nomenclature Enantiomers and Chirality (Stereochemistry) 6 STEREOCHEMISTRY Stereoisomers are molecules whose atomic connectivity is the same but whose three- dimensional arrangement of atoms in space is different. This has sweeping implications in biological systems. ✓ For example, most drugs are often composed of a single stereoisomer of a compound, and while one stereoisomer may have positive effects on the body (since it has the right three- dimensional shape to bind to the protein receptor), another stereoisomer may not bind, or could even be toxic. An example of this is the drug thalidomide which was used during the 1950s to suppress morning sickness. The drug, unfortunately, was prescribed as a mixture of stereoisomers, and while one stereoisomer actively worked on controlling morning sickness, the other stereoisomer caused serious birth defects. Ultimately the drug was pulled from the marketplace. Because of these implications, a great deal of work done by synthetic organic chemists is in devising methods to synthesize compounds that are purely one stereoisomer. The ability to visualize and manipulate molecules in three-dimensions is vitally important in order to study and understand the structural features that give rise to stereoisomerism. 7  ✓ Enantiomers occur only with those compounds whose molecules are chiral. A chiral molecule is defined as one that is not identical with its mirror image. The chiral molecule and its mirror image are enantiomers, and the relationship between the chiral molecule and its mirror image is defined as enantiomeric. ✓ The word chiral comes from the Greek word cheir, meaning “hand.” Chiral objects (including molecules) are said to possess “handedness.” ✓ The term chiral is used to describe molecules of enantiomers because they are related to each other in the same way that a left hand is related to a right hand. When you view your left hand in a mirror, the mirror image of your left hand is a right hand (Fig. 5.1). Your left and right hands, moreover, are not identical, and this can be shown by observing that they are not superposable* (Fig. 5.2). Many familiar objects are chiral and the chirality of some of these objects is clear because we normally speak of them as having “handedness.” ✓ We speak, for example, of nuts and bolts as having right- or left-handed threads or of a propeller as having a right or left-handed pitch. The chirality of many other objects is not obvious in this sense, but becomes obvious when we apply the test of nonsuperposability of the object and its mirror image. Objects (and molecules) that are superposable on their images are achiral. Most socks, for example, are achiral, whereas gloves are chiral. ` 8  ✓ How do we know when to expect the possibility of enantiomers? One way (but not the only way) is to recognize that a pair of enantiomers is always possible for molecules that contain one tetrahedral atom with four different groups attached to it. * ✓ Refer to the figure below: Models of Two Butanols In 2butanol this atom is C2. The four different groups that are attached to C2 are a hydroxyl group, a hydrogen atom, a methyl group, and an ethyl group. ✓ An important property of enantiomers such as these is that interchanging any two groups at the tetrahedral atom that bears four different groups converts one enantiomer into the other. ✓ In Fig. b it is easy to see that interchanging the hydroxyl group and the hydrogen atom converts one enantiomer into the other. You should now convince yourself with models that interchanging any other two groups has the same result. ✓ Because interchanging two groups at C2 converts one stereoisomer into another, C2 is an example of what is called a stereocenter. ✓ A stereocenter is defined as an atom bearing groups of such nature that an interchange of any two groups will produce a stereoisomer. Carbon-2 of 2-butanol is an example of a tetrahedral stereocenter. ✓ Not all stereocenters are tetrahedral, however. Thus, we would not predict the existence of enantiomeric forms of 2-propanol, and experimentally only one form of 2-propanol has ever been found. 9 Stereoisomers that are not mirror images are called diastereoisomers. ✓ Note the difference between enantiomers and diastereoisomers: enantiomers must have opposite (mirror image) configurations at all stereogenic centers; diastereoisomers must have opposite configurations at some stereogenic centers, but the same configuration at others. ✓ These relationships are summarized below: 10 Hierarchy of Molecular Components in a Cell The Cell And its Organelles Supramolecular Complexes e.g Enzyme complexes, ribosomes,chromosomes Macromolecules Proteins, Carbohydrates, Lipids, DNA, RNA Biomolecules (Building Blocks) Amino acids, Sugars, Fatty acids, Glycerol, Nucleic acids Metabolites Pyruvate,citrate, succinate, Glyceraldehyde 3 phosphate, Fructose-1,6-bisphosphate Precursors H2O, CO2, NH4+, NO3- and N2 ✓ Precursors or metabolites (H2O, CO2, NO3-, NH4+ and N2) react chemically to produce biomolecules such as amino acids, sugars (monosaccharides), nucleic acids, fatty acids, glycerol. ✓ These biomolecules are building blocks or monomers for the formation of the polymers which are macromolecules ✓ Each type of macromolecule is made up of a different type of building block. ✓ Macromolecules are assembled into supramolecular complexes (e.g chromosomes, ribosomes, enzyme complexes) which are responsible for specialized functions ✓ Supramolecular complexes are localized into organelles within each cell. Organelles also have specific functions Properties of Biomolecules Which Reflect their Suitability for Living Systems 1. Macromolecules are made up of building blocks which make them non-symmetrical. They have structural polarity 2. Because of this structural polarity, they are able to store information. The sequence of building blocks which make up the macromolecules allows different bits of information to be stored e.g proteins (made up of amino acids) and DNA (made up of nucleic acids) 3. They have unique 3D shapes because of their sequences which give them different chemical and physical properties and allow them to perform different functions 4. Weak chemical forces (non-covalent) link macromolecules together which allow constant formation and breaking of interactions between macromolecules. These forces include hydrogen bonds, van der Waals forces, ionic and hydrophobic interactions. 5. There is structural complementarity between certain macromolecules which allow them to recognize each other. Weak chemical forces hold these macromolecules together when necessary so that their functions can be carried out, after which the attractions are broken e.g an enzyme and its specific substrate Generalization Keep in mind students! ✓ Biochemistry is concerned with the chemical basis of life. 11 ✓ It is concerned with the various molecules that occur in living cells and organisms and with their chemical reaction. ✓ It scope is on structure and function of cellular components ✓ proteins, carbohydrates, lipids, nucleic acids and other biomolecules. ✓ It also discusses Metabolism and regulation, Gene expression and modulation ✓ Organic compounds contain carbon, which is able to form straight chains and branched chains. ✓ Hydrocarbons are organic substances composed of carbon and hydrogen. ✓ Hydrocarbons are classified into three: Alkane (single bond); Alkene (double bonds); Alkyne (triple bonds) ✓ A molecule that is not superimposable on its mirror image is said to be chiral. ✓ A chiral molecule is one that does not contain a plane of symmetry. The most common cause of chirality is the presence of a tetrahedral sp3-hybridised carbon atom bonded to four different groups, this is referred to as a stereogenic center. ✓ Compounds that contain such stereogenic centers exist as a pair of non-superimposable mirror image stereoisomers called enantiomers. ✓ Diastereoisomers are stereoisomers that are not mirror images. Diastereoisomers have different spectra and physical properties. 12