Biochemistry Prelims 1 PDF

INTRODUCTION TO BIOCHEMISTRY WHAT IS BIOCHEMISTRY? atoms present in the molecule - they give molecules specific  All living organisms have common features that they properties such as polarity and pH. use to sustain...

INTRODUCTION TO BIOCHEMISTRY WHAT IS BIOCHEMISTRY? atoms present in the molecule - they give molecules specific  All living organisms have common features that they properties such as polarity and pH. use to sustain life functions - they use the same type of biomolecules.  Studies the function and properties of these biomolecules - these molecules are still governed by chemical and physical laws, hence basic knowledge in chemistry and physics is important. WHY STUDY BIOCHEMISTRY? - It is a multidisciplinary subject that answers questions about molecular nature of life processes. - Understanding health and disease at the molecular level leads to more effective treatment of illnesses. TRANSPORTATION OF MOLECULES - The inside of the cell is similar to the transportation system of a city: there are roads, cars, buses, and trucks - These vehicles correspond to molecules that are involved CHEMICAL BONDS in a series of reactions. - is a lasting attraction between atoms, ions, or molecules. - There are molecules that travel multiple routes while there - without chemical bonds, no compounds will be formed. No are also others that are specialized, being confined to complex form of matter will be present. single pathways - may be a result of electrostatic forces between opposite charges or though sharing of electrons. WHY STUDY BIOCHEMISTRY: AN APPROACH TO MEDICINE A. IONIC BONDS  Biochemistry is essential to all life sciences - also known as electrovalent bond.  Biochemistry of nucleic acid lies at the heart of - involves the transfer of electron from one element to genetics. another resulting in a net difference in atomic charges.  Physiology and biochemistry overlaps almost - the difference creates a strong electrostatic attraction completely between the two oppositely charges ions. - compounds formed through this process are known as  Immunology uses techniques that are derived from ionic compounds. biochemical studies.  Pharmacology and pharmacy rests on a sound B. COVALENT BONDS knowledge of biochemistry and physiology. - a chemical bond that involves the sharing of electron  Normal biochemical processes are the basis of health pairs between atoms (bonding pairs).  Researches in biochemistry has impact on nutrition and - results in a stable balance of attractive and repulsive preventive medicine forces between atoms.  Most of all diseases have biochemical basis. - compounds formed through this process are known as covalent compounds. FOUR TYPES OF BIOMOLECULES 1. Carbohydrates : important for structural and energy- C. HYDROGEN BONDS storage properties. - a special type of bond unique to polar molecules. 2. Amino Acids : major structural elements. Also serves - a weak electrostatic attraction between a partially as transporters, catalysts, and hormones. positively-charges hydrogen atom of a molecule and an 3. Lipids : fulfill a variety of roles as messengers, fuel electronegative atom of another molecule. source, key component of cell membranes. - relatively weak, but is responsible for many physical 4. Nucleic Acids : stores the genetic code of organisms, properties of water including high heat capacity, cohesive which are of critical importance to life. ad adhesive properties, and high surface tension. FUNCTIONAL GROUPS - These are specific groupings of atoms in molecules that have their own characteristic properties regardless of other 1  WATER, ACIDS, AND BASES WATER - principal component of most cells (at least 70%) - underlying physical principle for dissolving solutes: - it’s shape and properties as a solvent play a major role electrostatic attraction. in determining properties of living systems. - since hydrocarbons are non-polar, the favorable  Oxygen is a very electronegative atom, it tends to interaction with water do not occur. attract the electrons of other atoms when in a chemical - however, water can induce a temporary dipole in bond. nonpolar molecules by disorting spatial arrangements of  This accounts for water’s polarity: partial positive and the electron in the nonpolar molecule partial negative. - nonpolar molecules that do not dissolve in water are termed as hydrophobic molecules ELECTRONEGATIVES OF SELECTED ELEMENTS PHYSICAL PROPERTIES OF WATER BIOCHEMICAL PROCESSES IN AQUEOUS  Has high specific heat capacity SOLUTIONS  Is a polar molecule - when solutions are dissolved in water, the resulting  An excellent solvent solution is termed aqueous solutions (aq.)  Can form hydrogen bonds - compounds that are necessary for life processes are  Has high surface tension dissolved in water for a number of reasons  Is cohesive and adhesive  For a chemical reaction to occur, atoms, molecules, or  Is miscible with many liquids ions must collide. This collision is not possible if the  Has unusual density curve molecules are in the solid state.  Being dissolved increases the reactivity of the molecules involved by being equally exposed to CHEMICAL PROPERTIES OF WATER catalysts and other molecules that can induce a  Is an amphoteric reaction.  Can be oxidized and reduced  Is neither acidic or basic ACIDS AND BASES a. Arrehenius Acid : a compound that increases the WATER AND POLARITY number of hydronium ions (H2O or protons) in an aqueous - the polarity of a molecule: dependent on the solution. electronegativity of the atoms b. Arrehenius Base : a compound that increases the - high difference between the electronegativity of atoms number of hydroxide ions (OH) in an aqueous solution. resulting to dipole moment: a more negative charge on c. Bronsted-Lowry Acid : a compound that donates a one side and more positive on the other side. proton to another molecute - bonds with partial charges: polar bonds - if d. Bronsted-Lowry Basic : a compound that accepts a electronegativity difference is too small: non-polar proton from another molecule. - there are instances where the bonds may be polar, but e. Lewis Acid : a compound that accepts an electron the molecule itself is non-polar because of its geometry pair from another molecule. (linear, trigonal planar, etc) f. Lewis Base : a compound that donates electron pair to another molecule SOLVENT PROPERTIES OF WATER - because of polarity (having partial negative and positive WATER: A SPECIAL CASE OF AN ACID AND BASE charges), water tends to dissolve almost all molecules that - water is the primary solvent inside most biological are necessary for life processes to proceed. systems. It acts as both a proton donor and a proton - dissolves ionic compounds: NaCl and other polar acceptor by dissociating itself. Because of this, water is compounds such as alcohol and ketones. known as an amphiprotic molecule. Water, acids, and bases 2  WATER AS THE BASIS OF THE PH SCALE - in the same way, Kb values indicates the strengths of a - water can dissociate itself to yield a hydronium ion and a base using the concentration of OH. hydroxide ion. This means that pure water has a fair amount of protons that can be measured. It also means that EQUILIBRIUM AND DISSOCIATION CONSTANT the amount of H3O and OH- is equal. - Ka, pKa, Kb, and pKb are helpful in predicting whether a - Ke = [H30] + [OH] species will donate or accept protons - this expression indicates the dissociation of hydronium - these values will describe the degree of ionization of an ions and hydroxide ions from H2O and is the basis of the acid or base. pH scale. The expression [H3O] and [OH] indicates the They are true indicators of acid and base strength. molar concentration of both ions in the solution. To get the -similar to pH and pOH, these values also account for value, solve for the concentration using stoichiometry. hydrogen and hydroxide ion concentration. Because hydronium and hydroxide ions are equal, they have the same value which is 1.0 x 102. WHY IS PH IMPORTANT? - in biochemistry, the acidity or basicity of a solution is of THE CONCEPT OF PH utmost importance because it affects the reactions that pH (potential of hydrogen or power of hydrogen) is a need to take place in the system. scale used to specifically determine the acidity and basicity of an aqueous solution.  Optimal pH: the range of pH needed for reactions to  Acids have a lower pH and are usually below 7. take place.  Bases have a higher pH and are above 7 in the scale. - important biological macromolecules lose activity when - pH is the negative logarithm of the hydrogen ion extreme deviation from their optimal pH occurs. concentration which is responsible for the acidity of a - other drastic physiological consequences can result from solution. pH fluctuations in the body. - the higher the H concentration, the lower the value in the pH scale, the stronger the acid PH AND HOMEOSTASIS THE CONCEPT OF P IN BIOCHEMISTRY  Homeostasis: any biological process that living things - other important terms in describing acidity and basicity: use to maintain a stable condition necessary for survival pOH, pKa, and pKb.  If the body loses too much heat due to cold  the p means negative logarithm (or how many times temperature, the muscle starts to oscillate more you divide a value). Typically used in chemistry rapidly to compensate the lost body heat. because concentrations have values less than 1. - the lower the number of the negative logarithm, the  If the body is too hot due to extreme activity, the higher the concentration pores on the skin will produce more water that will absorb the heat which will evaporate from the skin THE EQUILIBRIUM CONSTANT surface from bringing with it some of the heat, thus - the equilibrium constant (K) is the quotient of the lowering body temperature. concentrations of two chemical species in a reversible  The maintenance of internal body pH is a known reaction. homeostatic process.  When a reversible reaction occurs, the reactant will form the product and the product will reform the  Buffer systems are responsible for maintaining the reactant simultaneously. optimal pH of the body - the value represents the rate of reaction to achieve - Plasma Proteins (buffers blood pH) equilibrium, where the concentration of the reactants and - Hemoglobin (buffers blood pH) products is not considerably changing even if the reaction - Phosphate Buffer System (buffers is still occurring. intercellular pH) - Bicarbonate-Carbon Acid Buffer THE DISSOCIATION CONSTANT (buffers blood pH) - pKa and pKb are the negative logarithms of the values of Ka and Kb. - a large Kb values indicates a strong acid because the concentration of H is relatively high. A small Ka means little of there H dissociates from the molecule, hence a weak acid. 3  THE CELL AND ITS ORGANELLES : PROKARYOTES AND EUKARYOTES THE PROPERTIES OF LIFE TYPICAL CELL STRUCTURES  Living organisms exhibit a high degree of chemical  Plant Cell : complexity, allowing them to respond to stimuli,  Cell wall extract and transform energy, maintain defined  Cell membrane functions of their parts, replicate and maintain  Nucleus themselves, and have a history of evolution.  Endoplasmic reticulum with ribosomes  Lysosomes KEY PROPERTIES OF LIFE  Mitochondria  High degree of chemical complexity  Chloroplasts  Ability to respond to stimuli  Golgi apparatus  Capacity to extract and transform energy  Vacuole  Defined functions of its parts  Ability to replicate and maintain itself  History of evolution CLASSIFICATION OF CELLS BASED ON METABOLIC ACTIVITY  Cells can be classified based on their source of energy and carbon: 1. Phototrophs  Obtain energy from sunlight  Examples: Cyanobacteria, Heliobacteria, Sulfur- oxidizing bacteria  Animal Cell:  Cell membrane 2. Chemotrophs  Nucleus  Obtain energy from chemical compounds  Endoplasmic reticulum with ribosomes  Examples: Most bacteria, Vascular plants  Lysosomes  Mitochondria A. Autotrophs  Obtain carbon from inorganic sources (e.g.,CO2)  Examples: Cyanobacteria, Heliobacteria, Sulfur- oxidizing bacteria, Most green plants B. Heterotrophs  Obtain carbon from organic compounds  Examples: Animals, Non-sulfur bacteria WHY ARE CELLS SMALL? 1. Small Molecule Size : The size of themolecules that compose a cell is relatively small, allowing for faster diffusion. THE BIGGEST BIOLOGICAL DISTINCTION 2. Fast Diffusion Rate : The rate of diffusion of  All cells contain DNA, which is the total genetic molecules must be fast to support cellular processes. material of a cell.  Individual units of heredity controlling individual traits, 3. Minimum Biomolecules : Cells always have the coding for a specific protein or RNA, are called genes. minimum number of biomolecules required to function.  The earliest cells were likely simple, having only the minimum apparatus needed to sustain life functions. 4. Optimal Surface-to-Volume Ratio : The surface-to-  Living things that resemble these earliest cells are volume ratio must be optimal to avoid long diffusion times known as prokaryotes, which include bacteria and cyanobacteria.  Prokaryotes are single-celled but can form colonies with some simple differentiation. 1  THE CELL AND ITS ORGANELLES : PROKARYOTES AND EUKARYOTES PROKARYOTES VS. EUKARYOTES EUKARYOTIC METABOLIC PROCESSES (PAA)  Photosynthesis  Plants and protozoans that contain chlorophyll rely on the energy from the sun to generate energy.   Aerobic and Anaerobic Respiration  Almost all eukaryotes are reliant on oxygen, with some considered facultative anaerobes. PROKARYOTIC METABOLIC PROCESSES (SAAN)  Sulfur Metabolism  Bacteria that rely on this are the "producers" in deep-sea ecosystems.  Aerobic and Anaerobic Respiration  Obligate aerobes need oxygen to live; obligate anaerobes need the absence of oxygen to live.  Facultative aerobes can live with oxygen but can resort to anaerobic respiration if it is absent.  Nitrogen Metabolism  Rely on nitrogen-based compounds such as ammonia and nitrite; important in agriculture. PROKARYOTIC METABOLIC DIVERSITY  Prokaryotes have a diverse way of obtaining energy from the environment, which is different from how humans and other eukaryotes obtain energy. While animals feed on other living organisms, and plants rely on the sun, prokaryotes rely on multiple ways to obtain their "food." 2  BIOENERGETICS AND METABOLISM LAWS OF THERMODYNAMICS IN METABOLISM A. First Law (Conservation of Energy):  Energy cannot be created or destroyed, only transformed. B. Second Law (Entropy): For spontaneous  processes, entropy (disorder) increases. METABOLISM AND ENERGY: BIOENERGETICS  Metabolism : Sum of all chemical reactions within an organism, divided into:  Catabolism : Breakdown of molecules to release THERMODYNAMIC QUANTITIES: energy.  Gibbs Free Energy (ΔG) : amount of energy capable  Anabolism : Synthesis of complex molecules, of work during reaction at constant temperature and requiring energy input. pressure  Bioenergetics : Study of how energy is produced,  Endergonic Reactions (ΔG > 0): Require energy consumed, and managed by organisms. input (+ΔG)  Exergonic Reactions (ΔG < 0): Release energy (- METABOLIC PATHWAYS ΔG)  Also known as “Biochemical Pathways”  Enthalpy (ΔH): Heat content; positive for endothermic  Series of chemical reactions within a cell where the reactions, negative for exothermic. product of one reaction serves as the substrate for the  Entropy (S): Measure of randomness or disorder. next. △G = △H - T△S TYPES OF PATHWAYS: DIFFERENCES BETWEEN CATABOLISM AND 1. Chain Reactions : Linear progression of chemical ANABOLISM reactions.  Catabolism 2. Cycles : Reactions that regenerate the initial  Purpose: Break down molecules (e.g., reactant (e.g., Krebs cycle). carbohydrates, fats, proteins) to release energy.  Processes: Glycolysis, Krebs cycle, beta-oxidation.  Anabolism  Purpose: Synthesize complex molecules (e.g., proteins, nucleic acids) from simpler ones.  Processes: Protein synthesis, DNA Replication, fatty acid synthesis. ENERGY  Capacity to do work or cause change  Potential Energy: stored energy  Kinetic Energy: energy in motion  Energy transformation is always governed by laws of thermodynamics 3  BIOENERGETICS AND METABOLISM OXIDATION AND REDUCTION IN METABOLISM  Coenzyme A (CoA) : Facilitates the oxidation of pyruvate  Redox Reactions: Involves transfer of electrons between and synthesis of fatty acids. molecules.  Not electron carrier, but is important in the activation of  Oxidation: Loss of electrons or hydrogen, or gain of metabolic pathway oxygen.  Flavin Adenine Dinucleotide (FAD/FADH2) : Electron  Reduction: Gain of electrons or hydrogen, or loss of carriers in the electron transport chain. oxygen.  Key Roles: In cellular respiration, photosynthesis, and COUPLING OF ENERGY PRODUCTION AND USAGE other metabolic processes.  Coupling: Exergonic reaction of hydrolysis provides energy,  Reducing Agent: Substance that loses electron which in turn drives the endergonic reaction.  Oxidizing Agent: Substance that gains electrons  Cycling of ATP and ADP in the metabolic process is a way of shunting energy from its production to its use LEORA = Loses Electrons Oxidation Reducing Agent when needed. GEROA = Gains Electrons Reduction Oxidizing Agent - comparison of the state of reduction of carbon atoms in biomolecules: IMPORTANT COENZYMES IN METABOLIC  ATP (Adenosine Triphosphate) PATHWAYS  Main energy currency of the cell.  Coenzymes : Organic molecules that assist enzymes by  ATP is hydrolyzed to yield energy and ADP. transferring electrons or functional groups.  Functions as intermediate carriers of electron during  ATP Hydrolysis : ATP → ADP + Pᵢ releases energy. reaction Important because without electron transporter, oxidation of nutrients to provide energy  ATP Synthesis : ADP + Pᵢ → ATP requires energy (from cannot take place. oxidation of nutrients).  Coupling Mechanism : Energy released from catabolic processes (like glucose oxidation) is used to drive anabolic processes.  NAD+/NADH : Electron carriers in redox reactions. 4