Biochemistry Reviewer P1 PDF - Southwestern University PHINMA

lOMoARcPSD|45282399 Biochemistry (Lec) - Reviewer P1 Biochemistry (Southwestern University PHINMA) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Angelo (arcnje...

lOMoARcPSD|45282399 Biochemistry (Lec) - Reviewer P1 Biochemistry (Southwestern University PHINMA) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399 BIOCHEMISTRY LESSON 1: Introduction to Biochemistry  What is Chemistry? Study of the composition and properties of matter.  What is Inorganic Chemistry? Study of Elements in the Periodic table.  What is Organic Chemistry? Study of carbon containing compounds. Examples: gasoline, plastics, detergent, etc.  What is Biochemistry? Study of compounds, chemical changes and reactions occurring in living systems.  What is Molecular Chemistry? This involves studying macromolecules in the body, covering their ingestion, digestion, absorption, utilization, integration into tissues, metabolism, and excretion.  Aspects of Biochemistry: o Molecular Anatomy – different biomolecules which comprise the cell. o Molecular Physiology – dynamic part of biochemistry which includes the functions and metabolic activities of biomolecules in the cell.  pH – is a logarithmic scale that we use to determine the acidity or the basicity of an aqueous  Buffer – is a solution that resists a significant change in pH upon addition of an acid or a base  Ionization – is the process by which atoms or molecules get a positive or negative charge. It is the formation of ion, occurs when an atom or a molecule gain or loses electron.  Dissociation – is the breakdown of substances into smaller particles such as atoms, ions or molecules. It is the formation small constituents from larger compounds.  Polar – occur when two atoms do not share electrons equally in a covalent bond, there is one positive end and one negative end.  Nonpolar – is a molecule that doesn't have two distinct charge sites, the electrons are evenly distributed.  Electrolytes – substances whose water solutions conduct electricity. 3 types of Electrolytes: o Strong Electrolytes – solution/solute that completely, or almost completely, ionizes or dissociates in a solution. o Weak Electrolytes – solution/solute that do not dissociate or ionized completely in their aqueous solution. o Non-Electrolytes - solution/solute that does not dissociate, or separate, into ions during the dissolving process.  Irreversible Reaction – a reaction which goes to completion, the products no longer react to form back the reactants.  Reversible Reaction – a reaction which does not go to completion, products can react to form back the reactants.  Chemical Equilibrium - state at which 2 opposing reactions proceed at the same rate. 1 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399 LESSON 2: pH and Buffer  pH – “potential of hydrogen”. It is a measure of how acidic or basic solution is. It is also a measure of hydrogen ion concentration.  High number of H+ = acidic  The range goes from 0-14: less than 7 = acidic more than 7 = basic 7 = neutral  Ways to measure pH: pH Test Paper – litmus paper is probably the most familiar pH paper.  3 types–red, blue, and neutral.  Red litmus turns blue in basic solutions  Blue litmus turns red in acidic solution  Neutral litmus (usually purple) turns red in acidic solutions and blue in basic solutions. pH Meter – measure a solution’s pH by measuring the electrical potential difference between the pH electrode and a reference electrode. The meter then coverts this potential to a pH reading. pH Indicator – liquid acid-base indicators are weak organic acids or bases that present as different colors in their acid and base forms. An indicator has a specific pH range over which it changes from its acid form to its base form.  Amphoteric substances – can both donate and accept protons. Examples: Water, amino acids, & hydrogen-carbonate ion.  Amphiprotic substances - can act both as an acid and as a base. Examples: Water, amino acids, proteins, metal oxides, & hydroxides.  All amphiprotic substances are amphoteric – since when they donate a proton they are acting as an acid, and when they accept a proton, they are acting as a base.  pH expression is introduced by a Danish biochemist by the name of Sorensen. The p stands for the German “Potenz”, meaning power or concentration, and the H for the “hydrogen ion” (H+).  pH Expression Formulas: pH= -log (log) [H3O+]  Legend: pOH= -log [OH-] pH – the negative logarithm of pKw= -log Kw hydrogen determines hydrogen pKw= pKa + pKb; 14 = pKa + pKb ion concentration pKw= pH + pOH pOH – the negative logarithm of 14 = pH + pOH hydroxide ions determines the pKa = -log Ka ; ionization constant of weak acid hydroxide ion concentration pKa = -log Kb ; ionization constant of weak base pKw – the negative logarithm of [H3O] = antilog - pH the water dissociation constant [OH-] = antilog - pOH pKa – the negative logarithm of the acid dissociation constant determines how weak/strong an acid is.  Buffer – a mixture of a weak electrolyte and its salt. A solution that can resist pH change upon the addition of an acidic or basic components. It is able to neutralize small amounts of added acid or base, thus maintaining the pH of the solution relatively stable.  Types of Buffer: Acidic Buffer – contain a weak acid and its salt. pH = below 7 Alkaline Buffers – contain a weak base and its salts. pH = above 7 2 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399  Buffers can either be prepared by mixing a weak acid with its conjugate base or a weak base with its conjugate acid.  Conjugate base – when an acid dissociates into its ions in water, it loses a hydrogen ion. The species that is formed is the acid’s conjugate base.  Conjugate acid – when a base dissociates in water, the species that gains a hydrogen (proton) is the base’s conjugate acid.  Neutralization Reaction – a chemical reaction in which an acid and base react together to form a salt and water as products. LESSON 3: Acidosis and Alkalosis  Blood pH – our blood is slightly basic.  Normal pH range = 7.35 to 7.45  Factors affecting Blood pH:  Nature of Diet – proteins, fats, ketogenic substances tend to acidify blood pH. Fruits and vegetables tend to alkalinize blood pH.  Vigorous Exercise – tend to alkalinize blood pH.  Acidosis – occurs when an acid builds up or when bicarbonate (HCO3), a base, is lost. When your blood pH drops below 7.35 and becomes too acidic.  Metabolic acidosis – excessive loss of bicarbonate in the blood. Causes: Sever ketosis & diabetes mellitus (DKA), Eclampsia, High lipid diet, Uriria  Respiratory acidosis – increased level of carbon dioxide (CO2) in the blood. Causes: Depression to respiration, Obstruction to respiration.  Alkalosis – occurs when there is an overabundance of bicarbonate (HCO3) in the blood. When your blood pH is higher than 7.45 and becomes too alkaline.  Metabolic alkalosis – excessive loss of potassium and chloride. Causes: overdosage of alkaline drugs, loss of gastric HCl, diarrhea (K+).  Respiratory alkalosis - decreased the CO2 level of the blood. Causes: abnormal deep breathing in relation to the amount of physical exercise.  ABG (Arterial Blood Gas) test measures the oxygen and carbon dioxide levels in your blood as well as your blood’s pH balance.  ABG measures the following:  pH – determine the acidity & alkalinity of the blood  paCO2 – partial pressure of arterial carbon dioxide in the blood  HCO3 – bicarbonate level in the blood  paO2 – partial pressure of arterial oxygen in the blood ACID BASE Acid Base pH pOH (MmHg) HCO3 (Meq/L) PCO2 Normal Values 7.35 - 7.45 35 - 45 22 - 26 35 -45 Respiratory LOW HIGH NORMAL HIGH Acidosis Respiratory HIGH LOW NORMAL LOW Alkalosis Metabolic LOW NORMAL LOW HIGH Acidosis Metabolic HIGH NORMAL HIGH LOW Alkalosis 3 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399 LESSON 4: The Cell HISTORY OF CELL DISCOVERY  ROBERT HOOKE – he used a microscope to examine cork (plant). He published a famous book called Micrographia, included sketches of various natural things under a microscope.  ROBERT BROWN – a Scottish Botanist who was responsible for the discovery of the nucleus of the cell in 1833.  MATTHIAS SCHLEIDEN – a German botanist who defined the cell as the basic unit of a plant structure.  THEODOR SCHWANN – a German physician and physiologist. His most significant contribution to biology is the extension of cell theory to animals.  RUDOLF VIRCHOW – he observed under microscope that cells are dividing. He concluded That cells come only from another preexisting cell. His theory now debunked the spontaneous generation theory.  CELL – basic building blocks of all living things. The human body is composed of trillions of cells.  Functions of cell: o Structure and Support o Growth (Process of Mitosis) o Transport of nutrients o Energy Production (Process of Photosynthesis & Respiration) o Metabolism o Reproduction (Process of Meiosis)  Types of Cell: o Prokaryotes – is a single-celled organism that lacks a nucleus and other membrane- bound organelles. (e.g., bacteria) o Eukaryotes – refers to any of the single-celled or multicellular organisms whose cell contains a distinct, membrane-bound nucleus. Types of Eukaryotic Cell:  Plant Cell - Plant cell, the basic unit of all plants. Plant cells are eukaryotic, meaning they have a membrane-bound nucleus and organelles.  Animal cell - Animal cell, the basic unit of all animals. They are also eukaryotic.  Cell Parts of Organelles: o CELL MEMBRANE – a thin layer of lipid and Protein. Regulates what gets in and out of the cell. Analogy: “Restaurant Doors” o CYTOPLASM – semi-fluid matrix and other components such as water. Keeps the organelles in their proper place. Analogy: “Restaurant Floor” o NUCLEUS – contains genetic material (DNA – Deoxyribonucleic acid). Controls what happens inside the cell. Analogy: “Restaurant Manager” o ENDOPLASMIC RETICULUM – produces various substances used within the cell and throughout the body. Analogy: “Restaurant Kitchen” 1. Rough ER – make proteins 2. Smooth ER – make lipids o GOLGI BODY - stack of flattened stack. Sort and transport substances in vesicles that are used within the cell. Analogy: “Front Counter/ Cashier” o MITOCHONDRIA – store energy obtained from food until other organelles need it. Analogy: “Burger drawers” o RIBOSOME – make protein needed by the cell. Analogy: “Hamburgers” o LYSOSOME – breakdown and recycle cellular debris, discarded cellular contents and foreign pathogens. Analogy: “Garbage Truck” 4 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399 o CENTROSOME – small, rounded chromatin bodies attached to the nuclear membrane. Regulates reproduction or division of cells. Analogy: “Shipping box” o VACUOLE – space occupied by water or fluid. Temporary dumping site for cellular garbage or debris. And storage of food – CHO, fats. Analogy: “Water Storage Tower” o CELL WALL – surrounds the plasma membrane of plant cells and provides tensile strength and protection against mechanical and osmotic stress. Analogy: “Outer Wall” o CHLOROPLAST – produce energy through photosynthesis and oxygen-release processes, which sustain plant growth and crop yield. Analogy: “Kitchen”. LESSON 5: Amino Acids  Amino Acids – are molecules that combine to form proteins. Amino acids and proteins are the building blocks of life.  The human body uses amino acids to make proteins to help the body: Break down food, Grow, Repair body tissue, Perform many other functions.  More than 300 amino acids are found in nature but only 20 amino acids are standard and present in protein because they are coded by GENES.  Other amino acids are modified amino acids and are called NON-PROTEIN amino acids.  CHARACTERISTICS OF AMINO ACIDS: OPTICALLY ACTIVE Dextrorotatory – plane polarized light shifted to the right Levorotatory – plane polarized light shifted to the left  CHARACTERISTICS OF AMINO ACIDS: AMPHOTERIC/AMPHOLYTE Can act as an acid and as a base COOH on the C terminal is a proton donor (acid) NH2 on the N terminal end is a proton acceptor (base)  CHARACTERISTICS OF AMINO ACIDS: ZWITTERION/DIPOLAR ION Possesses both a positive and a negative ion. The OH bond in COOH weakens so it easily gives up or losses a proton that is accepted by the lone pair in NH3.  CHARACTERISTICS OF AMINO ACIDS: ISOLECTRIC POINT The pH value at which zwitterion state exists at a maximum.  CLASSIFICATION OF AMINO ACIDS: ACCORDING TO R-GROUP Neutral amino acids: contain equal number of amino and carboxyl groups. (Glycine, Alanine) Branched chain amino acids (BCAAs): an amino acid having an aliphatic side-chain with a branch (a central carbon atom bound to three or more carbon atoms). (Valine, Leucine, Isoleucine) Acidic amino acids: Amino acids in which R-group is acidic or negatively charged. (Glutamic acid, aspartic acid) Basic amino acids: Amino acids in which R-group is basic or positively charged. (Lysine, Arginine, Histidine) Aromatic amino acids (non-polar): are relatively nonpolar (hydrophobic). All can participate in hydrophobic interactions. (Phenylalanine, Tyrosine, Tryptophan) Sulfur-containing amino acids: generally considered to be nonpolar and hydrophobic. (Methionine, cysteine). Hydroxy-containing amino acids: contain aliphatic hydroxyl groups (that is, an oxygen atom bonded to a hydrogen atom, represented as―OH). (Serine, Threonine) Imino acids: structurally related to amino acids, which have amino group instead of imine—a difference of single vs double-bond between nitrogen and carbon. (Proline, Hydroxyproline) 5 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399 Aliphatic R-group amino acids (non-polar): The R groups in this class of amino acids are nonpolar and hydrophobic. (Glycine, Alanine, Valine, Leucine, Iseoleucine, Methionine, Proline) Polar, Uncharged amino acids: The R groups of these amino acids are more soluble in water, or more hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that form hydrogen bonds with water. (Serine, Cysteine, Glutamine, Threonine, Asparagine)  CLASSIFICATION OF AMINO ACIDS: ACCORDING TO IMPORTANCE ESSENTIAL AMINO ACIDS – 9 amino acids that cannot be synthesized in the body and, therefore, must be present in the diet for protein synthesis to occur. NON-ESSENTIAL AMINO ACIDS - these amino acids can be synthesized in the body itself and hence do not necessarily need to be acquired through diet. CONDITIONAL AMINO ACIDS - Are usually not essential, except in times of illness and stress. LESSON 6: Proteins  Proteins – it is derived from the Greek word proteios , meaning “of first importance”. Organic compounds of high molecular weight (macromolecule) made up of many amino acids joined together by means of peptide linkages. They are essential for the structure, function, and regulation of the body’s tissues and organs.  Proteins are made up of building blocks called amino acids. There are about 20 different amino acids that link together in different combinations.  CLASSIFICATION OF PROTEINS  I. SIMPLE PROTEINS - On hydrolysis they yield only the amino acids and occasional small carbohydrate compounds. Those which give one amino acid only upon hydrolysis.  ALBUMIN - Soluble in water and dilute salt solution  GLOBULIN - Soluble in neutral dilute salt solutions but not in water  GLUTELINS - Soluble in dilute acid and alkalis but insoluble in neutral solvents. Found in grains and cereals.  PROLAMINES - Insoluble in ordinary solvent but soluble in 70% alcohol at about neutral point. Present in plants.  HISTONES - Thymus gland, pancreas and nucleohistones. Soluble in water, salt solutions & dilute acids. Insoluble in ammonium hydroxide.  PROTAMINES - These are present in sperm cells. They are relatively smaller size.  SCLEROPROTEINS - Fibrous protein insoluble in all solvents. Resistant to digestion.  ll. CONJUGATED PROTEINS - made up of protein molecules combined with non- protein groups.  Nucleoproteins - It contains nucleic acid, nitrogen and phosphorus. It is present in chromosomes and in all living forms as a combination of protein with either DNA or RNA.  Glycoproteins - compounds of proteins with a carbohydrate component.  Phosphoproteins - have the prosthetic group (H3PO4) joined to the protein molecule.  Chromoproteins – protein compounds with hematin or similar pigments in their molecules. 6 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399  Lipoproteins – present in the blood serum, brain tissues, cell nuclei, egg yolk and milk.  III. DERIVED PROTEINS - Include substances formed from simple and conjugated proteins. 1. PRIMARY PROTEIN DERIVATIVES - have undergone slight intramolecular rearrangement through the hydrolytic action of certain physical and chemical agents.  Proteans - are insoluble substances resulting from the preliminary action of water, dilute acids or enzymes.  Metaproteans – soluble in weak acids and alkalies but insoluble in neutral salt solution.  Coagulated Proteins – insoluble products resulting from either the action of heat, alcohol, ultraviolet rays or even simple mechanical shaking. 2. SECONDARY PROTEIN DERIVATIVES - products of more extensive hydrolysis, mixtures of fragments of original protein varying in composition and size.  CLASSIFICATION OF PROTEINS: ACCORDING TO BIOLOGICAL SIGNIFICANCE  TRANSPORT PROTEINS - carry/circulate small molecules and ions  Hemoglobin - carries O2 from lungs to other tissues  Serum albumin - distribute fatty acids between fat tissues and other organs  STORAGE PROTEINS - store small molecules and ions, reservoirs of amino acids and metal ions that are needed by growing organisms.  Ovalbumin – used to store amino acids used as nutrients by chicken embryos found in eggs.  Ferretin (“liver protein”) – store Fe in humans and other animals.  CONTRACTILE PROTEINS - conduction of nerve impulses. Muscular motion and coordination of motion.  myosin + muscle protein for contraction  STRUCTURAL PROTEINS - are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles.  collagen  actin  myosin  keratin  PROTECTION PROTEINS - “natural defense proteins”  Antibodies  CATALYTIC PROTEINS - Used to catalyze biochemical reactions  Enzymes  CHEMICAL MESSENGERS - hormonal action  Hormone – internally secreted compounds that affect the functions of organs and tissues when transported by the body fluids.  CLASSIFICATION OF PROTEINS: ACCORDING TO CONFORMATION/SHAPE  FIBROUS PROTEIN - are made up of polypeptide chains that are elongated and fibrous in nature or have a sheet like structure. 7 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399  GLOBULAR PROTEIN – are spherical ("globe-like") proteins and are one of the common protein types. LESSON 7: Proteins (Peptides, Protein Structure and Denaturation)  PEPTIDE BONDS - Are chains of amino acid.  Two amino acid molecules can be covalently bonded through a peptide bond, to yield a dipeptide.  Three amino acids can be joined by two peptide bonds to form a tripeptide; similarly, four amino acids can be linked to form a tetrapeptide, and so forth.  When a few amino acids are joined in this fashion, the structure is called an oligopeptide. When many amino acids are joined, the product is called a polypeptide. NAMING A PEPTIDE:  Begin from the N terminal.  Change the ending of the 1st succeeding amino acids into –yl but retain the name of the last amino acid  Give the full name of amino acid at the C terminal  CHARACTERISTICS OF PEPTIDE BOND  The peptide bond is a partial double bond.  The C–N bond is ‘trans’ in nature and there is no freedom of rotation because of the partial double bond character.  The distance is 1.32Å which is midway between single bond (1.49Å) and double bond (1.27Å).  PROPERTIES OF PROTEINS: (PHYSICAL)  colorless, odorless, and tasteless except protein hydrolyzates  Solubility in solvents such as acids, bases, and salt solutions  Form colloidal dispersion, thus do not pass-through membranes  Those of low molecular weight are soluble in H2O  Those of high MW are macromolecular are totally insoluble in water  PROPERTIES OF PROTEINS: (CHEMICAL) a) Amphoteric /ampholyte  Possess both a positive and negative ion  Due to the presence of -COOH (proton donor)  Due to the presence of –NH2 (proton acceptor)  Are generally good buffers b) Proteins are precipitated by:  High concentration of a neutral salt solution or “salting out”  Process which lead to the destruction of the destruction of the 4 levels of organization of CHON 8 Downloaded by Angelo ([email protected])  lOMoARcPSD|45282399  As a general rule, higher the molecular weight of a protein, the salt required for precipitation is lesser.  Alcohol (powerful protein precipitating agent). LESSON 8: Protein (Protein Energy) Malnutrition - Caused by a deficiency or excess in one or more essential nutrients in the diet. Characterized by a wide array of health problems including weight loss, stunted growth, weakness, resistance to infection, and impairment of intellect. Types of Undernutrition: o Underweight - underweight for one’s age (weight for age) o Stunted - A chronic malnutrition manifested by being too short for one’s age (height for age). o Wasted - An acute malnutrition manifested by being dangerously thin (weight for height). Two major types of malnutrition: o Protein-energy malnutrition - resulting from deficiencies in any or all nutrients o Micronutrient deficiency diseases - resulting from a deficiency of specific micronutrients PROTEIN-ENERGY MALNUTRITION - Due to the foods people eat which are low in protein. PROTEIN-ENERGY (KWASHIORKOR) - Due to a diet deficient in protein and energy- producing foods. This condition usually appears at the age of about 12 months when breastfeeding is discontinued, but it can develop at any time during a child’s formative years. PROTEIN-ENERGY (MARASMUS) - Severe lack of protein intake and other nutrients. Also called the dry form of protein-energy malnutrition. In developing countries, marasmus is the most common form of PEM in children. SICKLE-CELL DISEASE a.k.a “depranocytosis” - A hereditary blood disease caused by a deficiency in protein globulin found in RBC. It is characterized by the production of an abnormal type of hemoglobin- SICKLE CELL HEMGLOBIN (HbS)- in the RBC 9 Downloaded by Angelo ([email protected])