Biochem lecture transes haahaahahahaahaahh khnkhukj PDF

Preview

Summary

Download Biochem lecture transes haahaahahahaahaahh khnkhukj PDF

Description

Biochemistry LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY) INTRODUCTION - Biochemistry is sometimes called biological chemistry. - It can be seen as a study of the components and composition of living things and how they come together to become life. - It is the study of chemical processes that give rise to the complexity of life. - It is also related to molecular biology that concerns genetic information encoded in DNA as well as understanding the structures, functions, and interactions of biological macromolecules. LESSON 11:: SIGNIFICANCE AND RELATION OF BIO BIOCHEMISTRY CHEMISTRY TO OTH OTHER ER FIELDS OF SCIENCES WHAT IS BIOCHEMIS BIOCHEMISTRY? TRY? > Biochemistry is the study of the chemical substances found in living organisms and the chemical interactions of these substances with each other. > Biochemistry is a field in which new discoveries are made almost daily about how cells manufacture the molecules needed for life and how the chemical reactions by which life is maintained occur. The knowledge explosion that has occurred in the field of biochemistry during the last decades of the twentieth century and the beginning of the twenty-first is truly phenomenal. WHAT IIS S BI BIOCHEMIC OCHEMIC OCHEMICAL AL SU SUBSTANCE BSTANCE BSTANCE?? - a chemical substance found within a living organism and are divided into two groups: Bioinorganic Subst Substances ances Bioorganic Substances - includes water and - includes carbohydrates, inorganic salts lipids, proteins, and nucleic acids As isolated compounds, bioinorganic and bioorganic substances have no life in and of themselves. Yet when these substances are gathered together in a cell, their chemical interactions are able to sustain life.

Figure: Mass composition for the human body in terms of types of biochemical substances present.

Although the human body is usually thought of as containing mainly organic (biochemical) substances, such substances make up only about one-fourth of total body mass. The bioinorganic substance water constitutes more than two-thirds of the mass of the human body, and another 4%–5% of body mass comes from inorganic salts.

BIOCHEMICAL IMPORTANCE Biochemistry and medicine enjoy a mutually cooperative relationship. Biochemical studies have illuminated many aspects of health and disease, and the study of various aspects of health and disease has opened up new areas of biochemistry. The medical relevance of biochemistry both in normal and abnormal situations is emphasized throughout this module. Biochemistry makes significant contributions to the fields of cell biology, physiology, pathology, pharmacology, microbiology, immunology, nutrition, forensic medicine, and toxicology, as well as the fields of inflammation, cell injury, and cancer. These close relationships emphasize that life, as we know it, depends on biochemical reactions and processes. Aside from medicine, biochemical research is also applied in industry, agriculture, and food production. LESSON 2: PROPERTIES OF WATER AND CHEM CHEMICAL ICAL REACTIONS IN THE CELL WHAT IS WATER? - one of the most plentiful compounds on earth. - major component of the cell (70-90% of its weight) and is referred to as inert space filler in a living organism. - comprises 62% of an adult body weight, higher in young children and lower in the elderly. - has many important roles in human and all living organisms. - Every day we take up about 2700 mL of water from various sources: drinking, water of metabolism and preformed water in food. HOW LONG CAN A PERSON LIVE WITHOUT WATER? - we can live without food for weeks, but we could be dead in about 3 days without water. - death usually occurs when water loss is over 10% of the person’s body weight. - impossible to answer for many variable factors determine a person’s survival time. Under the most extreme conditions, death can come rather quickly. Ex: a child left in a hot car / an athlete exercising on a hot weather can dehydrate, overheat & die in a period of a few a hours. An adult in a comfortable surroundings, in contrast, can survive for a week or more. PROP ROPERTIES ERTIES OF WATER & BIOLOGICAL IMPORTANCE 1. Water a ass a SSolvent olvent - All of our body fluids (blood, urine, lymph, sweat, and digestive juices) are mostly water. - All the chemical reactions in the body take place in water, UNIVERSAL SAL SOL SOLVENT VENT because it dissolves both - UNIVER polar (like) and non-polar (unlike) substances. hydrolysiss - Used during digestion in a series of hydrolysi reactions, i.e., breakdown of large compounds into smaller, more easily absorbed compounds. 2. Water a ass a Transporter

JALN | 1

Biochemistry LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY) - Water in blood carries nutrients from the eaten foods to tissues throughout the body. - Also transports waste products from cells to lungs, kidneys, and skin to be discarded as CO2, urine or sweat. - Urine & sweat help eliminate excess nitrogen % salt, are both over 95% water. - Plasma (liquid portion of blood) caries hormones to their specific target sites throughout the body. - It is essential for blood circulation - Also transports materials within cells. 3. Water a ass a Temperature R Regu egu egulator lator - Water retains heat better than most liquids. It takes a great deal of heat to turn liquid water into vapor. With that, a lot of heat is lost when we perspire, and the body is greatly relief from that small amount of sweat that has evaporated. - INSENSIBLE PERSPIRA PERSPIRATION TION – water loss due to the constant evaporation of water from skin and the lungs, even when temperatures are not very hot. We don’t see/feel it, but it balances the heat produced through metabolic processes in the cells in order that our body temperature remains constant. 4. Water a ass a Lubricant - Present in synovial fluid that helps the joints (knees & elbows) to move easily; tears protects the surface of the eyes; - Lubricates thin spaces around internal organs; - In the chest, water serves as lubricant as the rib cage slides over several internal organs during breathing. - Moistens food during digestion and ending with the passage of water-softened feces through the anus. - Principal component of mucus and every other lubricant fluid in the body, CHEMICAL REACTIONS IN THE CELL 1. OXIDATION OXIDATION--REDUCTION (REDOX) REAC REACTIONS TIONS Oxidation-reduction (redox) reactions are important because they are the principal sources of energy on this planet, both natural or biological and artificial. Most of the metabolic pathways that will be discussed in later modules are combinations of oxidation and reduction reactions. This is where mnemonics can be applied to remembering important facts. REDUCTION (VDGEHROA) When the Valence / oxidation number of an element that means it Decreases Gained Reduced d Electrons/Hydrogens, it (substance) was Reduce and its compound is the Oxidizing Age Agent nt. OXIDATION (VILEHORA) If the Valence / oxidation number of an element Increases that means it Lost Electron/Hydrogen, it (substance) was Oxidized and its compound acts as the Reducing Agent.

Examp Examples: les:

IN ALCOHOLS a. Primary (1° ) alcohols alcohols are first oxidized to aldehydes (RCHO), which are further oxidized to carboxylic acids (RCOOH) by replacing one and then two C–H bonds by C–O bonds.

- Since the enzymes have a higher affinity for ethanol than methanol, methanol poisoning is treated by giving ethanol to an individual. With both methanol and ethanol in a patient’s system, the enzymes react more readily with ethanol, allowing the methanol to be excreted unchanged without the formation of methanol toxic oxidation products.

Secondaryy ((22° ) alcohols are oxidized to ketones (R2 b. Secondar CO), by replacing one C–H bonds by one C–O bonds.

JALN | 2

Biochemistry LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY) more molecule of H2O are eliminated. Ex: Glucose + Glucose à Maltose 3. ISOMERIZATIO ISOMERIZATION N - In isomerization reactions, a single molecule is rearranged such that it retains the same molecular formula but now has a different bonding order of the atoms forming a structural or stereoisomer.

c. Tertia Tertiary ry (3°) alcohols have no H atoms on the carbon with the OH group, so they are not oxidized. EPIMIRIZATI EPIMIRIZATION ON - Interconversion of two aldoses - D-mannose / D-galactose à D-glucose

2. HYDROLYSIS AND CONDE CONDENSATION NSATION HYDROLYSIS - Greek “water loosening” - A molecule of water, with the help of enzymes, interacts with the reactant to break up the reactants’ bond; - Water converts a complex substance to smaller / simpler substances.

The first stage of catabolism, digestion, is the hydrolysis of large molecules to small molecules; polysaccharides such as starch are hydrolyzed to monosaccharides, proteins are hydrolyzed to their component amino acids, and triacylglycerols are hydrolyzed to glycerol and fatty acids. Each of these molecules enters its own metabolic pathway to be further broken down into smaller components, releasing energy.

- Hydrolysis is important to the body for large molecules of protein, nucleic acid, and fats are broken down into simpler, smaller, more usable molecules. - Generally, almost all digestive and degradative processes in the body occur by hydrolysis. Examp Examples: les: - Chemical reactions occurring in a living matter a. C12H22O11 + H2O à C6H12O6 + C6H12O6 b. Sucrose + H2O à Glucose + Fructose c. Maltose + H2O à Glucose + Glucose d. Lactose + H2O à Glucose + Galactose CONDENSATION / DEHYDRATIO DEHYDRATION N - Essentially hydrolytic reactions in reverse; small molecules united into larger molecules and one or

TAUTOMERISM - Interconversion of aldose to ketose - D-glucose à D-fructose (or vise versa)

PROP ROPERTIES ERTIES OF WATER & BIOLOGICAL IMPORTANCE The pH Scale - Measures how acidic or basic a substance is. - Ranges from 0-14 related to the [H3O+] (hydronium) of the solution. - Scientists uses a pH number to show the strength of an acid or base. - A pH is measured by dipping litmus into solution such as water and other liquids.

- First introduced by a Danish chemist Soren Sorensen at the Carlsberg Laboratory in 1909. - p exact definition is unknown. - H stands for Hydrogen. - For convenience, Sorensen suggested ‘pH’ as “power of Hydrogen” - Gave doctors, chemists, and technologists a measurement that could tell them exactly how acidic, alkaline or neutral a substance is.

JALN | 3

Biochemistry LECTURE | MODULE 1 (INTRODUCTION TO THE STUDY OF BIOCHEMISTRY) - All fluids in the human body is aqueous, the only solvent present is water. - Consequently, all body fluids have a pH value. Some of them have narrow range, some are wide. Ex: pH of blood = 7.35 – 7. 7.45 45 8.44 pH of urine = 4.8 – 8.

pH and Buffer Computat Computations ions

JALN | 4

Biochemistry LECTURE | MODULE 2 (CARBOHYDRATES) INTRODUCTION - Carbohydrates is the most abundant of all the organic compounds in nature. - About 65% of the foods in our diet consist of carbohydrates. - Each day, we utilize carbohydrates in foods such as bread, pasta, potatoes, and rice. Other carbohydrates called disaccharides include sucrose in table sugar and lactose in milk. - During digestion and cellular metabolism, carbohydrates are converted into glucose, which is oxidized further in our cells to provide our bodies with energy and to provide the cells with carbon atoms for building molecules of proteins, lipids, and nucleic acids. - In addition to providing the structural framework of plants, cellulose has other important uses too. The wood in our furniture, the pages in our book, and the cotton in our clothing are all made of cellulose. - Carbohydrates can be simple or complex, having as few as three or as many as thousands of carbon atoms. The glucose metabolized for energy in cells, the sucrose of table sugar, and the cellulose of plant stems and tree trunks are all examples of carbohydrates. - Carbohydrates on cell surfaces determine blood type, and carbohydrates form the backbone of DNA, the carrier of all genetic information in the cell. - Carbohydrates have many polar functional groups, whose structure and properties can be understood by applying the basic principles of organic chemistry. LESSON 11:: DEFINITION, SOURCES, PROPERTIES AND FUN FUNCTIONS CTIONS OF CARBOHYDRATE CARBOHYDRATES S WHAT ARE CARBOHYDRATES? > Are polyhydroxy ketones (ketose) or polyhydroxy aldehydes (aldose) or compounds that can be hydrolyzed from them; (CH2O)n ; Cn(H2O)y) ; carbon hydrates; sometimes referred also as sugars.

WHAT ARE ITS FU FUNCTIONS? NCTIONS? 1. Storage form of me metabolic tabolic fuel

2. Structural function / Supportive function a. Ce Cellulose llulose – most abundant in nature, no nutritive value, forms the cell wall of plants.

b. Chitin – exoskeleton of crustacean c. Peptidoglycan – found in the cell wall of bacteria 3. Transport function - Glycoproteins

4. Regulatory function - Follicle-stimulating hormones which regulates the development, growth, pubertal maturation and reproductive process. 5.. Catalytic funct function ion - Ribonuclease 6. Anti Anti--viral function - Interferon 7. Protective/Lubricating function a. Hyaluronic Acid – most abundant acid mucopolysaccharide found in connective tissue, vitreous humor of eye, synovial fluid

b. Mucin > Synovial Fluid – Multipurpose fluid surrounding all articular joints. Has both viscous (lubrication) and elastic (shock absorption) proportions (viscoelastic). 8. Other Biological Function a. Biological specificity of animal cell membrane. E.g. Blood Typing Focus on the Human Body Blood Type - There are 4 blood types – A, B, AB, and O. - It is based on 3 or 4 monosaccharides attached to a membrane protein of RBCs. - Each blood type has the monosaccharides below: N-acetyl D-glucosamine Type O D-galactose L-fucose

Type A

N-acetyl D-glucosamine N-acetyl D-glucosamine D-galactose L-fucose

Type B

N-acetyl D-glucosamine D-galactose D-galactose L-fucose

JALN | 5

Biochemistry LECTURE | MODULE 2 (CARBOHYDRATES) 2. FURANOSE – five-membered ring resembling furan; ketoses.

Type AB

N-acetyl D-glucosamine N-acetyl D-glucosamine D-galactose D-galactose L-fucose b. Components of clotting proteins - Heparin – an anti-clotting agent present in the body. 9. Precursors - Initiates biological processes for biosynthesis of: purine, pyrimidine, nucleotides, Vitamin C, and certain amino acids. LESSON 22:: CLASSIFICATIONS OF CA CARBOHYDRATES RBOHYDRATES TYPES OF CARBOHYDRATES A. ACCORDING TO NUMBER OF SIMPLE SUGARS OBTAINED BY H HY YDROLYSIS

1. Monosaccharides - Simplest form of sugar which cannot be further carbohydrates ates hydrolyzed; building blocks of carbohydr - Sweet tasting, with varying relative sweetness - Polar compounds with high melting points - Solids at room temperature, very soluble in water B. ACCORDING TO NUMBER OF CARBONS IN MONOSACCHARIDES 1. TRIO TRIOSE SE – contains 3 carbon atoms 2. TETROSE – contains 4 carbon atoms 3. PENTOSE – contains 5 carbon atoms 4. HEXOSE – contains 6 carbon atoms 5. HEPTOSE – contains 7 carbon atoms C. ACCORDIN ACCORDING G TO REACTIVE GROUP 1. ALDOSE – monosaccharides with an aldehyde group. - Carbonyl at C1; like Glucose 2. KETOSE – monosaccharides with a ketone group - Carbonyl at C2; like Fructose

C. ACCORDIN ACCORDING G TO RING STRUCTURE 1. PY PYRANOSE RANOSE – six-membered ring resembling pyran; aldoses.

CLASSIFICATIONS ALDOSES Aldotriose D-Glyceraldehyde Aldopentetroses D-Erythrose D-Threose D-Ribose (Rib) Aldopentoses D-Arabinose (Ara) D-Xylose (Xyl) D-Lyxose (Lyx) Aldohexoses D-Allose D-Altrose D-Glucose (Glc) D-Mannose (Man) D-Gulose D-Idose D-Galactose(Gal) D- Talose KETOSES Dihydroxyacetone Ketotriose D-Erythrulose Ketotetrose D-Ribulose Ketopentoses D-Xylulose Ketohexoses D-Psicose D-Fructose D-Sorbose D-Tagatose 2. Oligosaccharides - Polymers made up of 2-10 monosaccharides. Disaccharides à 2 Monosaccharides. Maltose = Glucose + Glucose Lactose = Glucose + Galactose Sucrose = Glucose + Fructose 3. Polysaccharides - Polymers more than 10 saccharide units. a. HOMOPOLYSACCHARIDES – one kind of monosaccharide. 1. Starch – Glucose 2. Glycogen – Glucose 3. Dextrin – Glucose 4. Cellulose - Glucose 5. Dextran - Glucose 6. Inulin - Fructose b. HETERO HETEROPOLYSACCHARIDES POLYSACCHARIDES – two or more kind of monosaccharides. 1. Hyaluronic Acid: d-glucuronic acid + d-glucosamine + acetic pain 2. Hepari Heparin n - Six sugar residues + N-acetyl D-glucosamine + Diduronate

JALN | 6

Biochemistry LECTURE | MODULE 2 (CARBOHYDRATES) 4. Derived Carbohydrates - Sugars with added with other substituents aside from OH. a. Sugar acid b. Sugar alcohol c. Amino sugar d. Deoxy sugar e. Phosphorylated sugar D. ACCORDIN ACCORDING G TO REDUCING POWER 1. REDUCING SUGARS – carbohydrates with free aldehyde or ketone group. - All monosaccharides and disaccharides except sucrose. 2. NON NON--REDUCING SUGARS– carbohydrates without free aldehyde or ketone group - Sucrose and all polysaccharides. LESSON 3 - ISOMERISM ISOMERISM:: FISCHER STRUC STRUCTURE TURE AND HAWORTH STRUCTURE DIF DIFFERENT FERENT FORMS OF ISOMERI ISOMERISM SM 1. Optical Isomers a. De Dextrorotator xtrorotator xtrorotatoryy – an optical isomer which rotates the beam of polarized light to the right or clockwise and indicated by a (+) sign or smaller letter d. Ex: (+) glucose or d-glucose b. Levorotatory – an optical isomer which rotates the beam of polarized light to the left or counterclockwise and indicated by a (-) sign or small letter l. Ex: (-) glucose or l-glucose

- Most biologically active monosaccharides are D isomers. - Most monosaccharides occurring in mammals are of the D-configuration and enzymes are responsible for their metabolism are specific for this configuration. 3. Alpha & Beta Anomers - Stereoisomers that differ configuration around an anomeric carbon of a cyclic ring structure or ring structure. a. Alp Alpha ha (α) – the OH is written below the anomeric carbon. - Most sugars are of α-anomers since our body can only utilize those of this anomers except in some cases. b. Beta (β ) – the OH is written above the anomeric carbon. > Pyranose – the anomeric carbon is C-1 and is obtained by cyclization of an aldehyde and an alcohol group.

2. D & L Enantiomers a. D – the enantiomer with the OH group on the right (dextro) side of the chiral carbon farthest from the carbonyl group. Naturally occurring. b. L – the enantiomer with the OH group on the left (levo) side of the chiral carbon farthest from the carbonyl group. Unnatural Enantiomer.

> Furanose – the anomeric carbon is C-2 and is obtained by cyclization of a ketone and an alcohol group.

JALN | 7

Biochemistry LECTURE | MODULE 2 (CARBOHYDRATES) b. Hemiketal – the product of the addition of an alcohol to the carbonyl group of a ketone. a. b.

4. Epimers - Stereoisomers that differ in configuration around a single carbon atom of a linear structure, using Dglucose as reference. - Two sugars which differs from one carbon only in the configuration.

SUMMARY De Dextro xtro – right, Levo – left, (-), l (+), d, D – OH group L – OH group on on the right, the left, Enantiomers naturally unnatural occurring Alp Alpha ha ( α) – OH Beta (β ) – OH Anomers written below written above Pyranose – 6- Furanose – 5membered ring, membered ring, C-1, aldehyde + C-2, ketone + alcohol alcohol Stereoisomers that differ in Epimers configuration around a single carbon atom of a linear structure. Optic Optical al Isomer

3. New Newman man Pro Project ject jection ion - Boat and chair structures.

GENERAL RULE TO TRANSLATE A FISHCER PROJECTION TO A HAWORTH PROJECTION 1. Classify given sugar as aldose (pyranose) or ketose (furanose). 2. Determine whether the given sugar is α- anomer or β- anomer. At the anomeric carbon, the α from is i...