BIO 1A03 Week 1 (CH 3&4 and 5&6).pdf

1 R2011 BIOLOGY 1A03: CELLULAR & MOLECULAR BIOLOGY '5▯▯.$-,85$¶6▯ UPDATED LECTURE OUTLINES ND TH WEEK 1 : MONDAY, MAY 2 TO WEDNESDAY MAY 4 2011 IMPORTANT The posted Biology 1A03 AVENUE Lecture Outlines are NOT detailed lecture notes. Students are expected to supplement the posted AVENUE Lecture Outlines with their own written notes. Since Supplementary Lecture Topics and Examples will be discussed EXCLUSIVELY in lectures (they are NOT found in the textbook), it is very important that students attend ALL Biology 1A03 Lectures. Note that Chapter 2 in the Biology 1A03 textbook is considered assumed knowledge that should have been previously obtained in high school biology 12U. CHAPTER 3: PROTEIN STRUCTURE AND FUNCTION MONOMER - subunit or building block of a polymer POLYMER - large molecule composed of several connected subunits, which are identical or similar MACROMOLECULES - large organic polymers Fig.3.1 Miller Spark-Discharge Experiment WHY WAS STANLEY 0,//(5¶6▯(;3(5,0(17▯SO SIGNIFICANT? 6WDQOH\▯0LOOHU¶V▯H[SHULPHQW▯VLPXODWHG▯WKH▯HDUO\▯HDUWK▯FRQGLWLRQV. His results and those of other subsequent researchers supported chemical evolution. NOTE that there are other alternative perspectives related to Hydrothermal Vents and the Murchison Meteorite AMINO ACIDS Fig. 3.2 Amino Acid Structure Fig. 3.3 The 20 Major Amino Acids Found in Organisms - R group is variable - 20 different R groups o 20 different amino acids 2 Fig. 3.4 Structural, Geometric, and Optical Isomers STRUCTURAL ISOMERS Students were advised to take notes during the in-class discussion of this topic. GEOMETRIC ISOMERS Students were advised to take notes during the in-class discussion of this topic. OPTICAL ISOMERS - are isomers which are mirror images of each other - carbon is asymmetric, D-carbon - exists as 2 isomers, rotates a beam of polarized light to the left or to the right REAL WORLD EXAMPLE THE PHARMACOLOGICAL IMPORTANCE OF OPTICAL ISOMERS IN THE 75($70(17▯2)▯3$5.,1621¶6▯',6($6( L- DOPA & D- DOPA DOPA = Dihydroxy Phenyl-Alanine Students were advised to take notes during the in-class discussion of this topic. Refer to the supplementary figure (DOPA) posted on the Biology 1A03 Avenue website. PROTEINS Summary Table 3.1 Protein Functions ± proteins serve several roles in cells and in organisms CONDENSATION (DEHYDRATION) REACTION - a peptide bond forms between 2 amino acids Fig. 3.6 Polymers can be Extended or Broken Apart 3 Fig. 3.8 Amino acids Polymerize to Form Polypeptides PRIMARY (1q) Structure - unique and specific amino acid sequence encoded in DNA - the amino acid sequence provides specificity in function and folding conformation REAL WORLD EXAMPLE Fig. 3.11 CHANGES IN PRIMARY STRUCTURE AFFECT PROTEIN FUNCTION SICKLE CELL DISEASE Students were advised to take notes during the in-class discussion of this topic. SECONDARY (2q) STRUCTURE (Fig. 3.12 Secondary Structures of Proteins) - D-helices & E-pleated sheets - H bond forms between ±C=O & -N-H of two peptide bonds - H bonds do not involve R groups - regular repeating units, contributes to structure (strong) - on average, 60% of polypeptide structure is in D-helix or E-pleated sheet form. Fig. 3.13 Tertiary Structure of Proteins Results from Interactions Involving R-Groups TERTIARY (3q) STRUCTURE - consists of irregular contortions due to interactions (disulphide bridges, ionic bonds, hydrogen bonds, hydrophobic interactions, van der Waals interactions) between various side chains of amino acids 4 Fig. 3.14 Quaternary Structure of Proteins is Created by Multiple Polypeptides QUATERNARY (4q) STRUCTURE - shape (or conformation) of a complex aggregate protein, that is attributed to the three-dimensional arrangement of its subunits (polypeptides) Table 3.3 A SUMMARY OF PROTEIN STRUCTURE Fig. 3.15 Proteins Fold into their Normal, Active Shape - heat causes denaturation, then spontaneously in solution o renaturation - assisted by chaperones REAL WORLD EXAMPLE Box 3.1 PRIONS Fig. 3.16 PRIONS ARE IMPROPERLY FOLDED PROTEINS Students were advised to take notes during in-class discussion of this topic. 5 REAL WORLD EXAMPLE MOLECULAR HANDEDNESS AND THE THALIDOMIDE TRAGEDY ,Q▯WKH▯▯▯▯▯¶V▯▯7KDOLGRPLGH▯▯▯ZKLFK▯FRQVLVWHG▯RI▯▯▯mirror-image molecules, was used as a sedative. One of the optical isomers was safe as a tranquilizer, but the other optical isomer inhibited blood vessel formation and caused serious birth defects. This tragedy underscores the need to carefully assess drugs, since their structures are linked to characteristics and functions. NEW HOPE FOR THALIDOMIDE USE IN CANCER RESEARCH Currently, cancer research is investigating the use of thalidomide in inhibiting the blood vessel development of cancerous tumors. USEFUL TERMINOLOGY chemical evolution amino acids R-group hydrophobic hydrophilic polar nonpolar optical isomers structural isomers geometric isomer monomer polymer polymerization macromolecule protein condensation reaction dehydration reaction hydrolysis peptide bond primary structure secondary structure Į-helix ȕ-pleated sheet tertiary structure Van der Waals interactions quaternary structure denaturation chaperones 6 CHAPTER 4: NUCLEIC ACIDS AND THE RNA WORLD NUCLEIC ACIDS Fig. 4.1 The General Structure of Nucleotide NUCLEOTIDE - is the monomer of nucleic acids, it consists of a phosphate group, a pentose sugar, and a nitrogenous base - Nitrogenous base is attached at C #1 - Phosphate group at C #5 - C#3 OH is involved in bonding with the next nucleotide PHOSPHODIESTER LINKAGE: - C ± O ± P ± O ± C DNA and RNA are POLYNUCLEOTIDES Fig. 4.2 Nucleotides Polymerize via Phosphodiester Linkages Fig. 4.3 RNA has a Sugar-Phosphate Backbone GENETIC CODE - one specific sequence of base pairs forms one gene DOUBLE HELIX - nitrogenous bases point to the center of the double helix, sugar-phosphate backbone is on the outside - A pairs with T - G pairs with C - H bonds hold the double helix form Fig. 4.6 Complementary Base Pairing is Based on Hydrogen Fig. 4.8 Dimensions of DNA Secondary Structure Fig. 4.9 Making a Copy of DNA Box 4.1 The Human Side of Research USEFUL TERMINOLOGY nucleic acid ribonucleic acid deoxyribonucleic acid purine pyrimidine nitrogenous base phosphodiester linkage Chargaff sugar-phosphate backbone X-ray crystallography double helix adenine complementary base pairing thymine cytosine guanine uracil 7 CHAPTER 5: AN INTRODUCTION TO CARBOHYDRATES FUNCTIONS OF CARBOHYDRATES Energy source - glucose is rapidly metabolized Energy storage - starch & glycogen Structural support - cellulose, chitin, cartilage Transport of energy source - sucrose (plants), lactose (milk) Cell surface signals - cell communication and cell-cell recognition MONOSACCHARIDES - are single sugars (simple sugars) Ribose is present in RNA Deoxyribose is present in DNA Glucose is present in starch, cellulose, glycogen Galactose is present in cartilage Fig. 5.3 Sugars Exist in Linear and Ring Forms - note that glucose in aqueous solutions forms ring structures HOW CAN YOU DISTINGUISH BETWEEN THE TWO RING FORMS (ALPHA FORM & BETA FORM) OF GLUCOSE? D Glucose ± hydroxyl group at C#1 is below the plane of the ring E Glucose ± hydroxyl group at C#1 is above the plane of the ring Fig. 5.4 Monosaccharides Polymerize through Formation of Glycosidic Linkages DISACCHARIDES - are double sugars that consist of two monosaccharides, which are joined a condensation (dehydration) reaction GLUCOSE + GLUCOSE o MALTOSE GLUCOSE + FRUCTOSE o SUCROSE GLUCOSE + GALACTOSE o LACTOSE 8 REAL WORLD EXAMPLES LACTOSE INTOLERANCE AND GALACTOSEMIA (Box. 5.1) CLASS DISCUSSION Students were advised to take supplementary notes during the in-class discussion of this topic. LACTOSE INTOLERANCE Adults do not produce sufficient amounts of lactase. Lactase is an enzyme which splits lactose into glucose & galactose. GALACTOSEMIA Lacks the enzyme that converts galactose to glucose. Table 5.1 Polysaccharides Differ in Structure POLYSACCHARIDES - are polymers that consist of many sugars monomers STARCH GLYCOGEN CELLULOSE CHITIN PEPTIDOGLYCAN (Box 5.2) 9 Fig. 5.6 Cellulose, Chitin, and Peptidoglycan Form Tough Fibers or Sheets Fig. 5.7 Carbohydrates Are an Identification Badge for Cells USEFUL TERMINOLOGY carbohydrate carbonyl hydroxyl monosaccharide aldehyde pentose hexose JOXFRVH▯▯Į▯DQG▯ȕ▯ galactose linear chains ring forms polysaccharide disaccharides lactose intolerance JO\FRVLGLF▯OLQNDJH▯▯Į▯DQG▯ȕ▯ starch amylase amylopectin glycogen cellulose Į-1,4-glycosidic linkages cell wall Į-1,6-glycosidic linkages chitin ȕ-1,4-glycosidic linkages N-acetylglucosamine peptidoglycan glycoproteins cell-cell recognition cell signaling 10 CHAPTER 6: LIPIDS, MEMBRANES, AND THE FIRST CELLS MAJOR CLASSES & FUNCTIONS OF LIPIDS Phospholipids, glycolipids, and some steroids (cholesterol) - membrane structure and function Other steroids - hormones and regulators Triglycerides - food storage Waxes - bee hives and plant leaf surfaces for the protection2against H O loss Fig. 6.3 Fats are One Type of Lipid found in Cells Fats - consist of glycerol + 3 fatty acids , linked by ester linkages Fig. 6.4 Amphipathic Lipids Contain Hydrophilic and Hydrophobic Elements WHAT IS AN "AMPHIPATHIC" MOLECULE ? - has both a polar (hydrophilic) region AND a nonpolar (hydrophobic) region Fig. 6.5 Phospholipids Form Bilayers in Solution - Phospholipids spontaneously form bilayers in water. NONPOLAR o HYDROPHOBIC TAILS POLARo HYDROPHILIC HEADS IMPORTANT CONCEPT WHY ARE MEMBRANES IMPORTANT? Membranes allow for COMPARTMENTALIZATION. COMPARTMENTS: may contain different enzymes