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R2009 BIOLOGY 1A03: CELLULAR & MOLECULAR BIOLOGY WEEK 1 : Monday, September 14th to Thursday, September 17th, 2009

IMPORTANT The posted Biology 1A03 ELM Lecture Outlines are NOT detailed lecture notes. Students are expected to supplement the posted ELM 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.

CHAPTER 3: PROTEIN STRUCTURE AND FUNCTION

Fig.3.1 Miller Spark-Discharge Experiment

Why was Millers Experiment significant? Stanley Millers experiment simulated the early earth conditions. Results supported chemical evolution.

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. 3.2 Amino Acid Structure

AMINO ACIDS Fig. 3.3 The 20 Major Amino Acids Found in Organisms - R group is the only variable - 20 different R groups 20 different amino acids

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Fig. 3.4 Structural, Geometric, and Optical Isomers STRUCTURAL ISOMERS
differ in the order which their atoms are attached. C-C-OH C-O-C ethanol(C2H6O) Dimethyl ether(C2H6O)

GEOMETRIC ISOMERS
differ in arrangement of atoms around a double bond trans-across cis-same side different properties, different functions, same molecular formula

OPTICAL ISOMERS

OPTICAL ISOMERS - are isomers which are mirror images of each other non-superimposable - carbon is asymmetric, -carbon - exists as 2 isomers, rotates a beam of polarized light to the left or to the right

TEST QUESTION REAL WORLD EXAMPLE

The Pharmacological Importance of Optical Isomers in the Treatment of Parkinsons Disease Supplementary Figure of L- Dopa & D- Dopa Dihydroxy Phenyl-Alanine

PROTEINS CONDENSATION (DEHYDRATION) REACTION - a peptide bond forms between 2 amino acids monomers Fig. 3.6 Polymers can be Extended or Broken Apart
polymers

Fig. 3.8 Amino acids Polymerize to Form Polypeptides

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PRIMARY (1) 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

Fig. 3.12 Secondary Structures of Proteins SECONDARY (2) Structure - -helices & -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 -helix or -pleated sheet form. Fig. 3.13 Tertiary Structure of Proteins Results from Interactions Involving R-Groups TERTIARY (3) 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

Fig. 3.14 Quaternary Structure of Proteins is Created by Multiple Polypeptides QUATERNARY (4) Structure

- shape (or conformation) of a complex aggregate protein, that is attributed to the three-dimensional arrangement of its subunits (polypeptides)

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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 renaturation - assisted by chaperones

REAL WORLD EXAMPLES Box 3.1 Prions & Fig. 3.16 Prions Are Improperly Folded Proteins

and Molecular Handedness and the Thalidomide Tragedy In the 1950s, Thalidomide , which consisted of 2 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. Currently, cancer research is investigating the use of thalidomide in inhibiting the blood vessel development of cancerous tumors.

USEFUL TERMINOLOGY chemical evolution hydrophilic structural isomers polymerization dehydration reaction secondary structure Van der Waals interactions chaperonins amino acids polar geometric isomer macromolecule hydrolysis -helix quaternary structure R-group nonpolar monomer protein peptide bond -pleated sheet denaturation hydrophobic optical isomers polymer condensation reaction primary structure tertiary structure renaturation

Enzymatic reactions - no study *What's minor + major grove used for? No RNA/evolution - no study Test #1 - 3,4,5,6 X-ray crystallography + Marie Curey Topics covered: proteins; N.A next week: carbs, lipids CHAPTER 4: NUCLEIC ACIDS AND THE RNA WORLD online quiz will get extended Study from 4 sources: - lectures NUCLEIC ACIDS - Read key concepts not beginning Fig. 4.1 The General Structure of Nucleotide - In-class discussions

NUCLEOTIDE - is the monomer of nucleic acids, it consists of a phosphate group, a pentose sugar, and a nitrogenous base
Fig. 4.1(a)

- Nitrogenous base is attached at C #1 - Phosphate group at C#5 - C#3 OH is involved in bonding with the next nucleotide

5 carbon sugar

double ring single ring - pyrimidines and purines be able to recognize them + label + explain

PHOSPHODIESTER LINKAGE: -C-O-P-O-C DNA and RNA are POLYNUCLEOTIDES

Fig. 4.2 Nucleotides Polymerize via Phosphodiester Linkages know: condensation reaction
label

Fig. 4.3 RNA has a Sugar-Phosphate Backbone

repeating units be able to recognize the diagram

GENETIC CODE Why is it important? - 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
when it opens replication can take place

- A pairs with T
Chargaff's rule Crick + Watson = Structure

- G pairs with C - H bonds hold the double helix form

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Fig. 4.6 Complementary Base Pairing is Based on Hydrogen
b) 3' and 3' never opposite to one another or weak H bonds to allow bond breaking so replication 5' and 5' can take place always anti-parallel
less energy taken

Fig. 4.8 Dimensions of DNA Secondary Structure

know dimensions of DNA - dimens important for design * - know major + minor groove

email

enzymes + why DNA polymerase can attach

stability

Fig. 4.12 Making a Copy of DNA

9 nucleotides floating around in the cell Rosalind Franklin X-ray crystallography

Box 4.1 The Human Side of Research

USEFUL TERMINOLOGY nucleic acid pyrimidine sugar-phosphate backbone complementary base pairing guanine ribonucleic acid nitrogenous base gel electrophoresis adenine uracil deoxyribonucleic acid phosphodiester linkage X-ray crystallography thymine purine Chargaff double helix cytosine

This information is copyright material (intellectual and academic property) of Dr. L. Kajiura, Department of Biology, McMaster University. It may be used only for study purposes and only by students enrolled in Fall 2009 Biology 1A03 Cellular & Molecular Biology, September-December 2009). This information may not be reproduced for any other purpose, nor distributed to any person (using any type of media), who is not enrolled in the course, except by written permission of the Biology 1A03 professor, Dr. L. Kajiura. Copyright 2009