Lecture 1

Lecture 1 - Welcome to BCMB / BIOL / CHEM 3100...

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Unformatted text preview: Welcome to BCMB / BIOL / CHEM 3100 Introductory Biochemistry www.biology.arizona.edu 1 BCMB 3100 Lectures: 9:00-9:50 AM, (Mon, Wed & Fri) C127 - Life Sciences Breakout Session: 5:00-5:50 PM, (Mon) C127 – Life Sciences INSTRUCTORS 1st half of course (Horton Chapters 1-9): Dr. John Rose Department of Biochemistry and Molecular Biology Room B204 F.C. Davison Life Sciences Complex Phone: 706-542-1750 email: [email protected] 2nd half of course (Horton Chapters 10-11, 13-22): Dr. Stephen Dalton Department of Biochemistry and Molecular Biology Coverdell Center, Room 245B Email: [email protected] Phone 706-583-0480 Rose REVISED Lecture Schedule The lecture schedule is subject to change. The schedule above is just to provide a general guideline for the semester. Dalton Lecture Schedule The lecture schedule is subject to change. The schedule above is just to provide a general guideline for the semester. IMPORTANT - See Class Syllabus for additional information •  Partial Class Notes will be available on the website at least one day prior to lecture •  These will be posted on the eLearning Commons website –  https://www.elc.uga.edu/ •  Grading: 100% from 4 exams –  The first two exams will be mainly multiple choice. –  You will select one answer from five possibilities for each question –  The second two exams will be short answers See syllabus for important information about missed exams and grading errors BCMB 3100 – Lecture 1 Horton Chapter 1 •  History of BIOCHEMISTRY •  Chemical elements of life •  Macromolecules •  Energetics •  Cells What is Biochemistry ”… the central goal of the science of biochemistry is to determine how the collections of inanimate molecules found in living organisms interact with each other to constitute, maintain, and perpetuate the living state. From Biochemistry, Albert L. Lehninger, 1975 Biochemistry is the study of the molecular basis of life. It is an empirical, reductionist and rapidly evolving discipline. History of Biochemistry •  1770 – 1774 - Priestly Plants produce oxygen, O2 consumed by animals •  People believed in vitalism-Special chemical and physical laws operate in living cells –  Vitalism belief that the animate world obeyed different chemical laws than the inanimate world •  1828 - Friedrich Wöhler Organic molecule (urea) synthesized from inorganic molecule (ammonium cyanate). –  Molecules of life can be synthesized from common chemicals outside living organism DEATH OF VITALISM •  1862 - Louis Pasteur – disproved spontaneous generation –  Showed sterilized solutions did not spontaneously form life. •  1897 - Eduard & Hans Buchner –  Fermented sucrose into alcohol using yeast extract. –  Chemical reactions can occur outside living cells! –  Enzymes = cell-derived catalysts. –  DEATH OF VITALISM. Advances in Biochemistry rapid from 1900s •  Early 1900s - 1st biochemistry departments established. •  Metabolic biochemistry –  1930s; Hans Krebs discovered the citric acid and urea cycles •  Nobel prize winner in 1953 •  What is the longest wait for a Nobel prize?   Peyton Rous, 30-year-old research worker at the Rockefeller Institute   Discovered Rouse Sarcoma virus in 1910   Won Nobel prize in 1966!   56 years later Advances in Biochemistry rapid from 1900s •  1950s - 3D structure of 1st proteins by X-ray crystallography –  Max Perutz → hemoglobin –  John Kendrew → myoglobin –  David Philips and Louise Johnson → lysozyme Advances in Biochemistry rapid from 1900s •  1953 – James Watson & Francis Crick – 3D and chemical structure of DNA. •  –  Who else got the Nobel Prize and who didn’t?   Wilkins and Franklin –  Brenner: 3 bases codes for an amino acid 1950s. –  Khorana: Worked out the genetic code in 1960s Advances in Biochemistry rapid from 1900s •  Methodology* –  Sanger in 1955 & 1975: Protein and DNA sequencing –  Cohen, Berg & Boyer 1973: Gene cloning –  Mike Smith & Kary Mullis 1983: PCR and mutagenesis •  Underpinned Omics technology –  Genome sequencing, transcriptomics, proteomics, etc •  Underpinned Structural Biology –  153 PDB structures (1983) –  70213 PDB structures (2011) *Aided by advances in computing and information management Fred Sanger Current biochemical generalization regarding living things 1. Life requires life 2. Biochemical reactions require catalysts 3. The information of life is transmitted in the genome 4. The Central Dogma of life information flow DNA → RNA → Protein Chemical elements of life Common types of molecules Common functional groups Common molecular linkages Also called [email protected] Bond Know: Figures 1 ­2a, 1 ­2b and 1 ­2c (Horton). N R H O C OC N H R O C C R H NH3+ H Resonance O H C C O- R OC N+ H C R H NH3+ sp3 H Tetrahedral sp2 [email protected] is due to double bonds and two sp2 sp2 R R N H Hybridized Atoms lead to resonance. Know the [email protected] plane. Trigonal Planar Important macromolecular polymers Proteins – made up of 20 amino acids Polysaccharides – made up of monosaccharides Nucleic acids – made up of the nuclotides A,T,C,G, U Lipids – a diverse class of insoluble molecules rich in carbon and hydrogen (little oxygen) - usually associated with membranes. Proteins Proteins are composed of amino acids linked by the [email protected] bond O + O + O + O +H 3N H3N CH CH3 C O - H3N CH CH H3C C O- H3N CH C O- C CH CH O- Alanine Ala A H3C CH3 CH2 CH CH3 Aliphatic O +H N 3 Valine Val V O Leucine Leu L O H2C CH3 CH3 Isoleucine Ile I O C CH O- H2 + N C O- +H 3N C CH CH2 O- +H N 3 C CH CH2 O- Glycine Gly G H Aliphatic/Structural O + Proline Pro P HS Cysteine Cys C H3C H2C S O +H 3N Sulfurcontaining O + Methionine Met M O C CH CH2 O- H3N CH C O- C CH CH2 O- H3N CH C O- + H3N N CH2 HN Histidine His H O H2C C O O- Glutamate Glu E O C O CH2 Acidic Aspartate Asp D Phenylalanine Phe F O +H N 3 Amino acid O + O +H 3N H3N CH C O+H N 3 C CH O- C CH O- C CH CH2 O- B A S I C CH2 H2C CH2 H2C NH3+ CH2 Lysine Lys K O H2C C O NH2 Glutamine Gln Q H2N C O CH2 Asparagine Asn N HO Tyrosine Tyr Y O +H 3N Amide OO + +H 3N C CH CH2 A R O M A T I C Condensation C CH CH2 O- O + H2C CH2 + H3N CH CH2 HO C O- H3N CH CH H3C C O- HN OH HN C H2N NH2 Arginine Arg R Serine Ser S Threonine Thr T Alcohol Tryptophan Trp W 20 amino acids Proteins The protein amino acid chain can fold into [email protected] structures Binding cleL Bound substrate Lysozyme is an enzyme and is part of the innate immune system. It protects [email protected] from Gram ­[email protected] bacteria such as Salmonella, E. coli, and Pseudomonas. Polysaccharides Glucose Ribose Deoxyribose Cellulose Figs 1.06, 1.07 Lipids Figs 1.11, 1.12, 1.13 Nucleic acids ATP Figs 1.08, 1.09 The DNA strand has [email protected] The 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. Energetics & Gibb’s Free Energy Substrates A + B C + D Products Free Energy Rules the World! ΔG = ΔH  ­ TΔS Gibb’s Free Energy is defined in terms of Enthalpy (Heat) and Entropy (Disorder) at a given Temperature (Kelvin). ΔG < 0 then the [email protected] is spontaneous and releases energy ΔG = 0 then the [email protected] is at equilibrium ΔG > 0 then the [email protected] is not favorable, requires energy Says nothing about the [email protected] rate! 1 kcal = 4.184 kJoules = The amount of energy to heat one kilogram of water 1° Celsius. Gibb’s Free Energy & Equilibrium The change in Gibb’s Free Energy ΔG can be calculated at Chemical Equilibrium Keq A + B C + D Keq = [Products] [C][D] = [Reactants] [A][B] Keq > 1, ΔG is [email protected] Keq = 1, ΔG is zero Keq < 1, ΔG is [email protected] ΔG =  ­RT ln Keq Le Chatelier’s Principle A system will strive towards equilibrium.! A + B C + D Keq = Keq [Products] [C][D] = [A][B] [Reactants] EA A+B EA ΔG ΔG A+B C+D C+D The Arrhenius Equation If you know the rates of a [email protected], then you can calculate the Chemical Equilibrium k+1 A + B C + D k ­1 A+B EA ΔG C+D k+1 [Products] Keq = = [Reactants] k ­1 The Arrhenius [email protected] shows rate is inversely [email protected] to [email protected]@on energy. k = Ae − E a / RT € Viruses: Adenovirus, HIV, Ebola, Polio Adenovirus Viruses consist of a nucleic acid molecule (DNA or RNA) surrounded by a protein coat. Viruses require a host cell machinery to replicate. Prokaryote Cells: Escherichia coli Biochemists concentrate on certain “model” organisms for their studies. Fig. 1.14 Prokaryotic cells contain no nucleus or intracellular membranes and are usually unicellular Eukaryote: humans, mice, rats, yeast, arabidopsis, drosophila Eukaryotic cell (animal) Eukaryotic cell (plant) Fig 1.15 (a) Fig 1.15(b) Eukaryotic cells contains membrane-bound organelles: nucleus, ER, Golgi, mitochondria, lysosomes, peroxisomes, chloroplasts The ER & Golgi organelles Endoplasmic Reticulum Site of protein synthesis Golgi Apparatus Site of protein modifi[email protected] P. 19, P. 20 Mitochondria & Chloroplasts Both are sites of energy transduction - Mitochondria main sites of oxidative energy metabolism (ATP production) - Chloroplasts sites of photosynthesis Both derived from bacteria that that entered into a symbiotic relationship with a primitive eukaryotic cell over a billion years ago P. 20, P. 21 The cell is a crowded place 1mm = 1nm Contents of the cytosol of an E. coli cell magnified 1 million times (left) Crowding effects diffusion rates in the cell Key 10mm = 1nm P. 23 ...
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This note was uploaded on 02/07/2011 for the course BCMD 3100 taught by Professor Rose during the Spring '11 term at UGA.

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