Principles of Biochemistry Week 2
Principles of Biochemistry Week 2 CHE 420
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This 10 page Class Notes was uploaded by Bethany Shay Edgeworth on Thursday August 27, 2015. The Class Notes belongs to CHE 420 at University of Southern Mississippi taught by Vijay Rangachari in Summer 2015. Since its upload, it has received 60 views. For similar materials see Principles of Biochemistry in Chemistry at University of Southern Mississippi.
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Date Created: 08/27/15
Principles of Biochemistry Dr Rangachari Week 2 August 25 2015August 28 2015 12 BIOMOLECULES DNA Blueprint of cell Deoxyribonucleic acid Encodes genetic information of an organism Structure 2 antiparallel polynucleotide strands forming a righthanded double helix 4 basic DNA nucleotides 1 Adenine 2 Guanine 3 Thymine 4 Cytosine DNA strands are held together by hydrogen bonds amp hydrophobic interactions Genome organism s entire set of DNA sequences Human genome proiect find entire length of gene encoding of gene if there are any mutations find risk factors etc RNA Singlestranded polynucleotide with ribose sugar instead of deoxyribose Synthesized via transcription 4 bases 1 Adenine 2 Cytosine 3 Guanine 4 Uracil 3 main types of RNA 1 Messenger RNA mRNA 2 Ribosomal RNA rRNA 3 Transfer RNA tRNA Noncoding small RNAs 1 siRNA 2 miRNA 3 snRNA 4 snoRNA Gene Expression Controls when the information encoded in a gene will be accessed Transcription factors class of proteins that regulates expression of proteinencoding genes 13 IS THE LIVING CELL A CHEMICAL FACTORY O P O P O CHZ Adenosine diphosphate The properties of even the simplest cells are REMARKABLE Autopoiesis remarkable properties of living organisms Metabolism acquisition amp utilization of energy synthesis of molecules needed for cell structure amp function growth amp development removal of waste products Metabolic reaction may require large amounts of energy comes mainly from biochemical reactions Biochemical Reactions NucleOphilic substitution reaction atom with an unshared pair of electrons displaces a leaving group A B X 9 A B X A is the nucleophile amp X is the leaving group Hvdrolvsis reaction addition of water Nucleophile donates pair of electrons Electrophile accepts pair of electrons electron deficient N9E H H NH2 0 N N k H i if if H N N quotO P O P O O CH2 Adenosine triphosphate l NH2 N N A l gtH H N N OH OH O O P O39 H Energy 9 o l 0 Inorganic phosphate OH OH water is added which is a nucleophile because of lone pair of electrons bond is broken in adenosine triphosphate OH is attached to phosphate group phosphate is hydrolyzed by water Elimination reaction forms a double bond when atoms in a molecule are removed water is removed Addition reaction 2 molecules combine to form a single product water is added lsomerization reaction results in atoms or groups undergoing intramolecular shifts same molecular formula just different positions of H atom Oxidationreduction reaction electron transfer results in this 1 Reducing agent electron donor 2 Oxidizing agent electron acceptor 3 Oxidation loss of electrons when reducing agents donate electrons they become oxidized oxygen is added hydrogen is removed 4 Reduction gain of electrons when oxidizing agents accept electrons they become reduced oxygen is removed hydrogen is added Energy Capacity to do work Cells generate most of their energy with redox reactions Energy captured when electrons are transferred from an oxidizable molecule to an electron deficient molecule is used to drive ATP synthesis Acquiring energy from the environment happens in 2 ways 1 Autotrophs using energy from light or inorganic chemical reactions 2 Heterotrophs obtains carbon from organic compounds can t synthesize own food Overview of Metabolism Metabolic pathways come in 2 types 1 Anabolic large complex molecules polymer amino acids synthesized from smaller precursors amino acids needs energy ATP consumed from catabolic process small to large 2 Catabolic large complex molecules degraded into smaller simpler products oxidative leads to carbon dioxide releases ATP large to small Energy transfer pathways capture energy amp transform it into a usable form energy is never lost Signal transduction pathwaJ allow cells to receive amp respond to signals without penetrating cells Biological order Coherent unity that is observed in all organisms 1 Biomolecule synthesis 2 Transport across membranes 3 Cell movement 4 Waste removal LIVING CELLS OVERVIEW Section 21 Basic Themes Section 22 Structure of Prokaryotic Cells Section 23 Structure of Eukaryotic Cells more advanced 21 BASIC THEMES 0 Understanding of the biological context of biochemical processes is enhanced by examining 6 key concepts 1 2 VVater Unique polar structure unequal charge distribution Interacts with wide range of substances amp dissolves Biological membranes Gives shape amp identity Protects from degradation Phospholipid bilayer quotocean of grease embedded nonembedded proteins contains hydrophilicpolar heads and in the middle is the hydrophobicnonpolar tails contains integral amp peripheral membrane proteins Permeability barrier entryexit control selective Processing of information from environment Energy ATP generation Thin flexible amp stable sheetlike structures Selfassembly Many biomolecules spontaneously undergo selfassembly into supermolecular structures Proteinsynthesis takes place in ribosome Molecular machines Contains cargo motor proteins and microfilament Motor proteins walk along microfilament Microfilament is formed by actin Macromolecular crowding Interior space within cells is dense amp crowded Excluded volume may be between 20 amp 40 Signal transduction 1 Signal goes through receptor 2 Signal is transduced amp multiplied until reaches target 3 Response is formed THE LIVING WORLD 1 Archaea Bacteria Singlecelled organisms amoeba DNA in nuclear region nucleoid PROKARYOTES 2 E ukaryotes Singlecelled or multicellular Welldefined nucleus with nuclear envelope Organelles surrounded by membranes mitochondria all eukaryotes chloroplasts plants only BACTERIA DNA wrapped m O C 3 Q I C protein Ribosomes gt Inner A v membrane Peptidoglycan Outer membrane Flagellum o Flagella directed amp random movement used for locomotion o Nucleoid region circular DNA few million nucleotide pairs contains genetic material 0 C oplasm organized contains organelles amp proteins r o Pili for attachment amp sex 22 STRUCTURE OF PROKARYOTIC CELLS Includes bacteria amp Archaea 2 types of bacteria 1 Gram positive takes initial stain purple thick layer of peptidoglycan 2 Gram negative doesn t take initial stain pink Common features 1 Cell wall Complex semirigid structure primarily for support amp protection Primarily composed of peptidoglycan absent in animal cells 2 Plasma membrane Directly inside cell wall Selectively permeable membrane that may be involved in photosynthesis or respiration Have pili for attachmentsex amp flagella for locomotion Cytoplasm contains a Nucleoid centrally located amp contains circular chromosome b Small DNA plasmids c Inclusion bodies large granules that contain organic or inorganic compounds 3 Circular DNA 4 No membranebound organelles 23 STRUCTURE OF EUKARYOTIC CELLS Plasma membrane Isolates cell and is selectively permeable Outside plasma membrane contains the glycocalyx amp extracellular matrix Ribosomes All cells have ribosomes gt50 ribosomal proteins function in protein synthesis Contains large subunit amp small subunit Endoplasmic Reticulum Series of membranous tubules vesicles amp flattened sacs ER lumen internal space Rough ER studded with ribosomes protein synthesis protein glycosylation nearest nucleus Smooth ER different functions lipid synthesis Ca2 storage Golgi Apparatus Flattened membrane stacks that function in 1 Protein glvcosvlation process by which carbohydrates are added to a protein 2 Intracellular proteinlipid distribution 3 Proteinlipid export Like post officefunctions in packaging Cisternal maturation model vesicles recycled back to cis golgi from trans golgi Secretory products concentrated at the trans golgi into secretory vesicles Involved in exocytosis transports outside not towards the nucleus o Nucleus Surrounded by 2 biological membranes NUCLEAR ENVELOPE continuous with RER Contains bulk of cellular DNA Transcription of DNA into RNA RNA export to cytoplasm Nucleolus assembly of ribosomes 90 of DNA found in nucleus 0 Vesicular Organelles Surrounded by 1 biological membrane No DNA Examples 1 Lysosomes degradative enzymes low pH recycling degradation quotgarbage cans contain digestive enzymes enzymes are acid hydrolases involved in autophagy removes junk degrade debris in cells 2 Peroxisomes oxidative enzymes degradation synthesis peroxides toxic to cell 3 Vacuoles degradative enzymes recycling degradation quotgarbage cans quotstorage bags cell turgor found in plants Vesicles found in eukaryotic cells Endocytosis vesicles originate in the ER golgi andor via endocytosis Phagoc osis process of engulfing and ingesting particles by the cell or phagocyte a process in which cell takes in materials from the outside by engulfing and fusing them with its plasma membrane Receptormed ted endocvtosis a process by which cells absorb metabolites hormones other proteins specific molecules Endocytic cycle used for recycling and remodeling of membranes 0 Mitochondria Factory of power Enclosed by 2 biological membranes Contain their own mtDNA Functions in 1 Aerobic metabolism 02 consumption 2 ATP generation 02 dependent Outer membrane permeable to molecules lt10000 Da Inner membrane permeability barrier invaginated cristae 02 reduction amp ATP synthesis Matrix soluble proteins small molecules amp ions ribosomes DNA and RNAs oxidative degradation of nutrients Why folds More surface area means more ATP production In internal organelles 1 Efficiency high concentration of enzymes reactants 2 Control traffic across membranes controlled 0 Plastids Organelles found only in plants algae and some protists 2 types 1 Chromoplasts specialized for photosynthesis produce amp store pigments 2 Leucoplasts nonpigmented store starch lipids or protein 0 Cytoskeleton Intricate supportive network of fibers filaments and associated proteins Main functions include 1 Cell shape amp structure 2 Large and smallscale movement 3 Solidstate biochemistry 4 Signal transduction 3 main components 1 Microtubules transport amp structural support 25 nm in diameter amp 200 nm 25 micrometers long 2 Microfilaments also known as actin filaments thinnest filaments of cytoskeleton 3 Intermediate filaments larger than microfilaments but smaller than microtubules Cilia amp Flagella whiplike appendages encased in plasma membrane highly specialized for their roles in propulsion bending occurs via ATPdriven structural changes in dynein molecules What do Biochemists do Break cells apart Fractionate cells organelles other subcellular structures etc Purify structures molecules of interest Chemical physical tests what who how how well with whom Try to put everything back together again C oplasm aqueous cell contents amp suspended particles amp organelles Supernatant cytosol concentrated solution of enzymes RNA monomeric subunits metabolites amp inorganic ions M particles amp organelles ribosomes storage granules mitochondria chloroplasts lysosomes endoplasmic reticulum Cell fractionation cell breakage differential centrifugations pellet amp supernatant density gradient centrifugation 31 MOLECULAR STRUCTURE OF WATER Learning objectives Why is water important for biological processes Understanding physiochemical properties of water which include 1 Chemical stability 2 Solvent properties 3 Hydration 4 Ionization 5 Buffers Overview Section 31 Molecular Structure of Water Section 32 Noncovalent Bonding Section 33 Thermal Properties of Water Section 34 Solvent Properties of Water Section 35 Ionization of Water Water is essential for life Important properties of water include 1 Chemical stability 2 Remarkable solvent properties 3 Role as a biochemical reactant 4 Hydration We are composed of 70 water Potable water is a precious commodity o Covalent bonds shared pair of electrons Nonpolar no strong charge separation Why is C02 a nonpolar molecule Some molecules have polar bonds but because of their geometry are nonpolar molecules they have a zero dipole moment Polar unequal charge distribution dipole moment occurs extremely polar ionic bonds Water is a polar molecule 1 Has tetrahedral geometry 2 Oxygen is more EN than hydrogen 3 Larger oxygen atom has partial negative charge amp hydrogen atoms have partial positive charges 4 Structure of water different in liquid amp solid states Molecu r dipoles orient themselves in an electric field interact with other molecular dipoles electrostatic attraction of unlike charges lonic bonds extreme electrostatic interaction 0 Electronegativitv measure of an atom s attraction for the electrons it shares covalent bond with another atom oxygen nitrogen amp fluorine are EN atoms F most EN 0 Ionic Interactions Oppositer charged ions attract one another Ionized amino acid side chains can form salt bridges acid and base forms salt with one another Biochemistry primarily investigates the interactions of charged groups on molecules which differs from ionic interactions like those of ionic compounds NaCl 0 Hydrogen Bonds Electrostatic attraction between dipoles Noncovalent order of magnitude weaker than covalent Positive end of one dipole hydrogen atom bonded to O N high EN Mative end of other dipole atom with a lone electron pair 0 N 3 things are needed for hydrogen bonding to occur 1 Hydrogen atoms 2 EN atoms bonded O N F 3 180 degree angle H bonding is strongest when 180 degree angle Remember Boiling point when vapor pressure amp atmosphere pressure are equal
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