Week 3 Notes: Finished CH2
Week 3 Notes: Finished CH2 BIO 355-02
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This 11 page Class Notes was uploaded by Santa's Little Helper on Saturday September 5, 2015. The Class Notes belongs to BIO 355-02 at DCH Regional Medical Center taught by Paul A. Steimle in Summer 2015. Since its upload, it has received 172 views. For similar materials see Cell Biology in Biology at DCH Regional Medical Center.
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Chapter 2 Notes Chemical Components of Cells Chemistry of living systems based on carbon compounds depends on chem Rxns that happen in aqueous environments in a small range of temperatures Highly complex Involves large polymeric molecule collections Tightly regulated Chemical Bonds Not many atoms make up a cell Atom smallest particle of an element with its own distinctive chemical properties 0 Approximately 02 u 0 At the center of an atom is a dense positively charged nucleus that is surrounded by a negative cloud that is held in tact by the electrostatic attraction of the positively charged nucleus I This negative cloud is made of electrons 0 Electrons negatively charged subatomic particle found around the nucleus e O 0 Outer electrons determine how an atom interacts Undergo rearrangement and specify how a atoms combine to form molecules Always moving around the nucleus in things called orbitals An orbital can only hold so many electrons so certain quottypesquot of electrons are housed in specified electron shells I Electrons held more closely to the positive nucleus are held in the inner most tightly bound electron shell I The further from the nucleus the shell is the weaker the bond I INNER FIRST SHELL HOLDS ONLY 2 ELECTRONS I SECOND SHELL HOLDS UP TO 8 ELECTRONS I THIRD SHELL HOLDS UP TO EIGHT ELECTRONS I FOURTH FIFTH SHELLS HOLD UP TO 18 ELECTRONS When the electrons are tightly bound near to the nucleus the atom is more stable thus when distributing electrons throughout the shells we fill the first ones first If the outermost shell of an atom is completely filled ie the second shell has exactly 8 electrons no more and no less is both stable and chemically unreactive o If a shell is only partially filled it is reactive and unstable because it is looking to take share give electrons to another atom by forming chemical bonds 0 Chemical properties of an element are determined by the outer electron shell 0 The periodic table is arranged in accordance with the fullness or lack thereof of the outermost electron shell I There are two types of particles found in the nucleus and one keeps the electrons from leaving protons and neutrons 0 Proton positively charged particle in the nucleus of EVERY atom also called a hydrogen ion Hthese keep the electrons around 0 Atomic number is the number of protons present in an atom but is also the number of electrons because in a neutral atom these number the same 0 Neutron an electrically neutral particle in the nucleus of EVERY atom 0 Same mass as proton 0 Without the stability provided by the neutral balance of neutrons in the nucleus the nucleus would disintegrate by radioactive decay o SAME NUMBER OF ELECTRONS AND PROTONS NEUTRALLY CHARGED ATOM 0 Mass number number of protons and neutrons in an atom Element substance that cannot be broken down into another chemical form and is made of a single atom o Isotope a variation of an element that has the same number of protons but has a different atomic weight due to differing numbers of neutrons ie 12C 14Cisotopes of carbon I Most occur naturally but some are unstable ie radioactive o 4 Elements that make up 96 of biological matter C H O N o The last 4 of biological matter is made from Ca P K S Na Cl Mg trace elements 0 Atomic weight molecular weight mass an atoms mass relative to a hydrogen atom or the number of protons plus the number of neutrons in the atom molecule I Example Carbon has 6 protons and 6 neutrons thus the atomic weight is 12 0 This can be understood to mean that 12 grams contains 6 x 1023 atoms Avogadro s number 6 x 1023 allows us to relate normal daily quantities of chemicals to individual atom molecule numbers o If a substance has a molecular weight of M then M grams of the substance will have 6 x 1023 molecules M Mole the amount of a substance in units of grams that equals a substance molecular weight Will contain Avogadro s Number 0 1M sln has concentration of 1M of a substance in 1L sin I EX 1M sln glucose 180gL and 1mM sln 180 mgL Chemical Bonds Chemical bonds exchange of electrons that holds two atoms together There are two bond types Covalent and ionic I Covalent bond a link between two atoms because they M one or more pairs of electrons 0 Characterized by geometries 0 Electron density holds atoms together by offsetting the positive charge of the nucleus with a dense negative shared region of electrons that counteracts the repulsion of the nuclei 0 Covalent bonds vary in strength 0 Single bond Covalent bond where only 2 electrons are shared one shared by each participating atom 0 Double bond when four electrons are shared between two atoms two coming from each participating atom I Double bonds are shorter thus they are stronger than single bonds by preventing rotation making the geometry more rigid and less flexible I Polar Covalent Bonds When electrons are shared unequally between two atoms of different elements 0 The bond between oxygen and hydrogen in water H20 is polar because the oxygen has a higher electronegativity 0 Electronegativity the force with which the atomic nucleus attracts electrons o Depends on the number of positive charges and distance between nucleus and electrons o Atoms with strong electronegativity pull shared electrons to them causing covalent bonds to become polar electrons spend more time with the more electronegative atom o Nonpolar bonds covalent bond between two similarly electronegative atoms I The bond between carbon and hydrogen in methane is nonpolar because carbon and hydrogen essentially have the same electronegativity 0 Polar structure has a positive charge concentrated toward one end of the molecule and the negative charge is on the other end creating positive and negative quotpolesquot 0 Some can form acids and bases in water I A molecule is a cluster of atoms held together by a covalent bond 0 Ionic bond interaction where one atom donates electrons to another atom causing both atoms to become electrically charged Most common elements in living cells C N O with incomplete second shells P and S have incomplete 3rel shells typically share electrons to fill their outer shell with Be The number of electrons an atom gives or takes via sharing or transferring to fill its outer shell and stabilize is equal to the number of bonds the atom can make Noncovalent bond bonding that does not involve sharing electrons are weak alone but put together noncovalent bonds are strong and have highly specific interaction between molecules O 0 Help bring molecules together in cells Hydrogen bonds form when a hydrogen atoms is covalently bonded to strongly electronegative atom and is drawn to another electronegative atom I Any polar molecule can interact with other polar molecules via hydrogen bonds I a weak noncovalent interaction bw positively charged H and negatively charged atom ie N 0 KEY TO STRUCTURE OF WATER WATER UNIVERSAL SOLVENT it will dissolve just about anything given enough time 0 O O O 0 Water expands upon freezing Water has unique properties due to its tendency to form hydrogen bonds with itself charged polar covalent molecules Can dissolve large molecules and proteins if they have either polar or ionic regions pH of water is essentially a neutral 7 with a small tendency to ionize Pure water has equal numbers of hydrogen ions and hydroxide ions I Solution liquid that is homogeneous mixture of 2 substances I Solvent liquid where substance dissolve to form a solution I Solute substance that dissolves in liquid Hydrophilic WATER LOVING O O 0 Polar molecules are typically soluble in water Dissolve readily in water Have ions and polar molecules that attract the water molecules via electrical charge effects Water molecules surround ion polar molecule and usher it into the solution Ionic substances dissolve in water because the water molecules are attracted to the charges on the ion Polar substances dissolve because their molecules form hydrogen bonds with the surrounding water molecules Hydrophobic WATER HATNG O O Nonpolar molecules are usually insoluble in water Water molecules really want nothing to do with hydrophobic molecules so water molecules will not surround a hydrophobic molecule pH concentration of hydrogen ions in a solution 0 00000 Each pH unit represents 10x change in hydrogen ion concentration Scale ranges from 014 pH 70 neutral pH lt 70 is acidic pH gt 70 is basic To maintain constant cellular pH values biological fluids have buffers Name Base of Interaction Nonpolar Covalent Bond Equal sharing of electrons Ionic Bond Attraction of opposite charges Hydrogen Bond Sharing of H atom Hydrophobic interaction Interaction of nonpolar substances with a polar substance present water Van Der Waals Interaction Interaction of electrons of nonpolar substance Polar Covalent bonds Electrons shared unequally Acids and Bases Changes in hydrogen hydroxide ion concentrations can drastically affect proteins and other cellular molecules By adding acids and bases to solutes can disrupt the equilibrium the alter the concentration of hydrogen hydroxide ions Acid solution solution containing more hydrogen ions than pure water is more positively charged 9 electron acceptor Basic solution solution containing fewer hydrogen ions than pure water is more negatively charged 9 electron donor Chemical Composition of Cells Cells have 4 major families of small organic molecules 1 Sugars polysaccharides glycogen plant starch 2 Fatty Acids fats and membrane lipids 3 Amino Acids proteins 4 Nucleotides nucleic acids Simplest sugars monosaccharides I Monosaccharide formula CH20n n345 or 6 Large molecules made from sugars carbohydrates 2 monosaccharides together disaccharide ie glucose fructose sucrose I Glucose plays a central role in the energy production in a cell by breaking down into smaller molecules Condensation reactions when an OH group from one sugar forms a bond with another OH group on another sugar Products of condensation reactions can be revered by hydrolysis through the consumption of a water molecule Sugars DO NOT function exclusively Used to make cellulose forms plant cell walls most organic molecule on Earth are a polysaccharide of glucose Cellulose glucose polymer makes up plant cell walls I Has a 3D shape cellulose easily makes hydrogen bonds to hold cellulose polymers parallel and together o Chitin organic substance that makes up insect exoskeleton fungal cells walls are made from polysaccharide linear polymer of sugar derivative called Nacetylglucosamine o Glycogen storage polysaccharide in animal cells Glycogen Starch Cellulose Branched chain Linear w no bends Monomers linked with 0L bonds Monomers linked with B ct hl 3 Llhll S The I lin mxyl group on th carbon that E r Et the aldehyde tut hatme can rapidly thatage from one pg lan39tn the other These tum Ful llcine are calla 1 and Hi Evhy ruxj39l hydlrnzjrl 0 Sugar derivatives hydroxyl groups of simple monosaccharides glucose that can be replaced by other functional groups ie amines carboxylic acids 0 Carbohydrates organic molecules made of sugars with polymers that play roles in energy storage structure formation and cellular recognition I Saccharides sugars Low molecular weight Water soluble Sweet Divided into monosaccharides and disaccharides Monosaccharides simple sugars that can be individually active or work as a monomer link in a disaccharide or polysaccharide Disaccharides double sugars o The carbon that carries aldehyde ketone can react with any hydroxyl group 0 Common disaccharides are 1 Maltose glucose glucose 2 Lactose galactose glucose 3 Sucrose glucose fructose I Polysaccharides complex sugars Fatty Acids High molecular weight Water insoluble Tasteless Made of multiple sugars Large linear amp branched molecules made from repeating simple sugar unites with short chains oligosaccharides and long chains polysaccharides Typically have two chemically distinct regions 1 Long hydrocarbon chain hydrophobic and not very reactive 2 Carboxyl group COOH very hydrophilic and reactive Typically covalently linked to other molecules via carboxylic acid group Amphipathic Possess both hydrophilic and hydrophobic regions Stearic acid a fatty acid has a saturated hydrocarbon tail with no double bonds bw the carbon atoms and has the max possible hydrogens Oleic acid a fatty acid has unsaturated hydrocarbon tail with 1 double bonds creating kinks in the hydrocarbon tail that disrupt its ability to pack together I Presence absence of double bonds is what makes butter hard saturated or soft unsaturated llTh is double llmndl is rigid ind Hittite quotfa kinkinthuhaim L mam If Whereatefthe thaln 739 acid t iifheet mtate t quot about thea her EIE I handi F spateu illing model carbrtmilzelemm 1 a UHWE TUH TED 393 EAIUHE39FED Found in cell membranes Function as concentrated food reserves in cells Stored in cytoplasm of most cells in droplets made of triacylglycerol molecules compounds made from 3 fatty acid chains covalently joined to glycerol Triacylglycerol is a fatty acid derivative that is an example of a lipid I Lipids water insoluble molecules but are soluble in fat and organic solvents benzene 0 Important lipid groups fats phospholipids steroids and waxes Glycerol has three hydroxyl groups that can bond to fatty acids to make triglyceride glycerol 1 HFEWI aaturated unsaturted fatty acid tails fatty acidtails 0 Forms a lipid bilayer basis for cell membranes which is made largely from phospholipids I Phospholipids a molecule with a hydrophilic head and a hydrophobic tail causing it to eagerly form chains membranes because the hydrophilic heads want to be near the water and are drawn together toward the water while the hydrophobic tails do not want to be near the water so they happily come together and hide behind the hydrophilic heads 0 Steroids lipids with four fused carbon rings that have various functional groups attached Amino Acids small organic molecules that ALL possess a carboxylic acid group and an amino group and are both linked to their a carbon o 20 amino acid types 0 Side chains on amino acids are what distinguish one amino acid from another 0 Building blocks of proteins 0 Headtotail joined amino acid monomer joined to form long chains folded into unique 3D polymer structures of each protein I STRUCTURE SHAPE CONFOMATION 9 FUNCTION I Hierarchy of Protein Structure iaetevtomiaeeoaernwe 39t J quoti i P m l y ElmElma Secondary structure IQuaternaryr structure Tertiary structure h Primary structure proteins amino acid sequence AMINO ACID SEQUENCE Secondary structure has 0L helices and 3 sheets that occur at given segments on along the polypeptide chain IT FOLDS Tertiary structure 3D conformation occurs when entire polypeptide chain coils with loops and folds COILS AROUND ITSELF Quaternary structure if protein molecule is formed as a complex 1 polypeptide chain BIG BUNCH OF POLYPEPTIDE CHAIN Peptide bond covalent bond bw adjacent amino acids in protein chain I Formed by condensation rxns I ALWAYS has NH2 group at one end and a COOH carboxyl group on the other end 0 Polypeptide chain of amino acids Nucleotides o Subunits of DNA and RNA 0 NUCLEIC ACID long polymer chain where nucleotide subunits are linked via covalent phosphodiester bonds bw phosphate group attached to nucleotide and hydroxyl group sugars next to the nucleotide I Made from energyrich nucleoside triphosphate via condensation rxns I Two main types are RNA and DNA 1 RNA Ribonucleic acid ribose sugar based nucleic acid with bases A Adenine C Cytosine G Guanine and U Uracil I Occurs in singlestranded polynucleotide chain 2 DNA Deoxyribonucleic acid based on deoxyribose and have bases C Cytosine G Guanine A Adenine and T Thymine I Occurs in doublestranded molecule called a Double Helix Cytsine I lull2 3 Maine 39I39 E J ltlcleotIHSEE H112 Liracil 39 39 Nuclei bungee H ucleo page Izat Dhl t F MA in quotA DNA Ribonucleic acid Deoxyribonucleic acid 0 Nucleotides are nucleosides that have 1 phosphate group attached to the sugar and come in two main forms 1 Ribonucleotides ribose containing 2 Deoxyribonucleotides deoxyribose containing I Nucleosides structure made of nitrogencontaining ring compounds linked to 5 carbon sugar and can either be ribose or deoxyribose Most macromolecules are polymers n uclem ide nuclei acid mih ill 39 ml i I