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Lecture 2

Textbook Readings - Week 2

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Melody Neumann

BIO 130 – Week 2 THE CHEMICAL COMPONENTS OF A CELL An Atom Often Behaves as if it Has a Fixed Radius • Van der Waals radius is the radius of the electron cloud at which strong repulsive forces prevent a closer approach of any second, non-bonded atom o The amount of repulsion increases very steeply as two such atoms approach each other closely o At slightly greater distances, any two atoms will experience a weak attractive force, known as van der Waals attraction  Therefore, there is a distance at which repulsive and attractive forces precisely balance to produce an energy minimum in each atom’s interactions with an atom of a second, non-bonded element Water is the Most Abundant Substance in Cells • Water accounts for about 70% of a cell’s weight, and most intracellular reactions occur in an aqueous environment • The bonds between H and O in water is a polar bond, with the H side of the molecule being slightly more positive and the O side of the molecule being slightly more negative o When a positively charged hydrogen side of one molecule comes into contact with the negative oxygen side of another molecule, a hydrogen bond is formed  Hydrogen bonds are much weaker than covalent bonds and are easily broken by the random thermal motion • Molecules that contain polar bonds can form hydrogen bonds with water and will dissolve readily, same goes for molecules carrying plus or minus charges o Such molecules are termed hydrophilic, meaning water-loving o Sugars, DNA, RNA, and most proteins are hydrophilic • Molecules that are uncharged and form few or no hydrogen bonds do not dissolve in water o Such molecules are termed hydrophobic, meaning water-hating o Hydrocarbons are an example of hydrophobic molecules  In hydrocarbons, carbon is linked to hydrogen covalently in a largely nonpolar bond Some Polar Molecules Are Acids and Bases • A molecule containing a highly polar covalent bond between a hydrogen and a second atom will dissolve in water BIO 130 – Week 2 o They hydrogen atom in such a molecule has largely given up its electron to the companion atom and so resembles an almost naked positively charged hydrogen nucleus – a proton (H+) o When surrounded by water, the proton will be attracted to the partial negative charge on the O atom of the water molecules o This attraction can cause the proton to dissociate from its original partner to associate instead with the oxygen atoms of the water molecule to generate a hydronium ion (H O )3 + o The reverse of this reaction will also take place, reaching an equilibrium state • This reaction takes place in pure water, therefore pure water contains an equal, very low concentration of H O3and OH ions, both being present at 10-7 M. + • Substances that release protons to form H O w3en they dissolve in water are terms acids o The higher the concentration of H O , the more acidic the solution 3 + o As H 3 rises, the concentration of OH- falls o The H O3concentration is usually referred to as the H+ concentration, and expressed using the logarithmic pH scale o The acidity inside a cell is closely regulated, kept close to neutrality, and is buffered by the presence of many chemical groups that can take and release protons near pH 7 • The opposite of an acid is a base – it accepts protons so as to lower the concentration of + - H 3 ions, thereby raising the concentration of hydroxyl ions (OH) • Molecules that accept protons from water will do so most readily when the concentration of H3O is high, (acidic solutions). Likewise, molecules that donate protons do so more + readily if the concentration of H3O in solution is low, (basic solutions), and they will tend to receive them back if this concentration is high Four Types of Non-covalent Attractions Help Bring Molecules Together in Cells • Much of biology depends on the specific binding of different molecules to each other. This binding is mediated by a group of non-covalent bonds that are individually quite weak, but can sum to create an effective force between two separate molecules. 1. Electrostatic Attractions: a. Result from the attractive forces between oppositely charged atoms b. Quite strong in the absent of water c. Readily form between permanent dipoles, but are greatest when the two atoms involved are fully charged, (ionic bonds) BIO 130 – Week 2 d. Polar water molecules cluster around both fully charged ions and polar molecules that contain permanent dipoles. This reduces the attractiveness of these charged species for each other in most biological settings 2. Hydrogen Bonds: a. Electropositive hydrogen atom is partially shared by two electronegative atoms. Hydrogen can be viewed as a proton that has partially dissociated from a donor atom, allowing it to be shared by a second acceptor atom b. Bond is highly directional – being strongest when a straight line can be drawn between all three involved atoms c. Water weakens these bonds by forming competing hydrogen-bond interactions with the involved molecules 3. Van der Waals Attractions: a. The electron cloud around any nonpolar atom will fluctuate, producing a flickering dipole b. Dipoles will transiently induce an oppositely polarized flickering dipole in a nearby atom c. This interaction generates a very weak attraction between atoms d. The net result of many atoms in contact is often significant e. Water does not weaken these attractions 4. Hydrophobic Force: a. Not technically a bond b. Caused by a pushing of nonpolar surfaces out of the hydrogen- bonded water network c. Central to the proper folding of protein molecules d. Water forces hydrophobic groups together in order to minimize their disruptive effects on the hydrogen-bonded water network A Cell is formed from Carbon Compounds • Nearly all the molecules in a cell are based on carbon • Molecules have different chemical groups, such as methyl (-CH ), h3droxyl (-OH), carboxyl (-COOH), carbonyl (-C=O), phosphate (-PO ), s3lfhydryl (-SH), and amino (- NH 2 o Each chemical group has distinct chemical and physical properties that influence the behaviour of the molecule in which the group occurs BIO 130 – Week 2 Cells Contain Four Major Families of Small Organic Molecules • All organic molecules are synthesized from and are broken down into the same set of simple compounds • The compounds in a cell are chemically related and most can be classified into a few distinct families o (1) sugars o (2) fatty acids o (3) amino acids o (4) nucleotides Sugars Provide an Energy Source for Cells and are the Subunits of Polysaccharides • The simplest sugars – the monosaccharides – are compounds with the general formula (CH 2) n where n is usually, 3, 4, 5, 6, 7, or 8 • Sugars are also called carbohydrates because of the aforementioned formula • Most sugars can exist in either of two forms: the D-form and the L-Form o Each form is a mirror image of the other o Isomers are two structurally different molecules that share the same chemical formula, mirror-image pair are called optical isomers • Sugars can exist as rings or as open chains o In the open chain form, sugars contain a number of hydroxyl groups and either one aldehyde or one ketone group o The aldehyde or ketone group can react with a hydroxyl group in the same molecule to convert the molecule into a ring, (in the ring the original aldehyde or ketone group can be recognized as the only one that is bonded to two oxygens)  Once the ring is formed, the same carbon can become further linked, via oxygen, to one of the carbons bearing a hydroxyl group on another sugar molecule, creating a disaccharide • Large sugar polymers range from oligosaccharides, (tri-, tetra-, etc) up to giant polysaccharides, which can contain thousands of monosaccharide units • Sugars link together by their respective –OH groups to form polymers by condensation reactions o In a condensation reaction, a molecule of water is expelled as the bond is formed o Bonds formed by condensation reactions can be reversed by hydrolysis, in which a molecule of water is consumed BIO 130 – Week 2 • Because each monosaccharide has several free hydroxyl groups that can form a link to another monosaccharide, sugar polymers can be branched, and the number of possible structures is extremely large o For this reason, it is a complex task to determine the arrangement of sugars in a polysaccharide • The monosaccharide glucose is a key energy source for cells o In a series of reactions, it is broken down to smaller molecules, releasing energy that the cell can harness to do useful work • Cells use simple polysaccharides composed only of glucose units – principally glycogen in animals and starch in plants – as energy stores • Sugars do not function only in the production and storage of energy, they also can be used, for example, to make mechanical supports o The most abundant organic chemical on Earth – the cellulose of plant cell walls – is a polysaccharide of glucose  The glucose-glucose linkages in cellulose differ from those in starch and glycogen, and thus humans cannot digest cellulose and use its glucose o The chitin of insect exoskeletons and fungal cell walls, is also an indigestible polysaccharide o Other polysaccharides are the main components of slime, mucus, and gristle • Smaller oligosaccharides can be covalently linked to proteins to form glycoproteins and to lipids to form glycolipids, both of which are found in cell membranes o These molecules get posted on the outside of cells and can be recognized selectively by other cells o Differences between people in the details of their cell-surface sugars are the molecular basis for the different major human blood groups Fatty Acids are Components of Cell Membranes, as well as a Source of Energy • A fatty acid molecule has two chemically distinct regions o (1) a long hydrocarbon chain, which is hydrophobic and not very reactive chemically o (2) a carboxyl (-COOH) group, which behaves as an acid, (carboxylic acid). It is extremely hydrophilic, and chemically reactive • Almost all the fatty acid molecules in a cell are covalently linked to other molecules by their carboxylic acid group • A fatty acid molecule can be saturated, containing no double bonds between carbon atoms and contains the maximum possible number of hydrogen BIO 130 – Week 2 • A fatty acid molecule can also be unsaturated, with one or more double bonds along their length o The double bonds create kinks in the molecules, interfering with their ability to pack together in a solid mass, which accounts for why margarine is hard, (saturated) and why vegetable oils are liquid, (unsaturated) • The many different fatty acids found in cells differ only in the length of their hydrocarbon chains and the number and position of the carbon-carbon double bonds • Fatty acids are stored in the cytoplasm of many cells in the form of droplets of triacylglycerol molecules, which consist of three fatty acid chains joined to a glycerol molecule o When required to provide energy, the fatty acid chains are released from triacylglycerols and broken down into two-carbon units • Fatty acids and their derivatives are examples of lipids: o Lipids comprise a loosely defined collection of biological molecules that are insoluable in water, which being soluble in fat and organic solvents such as benzene o They typically contain either long hydrocarbon chains, as in the fatty acids and isoprenes, or multiple linked rings, as in the steroids • The most important function of fatty acids in cells is in the construction of cell membranes o Cell membranes enclose all cells and surround their internal organelles o Composed largely of phospholipids, which are small molecules that are constructed mainly from two fatty acids chains and a glycerol. The “third” site on the glycerol is linked to a hydrophilic phosphate group, which is in turn attached to a small hydrophilic compound such as choline  This composition leads to phospholipids having a hydrophobic tail, (the fatty acid chains) and a hydrophilic head, (the phosphate group), whereas triacylglycerols are dominantly hydrophobic  Molecules such as phospholipids, with both hydrophobic and hydrophilic regions, are termed amphiphillic o The membrane-forming property of phospholipids results from their amphiphilic nature  Phospholipids will spread over the surface of water to form a monolayer of phospholipid molecules, with the hydrophobic tails facing the air and the hydrophilic heads in contact with the water  Two such molecular layers can readily combine tail-to-tail in water to make a phospholipid sandwich, or lipid bilayer BIO 130 – Week 2 • This bilayer is the structural basis of all cell membranes Amino Acids are the Subunits of Proteins • Amino acids are a varied class of molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to a single carbon atom called the α-carbon • Proteins are polymers of amino acids joined head-to-tail in a long chain that is then folded into a three-dimensional structure unique to each type of protein • The covalent linkage between two adjacent amino acids in a protein chain forms an amide, and it is called peptide bond; the chain of amino acids is also known as a polypeptide • A polypeptide has an amino, (NH ) 2roup at one end, (its N-terminus) and a carboxyl (COOH) group at its other end (its C-terminus) o This gives it a definite directionality – a structural polarity • All organisms have proteins made of the same 20 amino acids • Like sugars, all amino acids, except glycine, exist as optical isomers in D- and L-forms, but only L-forms are ever found in proteins • Five of the twenty amino acids have side chains that can form ions in neutral aqueous solution and thereby can carry a charge. The others are uncharged; some are polar and hydrophilic, and some are nonpolar and hydrophobic o These properties underlie the diverse and sophisticated functions of proteins Nucleotides are the Subunits of DNA and RNA • A nucleotide is a molecule made up of a nitrogen-containing ring compound linked to a five-carbon sugar, which in turn carries one or more phosphate groups o Five carbon sugar can be either ribose or deoxyribose o Nucleotides containing ribose are known as ribonucleotides, and those containing deoxyribose as deoxyribonucleotides o The nitrogen-containing rings are generally referred to as +ases for historical reasons: under acidic conditions they can each bind an H , thereby increasing OH ions in aqueous solutions • There is a strong family resemblance between the different bases: o Cytosine (C), thymine (T), and uracil (U) are called pyrimidines because they all derive from a six-membered pyrimidine ring o Guanine (G) and adenine (A) are purine compounds, and they have a second, five-membered ring fused to the six-membered ring BIO 130 – Week 2 o Each nucleotide is named for the base it contains • Nucleotides can act as short-term carriers of chemical energy: o The ribonucleotide adenosine triphosphate, or ATP, transfers energy in hundreds of different cell reactions o ATPs three phosphates are linked in series by two phosphoanhydride bonds, whose rupture releases large amounts of useful energy • The most fundamental role of nucleotides is in the storage and retrieval of biological information: o Nucleotides serve as building blocks for the construction of nucleic acids – long polymers in which nucleotide subunits are covalently linked by the formation of a phosphodiester bond between the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide o Nucleic acid chains are synthesized from energy-rich nucleoside triphosphates by a condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation • There are two main types of nucleic acids, differing in the type of sugar in their sugar- phosphate backbone o Those based on the sugar ribose are known as ribonucleic acids, or RNA, and normally contain the bases A, G, C, and U  RNA usually occurs in cells as a single polynucleotide chain o Those based on deoxyribose (in which the hydroxyl at the 2’ position of the ribose carbon ring is replaced by a hydrogen) are known as deoxyribonucleic acids, or DNA¸ and contain the bases A, G, C, and T  DNA is virtually always a double-stranded molecule – a DNA double helix composed of two polynucleotide chains running antiparallel to each other and held together by hydrogen-bonding between the bases of the two chains The Chemistry of Cells Is Dominated by Macromolecules with Remarkable Properties • The macromolecules in cells are polymers that are constructed by covalently linking small organic molecules (called monomers) into long chains. o They have properties that could not have been predicted from their simple constituents • Proteins perform thousands of distinct functions inside cells. o Proteins functions include: serving as enzymes, building structural components of the cell, serving as histones that compact the DNA in chromosomes, acting as molecular motors the produce force and movement BIO 130 – Week 2 • Although the chemical reactions for adding subunits to each polymer are different in detail for proteins, nucleic acids, and polysaccharides, they share important features: o Each polymer grows by the addition of a monomer onto the end of a growing polymer chain in a condensation reaction, in which a molecule of water is lost with each subunit added o Apart from some of the polysaccharides, most macromolecules are made from a set of monomers that are slightly different from one another o The subunits are added to a polymer in a particular order or sequence Noncovalent Bonds Specify Both the Precise Shape of a Macromolecule and its Binding to Other Molecules • Most of the covalent bonds in a macromolecule allow rotation of the atoms they join, giving the polymer chain great flexibility o This allows a macromolecule theoretically to adopt an almost unlimited number of shapes, of conformations, as random thermal energy causes the polymer chain to writhe and rotate o The shapes of most biological macromolecules in reality are highly constrained because of the many weak noncovalent bonds that form between different parts of the same molecule  If these noncovalent bonds are formed in sufficient numbers, the polymer chain can strongly prefer one particular conformation, determined by the linear sequence of monomers in its chain  Most proteins and many small RNA molecules found in cells fold tightly into one highly preferred conformation in this way • Although individually these noncovalent interactions are quite weak, they cooperate to fold biological macromolecules into unique shapes o They can also add up to create a strong attraction between two different molecules when these molecules fit together very closely PROTEINS: The Shape of a Protein is specified by its Amino Acid Sequence • A protein molecule is made from a long chain of amino acids, each linked to its neighbour through a covalent peptide bond o Proteins are thus also known as polypeptides BIO 130 – Week 2 • The repeating sequence of atoms along the core of the polypeptide chain is referred to as the polypeptide backbone o Attached to this repetitive chain are those portions of the amino acids that are not involved in making a peptide bond and that give each amino acid its unique properties: the 20 different amino acids side chains o Some of these side chains are nonpolar and hydrophobic, others are negatively or positively charged, some readily form covalent bonds, and so on • In addition to the three weak noncovalent interactions, (hydrogen bonds, electrostatic attractions, and van der Waals attractions), that cause the various conformations of proteins, there is a fourth weak force: o Nonpolar side chains of particular amin
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