Essential Cell Biology 3rd ed: Ch2 Chemical Components of the Cell

• INTRO

• One of the hardest things to wrap your head around in biology is the fact that all living creatures are just chemical systems.

• Until the 19th century it was mostly believed that animals contained a vital force, "animus", that was responsible for the behavior of living organisms. But this doesn’t mean that the chemistry of life is not a special one

• Organic chemistry

• Almost all chemical reactions take place in aqueous solutions.

• The chemistry involved is extremely complicated

• It is coordinated by polymeric molecules, whose properties enable cells and organisms to grow and reproduce and do all of the other things that they do.

• CHEMICAL BONDS

• Matter is made up of elements

• The smallest particle of an element that still retains its distinctive chemical properties is an atom. These are then grouped together to form molecules

• Cells are made of relatively few types of atoms

• Hydrogen - has an atomic number of 1 and is the lightest element.

• Carbon - atomic number of 6, can be the stable Carbon-12 (the most common) Carbon-13, and Carbon-14 also play a role in chemistry.

• The outer most electrons determine how atoms interact.

• Electrons are in constant motion and move in orbitals call electron shell. But the outermost electrons are the ones that interact with other atoms electrons to form molecules and compounds.

• The state of the outer electron shell determines the chemical properties of an element.

• Ionic bonds are formed by the gain or loss of electrons, and are a type of electrostatic attraction. While covalent bonds are formed when atoms share electrons (molecules are always covalent).  

• Electrostatic attractions help bring molecules together in cells

• In aqueous solutions, covalent bonds are between 10 and 100 times stronger than the other attractive forces between atoms, allowing their connections to define the boundaries of one molecule from another.

• Polar covalent bonds are extremely important in biology because they allow molecules to interact though electrical forces, using positively and negatively charged regions to interact with specific portions of other molecules.

• Water is held together by hydrogen bonds.

• 70% of a cell's weight is water, and most intercellular reactions occur in an aqueous environment.

 

 

• Hydrogen bonds are much weaker than covalent bonds and are broken relatively easily by random thermal motions, so each bond only lasts a short time.

• These bonds can form when a positively charged hydrogen is held in one molecule by a polar covalent bond and then comes into close proximity to a negatively charged atom- usually oxygen or nitrogen, but there are others.

• Like dissolves like is the rule of thumb. Polar will mix with polar and non polar will mix with non polar.

• Hydrophilic- water loving

• Hydrophobic- water fearing, these are uncharged and will form few if any hydrogen bonds, and will not dissolve in water.

• Hydrocarbons fall into this category

• Some polar molecules form acids and bases in water.

• Hydronium ion (H3O+) is made when a highly polar covalent bond between a hydrogen and another atom dissolves in water, then hydrogen is given up and is made into a hydronium ion when it is surrounded by water. So this will be common in the cell.

• Many of the acids that are important in the cell are weak acids.

• Many bases of biological importance are weak bases containing an amino group. (NH2) and can generate OH- by taking a hydrogen from water.

• These two concentrations are in a biological tug-a-war, in that an increase in the OH concentration forces a decrease in the other and vice versa.

• Pure water can act as a buffer: where acid and bases can react while the environment of the cell is kept relatively constant under a variety of conditions.

• Molecules in cells

• Carbon compounds make up the cell's of living things and are able to make large and complex molecules with not upper limit to their possible size.

• Functional groups are combinations of atoms that occur repeatedly and have distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs.

• Methyl CH3

• Hydroxyl OH

• Carboxyl COOH

• Carbonyl C=O

• Phosphoryl PO3

• Amino NH2

• The combination of a phosphate and a carboxyl group, or two or more phosphate groups, gives an acid anhydride. (PICS !!!)

• Cells contain four major families of small organic molecules

• Sugars

• Monosaccharides (CH2O)n- the simple sugars where n is usually 3, 4, 5, or 6 make up and compose compounds called carbohydrates. Each sugar can exist in two forms, D or L, mirror images of each other (isomers)

• Glycosidic bonds = covalent bonds that hold monosaccharides together to form larger carbohydrates.

• These can then be labeled as disaccharides, trisaccharides, tetracaccharides, and so forth. The prefix "oligo-" is used for a small number of monomers, between 3 and 50, polymers would indicate more.

• The carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide.

• Maltose (glucose + glucose)

• Lactose (galactose + glucose)

• Sucrose (glucose + fructose) 

 

• The OH- group of one sugar can be bonded to the OH- group of another sugar through a condensation reaction (water expelled) and they can be  separated by hydrolysis (consumption of water). Because each monosaccharide has several OH groups they can link together in several different ways, and even branch making it relatively difficult to determine the arrangement of the sugars in polysaccharides.

• Glucose has a central role as the energy source for the cell. Animals will use glycogen and plants will use starch as long term storage of glucose, both of which are composed only of glucose units.

• Polysaccharides also make up cellulose, chitin (insect exoskeletons/fungal cell walls), and are the main component of slime, mucus, and gristle.

• Glycolipids- small oligosaccharides that are covalently linked to proteins. These tend to be found in cell membranes.

• These sugar side chains can be recognized selectively by other cells, (blood type)

• Fatty acids

• This molecule has two main regions; a long hydrocarbon chain that is hydrophobic and not very reactive, and a carboxyl group (COOH-) which is very hydrophilic and acts as an acid.

 

• If the hydrocarbon tail is saturated, that means that it has no double bonds between its carbon atoms, containing the maximum number of hydrogens. But there are types of fatty acids that are termed unsaturated, and may contain one or more double bond along their length. 

 

• Different fatty acids differ only in the length of the carbon chain, and the number and placement of the double bonds. 

• Amphipathic- molecules that possess both hydrophobic and hydrophilic regions.

• Triacylglycerol- a compound made of three fatty acid chains joined to a glycerol molecule.

• This compound is found in the cytoplasm, and how fatty acids are stored in many cells. When the cell needs energy, the fatty acid chains can by released and broken down into two carbon units which are identical to  those made from breaking down glucose, and will enter the same energy producing reaction pathways as well.

• Lipids- a derivative of fatty acids, typically containing long hydrocarbon chains and isoprenes (2-methyl-1,3-butadiene) or multiple linked aromatic rings.

• This class of molecules has the common feature of being insoluble in water but soluble in fat and organic solvents.

• Lipids and their derivatives can form larger aggregates help together by hydrophobic forces.

• Micelle

 

• Phospholipids- similar to triacylglycerol, but the glycerol is joined to two fatty acids here, and in the place of the third glycerol us a hydrophilic phosphate.

• This is what makes up cell membranes.

• Other lipids present in the cell membrane may contain one or more sugar instead of the phosphate (glycolipids) and play an important role in intracellular cell signaling.

• When these sheets of phospholipids are arranged tail to tail, they form what is known as the phospholipid bilayer. 

 

• Amino acids

• These are a varied class of molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to the same carbon atom called the Alpha carbon. Their chemical variety comes from the side chain that is also attached to the alpha carbon.

• These are used to build proteins, which are polymers of amino acids joined head to tail in a long chain that is then folded into a three dimensional structure.

• Peptide bond- the covalent linkage between two adjacent amino acids in a protein chain. These are also formed through condensation reactions.

• The four atoms in the peptide bond form a rigid planar unit, so there will be no rotation around the C-N bond.

• Amino acids will always have an amino (NH2) group at one end (N-terminus) and a carboxyl group at the other end (C-Terminus)

• 20 types of amino acids are commonly found in proteins. 

 

• Similar to sugars, all amino acids, with the exception of glycine, exist as optical isomers. Proteins will only have the L-isomer, while some D-amino acids will occur in parts of bacterial cell walls and in some types of antibiotics. 

• Five of the twenty amino acids have side chains that can be positively charged, all the others are uncharged.

 

• Nucleotides

• Nucleoside- a molecules made of a nitrogen-containing ring compound linked to a five-carbon sugar, which can be either ribose of deoxyribose. A nucleoside that has one or more phosphate groups attached to the sugar is a nucleotide. 

 

• Pyrimidines- these are all derived from a six-membered pyrimidine ring; Cytosine, Thymine, and Uracil.

• Purine- these are similar to pyrimidines except they have a five-membered ring attached to the six-membered ring; Guanine and adenine.

• Adenosine triphosphate (ATP)- this is an example of how nucleotides can act as short term carriers of chemical energy.

• ATP is formed through the reactions that are driven by the energy released by the breakdown of food. The phosphates are linked in series by two phosphoanhydride bonds, when these bonds are broken, large amounts of energy are released. The terminal phosphate tends to be the one that is lost through hydrolysis, providing the energy required for biosynthetic reactions. 

 

• The most fundamental role of nucleotides though, is the storage and retrieval of biological information. When this is the case they will form long chains linked by 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. (between the 5' carbon and the 3' carbon)

• As these chains are formed from nucleoside triphosphates through a condensation reaction, a phosphodiester bond will form with the release of an inorganic pyrophosphate.

• They are given names DNA or RNA depending on the sugar that is being used.

• RNA -adenine, guanine, cytosine, and uracil

• DNA - adenine, guanine, cytosine, and thymine.

• Not all compounds fit into these categories. (enzymes and macromolecules)

• Polymers grow by the addition of a monomer onto one end of the polymer chain via a condensation reaction, and are catalyzed by specific enzymes to ensure that only monomers of the appropriate type are incorporated into the polymer and in the right sequence.

• This reaction will occur over and over again to extend the length of the polymer chain. 

 

• Most of the single covalent bonds in a macromolecule allow rotation of the atoms they join, allowing the polymer chain to have a high level of flexibility and allows the macromolecule to adopt an almost unlimited number or conformations. But these shapes tend to be highly constrained because of the formation of noncovalent bonds that form in different parts of the molecule.

• While these bonds are weak, in large numbers they can cause the chain to adopt one particular conformation that is dependent on the linear sequence of monomers in the polymer chain.  These bonds will be primarily formed by electrostatic attractions and hydrogen bonds, and at times the van der Waals attraction.

• Water is also present in most if not all of the cell, and can also play a roll in the shape of these molecules. Water will force hydrophobic groups together in order to minimize the disruptive effect water will have on the hydrogen bonds. This is referred to as hydrophobic interaction, and is responsible for the globular shape that most protein molecules and is the force that pushes the phospholipid molecules together in cell membranes.

• These shapes that the polymers are forced into will effect which polymers they can interact with. This underlines all biological catalysis, making it possible for proteins to function as enzymes, and allow macromolecules to be used as building blocks for the formation of much larger structures. ( an example of this would be histones or any of the polymerase that interact and catalyze the replication/repair of DNA.

• All organic molecules are synthesized from, and are broken down into- the same set of simple compounds. Both their synthesis and their breakdown occur through sequences of simple chemical changes that are limited in variety and follow definite step-by-step rules.