Class 03: Molecules of Life - Lecture Notes

9/3/24 Class 03 Molecules of Life, pt I Sept 3, 2024 1 Recap – Have been introduced to Scientific Method Philosophy of Rules Disease Usual Suspects and some of their diffe...

9/3/24 Class 03 Molecules of Life, pt I Sept 3, 2024 1 Recap – Have been introduced to Scientific Method Philosophy of Rules Disease Usual Suspects and some of their differences Bacteria Archaea Eukarya Viruses Viroids Prions 2 1  9/3/24 Today – Legos and Tinker Toys Review of the parts of Chemistry that apply to living Cells The general molecules reviewed here are shared by all forms of cellular life Some of them are also used by acellular agents! è no general differences. àare differences in specifics (will come in later chapters) Chapter parts 2.1, 2.2, 2.3 – should be a review Will walk through the key parts as apply to life If there are parts you do not understand – see me to catch up. Will spend more time (Thursday) on the second part of Ch 2.4 as we get into some very specialized molecules à apologies – class today and Thursday will not have much for clickers 3 Class 03 Agenda Reading provided overview (just had it) on atoms, elements, electrons, and bonding In class we are going to build from there Expand on types of bonding and why Expand on chemical reactions of life àcentrality of WATER. (solution chemistry) Add concepts of equilibirium and catalysis But my order of presentation will be different from the book… As time permits, we will move to the special role of assembly of legos and tinkertoys… Carbohydrates Lipids and sterols 4 2  9/3/24 By the time I was in college -- Chemists and Physicists had identified 103 elements (more added since then – but none that occur naturally) They have leaned a lot about the physical laws that create those elements and their individual properties Protons, neutrons in the nucleus, electrons in shells. All important – but not for what we are talking about in this course MOs learned about elements and their properties by trial and error – and learned to use them. We will focus on what the characteristics are and how MOs use them I will leave it to others to explain where those traits come from. 5 The molecules of life, the “compounds”, center around six elements (CHONPS) Carbon, Hydrogen, Oxygen Nitrogen, Phosphorus, Sulfur There are many more elements that play important roles as electrolytes, metals, and more. They will show up on later talks. But these six easily form COVALENT bonds (where electrons are shared) to form new, more complex compounds essential for life chemistry. And among those elements, CARBON is King 6 3  9/3/24 Carbon Most stable when it has four covalent bonds Allows it to bind to itself in chains of any length while still having other bonds to add variety of structure and activity. The definition of “Organic Chemistry” And the other five elements? At least remember… Hydrogen – 1 covalent bond Oxygen & Sulfur – 2 Nitrogen – 3 Phosphorus – 5 7 Table 2.5 Biologically Important Functional Groups Functional Group Structure Where Found Aldehyde Carbohydrates Amino Amino acids, the subunits of protein Carboxyl Organic acids, including amino acids and fatty acids Hydroxyl Carbohydrates, fatty acids, alcohol, some amino acids Keto Carbohydrates, polypeptides Methyl Some amino acids, attached to DNA Phosphate Nucleotides (subunit of nucleic acids), ATP, signaling molecules Sulfhydryl Part of the amino acid cysteine 8 8 4  9/3/24 Water is Key! Life as we know it can only occur in the presence of water. MOs might be able to survive in stasis w/o water, but none can grow. The essential chemistry of life is mostly solution chemistry And even the “exceptions” require structures that can only exist in water. Highlights another key feature of covalent bonds – They can largely retain their connection between atoms when put into a water environment! 9 Chemical Reactions These atoms are most stable when all possible bonds are in place Can still shift those bonds… Chemical reactions transfer electrons, often involving rearrangement of bonds to form new stable structures When considered as running in only one direction, Reactants are starting components of a reaction that are changed to products Synthesis reaction A + B → AB Decomposition reaction AB → A + B Exchange reactions AB + CD → AD + CB or AB + C → AC + B Book presents all these as going in one direction, only. For Life Chemistry, most (all?) reactions are reversable! 10 5  9/3/24 Equilibrium Reactions can run both ways: AB + CD AD + CB But prefers to run to the most stable compounds. Extreme example: CH4 + 2O2 CO2 + 2H2O Symbolically map as “energy levels” CH4 + O2 CO2 + H2O 11 Sidebar – balancing chemical equations May have noticed I threw some extra numbers into the chemical reaction. Needed to balance the number of each kind of atoms on each side. In much of Life Chemistry, you also need to pay attention to the number of reduced or oxidized electrons – balancing “redox” elements. Not going to go into detail on how – but know that it will come up again in metabolism. à if you run out of atoms or reduced or oxidized electrons on either side, the reaction cannot run! Important, later. 12 6  9/3/24 In Water, things go both directions more readily. Water itself – Oxygen covalently bonded to two Hydrogens But they can, at a low lever, separate in OH- and H+ ions. H–O–H OH- + H+ Equilibrium is the balance of products and reactants when the net rate of the reaction in each direction is the same. In pure water, the H+ concentration is 10-7 molar (= pH 7) In Acidified water (add acid), the concentration is higher, resulting in a lower pH. So, at pH 4, concentration of H+ is 10-4. Still not much, but results in a 1000x increase in availability of H+ 13 Back to Covalent Bonds for a moment We’ve found that some compounds are more stable than others (different energy levels) Also need to realize that in some covalent bonds, the sharing of electrons is not as equal as it could be. Nearly equal: C—C, C—H, and H—H Not so equal: O and N not as nice – hog the electrons Results in a dipole – (slight negative charge) O—H (slight positive charge) We know that + charges are attracted to – charges Same true for dipoles -- slight (+) weakly attracted to slight (–) è Hydrogen Bond 14 7  9/3/24 Hydrogen Bonds Very weak – roughly 1/100 the strength of a Covalent Bond Put a few thousand of them together, and things will stick… Locally, bonds form and unform continuously But across the structure, holds overall àFlexibility! Put a pin here – we will come back in a future class. Meanwhile – we suddenly realize that water is a dipole, hydrogen bonding to other water molecules è And things get interesting! 15 Covalent Bonds—Figure 2.6 Polar covalent bonds result in slight separation of charge Important in biological systems May result in formation of hydrogen bonds Access the text alternative for slide im ages. 16 16 8  9/3/24 Water, pH, and Buffers—Figure 2.9 Water (H2O) is a polar molecule Hydrogen bonding explains properties Liquid: hydrogen bonds continually form and break, allowing molecules to slide over one another Solid: each water molecule forms four hydrogen bonds with surrounding water molecules producing a less dense structure called ice ICE is LESS DENSE than LIQUID WATER Also capillary action! Access the text alternative for slide im ages. 17 17 Water—Figure 2.10 Polar nature makes water an excellent solvent in which solutes are dissolved Polar and charged substances are hydrophilic (“water loving”); dissolve in water Non-polar substances are hydrophobic (“water fearing”); do not dissolve in water Water with dissolved substances freezes at lower temperatures Access the text alternative for slide im ages. 18 18 9  9/3/24 Look back at our covalent bonds in Life Chemistry C—C, C—H combinations – equal sharing – no dipole HYDROPHOBIC Do not dissolve in water In fact, will try to HIDE from water, if possible Involve O or N – now have dipoles HYDROPHILIC Dissolve in water What happens if you have both features in one molecule? Things get interesting. Later topic….(another pin…) 19 Ions and Ionic Bonds Why did I skip? As far as life is concerned, solid salts are relatively boring. But now that we have added water, it gets interesting! Some elements don’t share electons at all. They either steal them or give them away Net result is a solid positive or negative charge on each atom. Salt crystals are a lattice of positive and negative charges, balanced overall, but with no identifiable “molecule”. But dissolve in water -- 20 10  9/3/24 Dissolve in water, and … Ions can take on individual lives of their own as “Electrolytes”. Individual “point” positive or negative charges can be diffused by hydrogen bonding capability of water. If you get fancy with membranes or attractive surfaces, can swap out negative ions for OH- and positive ions for H+, all courtesy of water. And dissolution of salts in water can alter the properties of water Change the freezing or boiling points of water. Change the pH of water to acidic or basic. Change the effective concentration of water. Transport electricity And life will use all of these characteristics to its advantage. 21 A couple closing thoughts on Chemical Reactions: Challenge #1 Discussed earlier about how reactions run in both directions -- but favor the direction of the most stable (least energy) compounds. Second Law of Thermodynamics – Entropy increases. But life generally wants to go the other direction – higher energy compounds and lower entropy structures. How does life break the law? 22 11  9/3/24 Life doesn’t break the law, just hires a good lawyer… Seems you can do pretty much anything you want, as long as you pay for it somehow! General solution – Artificially link together two reactions One, that you really want, that is energetically not favored. And one that you don’t care about much, except that it is energetically favored When run together, net reaction is favorable, and law is satisfied. Example of a can of paint needed on the roof. 23 Chemical Reactions, Challenge #2: How to control reaction Think about a Snickers Bar Family size is about 500,000 calories. Enough energy to boil the blood in my hand and fingers Or if released all at once, probably blow my hand right off Yet, if I were to offer to give it away, any takers? 24 12  9/3/24 Experience has taught us, safer than it sounds. 25 If you can reduce the activation energy to a level sufficiently low… Energy at room temperature can be enough to let it Catalyst/Enzyme find equilibrium. 26 13  9/3/24 Enzymes (usually protein) Most biologically important chemical reactions occur too slowly at livable temperatures to be useful to a cell Enzymes are biological catalysts that speed the rate of reactions Bind to one or more reactant molecules Stabilize the transition state of the reaction, lowering the required activation energy. CAN ALSO LINK UNRELATED CHEMICAL REACTIONS TO DRIVE UNFAVORABLE REACTIONS. 27 Shifting gears: Major Classes of Compounds used by Cells Carbohydrates Lipids/Sterols Proteins Nucleic Acids Heavy use of building blocks for polymers or structures. 28 14  9/3/24 Major Classes of Organic Molecules—Table 2.4 TABLE 2.4 Major Classes of Organic Molecules Name Subunits Major Functions Carbohydrates Monosaccharides Structural components of cell walls; energy sources Lipids Varies—subunits are not Some types are important always similar components of cell membranes; energy storage Proteins Amino acids Enzyme catalysts; structural portion of many cell components Nucleic acids Nucleotides DNA Deoxyribonucleotides Genetic information of a cell RNA Ribonucleotides Various roles in protein synthesis; catalysis 29 29 Carbohydrates—Figure 2.13 Diverse group includes sugars and starches Energy source Energy storage Carbon source Component of DNA and RNA Structural components of cells Carbon, hydrogen, oxygen in 1:2:1 ratio Building block: CH2O Access the text alternative for slide im ages. 30 30 15  9/3/24 Monosaccharides—Figure 2.14 Monosaccharide: basic unit of carbohydrates 5-carbon sugars include ribose, deoxyribose 6-carbon sugars include glucose, galactose, mannose, fructose Structural isomers: same atoms, but different arrangement Distinct sugars with different properties Access the text alternative for slide im ages. 31 31 Disaccharides—Figure 2.15 Disaccharides composed of two monosaccharides Common disaccharides Sucrose (glucose + fructose) Lactose (glucose + galactose) Maltose (glucose + glucose) Dehydration synthesis forms covalent bond between hydroxyl groups of monosaccharides Hydrolysis breaks bond and yields two monosaccharides Access the text alternative for slide im ages. 32 32 16  9/3/24 Polysaccharides—Figure 2.16 Polysaccharides are chains of monosaccharides Structural diversity from branching, linkages Important polymers of glucose: Cellulose Starch Glycogen Dextran Chitin, agar also important Access the text alternative for slide im ages. 33 33 Lipids Lipids are non-polar, hydrophobic molecules Diverse group defined by slight solubility in water Important in structure of membranes Not all lipids are composed of similar subunits 34 34 17  9/3/24 Fatty Acids—Figure 2.17 Fatty acids are linear carbon skeletons with a carboxyl group (—COOH) at one end Saturated fatty acids No double bonds Tails pack tightly so solid at room temperature Unsaturated fatty acids Double bonds between carbon atoms Kinks prevent tight packing so liquid at room temperature (oils) Access the text alternative for slide im ages. 35 35 Simple Lipids Most natural fatty acids are cis: hydrogens attached to same side of double bond Trans: hydrogens on opposite sides of double bond (linked to certain health problems) Access the text alternative for slide im ages. 36 36 18  9/3/24 Triglycerides—Figure 2.18 Triglycerides: most common simple lipids Fats or oils composed of three fatty acids linked to glycerol Fatty acids: linear chains of bonded C, H atoms with carboxyl group at one end Access the text alternative for slide im ages. 37 37 Backtrack a bit: Chemical reactions Challenge #3: Dependence on concentration of reactants Higher concentration means faster reaction But reactants and products diffuse in water Other life forms can steal Need a container that limits diffusion, but flexible enough to allow controlled passage of compounds. 38 19  9/3/24 Remember that pin – hydrophobic and hydrophilic in one molecule? 39 Phospholipids—Figure 2.19 Compound lipids contain fatty acids and glycerol in addition to a non-lipid component Phospholipids contain hydrophilic phosphate group and hydrophobic fatty acid tails If oil floating on top of water – cluster at the interface, polar head in water, fatty acids in oil! Access the text alternative for slide im ages. 40 40 20  9/3/24 But carries its own “oil” Form lipid bilayer with phosphate groups oriented outward toward aqueous environments Essential component of cytoplasmic membranes Lipoproteins, lipopolysaccharides also compound lipids 41 Steroids—Figure 2.20 Steroids have characteristic four-ring structure Classified as lipids because they are poorly soluble in water Sterols such as cholesterol have hydroxyl group attached to one of the rings Often part of eukaryotic plasma membrane Role in Fungal disease treatment… Other steroids include hormones Cortisol, progesterone, testosterone Access the text alternative for slide im ages. 42 42 21  9/3/24 In Class Assessment Briefly describe two characteristics MOD of water that are important to Life. Signature Answer 43 Homework for Class 03 Both covalent bonds and hydrogen bonds are important in life chemistry. To be sure that you understand the circumstances where weak bonding is appropriate: 1). Give an example (from either life or chemistry) where many weak attachments or bonds is better than a few very strong attachments or bonds. Submit your answer either typed directly or as a word or pdf attachment to the assignment page for HW 03 in Blackboard. You do not need to copy the question. 44 22