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Date Created: 05/14/16
Valence shell in a polar molecule to the Usually a solid that is is bonded to 4 different The outermost energy level opposite partial charge of dissolved or added to a atomic groups an atom in a separate Enantiomer of an atom where electrons solvent or liquid of some orbit molecule kind Stereo Isomer where Electronegativity Solvent molecules with the same The measurement of an Dispersion Forces Usually a liquid (water) that molecular formula but cannot be transposed on atoms ability, in comparison Attractive forces that occur can have a solute or solid to other atoms in a between molecules when dissolved in it one another because they molecule, to pull electrons they are close enough are mirror images towards it, causing those together because at any Identical phys/chem time a molecule may have properties except when electrons to orbit the atom Hydration Shell with higher EN more of the a higher concentration of The sphere of water that exposed to plain light. One time electrons in one region, surrounds ions of a solute will rotate one direction, the Ionic Compound attracting it to the region of being dissolved. other will rotate the another molecule where opposite at same degree. A combination of elements Hydrophilic formed from two ions (atom electrons may not be as Any substance that can Referred to as L&D isomers loses e, atom gains e) concentrated at the interact with water Hydroxyl attracting eachother moment. Hydrophobic Functional group of atoms Covalent Compound Cohesion with an Oxygen bonded to Substances that are A combination of two The linkages of water nonionic and nonpolar a Hydrogen that is elements formed from two molecules because of the (cannot form hydrogen connected to an R group atoms with open space in hydrogen bonds that form bonds) that repel water (rest of the molecule) their valences shells between partially positive Carbonyl Amphipathic sharing e hydrogen of one molecule Have both hydrophobic and Functional group of atoms Molecule and partially negative hydrophilic regions on a with carbon double bonded A single structure made up oxygen of the next molecule to oxygen, single bonded to of two or more atoms molecule hydrogen, and the R group Adhesion Acid Polar Covalent Bond A substance that increases Aldehyde A bond where e are shared Clinging of molecules to the hydrogen ion If carbonyl group is at the between two atoms with e another object by hydrogen concentration of a solution end of a carbon chain bonds Ketone density focused around one Specific Heat Base atom more than the other A substance that reduces If carbonyl group is in the Dipole The amount of heat that hydrogen ion concentration middle of a carbon chain A condition of a molecule must be absorbed or lost of solution sometimes by Carboxyl for 1g of that substance to where two polar bonds change its temperature by increasing hydroxide ion Functional group of atoms occur and the slightly concentration with Carbon double bonded positive charges of that 1c Buffer to an oxygen atom and molecule push towards or Kinetic Energy A substance that minimizes single bonded to a hydroxyl away from eachother The energy of motion, group. Group is ionic if it changes in the Nonpolar Covalent Bond usually related to particle concentrations of H+ and loses a Hydrogen (p+) A bond where e are shared movement. Faster OH in a solution. Accepts Amino between two atoms with no movement means, higher H+ ions from solution when Functional group of atoms kinetic energy, means distinction between where increase in temperature they are in excess and with Nitrogen bonded to 2 the e density is most of the donates H+ when depleted hydrogen atoms. Group is time Temperature Structural Isomer positive if it gains a Ionic Bond Average kinetic energy in a A molecule with the same hydrogen (p+) body of matter regardless Phosphate The connection formed formula as another but with between two atoms when of volume different covalent Functional group of atoms one atom loves an e and Heat connectivity causing with phosphorus covalently the other gains it The transfer of thermal different physical/chem bonded to 4 oxygen atoms Anion energy from one body of (one double bonded) properties Atom of an element that matter to another Cis/Trans (Geometric) Isomer Contains to full negative gained e in an ionic bond Calorie A stereo isomer where one charges making group ionic Cation Amount of energy required molecule has two atoms on Found in subunits of DNA to raise 1g of water by 1c Methyl The atom of an element the same side (Cis) and the that lost an e in an ionic Solution other has the same atoms Functional group of atoms bond The combination of a solute but opposite each other on with carbon bonded to 3 Hydrogen Bond being dissolved in a solvent the molecule (Trans) hydrogen atoms and R in a specific ratio group The force of attraction Chirality between a hydrogen atom Solute When an atom (usually C) Sulfhydryl Functional group of atoms Amylose is a polymer that which contributes to serine, or inositol) with sulfur bonded to exists as a single chain with specificity of molecular Amphipathic molecule hydrogen atom no sugar groups branching interactions o “head” contains Slightly polar and can off the main chain Glucose phosphate and glycerol is undergo oxidation reactions Amylopectin is similar but 6 carbon monosaccharide hydrophilic/polar to yield disulfide bonds does have sugar branching used for energy when o “tail” contains 1 saturated Disulfide bonds found in about every 20 units bond with another glucose and 1 unsaturated fat is proteins used to stabilize Glycogen is broken via dehydration hydrophobic/nonpolar Dehydration Synthesis The starch that exists in synthesis component of bilayer in cell Enzymatic combination of animals with more frequent Hexose membrane that creates molecules that causes the sugar branching (about 6 carbon monosaccharide “fluid mosaic” removal of a molecule of every 8 units) Aldose Sphingolipid water More branches exist for Sugar with carbonyl part of cell membrane enzymatic cleaving to groups at the end of the structure expose more ends for carbon chain not based on backbone of energy release Ketose glycerol but on Sphingosine Glycosidic Bond Sugar with carbonyl group o Sphingosine contains The bond that links to in the middle of the carbon large hydrocarbon tail and monosaccharides via an chain fatty acid covalently oxygen atom that was left Lipid bonded to the Nitrogen Hydrolysis behind after dehydration Hydrophobic, non polar and another group Bonds are broken by the synthesis biomolecule used for (usually phosphocholine) addition of a water Cellulose energy storage on an oxygen atom molecule when the Polymer of betaglucose o Stored as triglycerides Glycolipid Hydrogen molecule linked 1,4 that is the main Make up phospholipids in Carbohydrates bonded to attaches to one molecule component of plant cell cellular membranes lipids and the hydroxyl attaches walls Signaling molecules such Saturated Fatty Acid to another Betaglucose links together as steroid hormones and Single bonds along carbon Monosaccharide when one is inverted and inflammation signaling chain to max number of Polar molecule consisting they stack in linear fashion pathways hydrogens (2) of a carbon chain, hydroxyl held together Triacylglyceride Linear and can stack which and carbonyl groups INTERrmolecularly by Glycerol and 3 fatty acids attributes to their high Ring structure in aqueous hydrogen bonds covalently bonded via melting point solution when chain folds Chitin dehydration synthesis Butter/animal fats back on itself to create new Similar to cellulose o Glycerol is an alcohol Trans position compared to chiral center—brings structure but fibers are whose 3 carbons have Unsaturated fatty acid carbonyl closer to hydroxyl wrapped in a protein hydroxyls bonded Unsaturated Fatty Acid group Presence of amino group Energyrich molecule can 1 or more double bonds Disaccharide (Nacetyl) on Carbon 2 be stored in adipose tissue along carbon chain to only Linking of two Proteoglycan in animals and oil droplets 1 hydrogen monosaccharides by Proteins connect to in plants (seeds for Lower melting point dehydration synthesis branching carbohydrates to embryonic development) Usually an oil (liquid at causing the remaining form a network in Fatty Acid room temperature) because oxygen molecule to create extracellular matrix Long hydrocarbon chains of Cis orientation that a glycosidic bond between o Molecular meshwork which are non polar (fatty) creates a bend making the two molecules outside of cells that and a carboxyl group (acid) them unable to stack like Polysaccharide provide support at the end of the chain saturated fats Linking of multiple o Cartilage Essential Fatty Acid Steroid monosaccharides by Glycosaminoglycan Fatty acids that are not Carbon skeleton consisting glycosidic bonds via Branching carbs that are created in the body of four fused rings dehydration synthesis covalently bonded naturally and must be Enzymatically modified Amylose/Amylopectin Sugar molecule with amino obtained through the diet from cholesterol 2 different kinds of starch group and other (usually Phospholipid Cholesterol is a common found in plants. sulfate) polar functional Similar to triglyceride component of animal cell o Starch is a polymer of groups attached except only 2 fatty acids membranes is also the alphaglucose linked 1,4 Negatively charged and linked to 2 carbons and the precursor form which other o Forms helical coil shape hydrophilic third is linked to phosphate steroids such as when partially + oxygen Chondroitin sulfate group ( charge). The testosterone and estrogen and partially – hydroxyl Glycoprotein phosphate group is then are synthesized. attract (INTRAmolecular Carbohydrates attached to linked to an Rgroup (polar, Enzyme bonding) proteins by glycosylation ionic group usually choline, Protein Complex that catalyzes reactions Secondary Structure o Proteins that are fully o mRNAProteincoding nd Glycine The 2 step in protein functional with only messenger RNA that is Smallest Amino acid with synthesis created by local secondary structure and copied from protein only a Hydrogen atom for folding of interactions by remain linear coding genes, specifies o Structural support roles amino acid sequence in its Rgroup and no chiral functional groups and Carbon hydrogen bonds between o Hbonds and covalently proteins. Translated at Proline the backbone functional bonds with other fibrous the ribosome cell Nonpolar amino acid with groups proteins to form networks structure either within or outside o tRNA (Transfer RNA) Rgroup bonded to the Carbonyl and amino groups chiral carbon and the hbond with each other the cell Nonproteincoding RNA nitrogen of the amino Alpha helix Collagen: main protein used for transporting functional group Coil structure that forms component of correct amino acid extracellular matrix sequence to ribosome Cysteine during secondary structure Polar amino acid with a because of local folding and Keratin: protein during protein synthesis sulfhydryl group that can hbonds structural support inside o rRNA (Ribosomal RNA) become disulfide bond Rgroups all face out to be cells called the Nonproteincoding RNA cytoskeleton which is part of the when oxidized for protein able to bond structure stabilization Beta strand/sheet Quaternary Structure Ribosome Disulfide Bridge When Hbonds are Combination of two or more o miRNA (Micro RNA) Covalent bond that forms protein chains called nonproteincoding RNA interrupted because of used to regulate the where two molecules certain amino acid protein complexes (usually in cysteine sequences causes linear Chaperonin expression of genes by monomers) are brought structure/strands hbond to Protein structure that interacting directly with close together so the sulfur adjacent strand causes protects synthesizing DNA or with mRNA copy. Also determines whether of each molecules sheets made of strands proteins from hydrophobic sulfhydryl group bond via o Sequences that form ionic conditions that may cause proteins get synthesized dehydration synthesis. bonds—stronger than H misfolding or not Peptide Bond bonds Denaturation Nucleotide Linkage between two amino o Large Rgroups (carbon The detrimental unfolding of the monomeric unit of acids so that the carboxyl rings) cause steric a protein caused by heat or nucleic acids. group of one joins the hindrance cause groups a detergent that breaks Consists of a 5carbon to “bump” into each other bonds within the complex sugar covalently bonded to amino group of the other through dehydration o Rgroup bonding to amino Invariant Residue a nitrogenous base synthesis. group (Proeline“helix Amino acids in a sequence Sugar is covalently bonded Peptide/Polypeptide breaker”) prevents that that would be detrimental to to 1 or more phosphates group from Hbonding Nucleoside When two monomer units the protein if it were known as amino acids they elsewhere substituted for another The combination of the form a peptide. A polymer Rgroups alternate up/down amino acid nitrogenous base and the of these units is a position ie a polar for a nonpolar sugar polypeptide. substitution or an acidic for Depending on how many Protein Tertiary Structure a basic substitution phosphate groups are Complex of two or more 3 step in protein synthesis Conservative Substitution bonded to the nucleoside – polypeptides by Rgroup interactions substitution of an amino monophosphate, Nterminus creates 3D structure and acid with similar properties diphosphate, The open amino group end fullyfunctional polypeptides that would not drastically triphosphate. of a chain of polypeptides o Ionic bonds between (+) affect the structure of a Nucleic Acid basic side chains and () protein Polymeric unit of multiple Cterminus The open carboxyl group acidic side chains ie polar for polar nucleotides bonded end of a chain of o Hbonds between polar substitution together polypeptides groups Deoxyribonucleic Acid Phosphodiester Bond o Covalent linkages DNAthe blueprint used to Bond between the hydroxyl Phosphorylation (disulfide bonds) The addition or removal of store genetic info by all of the 3’ carbon on the a phosphate group from a o Nonpolar interactions by cells. preceding sugar to the first molecule (usually in the hydrophobic interactions Genetic info storage for phosphate group on the 5’ with water causing groups carbon on the nucleotide enzymatic reaction of ATP to be pushed together proteins and other to ADP and visa versa) functional molecules Bonds are created in this Primary Structure Globular Protein Ribonucleic Acid directionality from 5’ to 3’ The sequence of amino o Proteins with bulky shape RNAcopied from DNA and along the polynucleotide that have tertiary and chain with new nucleotides acids that are dictated by a quaternary structure allows the info it encodes to gene in creating the 1 step be expressed as a useful being added to 3’ end of a protein Fibrous Protein cellular product Purine Nitrogenous bases with 2 RNA molecule Major Groove Nucleosome fused rings Deoxyribose The wider of 2 grooves of DNA with about 150 base Adenine and Guanine The sugar structure of the the DNA molecule where pairs is wrapped twice Pyrimidine DNA molecule proteins can bind around a complex of 8 B DNA Minor Groove histone proteins Nitrogenous bases with 1 ring The most common The smaller of 2 grooves Chromatin Cytosine, Uracil, and structural form of DNA of the DNA molecule Compacts DNA in an Thyamine 2 nm diameter, 10 base where proteins can bind organized fashion and pairings per turn of the Histone regulates DNA and its Ribose The sugar structure of the double helix DNA binding proteins expression. 1. How are the chemical properties and reactivity of an element related to atomic valence configuration? Whether or not an atoms valence shell is filled (duet rule of first shell, octet rule of valence shell) determines how reactive an element is. If the valence shell is full, it will not react, the more “space available” the more reactive it can be. 2. At the subatomic level, what is a covalent bond? A covalent bond forms when the there is a relatively small difference between the Electronegativity of two atoms, and the atoms “share” electrons to form a bond. Usually seen between two nonmetals, covalent bonds occur between the valence electrons of two atoms 3. What four elements are the principal atomic constituents of biological molecules, and how do they differ in terms of their covalent interactions? The four main elements in biological molecules are Hydrogen, Oxygen, Nitrogen, and Carbon. There valance shells have different numbers of electrons in them (hydrogen1, carbon4, nitrogen5, and oxygen6) allowing for different amounts of bonds to form between them and other atoms. Hydrogen can only covalently bond with 1 other atom, carbon can covalently bond with 4 other atoms, nitrogen can covalently bond with 3 other atoms, and oxygen can covalently bond with 2 other atoms because this would fill the octet rule for their valence shells. (No more than 8 electrons in a valence shell) 4. What is meant by the term electronegativity? How does electronegativity affect the properties of any given covalent bond? Electronegativity refers to an atom in a molecule’s “ability” to have the concentration of electrons in that molecule be around that atom more of the time while they move in the electron cloud. A covalent bond is formed usually when the difference of EN is less than 1.7 on the Pauling scale because this infers that neither atom in a bond has a “strong enough ability” to pull the electrons completely away from the other causing them to “share” 5. Compare the relative Electronegativities of the four principal atomic constituents of biological molecules, and relate that property to the formation of polar versus nonpolar covalent bonds between them. The least electronegative of the four main elements of biology is hydrogen (2.1), next is Carbon (2.5), Nitrogen (3.0), and finally oxygen (3.5). The only polar covalent bond of between these atoms is between oxygen and hydrogen because of the relatively large difference in their Electronegativities. Any other combination of interactions between these atoms yields nonpolar covalent bonds because the differences between their Electronegativities is relatively small and would not cause electrons in those molecules to “spend more time” around one atom compared to the other. 6. What drives the formation of stable ions? Why is a sodium ion more stable chemically than the sodium atom? Stable ions form when the atom of a certain element when that atoms valence shell is either completely full or completely empty. Sodium is more stable chemically as an ion because it only has one electron in its valence shell, so losing this electron (forming Na+ ion) is “easier” than gaining 7 more electrons to complete its valence shell to reach stability. 7. At the subatomic level, what is an ionic bond? An ionic bond forms when an atom (usually a metal) gains an electron to complete its valence shell (i.e. Cl) forming an anion and another atom (usually a nonmetal) loses an electron to have a complete valence shell (i.e. Na+) forming a cation. These two ions will then be attracted to each other because one now has a full negative charge while the other has a full positive charge. 8. What is a hydrogen bond? Is it more similar to an ionic bond or a covalent bond? Why? A hydrogen bond forms when a molecule with a partial positive end (due to it being a polar molecule) is attracted to another molecule’s partially negative end (due to it being a polar molecule). This is more similar to a ionic bond because it is the negative and positive charges that cause the attraction between the two molecules. 9. Why is it accurate to depict water as "sticky" molecules? Water can be depicted as “sticky” because of the hydrogen bonds that hold water molecules together giving it fluidity and its cohesion property 10. At the molecular level, what explains water’s cohesive and adhesive properties? How is this related to the existence of sequoias that are hundreds of feet tall? Water is cohesive because of the hydrogen bonds that form between the partial negative end (oxygen atom) of one water molecule and the partial positive end (hydrogen atom) of another. It is also the hydrogen bonds that form between water molecules and the cell walls of plants that allow the water to move up inside the trunk of a 100 ft. Sequoia for example. The water adheres to cell walls so it can defy gravity and the cohesiveness of water molecules allow the chain to keep moving up as water is absorbed through roots and evaporated out the top through the leaves. The evaporation actually pulls this water molecule chain up through the tree and keeps the “train” moving. 11. At the molecular level, what explains water’s high specific heat and heat of vaporization (compared to similarly sized nonpolar substances)? How is this related to the relative stability of earth’s temperature and our ability to moderate temperature changes in our bodies? Hydrogen bonds between molecules contribute to water’s high specific heat and heat of vaporization. Water has a high specific heat because any energy absorbed by water is first used to break the hydrogen bonds before the molecules start moving faster. Water’s high heat of vaporization is another property due to hydrogen bonds which must be broken before molecules can exit the liquid form and turn into gas. On earth, the ecosystems both in water and on land are sensitive to changes in temperature and the oceans absorb some of that heat given off by the sun and evaporate which help keep coastal climates cool. Oceans are so large that it may only change a few degrees over the coarse of a few months. In our bodies, we see sweat form on our skin when our body temperature raises. The sweat will evaporate and by pulling heat from our bodies out, thus attempting to cool the body down. 12. At the molecular level, what explains the fact that unlike most substances, frozen water is less dense than liquid water? How is this related to Earth’s fitness for life? Hydrogen bonds explain why water is less dense when it is frozen than when it is a liquid. When water moves from about 4 ℃ to 0 ℃ the hydrogen bonds stay at equidistance to 4 other water molecules in a crystalline structure which means there are less molecules in a given volume. On Earth, we see ice caps stay on the surface of bodies of water insulating the water below from the colder air. 13. At the molecular level, what explains the fact that water is an excellent solvent? Why is this important in a biological context? Water is a versatile solvent because of the polarity of the water molecule. Partial positive ends and partial negative ends of water molecules can surround solutes being dissolved in water by attraction the positive and negative ends of the solute’s molecules. Blood, sap in plants, and the liquid in cells act as solvents to the various solutes dissolved in them including biomolecules required to survive. 14. In aqueous solution, why are covalent bonds more stable than ionic bonds? In other words, why will ionic compounds dissociate into constituent ions, but molecular compounds do not dissociate readily into constituent atoms? In aqueous solutions, ionic bonds dissociate because the attraction between the polar ends of the water molecule have a stronger attraction the cations and anions that made up the ionic bond of the solute (compound). Molecular compounds stay together but a hydration shell will form around the molecule which is how it dissolves. 15. What determines if a compound is hydrophilic or hydrophobic? A compound is hydrophilic if it can interact with water molecules. A substance is hydrophobic if it has nonionic and nonpolar molecules that will not interact with water such as the bonds of carbon and hydrogen in oils. 16. At the molecular level, explain what is meant by the term “like dissolves like”. Like dissolves like means that water is a polar molecule and substances with polar molecules more easily dissolve in it. 17. What happens when a water molecule dissociates? When water dissociates the hydrogen atom participating in the hydrogen bond with another water molecules oxygen end leaves its electron behind and it forms a hydroxide ion (OH) That hydrogen atom is transferred away as a single proton (H+) and binds to another water molecule and a hydronium ion H30+ is formed. 18. What two chemical moieties associate to reform a water molecule? OH which is a hydroxide ion, and H3O+ hydronium ion can reform to form 2 H2O molecules. 19. What is meant by the dynamic equilibrium of association/dissociation in pure water? Dynamic equilibrium of association and dissociation in pure water means that at any given time the rate at which water dissociates into H3O+ and OH is the same as the rate in which water reforms back into H2O. 20. What number determines the pH of an aqueous solution, and why is this 7 for pure water? The number of H+ ions in a solution determines the pH of that solution. In pure water it is 7 because at room temperature 14 7 the product of the H+ and OH ions is constant at 10 with 10 of each ion. 21. What happens when an acid dissociates, and how does this affect the hydrogen ion/hydroxide ion concentrations in the solution? Hydrogen is dissociated from an acidic substance when it is added to water. 22. What chemical characteristics cause a substance to dissociate a hydrogen ion? When an acid dissociates a hydrogen ion (H+) is broken off resulting in an acidic solution—a solution that has more H+ than OH ions. 23. What happens when a base is added to an aqueous solution, and how does this change the hydrogen ion/hydroxide ion concentrations in the solution? Some bases accept H+ ions from a solution decreasing the concentration of the hydrogen ions making the solution more basic. Bases can also add OH ions to a solution which reduces H+ concentration because the hydrogen ions combine with the hydroxide ion to form water making the solution more basic. 24. What is a "weak acid," and why is it weak relative to a "strong acid"? A weak acid (H2CO3) is an acid that reversibly releases and accepts back hydrogen ions as opposed to strong acids (HCl) which only release the H+ ion into the solution. 25. Using carbonic acid/bicarbonate as an example, explain what happens in a buffered system when the concentration of hydrogen ion or hydroxide ion is increased. In our blood we have the presence of a buffer system that ensures that the pH of our blood will not swing to much away from the homeostatic 7.4 pH via carbonic acid/bicarbonate when CO2 reacts with water in the blood plasma. If there may is an increase in H+ ions (pH drops) more carbonic acid is created to by the combination of the bicarbonate the hydrogen ion to lower the hydrogen ions concentration. If there is a drop in H+ ions (pH rises/more basic) then carbonic acid is dissociated at a faster rate to bicarbonate and hydrogen ions to lower pH again. 26. What distinguishes structural isomers from stereoisomers like cis/trans isoforms or enantiomers? Structural isomers have different covalent connectivity which can lead to different physical/chemical properties where as stereoisomers have the the same connectivity between atoms but they differ in spatial arrangements. In cis/trans isomers, carbons are bonded to the same atoms but the because of a double bond the bonded atoms cannot rotate. The cis version of a molecule has the bonded atom on the same side of the molecule where the trans version has them opposite each other. Enantiomers are also stereoisomers that are mirror images of each other where one is referred to the L isomer and the other is the D isomer. This is caused by a chiral carbon with four different bonded atoms or molecules. 27. Why is understanding enantiomers important from a biological perspective? From a biological perspective there could be two enantiomers of a drug used to treat someone but they are received different in the body because certain binding sites may be able to accept one and not the other. 28. What are functional groups in general? Why is it important to understand their structure and properties in a biological context? Functional groups are the chemical groups directly involved in chemical reactions each with its own properties such as shape and charge that cause it to act in a certain way. There are seven recognizable functional groups known to contribute to a molecules overall physical and chemical attributes. It is important to understand the structure and properties of these from a biological context because the structure of the molecule has a direct correlation to the molecules function. 29. What is a carboxyl group? At physiological pH, what property(ies) does it confer to a molecule it is a part of? A carboxyl group is made of a carbon double bonded to an oxygen and a hydroxyl group (an oxygen bonded to a hydrogen). At physiological pH this molecule acts as an acid (can donate its H+) because the hydroxyl group is so polar and its hydrogen can be lost to another polar hydroxyl to form a water molecule making the carboxyl ionic. 30. What is an amino group? At physiological pH, what property(ies) does it confer to a molecule it is a part of? An amino group consists of a Nitrogen atom bonded to two hydrogen atoms. At physiological pH this acts as a base (can pick up a H+ from water) making it positively charged ionically. 31. What is a hydroxyl group? At physiological pH, how are its chemical properties different from the OH component of the carboxyl group? What property(ies) does it confer to a molecule it is a part of? A hydroxyl group consists of an oxygen atom bonded to a hydrogen atom. At physiological pH it is polar due to the relatively high electronegativity of oxygen compared to hydrogen. Forms bonds with water which contributes to solutes dissolving in water (solvent). It differs from the OH in a carboxyl group in that the whole –OH can bind with a free H+ whereas the oxygen in the –OH in the carboxyl group is already bound to a carbon and can only lose its H+. 32. What is a carbonyl group? What property(ies) does it confer to a molecule it is a part of? A carbonyl group consists of a carbon atom double bonded to an oxygen atom. This functional group is polar and is common in sugar molecules. Its position in the larger molecule contributes to its physical/chemical characteristics and function. 33. What distinguishes aldehydes from ketones? Aldehydes are classified as molecules with the carbonyl group at the end of a carbon chain and ketones are classified as such when the carbonyl group is in the center of the carbon chain. In sugars these are respectively referred to as Aldoses and Ketoses. 34. What is a sulfhydryl group? What property(ies) does it confer to a molecule it’s a part of? A sulfhydryl group consists of a sulfur atom bonded to a hydrogen atom. Two sulfhydryl groups can react forming a disulfide bridge during oxidation reactions. These disulfide bonds help stabilize protein structures because of the strong bond they form. 36. What is a phosphate group, and what property(ies) does it confer to the molecule it’s a part of? A phosphate group consists of a phosphorus atom covalently single bonded to 4 oxygen atoms (1 oxygen atom also bonded to Rgroup, 1 oxygen atom double bonded, and 2 with negative charges). Gives the molecule its attached to the ability to react with water and/or release energy. 37. Why are phosphate groups particularly important in a biological context? Phosphate groups are found in the subunits of DNA and they also play a role in energy transfer when ATP (adenosine molecule bonded to three phosphates) reacts with water and a phosphate group is enzymatically cleaved off releasing energy and the molecule ADP. 38. What “class” of organic molecule is associated with each of the functional groups we discussed? Carbohydrates—sugars contain hydroxyl and carbonyl groups. Sugars with carbonyl groups in the center of the molecule’s carbon chain are ketoses; sugars with carbonyl groups at the end of the molecule’s carbon chain are aldoses Lipids—fats consist of a glycerol molecule which is a 3 carbon chain (before dehydration synthesis it contains hydroxyl groups on all of the carbons) covalently bonded to 3 fatty acids (named so because the molecule is hydrophilic (fatty) and it contains a carboxyl at the end of the chain (acid)) creating the triglycerol molecule. Proteins—the primary structure of proteins are made up of amino acids which contain a central carbon with an amino group (amino), a carboxyl group (acid), and an Rgroup that contributes to its physical/chemical attributes o Polar Rgroups: contain hydroxyl, sulfhydryl, amino, and/or carboxyl o Acidic Rgroups: contain carboxyl causing a negative charge o Basic Rgroups: contain amino group causing a positive charge Nucleic Acids—the monomeric unit, nucleotides consist of a 5 carbon sugar (contains carbonyl and hydroxyl groups), covalently bonded to nitrogenous base (Nucleoside) and a phosphate group. 39. Compare the arrangement of phosphate groups in adenosine triphosphate and adenosine diphosphate. What is the biological significance of adenosine triphosphate? Adenosine triphosphate contains 3 phosphate groups bonded to each other and an adenosine molecule. When this molecule enzymatically reacts with water a phosphate is group is cleaved off to release energy and the Adenosine diphosphate molecule which consists of the adenosine molecule bonded to only two phosphate groups. The ADP molecule has the potential to interact with water causing the bond of a phosphate to break off the the rest of the ADP molecule releasing energy which is used in the cell. 40. Based on their chemical properties, which functional groups might be likely to interact with one another? Why? Hydroxyl groups are polar and can interact with other polar molecules because a slightly positive (hydrogen) or a slightly negative (oxygen) will attract to each other. Carbonyl groups are also polar and can interact in this way too. Carboxyl and phosphate groups at physiological pH have a () charge and can interact with any slightly positive pole of a polar functional group or atom as well as the (+) charge of Amino groups; Amino groups, in turn, can interact with any slightly negative pole of a polar functional group or atom. Sulfhydryl groups can interact with each other to create a disulfide bridge when the sulfur atoms of each bond after losing the hydrogen atoms they were originally bonded to. 41. Even though a methyl group contributes no polarity or charge to a molecule it’s a part of, one small methyl group added on to a molecule can nonetheless completely alter that molecule’s biological function. Explain this observation. Methyl groups do have mass and a 3D shape that will influence the molecule it's part of because of steric hindrance (bumping into other parts of the molecule) and because of its nonpolar structure it is hydrophobic and will repel polar molecules such as water causing the molecule its attached to to shift appropriately away from water. 42. In the case of a Dglucose molecule, what functional groups are present in the chain (linear) form, and what happens to the carbonyl when the molecule forms its more stable ring form? In the case of Dglucose molecule there are hydroxyl groups bonded to each carbon in the chain as well as a carbonyl group at the end of the chain (Aldose). The carbonyl carbon is labeled as Carbon #1 and when the molecule forms a ring, this carbon folds back on the molecule and remains bonded to the hydrogen it was originally bonded with but the oxygen it was double bonded to picks up the hydrogen from the hydroxyl group from Carbon #5. If this new hydroxyl group on Carbon #1 is below the plane of the ring (most of the time) it is called alphaglucose, if the hydroxyl group is above the plane (not as often) it is known as betaglucose. 43. What are monosaccharides and how are pentoses different from hexoses? Which class does glucose fall into? Monosaccharides (ie Glucose) are the monomer units of polysaccharides such as starches. Glucose is classified as a pentose which is a 5carbon chain compared to a hexose which is a 6carbon chain sugar. 44. What are disaccharides? Name one commonly found in nature and describe its “function” (in a biological context). Disaccharides are sugars composed of two monosaccharides bonded together by a glycosidic bond which occurs after dehydration synthesis causes a hydroxyl group to be broken apart causing an oxygen atom to be the bridge between the two monosaccharides. A common disaccharide is sucrose which is a combination of glucose and fructose commonly referred to as table sugar. Sucrose is used primarily in plants to transport carbohydrates from leaves to roots and other nonphotosynthetic organs. 45. How is the synthesis of large biological macromolecules like carbohydrates and proteins an example of a dehydration reaction? The synthesis of polymers from monomers is a dehydration reaction because a new bond forms between two monomers when each contributes part of water molecule. The first monomer contributes a hydrogen atom while the other contributes a hydroxyl group creating H2O to be removed from the combination of the molecules. 46. In the oppositeor hydrolyticreaction, where is the "hydrolysis" occurring (using carbohydrates as an example)? A hydrolysis reaction is when a water molecule is added to break a bond between two monomer units that were previously bonded. In a carbohydrate we see the carboxyl carbon (carbon #1) of the first monomer lose its hydroxyl group and the carbon #4 of the second monomer lose a hydrogen off the attached hydroxyl group causing what is referred to as a 1,4 glycosidic bond. 47. How is the alpha form of Dglucose different from beta Dglucose? How does the interconversion between the two forms take place? Alpha Dglucose is a ring formation where the hydroxyl group attached to Carbon #1 is below the plane of the ring whereas beta Dglucose has this hydroxyl group above the plane of the ring (less common). 48. How do the conformations of the alpha 1,4 and beta 14 polymers of Dglucose differ? At the biochemical level, what explains the difference in conformation between the two? Alpha 1,4 polymers of Dglucose (starch) link all facing the same orientation by a glycosidic bond at the 1 and 4 carbons with the hydroxyl group off carbon #2 facing down. Beta 1,4 polymers of Dglucose (cellulose) must alternate their orientation with the hydroxyl group on carbon #2 of the first monomer facing up and the next one facing down in order for the 1 and 4 carbons to form a glycosidic bond. Because of the flipped orientation of the hydroxyl group on Carbon 1 in beta Dglucose compared to alpha Dglucose, the whole molecule must orientate upside down in order for the dehydration synthesis to occur between the the two monomers. 49. How is the structural difference between the alpha 14 and beta 14 polymers of glucose related to their distinct biological functions? Alpha 1, 4 polymers of glucose can be used as stored energy in plants in a form called starch and in a form in animals known as glycogen. Plants have a simpler form of starch called Amylose which is a single chain polysaccharide and a more complex form called Amylopectin which contains some branches of polymer chains which can be cleaved by hydrolysis when the plant requires energy. Animals contain glycogen as stored glucose that contains many branching chains because animals require more access to the glucose more of the time which is used in cellular work. Beta 1, 4 polymers of glucose form hydrogen bonds between parallel cellulose chains and form microfibrils as bundles and are very rigid. The rigidity of the structure contributes to the hard “shell” of plant cell walls. 50. Why does the bulk of the plant material we eat go undigested (compared to, say, the plant matter eaten by a cow)? The bulk of plant material is made of cellulose which most animals do not digest because of the beta linkage structure of cellulose and the lack of enzymes to break the linkages down. During digestion the cellulose abrades to the lining of the intestine causing a mucus release to help fecal matter move out. This cellulose is referred to as insoluble fiber. There are microorganisms that can break down the bonds of cellulose polymers into glucose monomers which humans do not have for the most part (some exist in our large intestine) but a cow does have in its stomach to help it break down the hay and grass that makes up most of its diet. 51. How are the structure and properties of proteoglycans related to their function as part of the extracellular matrix? Proteoglycans consist of a small core protein with many carbohydrate chains covalently bonded. This molecule is bonded covalently to a polysaccharide molecule to form a complex. These complexes can then contribute structural rigidity to the extracellular matrix which is a meshwork of the eukaryotic cells, proteoglycans, polysaccharides, and glycoproteins. Structures called glycosaminoglycan structures are sugars and amino groups bonded with other functional groups (usually sulfate) to form polar molecules such as chondroitin sulfate which are negatively charged and can interact with water molecules which make up most of the extracellular fluid surrounding cells. 52. Explain how the difference in structure between large, structurally simple polysaccharides (think starch or cellulose) and small structurally complex polysaccharides (like those found on the cell surface glycoproteins) is related to their distinct functions. Large simple polysaccharides are considered storage and structural polysaccharides with only a few specific tasks such as storing glucose for later energy accessibility or creating rigid strong structures in plant cell walls. Smaller more complex polysaccharides such as glycoproteins have a wider array of functions because of the addition of diverse molecules such as a protein molecule. The glycosylation of proteins (enzymatically binding of a carbohydrate to a protein) creates way more opportunity for diversity in structure, and thus, more diversity in function. An example are the vast numbers of cell receptors on cell membranes looking to bind with many different types of molecules for many different types of reasons. (ie self/non self recognition of the body in the immune system) 53. What is the structure of glycerol? Of a fatty acid? How are these molecules related to triacylglycerols? A glycerol molecule is considered an alcohol. It is a 3 carbon chain with hydroxyl groups and hydrogens on each carbon. A fatty acid is a chain of hydrocarbons with a carboxyl group at the end. When three fatty acid chains covalently bond via dehydration synthesis to a glycerol it is referred to as a “fat molecule” or triglycerol. 54. What makes a fatty acid "saturated," as opposed to "monounsaturated" or "polyunsaturated," and how does the level of fatty acid saturation affect the physical/chemical properties of a triacylglycerol? When a fatty acid is “saturated,” it refers to a triglycerol molecule with no double bonds between the carbon atoms composing a chain because there are just as many hydrogens “saturating” the chain as there are carbons. An unsaturated fat contains one or more cis double bonds in the chain of carbons in the fatty acid chain causing a bend in the chain. When there is only one double bond
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