∙ The outermost energy level of an atom where electrons orbit
∙ The measurement of an atoms ability, in comparison to other atoms in a
molecule, to pull electrons towards it, causing those electrons to orbit the atom with higher EN more of the time
∙ A combination of elements formed from two ions (atom loses e, atom gains e)
∙ A combination of two
elements formed from two atoms with open space in their valences shells
∙ A single structure made up of two or more atoms
Polar Covalent Bond
∙ A bond where e are shared between two atoms with e density focused around one atom more than the other Dipole
∙ A condition of a molecule where two polar bonds We also discuss several other topics like What is a limited liability partnership?
occur and the slightly
positive charges of that
molecule push towards or away from eachother
Nonpolar Covalent Bond ∙ A bond where e are shared between two atoms with no distinction between where the e density is most of the time
∙ The connection formed between two atoms when one atom loves an e and the other gains it
∙ Atom of an element that gained e in an ionic bond Cation
∙ The atom of an element that lost an e in an ionic bond If you want to learn more check out What is cross-sectional survey design?
∙ The force of attraction between a hydrogen atom
in a polar molecule to the opposite partial charge of an atom in a separate
∙ Attractive forces that occur between molecules when they are close enough
together because at any time a molecule may have a higher concentration of electrons in one region,
attracting it to the region of another molecule where electrons may not be as concentrated at the
∙ The linkages of water molecules because of the hydrogen bonds that form between partially positive hydrogen of one molecule and partially negative If you want to learn more check out How do you calculate coefficient of performance?
oxygen of the next
∙ Clinging of molecules to another object by hydrogen bonds Don't forget about the age old question of What kind of isomers have the same formula and the same connectivity, but different spacial arrangement?
Specific Heat If you want to learn more check out What is manipulation variable?
∙ The amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1°c
∙ The energy of motion, usually related to particle movement. Faster
movement means, higher kinetic energy, means
increase in temperature
∙ Average kinetic energy in a body of matter regardless of volume
∙ The transfer of thermal energy from one body of matter to another
∙ Amount of energy required to raise 1g of water by 1°c Solution
∙ The combination of a solute being dissolved in a solvent in a specific ratio
∙ Usually a solid that is dissolved or added to a
solvent or liquid of some kind
∙ Usually a liquid (water) that can have a solute or solid dissolved in it
Hydration Shell We also discuss several other topics like What is another word for realization?
∙ The sphere of water that surrounds ions of a solute being dissolved.
∙ Any substance that can interact with water
∙ Substances that are
nonionic and nonpolar
(cannot form hydrogen
bonds) that repel water
∙ Have both hydrophobic and hydrophilic regions on a
∙ A substance that increases the hydrogen ion
concentration of a solution Base
∙ A substance that reduces hydrogen ion concentration of solution sometimes by increasing hydroxide ion concentration
∙ A substance that minimizes changes in the
concentrations of H+ and OH in a solution. Accepts H+ ions from solution when they are in excess and
donates H+ when depleted Structural Isomer
∙ A molecule with the same formula as another but with different covalent
Cis/Trans (Geometric) Isomer ∙ A stereo isomer where one molecule has two atoms on the same side (Cis) and the other has the same atoms but opposite each other on the molecule (Trans)
∙ When an atom (usually C)
is bonded to 4 different
∙ Stereo Isomer where
molecules with the same molecular formula but
cannot be transposed on one another because they are mirror images
∙ Identical phys/chem
properties except when
exposed to plain light. One will rotate one direction, the other will rotate the
opposite at same degree. ∙ Referred to as L&D isomers Hydroxyl
∙ Functional group of atoms with an Oxygen bonded to a Hydrogen that is
connected to an R group (rest of the molecule)
∙ Functional group of atoms with carbon double bonded to oxygen, single bonded to hydrogen, and the R group Aldehyde
∙ If carbonyl group is at the end of a carbon chain
∙ If carbonyl group is in the middle of a carbon chain Carboxyl
∙ Functional group of atoms with Carbon double bonded to an oxygen atom and
single bonded to a hydroxyl group. Group is ionic if it loses a Hydrogen (p+)
∙ Functional group of atoms with Nitrogen bonded to 2 hydrogen atoms. Group is positive if it gains a
∙ Functional group of atoms with phosphorus covalently bonded to 4 oxygen atoms (one double bonded)
Contains to full negative charges making group ionic ∙ Found in subunits of DNA Methyl
∙ Functional group of atoms with carbon bonded to 3 hydrogen atoms and R
∙ Functional group of atoms with sulfur bonded to
∙ Slightly polar and can undergo oxidation reactions to yield disulfide bonds
∙ Disulfide bonds found in proteins used to stabilize Dehydration Synthesis
∙ Enzymatic combination of molecules that causes the removal of a molecule of water
∙ Bonds are broken by the addition of a water
molecule when the
attaches to one molecule and the hydroxyl attaches to another
∙ Polar molecule consisting of a carbon chain, hydroxyl and carbonyl groups
∙ Ring structure in aqueous solution when chain folds back on itself to create new chiral center—brings
carbonyl closer to hydroxyl group
∙ Linking of two
causing the remaining
oxygen molecule to create a glycosidic bond between the two molecules
∙ Linking of multiple
glycosidic bonds via
∙ 2 different kinds of starch found in plants.
o Starch is a polymer of alphaglucose linked 1,4
o Forms helical coil shape when partially + oxygen
and partially – hydroxyl
attract (INTRAmolecular bonding)
∙ Amylose is a polymer that exists as a single chain with no sugar groups branching off the main chain
∙ Amylopectin is similar but does have sugar branching about every 20 units
∙ The starch that exists in animals with more frequent sugar branching (about
every 8 units)
∙ More branches exist for enzymatic cleaving to
expose more ends for
∙ The bond that links to monosaccharides via an oxygen atom that was left behind after dehydration synthesis
∙ Polymer of betaglucose linked 1,4 that is the main component of plant cell
∙ Betaglucose links together when one is inverted and they stack in linear fashion held together
∙ Similar to cellulose
structure but fibers are
wrapped in a protein
∙ Presence of amino group (Nacetyl) on Carbon 2
∙ Proteins connect to
branching carbohydrates to form a network in
o Molecular meshwork outside of cells that
∙ Branching carbs that are covalently bonded
∙ Sugar molecule with amino group and other (usually sulfate) polar functional
∙ Negatively charged and hydrophilic
∙ Chondroitin sulfate
∙ Carbohydrates attached to proteins by glycosylation
which contributes to
specificity of molecular
∙ 6 carbon monosaccharide used for energy when
bond with another glucose is broken via dehydration synthesis
∙ 6 carbon monosaccharide Aldose
∙ Sugar with carbonyl
groups at the end of the carbon chain
∙ Sugar with carbonyl group in the middle of the carbon chain
∙ Hydrophobic, non polar biomolecule used for
o Stored as triglycerides ∙ Make up phospholipids in cellular membranes
∙ Signaling molecules such as steroid hormones and inflammation signaling
∙ Glycerol and 3 fatty acids covalently bonded via
o Glycerol is an alcohol whose 3 carbons have
∙ Energyrich molecule can be stored in adipose tissue in animals and oil droplets in plants (seeds for
embryonic development) Fatty Acid
∙ Long hydrocarbon chains which are non polar (fatty) and a carboxyl group (acid) at the end of the chain
Essential Fatty Acid
∙ Fatty acids that are not created in the body
naturally and must be
obtained through the diet Phospholipid
∙ Similar to triglyceride
except only 2 fatty acids linked to 2 carbons and the third is linked to phosphate group ( charge). The
phosphate group is then linked to an Rgroup (polar, ionic group usually choline,
serine, or inositol)
∙ Amphipathic molecule o “head” contains
phosphate and glycerol is hydrophilic/polar
o “tail” contains 1 saturated and 1 unsaturated fat is
∙ component of bilayer in cell membrane that creates
∙ part of cell membrane structure
∙ not based on backbone of glycerol but on Sphingosine o Sphingosine contains large hydrocarbon tail and fatty acid covalently
bonded to the Nitrogen
and another group
(usually phosphocholine) on an oxygen atom
∙ Carbohydrates bonded to lipids
Saturated Fatty Acid
∙ Single bonds along carbon chain to max number of
∙ Linear and can stack which attributes to their high
∙ Butter/animal fats
∙ Trans position compared to Unsaturated fatty acid
Unsaturated Fatty Acid ∙ 1 or more double bonds along carbon chain to only 1 hydrogen
∙ Lower melting point
∙ Usually an oil (liquid at room temperature) because of Cis orientation that
creates a bend making
them unable to stack like saturated fats
∙ Carbon skeleton consisting of four fused rings
∙ Enzymatically modified from cholesterol
∙ Cholesterol is a common component of animal cell membranes is also the
precursor form which other steroids such as
testosterone and estrogen are synthesized.
∙ Protein Complex that
∙ Smallest Amino acid with only a Hydrogen atom for its Rgroup and no chiral Carbon
∙ Nonpolar amino acid with Rgroup bonded to the
chiral carbon and the
nitrogen of the amino
∙ Polar amino acid with a sulfhydryl group that can become disulfide bond
when oxidized for protein structure stabilization
∙ Covalent bond that forms where two molecules
(usually in cysteine
monomers) are brought
close together so the sulfur of each molecules
sulfhydryl group bond via dehydration synthesis.
∙ Linkage between two amino acids so that the carboxyl group of one joins the
amino group of the other through dehydration
∙ When two monomer units known as amino acids they form a peptide. A polymer of these units is a
∙ Complex of two or more polypeptides
∙ The open amino group end of a chain of polypeptides Cterminus
∙ The open carboxyl group end of a chain of
∙ The addition or removal of a phosphate group from a molecule (usually in the
enzymatic reaction of ATP to ADP and visa versa)
∙ The sequence of amino acids that are dictated by a gene in creating the 1st step of a protein
∙ The 2nd step in protein synthesis created by local folding of interactions by functional groups and
hydrogen bonds between the backbone functional groups
∙ Carbonyl and amino groups hbond with each other
∙ Coil structure that forms during secondary structure because of local folding and hbonds
∙ Rgroups all face out to be able to bond
∙ When Hbonds are
interrupted because of
certain amino acid
sequences causes linear structure/strands hbond to adjacent strand causes
sheets made of strands
o Sequences that form ionic bonds—stronger than H bonds
o Large Rgroups (carbon rings) cause steric
hindrance cause groups to “bump” into each other o Rgroup bonding to amino group (Proeline“helix
breaker”) prevents that
group from Hbonding
∙ Rgroups alternate up/down position
∙ 3rd step in protein synthesis by Rgroup interactions
creates 3D structure and fullyfunctional polypeptides o Ionic bonds between (+) basic side chains and () acidic side chains
o Hbonds between polar groups
o Covalent linkages
o Nonpolar interactions by hydrophobic interactions with water causing groups to be pushed together
o Proteins with bulky shape that have tertiary and
o Proteins that are fully functional with only
secondary structure and remain linear
o Structural support roles o Hbonds and covalently bonds with other fibrous proteins to form networks either within or outside
∙ Collagen: main protein component of
∙ Keratin: protein
structural support inside
cells called the
∙ Combination of two or more protein chains called
∙ Protein structure that
proteins from hydrophobic conditions that may cause misfolding
∙ The detrimental unfolding of a protein caused by heat or a detergent that breaks
bonds within the complex Invariant Residue
∙ Amino acids in a sequence that would be detrimental to the protein if it were
substituted for another
∙ ie a polar for a nonpolar substitution or an acidic for a basic substitution
Conservative Substitution ∙ substitution of an amino acid with similar properties that would not drastically affect the structure of a
∙ ie polar for polar
∙ DNAthe blueprint used to store genetic info by all
∙ Genetic info storage for proteins and other
∙ RNAcopied from DNA and allows the info it encodes to be expressed as a useful cellular product
o mRNAProteincoding messenger RNA that is
copied from protein
coding genes, specifies
amino acid sequence in proteins. Translated at
the ribosome cell
o tRNA (Transfer RNA) Nonproteincoding RNA used for transporting
correct amino acid
sequence to ribosome
during protein synthesis
o rRNA (Ribosomal RNA) Nonproteincoding RNA which is part of the
o miRNA (Micro RNA) nonproteincoding RNA
used to regulate the
expression of genes by
interacting directly with
DNA or with mRNA copy. Also determines whether proteins get synthesized or not
∙ the monomeric unit of nucleic acids.
∙ Consists of a 5carbon sugar covalently bonded to a nitrogenous base
∙ Sugar is covalently bonded to 1 or more phosphates Nucleoside
∙ The combination of the nitrogenous base and the sugar
∙ Depending on how many phosphate groups are
bonded to the nucleoside – monophosphate,
∙ Polymeric unit of multiple nucleotides bonded
∙ Bond between the hydroxyl of the 3’ carbon on the
preceding sugar to the first phosphate group on the 5’ carbon on the nucleotide
∙ Bonds are created in this directionality from 5’ to 3’ along the polynucleotide chain with new nucleotides being added to 3’ end
∙ Nitrogenous bases with 2 fused rings
∙ Adenine and Guanine Pyrimidine
∙ Nitrogenous bases with 1 ring
∙ Cytosine, Uracil, and Thyamine
∙ The sugar structure of the
∙ The sugar structure of the DNA molecule
∙ The most common
structural form of DNA
∙ 2 nm diameter, 10 base pairings per turn of the
∙ The wider of 2 grooves of the DNA molecule where proteins can bind
∙ The smaller of 2 grooves of the DNA molecule
where proteins can bind Histone
∙ DNA binding proteins
∙ DNA with about 150 base pairs is wrapped twice
around a complex of 8
∙ Compacts DNA in an organized fashion and
regulates DNA and its
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 the product of the H+ and OH ions is constant at 1014 with 107 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 it is referred to as monounsaturated, more than one double bond forms a polyunsaturated fatty acid.
∙ Saturated fats at room temp are usually solid (butter or lard) because the molecules are packed more tightly together. Unsaturated fats are usually a liquid (oil) at room temperature because the molecules cannot pack tightly because of kink(s) in the chains.
55. Why does it make some sense that tropical oils and mammal fats should contain a higher prevalence of saturated fatty acids compared to coldclimate plants or coldblooded animals?
∙ Tropical oils and mammal fats are usually saturated fats because fats are used to store energy and since animals are mobile it is important for them to be able to carry these stores around with them as fat in adipose cells which also act as cushion to protect internal organs. Tropical oils (coconut oil) needs to have a higher melting point because of warmer weather/environments. Lipids are considered smaller molecules that polysaccharides and are more efficient to store than large polysaccharide molecules that provide about half the amount of stored energy per gram.
∙ Plants are immobile and coldblooded animals live in cold (water) environments where a more liquid form of fat with a lower melting point is more structurally efficient. Plants can rely mostly on the starch they store for energy instead of tightly packed molecules of fat.
56. What is a phospholipid, and how is its structure related to but distinct from that of a triacylglycerol? ∙ A phospholipid is a molecule of a head section and a tail section that in a bilayer structure (tail to tail) creates the basis for the cell membrane in eukaryotic cells. The hydrophilic head consists of a glycerol (similar to a triglycerol) bonded to a phosphate group and an additional small charged or polar molecule such as a choline molecule. These heads face out toward extracellular fluid (mostly water) and in toward the cytoplasm (mostly water) inside the cell. The tails consist of hydrophobic molecules of two fatty acids (triglycerol has 3 fatty acids) that face in toward each other. 57. What is a sphingolipid, and how is its structure related to that of a phospholipid?
∙ Sphingolipids are also part of the cell membrane structure but not based on the backbone of glycerol molecules. They are based on the Sphingosine molecule which contains a large hydrocarbon tail and a fatty acid covalently bonded to the nitrogen of another group on an oxygen atom—Phosphocholine.
58. Phospholipids are described as being amphipathic. At the biochemical level, what is meant by this term and how does this property relate to the role of phospholipids in cellular membranes?
∙ Amphipathic refers to the molecule having a polar and a nonpolar end. The head of the phospholipid has a polar hydrophilic head that interacts with water inside (cytoplasm) and outside of the cell (extracellular fluid). The nonpolar hydrophobic tails interact with each other because the water on the outside has repelled them toward each other.
59. Why is the collection of lipids in the plasma membrane more accurately referred to as a macromolecular aggregate than a macromolecule (like carbs, proteins and nucleic acids)?
∙ The lipids in the plasma membrane are referred to as aggregate because the phospholipids that help make up the membrane are not all the same combinations of molecules. Some of the phospholipids which have the same main components of glycerols, fatty acids, and phosphate groups, there is an array of polar molecules such as choline that are bound to the phosphate. Also, not every lipid in the membrane are phospholipids—some can be sphingolipids or others depending on their specific function in the membrane. Carbs, proteins, and nucleic acids follow a stricter formula; lipids can vary in their composition.
60. What is cholesterol, and how does it affect the physical properties of the cellular membranes that it is a part of?
∙ Cholesterol is a type of steroid (a lipid with a carbon skeleton of 4 fused rings) which is synthesized in the liver and obtained from the diet that is an important precursor in the formation of sex hormones. Cholesterol has a short hydrocarbon tail that interacts with the nonpolar tails of phospholipids and a hydroxyl group bonded l that interacts with the hydrophilic heads of phospholipids. In animals, the phospholipid bilayer may stack too tight (colder conditions) cholesterol is produced to break this up and create more fluidity; if the bilayer stacks too loosely (warmer conditions) cholesterol’s tail end will help stabilize interactions between adjacent phospholipids.
61. Is cholesterol a component of all the plasma membrane in all organisms? Explain your answer. ∙ Cholesterol is found in all animal’s cell membranes but not in plants. Plants use phytosterols in their membranes in the same way animals use cholesterol.
62. How does cholesterol relate to the general class of nonpolar molecules known as steroids? ∙ Cholesterol is a steroid defined by its 4 carbon rings fused. However, cholesterol specifically contains a short hydrocarbon chain and a hydroxyl group.
63. What chemical groups are attached to the alpha carbon in a typical amino acid? Which of these is/are consistent across all kinds of amino acids, and which is/are variable?
∙ All amino acids contain a hydrogen, an amino group, and carboxyl group off the alpha carbon. The only group that changes is the Rgroup off the central carbon.
64. What determines if an amino acid is classified as "polar," "nonpolar," "chargedacidic," or "chargedbasic"? ∙ The variation in the Rgroup on amino acids will classify them differently:
o Nonpolar amino acids have Rgroups that are solely hydrocarbons
o Polar amino acids have Rgroups with hydroxyl, carbonyl, and/or amino functional groups
o Charged acidic () amino acids have Rgroups with a carboxyl functional group
o Charged basic (+) amino acids have Rgroups with an amino functional group
65. What is “special” about the three amino acids we highlighted (glycine, proline and cysteine)? ∙ Glycine is the smallest amino acid consisting of only one hydrogen atom for it's Rgroup making it the only amino with no chiral carbon center
∙ Cysteine contains a sulfhydryl group that can form a disulfide bond when it encounters another sulfhydryl group used to provide more stabilization for a protein structure.
∙ Proline contains an Rgroup that is bonded to the chiral carbon and the nitrogen in the amino group off the chiral carbon. 66. What is the "NCC backbone" of a polypeptide, and what is meant by an "amino" and a "carboxyl" terminus of a protein?
∙ The NCC backbone refers to the pattern of nitrogen, carbon, and carbon that always forms when amino acids bond to each other. The amino terminus is the open end of the polypeptide with the amino group present (Nterminus) and the carboxyl terminus is the open end of the polypeptide where the carboxyl group is and the next amino acid could bond to (C terminus).
67. What is the primary structure of a polypeptide and in what sense does it "dictate" higher levels of protein structure? ∙ Primary structure is the first step in forming a fully functioning protein and it is dictated by a gene that creates the sequence in which amino acids covalently link in linear fashion. It is this first structure that will lead to the higher levels of protein structure because of the Rgroups interaction with each other by intramolecular forces from their polar, nonpolar, full negative (acid) or full positive (base) charges.
68. Explain the observation that a mutation that changes one amino acid in a protein could have A) no effect on the protein’s structure/function, B) a moderate effect or C) ablate function altogether. What factors might allow you to predict the potential consequence of any such change?
∙ A mutation could cause a substitution of an amino acid of the same class (polar, nonpolar, acidic, or basic) that may have no effect on the proteins structure because the charges would be the same causing it to interact with the rest of the protein in the same way it would have. This would lead to the protein functioning correctly and causing little or no “problems” when physically expressed. Also referred to as a conservative substitution.
∙ A mutation could cause a substitution of an amino acid of the same class but maybe of a larger/smaller size that could moderately effect the rest of the structure. Depending on where this substitution takes place this could slightly change the functionality of the protein.
∙ A mutation could cause a substitution of an amino acid of a different class (polar for nonpolar, acidic for basic) that could totally change the structure and thus the function of the protein, perhaps causing it not to function properly at all. This could lead to serious problems when the characteristic is expressed physically depending on where the substitution in the protein occurs. Also referred to as Invarient Residue.
∙ When considering what the potential consequences might be, you can consider what the class of the amino acid being substituted is and how it will interact with the amino acids near by causing it to change its potential secondary structure. 69. What are the principal motifs in the secondary structure of proteins, and what type(s) of chemical interactions stabilize these structural motifs?
∙ Secondary structure is based on the interactions of the Rgroups of the amino acid sequence from the primary structure. This leads to intramolecular forces between the Rgroups of the amino acids (not adjacent amino acids, about every 4th group) via hbonding.
∙ Hbonds also form between the polypeptides functional groups, and carbonyl and amino groups dipole interactions. These interactions lead to the formation of the alphahelices.
∙ Interruptions to the hbonds lead to bstrands forming and come from the formation of ionic bonds between fully charged amino acids, steric hindrance of large Rgroups bumping into each other or in the case of Proline (“helixbreaker”) an amino group being bonded to an Rgroup and preventing it from Hbonding elsewhere.
∙ Reverse turns occur in the structure when hbonds form between backbone functional groups such as amino acids carbonyl oxygen and the amino hydrogen about 3 acids away causing the structure to fold back on itself.
71. What type(s) of chemical interactions stabilize a polypeptide's tertiary structure? Which of these forces are "strong" and which are "weak"?
∙ A polypeptides tertiary structure is a 3D fully functional folded polypeptide chain that gets its structure from a few different interactions.
o Strong interactions include ionic bonds between charged basic and charged acidic Rgroups and covalent linkages such as disulfide bridges between sulfhydryl functional groups
o Weak interactions are between Hbonds of polar Rgroups and nonpolar interactions that are forced together because of their hydrophobic characteristics.
72. What is quaternary structure? Do all proteins have quaternary structure? Explain your answer. ∙ Quaternary structure forms from the same interactions of the tertiary structure but is considered quaternary because it brings together two or more tertiary structures to be called a complex. Not all proteins have quaternary structure, however, some proteins are fully functional at their tertiary structure and do not need to combine with another protein. ∙ Proteins that reach tertiary and quaternary structure are referred to as globular. Some proteins function fully at secondary structure and are called fibrous. Fibrous proteins are structural support proteins and often hbond with other fibrous proteins to form networks in or outside of cells
o Collagen: main protein component of extracellular matrix (secondary structure)
o Keratin: protein structural support inside cells called the cytoskeleton (secondary structure)
73. At the molecular/biochemical level, why does heating up your egg in a skillet cause the egg white to turn white and solidify? Are all proteins equally sensitive to heat? Explain your answer.
∙ When an egg is heated it turns white because this is a sign that the proteins in the egg white have denatured. Denaturation occurs when the bonds holding a protein in its tertiary or quaternary structure are broken and it reverts to a more linear secondary structure. Most proteins can be denatured by heat, however, some can be denatured by transferring them to a nonpolar solvent causing the hydrophobic regions to refold the “wrong” way. Other chemicals can cause hydrogen, ionic, and disulfide bonds to be broken causing the protein to denature as well.
74. At the molecular/biochemical level, how can pH changes lead to denaturation of a protein? ∙ pH changes can cause denaturation of a protein because proteins function properly at physiological pH which is around 7 (neutral) and if they are transferred to a solution (or solution changes) this will affect how the Rgroups interact with the pH of the fluid they are in (extracellular fluid). For example, if a protein has acidic Rgroups interacting properly with extracellular fluid and that fluid becomes more acidic (less H+ available to bond with) this could cause the protein to lose functionality.
75. What role do chaperonins play in protein folding? Do all proteins require chaperonins? Explain your answer. ∙ Chaperonins act as a protective cylinder for proteins to properly fold before they are released into a watery environment. A proteins hydrophobic attributes could cause it to misfold if it is not ready to be exposed to water so the chaperonins act as a shelter until they are ready. Not all proteins require this, only those that could be influenced by potentially harmful hydrophobic interactions.
76. What is a functional domain on a protein, and what are some examples of functions of protein domains? ∙ Functional domains of proteins are areas on proteins where other molecules can bind to them to perform an important function in the cell.
o Alphahelices have transmembrane domains for DNA binding. These sites function for transcription factors that influence DNA gene expression. Alphahelices also bond with phospholipid bilayers of cell membranes at certain domains on the spiral
o Betasheets create structural rigidity and have flat surfaces called interaction domains. These domains interact with the cell membrane and can form betabarrels (hollow cylinders to allow the transfer of materials in/out of the cell)
77. What is the relationship between the structural diversity found in proteins and the functional diversity they exhibit? ∙ There are 20127different combinations of a polypeptide chain 127 amino acids long and every specific combination has a specific function in the cell. There are specific proteins for binding and transporting specific materials in and out of cells so the structure, starting from the primary structure, is extremely specific to its function.
78. How can comparison of a conserved protein’s amino acid sequence across species provide useful information regarding evolutionary relationships?
∙ When comparing the conserved protein’s amino acid sequence across species we can see that some of the proteins are absolutely necessary for life as we know it. They were preserved by natural selection through species evolving over millions of years because with out those proteins, life would cease to exist. We see that the more in common two species have, the more they are closely related and have descended from one another (share a common ancestor).
79. How can comparison of a conserved protein’s amino acid sequence across species provide useful information regarding the structural/functional significance of its primary structure?
∙ When comparing a conserved protein’s amino acid sequence across species we see that by natural selection, the more proteins that had been preserved the more necessary they are to survival. The more variation in amino acids within a protein the less important its specificity is to that protein. This means that primary structure is slightly less important (more substitutions can be made) to the functionality of that protein.
80. What are the parts of a ribonucleotide, and how is the structure of a deoxyribonucleotide different? ∙ A ribonucleotide consists of a ribose sugar (pentose) which has a hydroxyl group off Carbon 2’ bonded to a nitrogenous base at Carbon 1’ and a phosphate group at Carbon 5’. The nitrogenous bases of a ribonucleotide can be adenine, guanine, cytosine, and uracil.
∙ A deoxyribonucleotide consists of a deoxyribose sugar (pentose) which only has a hydrogen atom off Carbon 2’ (hence deoxyribose) bonded to a nitrogenous base at carbon 1’ and a phosphate group at carbon 5’. The nitrogenous bases of a deoxyribonucleotide can be adenine, guanine, cytosine, and thymine.
81. What are some examples of coenzymes whose structure is basically that of a mono or dinucleotide? ∙ ATP (adenosine triphosphate) is an example of a ribonucleotide used in the enzymatic release of energy. ∙ NAD is a coenzyme which is an important part of the catalysis of REDOX reactions in cells including those used to oxidize glucose for energy.
82. What are the nitrogenous bases, and which are purines and which are pyrimidines? What is the "sugarphosphate backbone" of a polynucleotide, and how does it specify both a 3' (threeprime) and a 5' (fiveprime) end? ∙ Nitrogenous bases are rings that contain nitrogen atoms that tend to take up H+ from solution causing it to act as a base. They are divided into two families based on their structure:
o Pyrimidine: one sixmembered ring of carbon and nitrogen atoms. Consist of cytosine, thymine, and uracil. o Purines: sixmembered ring fused to a fivemembered ring of carbon and nitrogen atoms. Consist of adenine and guanine.
∙ The sugarphosphate backbone of a polynucleotide consists of the pentose sugar (either ribose in RNA or deoxyribose in DNA) and a phosphate group bonded to the 5’ carbon of the sugar. The 5’ end of the backbone refers to the #5 carbon on the sugar bonded to the phosphate and the 3’ end refers to the #3 carbon on the sugar where new phosphate groups of new nucleotides are bonded on. A nucleotide back bone always builds in the 5’ to 3’ direction where new nucleotides are added to the 3’ end.
83. DNA can be described as a righthanded double helix with complementary, antiparallel strands. Explain what is meant by each of these terms.
∙ DNA is formed when the polynucleotide built 5’ to 3’ going down forms hydrogen bonds with the complementary nitrogenous bases (A with T or U, C with G) of another polynucleotide built 5’ to 3’ going up. This opposite direction refers to the anti parallel strands that forms a double helix shape.
84. Explain why the polymerization of mononucleotide triphosphates into nucleic acids does not require outside energy input whereas the dehydration synthesis of polysaccharides from monosaccharides does. ∙ The polymerization of mononucleotide triphosphates into nucleic acids does not require outside energy because of the enzymatic cleaving of an inorganic phosphorous off the triphosphate in order for the monomer to join with another. When
this bond is broken energy is released and is immediately used to create the bond between the mononucleotide and the next mononucleotide. In polysaccharides there is no triphosphate molecule available for cleaving and energy release so dehydration synthesis requires an enzyme and outside energy to create the glycosidic bond.
85. What chemical forces are primarily responsible for the structural stability of the DNA double helix? ∙ The main forces responsible for the structural stability of the double helix are the strong sugarphosphate backbones running antiparallel to each other and the nitrogenous base pairings that form hydrogen bonds. The pyrimidines form 3 hydrogen bonds while the purines form 2 hydrogen bonds.
86. What are B DNA, A DNA and Z DNA? Which is most relevant in a biological context?
∙ BDNA is the most relevant in a biological context and the most common blueprint of genetic information because of its symmetrical structure.
∙ ADNA is a form where DNA is being copied to make RNA and its structure is much shorter and wider ∙ ZDNA is a lefthanded helix with a backbone that is slightly staggered and uneven.
87. What is the significance of the major and minor grooves of DNA in terms of function and regulation? ∙ BDNA has two major grooves that can be seen in the double helix where proteins interact with the DNA molecule. 88. What chemical forces lead to the formation of stable secondary and tertiary structure in a molecule of RNA? What is the significance of RNA tertiary structure?
∙ RNA molecules are singlestranded molecules with intramolecular hydrogen bonding that leads to a diverse secondary and tertiary structure. Back folding within the molecule leads to the tertiary structure which forms to allow amino acids to bind to it. Its shape allows it to fit in a specific binding sight with a ribosome (tRNA).
89. Explain why ribonucleic acids are considered to be functionally more complex than deoxyribonucleic acid. What is the relationship between the structural complexity exhibited by cellular ribonucleic acids and this functional complexity?
∙ RNA is considered more functionally complex than DNA because of the various forms it takes and the specificity in function that these forms have.
o There is RNA specific for protein coding messaging called mRNA which is copied from protein coding genes and it specifies the amino acid sequence in proteins and is translated at the ribosome within the cell. o There is noncoding RNA, functional RNA, that carry out specific functions as RNA molecules based on their specific structure. tRNA transports correct amino acid sequence to ribosome during protein synthesis; rRNA is part of the ribosome itself. There are other forms of RNA as well including times when RNA serves as a catalyzing enzyme called ribozymes.