Biochem - Nucleotides, Sugars, Isomers Flashcards
Purines
Pure as gold
Short pure but big molecule
Pyrimidines
Cut the Py
Long name small molecule
Adenine
Guanine
Cytosine
Thymine
Uracil
Base pairs have how many purines and pyrimidines
1 purine
2 pydrimidines
Hydrogen bond acceptors and donors in DNA base pairing
Any nitrogen within these structures that has a hydrogen will be able to “donate” a hydrogen bond to any fluorine, oxygen or nitrogen that does not have a hydrogen. Note that if a given nitrogen has two hydrogens, it’ll only contribute one towards a hydrogen bond donation
Adenine, Thymine, and Uracil each have a single hydrogen bond donor and a single hydrogen bond acceptor.
Cytosine has a single hydrogen bond donor and two hydrogen bond acceptors
Guanine has a two hydrogen bond donors and a single hydrogen bond acceptor
Mnemonics for hydrogen pair acceptors and donors
theta TAU men are single” (theta tau is an engineering frat at my school that doesn’t allow cursing lmao) = thymine, adenine, and uracil have one H-donor and one H-acceptor
Guanine is generous” (selfless) = two H-donors but one H-acceptor
“Cytosine is a crafty” (selfish) = one H-donor but two H-acceptors
where does nitrogenous base attach to the sugar?
at C 1 to the right of O bond not on same side as chain piece
nucleotide vs nucleoside
nucleoside - nitrogenous base and sugar
nucleotide - nitrogenous base and sugar and phosphates
How are purines numbered?
Numbering always starts at Nitrogen
How are pyrimidines numbered?
Numbering always starts at N-H next to carbonyl and goes
ribose and deoxyribose hayworth
ribose fisher
deoxyribose fisher
fructose hayworth
fructose Fischer
glucose vs fructose hayworth
glucose epimers
mannose - C2 epimer
galactose - C4 epimer
explain epimers vs anomers
epimers are a sup type of Diastereomers (These molecules are chiral, share the same connectivity, #C, but are not mirror images of each other. They differ at some (but not all) of their multiple chiral centers)
anomers are a subtype of epimers
epimer = differs at ONLY 1 chiral carbon. ( ex: galactose is C4 epimer of glucose).
anomer = differs at the anomeric carbon (Ex : alpha DOWN/beta UP.)
mutarotation
The term “mutarotation” (literally “change in rotation”) refers to the observed change in the optical rotation of the α- and β- anomers of glucose upon dissolution in solvent. Due to ring-chain tautomerism, the α- and β- forms slowly interconvert until equilibrium is established.
anomer = differs at the anomeric carbon (Ex : alpha DOWN/beta UP.)
cyclic ring formation from Hayworth. How do you know what is up and down on ring?
things on left of carbon in fisher will be UP and things on right side of carbon in fisher will be DOWN
D vs L in fisher
R/S vs D/L vs +/- in molecules/sugars
R/S deals with absolute configuration at chiral centers within compounds. Thats it. The concept is not connected to polarization of light at all.
D/L deals with relative configuration of whole compounds compared to glyceraldehyde and it doesnt directly relate to direction of polarized light since this must be determined EXPERIMENTALLY
(+) and (-) notation corresponds to the optical activity of the substance, whether it rotates the plane of polarized light clockwise (+) or counterclockwise (-)
chirality
- identify most electronegative elements or paths (directions out from carbon
- number in priority where most EN is lower number
- Note if lowest priority (usually H) is wedged or dashed
If the #4 priority is on a dash its in back and no charge
- Clockwise = R
- Counterclockwise = S
If the #4 priority is on a wedge, reverse the typical rules:
- Clockwise = S
- Counterclockwise = R
if the #4 priority is in the plane (no wedge or dash):
- swap number 4 priority in plane with dash group and find R/S
- then flip the configuration
enantiomers vs diastereomers
Enantiomers are a pair of molecules that exist in two forms that are mirror images of one another but cannot be superimposed one upon the other. Enantiomers differ at their spatial arrangement around a chiral center
Diastereomers (These molecules are chiral, share the same connectivity, #C, but are not mirror images of each other. They differ at some (but not all) of their multiple chiral centers)
enantiomers
Enantiomers are a pair of molecules that exist in two forms that are mirror images of one another but cannot be superimposed one upon the other. Enantiomers differ at their spatial arrangement around a chiral center
Enantiomers have nearly identical physical properties and chemical properties, but they rotate plane-polarized light in opposite directions and react differently in chiral environments.
chiral
An object is considered chiral if its mirror image cannot be superimposed on the original object; this implies that the molecule lacks an internal plane of symmetry. Chirality can also be thought of as handedness.
The rule of thumb is: chiral carbon centers are carbon atoms that are attached to four different substituents, that are placed at the corners of a tetrahedron.
Chirality = handedness
chiral
Achiral objects have mirror images that can be superimposed; for example, a fork is identical to its mirror image and is therefore achiral.
molecules with 3 substituents are achiral as they can be rotated and superimposed on itself
constitutional isomers vs stereoisomers
constitutional isomers have diff connectivity but stereoisomers have same connectivity but different rotations (wedge/dash)
conformational vs configurational isomers
Conformational isomers or conformers differ in rotation around single (σ) bonds;
Conformational isomers arise from the fact tht varying degrees of rotation around single bonds can create different levels of strain (Newton projections)
configurational isomers can be interconverted only by breaking bonds.
Wherease trans cis double bond rotation is a conformational isomer
conformational isomers with newman projections
guache, anti, eclipsed and energy
cyclic conformations
ring strain arises from three factors: angle strain, torsional strain, and nonbonded strain (sometimes referred to as steric strain). Angle strain results when bond angles deviate from their ideal values by being stretched or compressed. Torsional strain results when cyclic molecules must assume conformations that have eclipsed or gauche interactions. Nonbonded strain (van der Waals repulsion) results when nonadjacent atoms or groups compete for the same space. Nonbonded strain is the dominant source of steric strain in the flagpole interactions of the cyclohexane boat conformation. To alleviate the strain, cycloalkanes attempt to adopt various nonplanar conformations.
The most stable conformation of cyclohexane is the chair conformation, which minimizes all three types of strain. The hydrogen atoms that are perpendicular to the plane of the ring (sticking up or down) are called axial, and those parallel (sticking out) are called equatorial. The axial–equatorial orientations alternate around the ring; that is, if the wedge on C-1 is an axial group, the dash on C-2 will also be axial, the wedge on C-3 will be axial, and so on.
chair flip
Cyclohexane can undergo a chair flip in which one chair form is converted to the other. In this process, the cyclohexane molecule briefly passes through a fourth conformation called the half-chair conformation. After the chair flip, all axial groups become equatorial and all equatorial groups become axial. All dashes remain dashes, and all wedges remain wedges. This interconversion can be slowed if a bulky group is attached to the ring; tert-butyl groups are classic examples of bulky groups on the MCAT.
For substituted rings, the bulkiest group will favor the equatorial position to reduce nonbonded strain (flagpole interactions) with axial groups in the molecule, as shown in Figure 2.7.
equitorial vs axial
For substituted rings, the bulkiest group will favor the equatorial position to reduce nonbonded strain (flagpole interactions) with axial groups in the molecule, as shown in Figure 2.7.
maltose
glucose + glucose
alpha 1-4
sucrose
glucose + fructose
alpha 1-2
lactose
galactose + glucose
beta 1-4
cellulose
Cellulose is the main structural component of plants. A homopolysaccharide, cellulose is a chain of β-D-glucose molecules linked by β-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chains together for support. Humans are not able to digest cellulose because we lack the cellulase enzyme responsible for hydrolyzing cellulose to glucose monomers. Therefore, cellulose found in fruits and vegetables serves as a great source of fiber in our diet, drawing water into the gut. Cellulase is produced by some bacteria found in the digestive tract of certain animals, such as termites, cows, and goats, which enables them to digest cellulose.
starches
Starches are polysaccharides that are more digestible by humans because they are linked α-D-glucose monomers.
Plants predominantly store starch as amylose, a linear glucose polymer linked via α-1,4 glycosidic bonds.
Another type of starch is amylopectin, which starts off with the same type of linkage that amylose exhibits, but also contains branches via α-1,6 glycosidic bonds.
Iodine is a well-known reagent that tests for the presence of starch and does so by fitting inside the helix conformation amylose typically makes, forming a starch–iodine complex.
breaking down starches amylose and amtlopectin
Amylose is degraded by α-amylase and β-amylase. β-Amylase cleaves amylose at the nonreducing end of the polymer (the end with acetal) to yield maltose, while α-amylase cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose. Because amylopectin is highly branched, debranching enzymes help degrade the polysaccharide chain.
glycogen
Glycogen is a carbohydrate storage unit in animals. It is similar to starch, except that it has more α-1,6 glycosidic bonds (approximately one for every 10 glucose molecules, while amylopectin has approximately one for every 25), which makes it a highly branched compound. This branching optimizes the energy efficiency of glycogen and makes it more soluble in solution, thereby allowing more glucose to be stored in the body. Also, its branching pattern allows enzymes that cleave glucose from glycogen, such as glycogen phosphorylase, to work on many sites within the molecule simultaneously. Glycogen phosphorylase functions by cleaving glucose from the nonreducing end of a glycogen branch and phosphorylating it, thereby producing glucose 1-phosphate, which plays an important role in metabolism.
glyceraldehyde
dihydroxyacetone
the simplest ketone sugar (ketose) is dihydroxyacetone, shown in Figure 4.2. Again, the carbonyl carbon is the most oxidized; in this case, the lowest number it can be assigned is carbon number two (C-2). This is true, in fact, for most ketoses on the MCAT: the carbonyl carbon is C-2. Ketoses can also participate in glycosidic bonds at this carbon. Notice that on every monosaccharide, every carbon other than the carbonyl carbon will carry a hydroxyl group.
stereoismers
When trying to figure out how many possible stereoisomers can exist for a multi-carbon compound, identify the number of chiral carbons (n) and plug into the formula 2n. For example, 21 = 2 stereoisomers and 22 = 4 stereoisomers.
convert chain to fisher
mutatrotation
hemiacetal formation
hemiacetal formation
