NS1: CPF Flashcards
how do ions contribute to osmosis
Ions cannot diffuse out of cells but water can, due to the phospholipid bilayer membrane.
Hypertonic solutions (high ion concentration in extracellular space) cause water to diffuse from the inside of cells to the outside via osmosis, causing shrinkage of the cells
Hypotonic solutions do the opposite
what is boiling point
Boiling point is defined as the temperature at which vapor pressure of a soln equals atmospheric pressure.
Adding more solute into soln reduces vapor pressure bc rate at which water molecules can break through the liquid surface decreases, thus requiring more energy to elevate the VP to AP → this is observed as a higher boiling point
why can ice (solid water) float in liquid water
Solid ice is less dense than fluid water due to its bent structure (104.45 degree angle) and the hydrogen bonding between water molecules, creating a solid crystalline structure with lots of empty space
nomenclature of oxyanions
Oxyanions (polyatomic anions that contain oxygen)
“Ite” vs “Ate” Suffix indicates lesser and greater numbers of oxygen, respectively → eg. Chlorite is ClO2- and Chlorate is ClO3-
“Hypo” vs “Per” prefixes indicates lesser and greater numbers of oxygen than “ite” and “ate” suffixes, respectively → eg. Hypochlorite is ClO- and Perchlorate is ClO4-
what is radioactive decay and what types are there
Radioactive decay is the spontaneous / irreversible transformation of one atomic nucleus into another via changing the number of protons or neutrons.
Alpha decay: emission of an alpha particle, containing two protons, two neutrons, and a +2 charge → new element should be 2 protons less than original
Beta decay
- Beta-positive decay: neutron is changed into a proton, thus requires electron emission for charge balance → new element should be 1 proton more than original
- Beta-negative decay: proton is changed into a neutron, thus requires positron emission for charge balance → new element should be 1 protron less than original
Gamma decay: emission of gamma ray (high energy photon from excited nucleus)
Electron capture: nucleus “grabs” an electron, changing a proton into a neutron → new element should be one less than the original
what is cancer
Tumor: any abnormal proliferation of cells
- Benign: harmless; localized and controlled
- Malignant: harmful, thus these are the kinds we refer to as “cancer”; not localized or controlled; invade other areas of the body via metastasis (breakage of cancer cells from the original tumor body to travel via blood or lymph systems to new locations)
Oncogenesis: most often associated with mutations that occur by random change, thus creating opportunities for cells to obtain the ability to proliferate uncontrollably
what is a chiral carbon
A chiral carbon must be attached to four different substituents. Given a molecule with n chiral centers, that molecule will have 2^n stereoisomers (excl meso compounds, which are molecules with multiple stereocenters that have an internal plane of symmetry that allows their mirror images to be superimposable).
aka tetrahedral stereocenter
describe a separation technique for substances that are liquids
distillation (which aims to separate liquids by utilizing their different boiling points)
This requires the use of a distilling flask held over a heat source, a column to connect this flask to a receiving one, and a condenser held through which cold water is pumped.
As the liquid with the lower BP is vaporized, the vapor will travel through the column and re-condense to fall into the receiving flask.
Thus, the end result should be the receiving flask containing all the liquid that had the lower BP while the original flask contains the liquid with the higher BP
(If the BPs are very high, a vacuum may also be used to lower atmospheric pressure, thus lowering the BPs of all substances involved)
describe a separation technique for substances that is a solid that contains impurities
recrystallization
obtain a pure solid produced by dissolving the solid in a solvent and subsequently heating the solution. Upn cooling, the lattice structure of solids tend to exclude impurities such that each subsequent recrystallization results in a progressively purer compound
describe a separation technique for substances that are variously mixed within a soln
chromatography can separate compounds based on relative affinity to a certain solvent or structure (ie the mobile phase vs stationary phase)
describe a separation technique for substances that vary by density
centrifugation utilizes a rapidly spinning apparatus to separate particles by density. More dense particles will gravitate towards the bottom (becoming the pellet) while less dense ones will remain at the top (becoming the supernatant).
what is the function of boiling chips or vacuums
Boiling chips are used to provide sites of nucleation (ie places to begin forming bubbles).
Use of a vacuum can reduce the boiling point of a substance by reducing the atmospheric pressure.
what are the physical properties and reactivity of alkanes
Alkanes (only have single C-C bonds) and alkenes (at least one C=C double bond) are hydrocarbons.
They interact with each other through weak London dispersion forces, have low melting and boiling points, and do not engage in meaningful acid-base chemistry.
what are the physical properties and reactivity of alcohols
Alcohols (RC-OH) and carboxylic acids (R(C=O)OH) have higher melting/boiling points than aldehydes and ketones, and can function as organic weak acids, thanks to hydrogen bonding.
The –OH group of carboxylic acids can be replaced by other functional groups to form carboxylic acid derivatives, the most notable are:
- amides (R(C=O)NR’R’’)
- esters (R(C=O)OR’)
- acid anhydrides (R(C=O)O(C=O)R’)
- acid halides (R(C=O)X)
- ** in increasing order of reactivity.
what are the physical properties and reactivity of carbonyls
Carbonyl (C=O) carbons have a significant partial positive charge and therefore often act as electrophiles.
what are the physical properties and reactivity of amines
Amines (R–NH2, R–NHR’, or R-NR’R”), imines (R=NH or R=NR’), and enamines (C=C–NH2, C=C–NHR, or C=C–NRR’) are nitrogen-containing compounds with medium melting/boiling points that can act as weak bases.
what are the physical properties and reactivity of sulfur-containing functional groups
Sulfur-containing functional groups contain the root “thio” and generally act similarly to the corresponding oxygen-containing groups.
what are formal charges
charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared equally between atoms, regardless of relative electronegativity
Formal charge = # of valence electrons - sticks - dots
where “sticks” refer to bonds and “dots” refer to lone-pair electrons.
what are some periodic trends
Due to the presence of protons, the nucleus of an atom is always positive. The attractive force of this positively-charged nucleus on the atom’s negatively-charged valence electrons is termed the effective nuclear charge (Zeff).
Moving left to right across a row, you will observe that the number of protons in the nucleus incrase.
Moving up and down across columns, you will observe that the principal quantum number of the outermost energy level increases, which effectively means that more shells of electrons are added between the nucleus and the outermost, or valence, electrons. These layers of core electrons partially shield the valence electrons from the effects of the positive charge in the nucleus. Thus, Zeff decreases as one moves down a group.
Atomic radius decreases from left to right across a period as Zeff increases and the addition of protons pulls the valence electrons closer to the nucleus. In contrast, atomic radius increases down a column as more electron shells are added and electron shielding decreases the attractive force of the nucleus on valence electrons. To summarize this trend, the atoms with the largest radii are found nearest the bottom left of the periodic table.
QB!
Given that a 65-kg man undergoes a turning acceleration of 5 m/s2 during a running turn, what is the magnitude of force experienced by the foot due to the ground?
We must account for the normal force exerted by the ground on the foot; this is a vertical force which occurs as a result of the runner’s weight. We also must consider the acceleration force, which (since the person is turning) is horizontal. These two force vectors are perpendicular and will form a right triangle.
We are looking for the overall force experienced, so we must find the hypotenuse. Specifically, we need to find the hypotenuse of a triangle with legs of Fnormal = mg = (65 kg)(10 m/s2) = 650 N and Fturning = (65 kg)(5 m/s2) = 325 N. The combined vector will be bigger than either component alone, so eliminate choices A and B. To solve, let’s round 650 N to 700 N and round 325 N to 300 N. With this in mind, this calculation can be approximated as:
√(3002 + 7002) = √(90000 + 490000) = √(580000) = √(58 x 104) = (√58) x 102
The square root of 58 falls between 7 and 8, so the overall value of our answer falls between 700 and 800, meaning that choice C must be correct (the actual value is 761)
what are the three types of inhibition
Competitive inhibition is when the inhibitor directly competes with the substrate for the active site on the enzyme. This increases Km since it now takes more substrate to ensure half of the active sites are occupied. If enough substrate is supplied, it will outcompete the inhibitor; therefore, Vmaxdoes not change, although more substrate is needed to reach it.
Noncompetitive inhibition is when the inhibitor does not compete with the substrate for the active site, but reduces enzyme activity by binding to another site (the allosteric site) on the enzyme. Since these inhibitors do not compete with the substrate, their activity is unaffected by substrate concentration. Since the inhibitor always affects a consistent proportion of the available enzyme, Vmax is reduced. However, Km remains the same since if Vmax, is reduced, Vmax/2 is reduced proportionally, and the amount of substrate required to reach this new, reduced Vmax/2 is the same as the original Km.
Uncompetitive inhibition is when the inhibitor binds to only the enzyme-substrate complex, and inactivates it. This causes the number of active enzyme-substrate complexes to decrease, thereby decreasing Vmax. Km also decreases to exactly the same degree as Vmax. The effects of an uncompetitive inhibitor cannot be overcome by increasing substrate concentration.
how can we determine whether an R group is protonated at a given pH?
Given the values of pKa of the R groups, one can determine whether or not that R group is protonated in a given pH.
At pH values greater than the pKa, the R group will predominantly be found in a deprotonated form.
At pH values lower than the pKa, the R groups will predominantly be found in a protonated form.
why is N2 important
N2 is considered a very inert gas (unreactive). It makes up approximately 80% of the air you breathe, yet has no significant chemical reactions with your lungs – or with anything other than nitrogen-fixing plants. As such, it would serve as a good artificial atmosphere when working with reagents that might react with oxygen or other gases.
what is acetone
Acetone has a central carbon atom that is double-bonded to an oxygen and single-bonded to two carbon atoms. Since it is bound to three substituents and has no lone pairs, the hybridization around this carbon is sp2, creating a trigonal planar geometry and a bond angle of 120º
what is power and its related equations
Power is measured in watts and can be solved through one of three power equations (derived from Ohm’s law).
P = IV
P = I2R
P = V2/R
Ohm’s Law: The three quantities of current, voltage, and resistance are linked together: V = IR
what is reduction
vs oxidation
Reduction is defined as a decrease in the oxidation state of an atom → eg. (1) gain of an electron, (2) decreased oxidation state, (3) formation of a C–H bond (e.g. alkene → alkane), and (4) loss of a C–O or C–N bond (or any bond between carbon and an electronegative atom)
Oxidation is defined as an increase in the oxidation state of an atom → eg. (1) loss of an electron, (2) increased oxidation state, (3) loss of a C–H bond (e.g. alkane → alkene), and (4) gain of a C–O or C–N bond (or any bond between carbon and a highly electronegative atom)
LEO goes GER
lose electrons = oxidation
gain electrons = reduction
rate oxygen containing compounds on the spectrum of oxidation (ie most reduced / least oxidized to least reduced / most oxidized)
alcohols (most reduced / least oxidized) to aldehydes and ketones (intermediate reduction / oxidation) to carboxylic acids (least reduced / most oxidized)
A primary alcohol can be oxidized to an aldehyde by a mild oxidizing agent or to a carboxylic acid by a strong oxidizing agent.
– A strong oxidizing agent will likewise oxidize an aldehyde to a carboxylic acid.
A secondary alcohol will be oxidized to a ketone by either a mild or a strong oxidizing agent.
A strong reducing agent can reduce a carboxylic acid directly to an alcohol, while weak reducing agents will not reduce carboxylic acids at all.
Both mild and strong reducing agents can reduce aldehydes and ketones to primary and secondary alcohols, respectively.
what are steroid hormones
derived from cholesterol, which means they share a four-ring lipid structure and are permeable to the cell membrane
- hydrophobic, therefore transported using plasma proteins in the blood
- lipophilic, therefore cannot be stored in vesicles (bc they would diffuse out easily) and only synthesized when needed
synthesized by the adrenal cortex and the gonads, in the mitochondria and smooth endoplasmic reticulum
how do steroid hormones function
three “S’s”: sex, salt, and sugar
– aldosterone, testosterone / estradiol, and cortisol respectively
Since steroid hormones diffuse freely through the plasma membrane due to their hydrophobicity, steroid hormone receptors are found on the inside of the cell, and these receptors form a complex with the hormone before entering the nucleus. Once inside the nucleus, the hormone-receptor complex binds to promoter regions of target genes and can stimulate or inhibit transcription of those genes. Thus, steroid hormones directly regulate gene expression in target cells.
Direct gene effects take time to manifest, so steroid hormone responses are generally slower than peptide hormone responses. However, since these changes are at the genetic level, they are much longer-lasting and sometimes permanent.
six important enzymes and their functions
“LIL HOT” mnemonic
Lyases break molecules into two smaller molecules without using water or redox reactions. → eg. decarboxylases
Isomerases convert a molecule from one isomer to another (including stereoisomers and constitutional isomers).
Ligases are used in catalysis where two substrates are stitched together (i.e., ligated) via the formation of C-C, C-S, C-N or C-O bonds while giving off a water (condensation) molecule.
Hydrolases catalyze reactions that involve cleavage of a molecule using water (hydrolysis). This cases usually involves the transfer of functional groups to water. → eg. amylases, proteases/peptidases, lipases, and phosphatases.
Oxidoreductases catalyze oxidation-reduction reactions where electrons are transferred. In metabolism, these electrons are usually in the form of hydride ions or hydrogen atoms. When a substrate is being oxidized, it is the hydrogen donor. Examples include reductases, oxidases, and dehydrogenases.
Transferases move functional groups from one molecule to another (such as kinases that move phosphate groups onto their substrates)
where do disulfide linkages form
Disulfide linkages only form between the side chains of cysteine (C) residues. When not part of such a linkage, cysteine side chains contain a thiol group (S-H). Through the process of oxidative folding, two thiol groups can connect and form an S-S bond. These linkages are an important part of protein tertiary and quaternary structure.
Note: Methionine does contain sulfur, but it cannot form disulfide bonds. This apparent contradiction can be explained by looking at the structure of methionine. The side chain of this amino acid includes a sulfur atom bound to carbon instead of hydrogen. As such, it cannot easily lose its proton and form a disulfide linkage through oxidation.
what are the four levels of protein structure
The first level, referred to as the primary structure, is the amino acid sequence that codes the protein. Each amino acid is coded for by a three-nucleotide sequence known as a codon.
The second level of protein structure refers to its two-dimensional arrangement (secondary structure). This folding is due to hydrogen bonds between groups along the peptide backbone that link different segments of the polypeptide chain to each other.
- In the alpha-helix, there are 3.6 residues per turn, which means that there is one residue every 100 degrees of rotation of the molecule.
- In beta-sheets, the protein is arranged into several β-strands, which are stretched segments of the polypeptide chain that are also kept together by hydrogen bonds. Beta-sheets may be parallel (the strands point in the same direction) or anti-parallel (the strands point in opposite directions).
The third level of protein structure, known as tertiary structure, refers to the actual three-dimensional shape of the native protein. These folds are caused and maintained primarily by hydrophobic/hydrophilic interactions and hydrogen bonds between the side chains of amino acids and between the amino acids and the protein’s environment.
The fourth level of protein structure, which is not present in all proteins, is quaternary structure. Quaternary structure exists when a single protein consists of two or more polypeptide chains (called subunits). The number of subunits will be reflected in the name given to its structure (dimer, trimer, pentamer). If the subunits are identical, the prefix “homo” is used, and if they differ, the term “hetero” is used. Thus, a protein with two identical subunits would be a homodimer, while a heterotetramer would be a protein with four subunits, at least some of which are different. These subunits can interact with each other, contribute to an active site or to the dynamics of the complex, or interact with some target molecules.
why are enzymes important
enzymes decrease the activation energy
note: enzymes are not changed or consumed in their associated reactions, do not affect the equilibrium constant (Keq) of these reactions, and do not affect any thermodynamic parameters of the reaction (ΔG, ΔH, and ΔS). For this reason, enzymes cannot make an energetically unfavorable reaction into a favorable one.
how do enzymes and substrates interact
Enzymes and substrates interact at the active site of an enzyme, which can be divided into a binding site and a catalytic site. The catalytic site is the very specific place where a reaction is catalyzed, while the binding site is a larger area where the substrate interacts with the enzyme through intermolecular interactions in a way that positions the substrate properly relative to the catalytic site. When the substrate interacts with the active site of an enzyme, it forms what is known as the enzyme-substrate complex.
The lock-and-key theory proposes that the active site of an enzyme and the substrate fit together like puzzle pieces, with no change in tertiary or quaternary structure. However, it eventually became clear that the lock-and-key theory was not sufficient to adequately explain enzyme-substrate interactions, leading to the development of the induced fit model.
In the induced fit model, the enzyme and substrate are seen as affecting each other; the initial stages of binding induce conformational shifts that allow closer attachment and more efficient catalysis.
what is spontaneity
The most basic definition of spontaneity is ∆G < 0, meaning that the reaction has a negative change in Gibbs free energy. Spontaneity is associated with exothermic (∆H < 0) reactions and those that increase entropy (∆S > 0) through the equation ∆G = ∆H – T∆S.
Note that a reaction can still be spontaneous even if it fulfills only one of these requirements.
it is important to automatically recognize that spontaneity is equivalent to ∆G < 0, Keq > 1, and E° > 0 where ∆G°rxn = −RTlnK eq
how do we determine orbital hybridization
One quick way to determine the orbital hybridization around the central atom is to simply count up the number of bonds and lone pairs.
For example, ammonia has three bonds and one lone pair around its central nitrogen atom, for a total of four regions of electron density.
This orbital hybrid therefore needs four orbitals to hybridize: s, p, p, and p. Thus, ammonia is an sp3 hybrid.
Next, XeF4 has two lone pairs and four bonds around the central xenon atom. We know this because the central Xe atom has eight valence electrons. It gets four of these eight electrons from the two lone pairs and four from the bonds — one electron from each bond.
Alternatively, we could try drawing the Lewis structure of XeF4, knowing that 8 electrons must come from the Xe atom and 7 from each of the F atoms, for a total of 8 + 7(4) = 36 electrons. Drawing XeF4 with Xe as the central atom and single bonds between the Xe atom and each F atom produces a structure with only 32 electrons, so we must add two lone pairs to the central Xe atom.
Two lone pairs and four bonds gives us six total regions of electron density. So we need six hybrid orbitals to hold those electrons: s, p, p, p, d, and d. That’s an sp3d2 hybrid.
how does L interact with different solvents?
Leucine is hydrophobic, since its side chain contains only carbon and hydrogen.
If the solvent were also hydrophobic, the face of a leucine zipper could interact just as favorably with the solvent as with the opposite alpha helix. Some leucine residues would likely interact only with the solvent, preventing formation of the dimer entirely.
how do different residues interact in different solutions
based on whether the residues are hydrophobic or hydrophilic
If hydrophilic (meaning you are polar), residues favor facing into the aqueous solution, thus promoting hydrogen bonding → yields high entropy, which is energetically favorable
If hydrophobic, residues favor facing away from the soln, thus limiting hydrogen bonding with nonpolar residues → yields low entropy, which is energetically unfavorable
electron rich molecules vs electron poor
Electron-rich molecules tend to act as nucleophiles when a covalent bond is being made; they also tend to act as Bronsted-Lowry bases when making a bond to an H+ or as Lewis bases when a coordinate bond is formed.
Vs. Electron-poor molecules tend to act as electrophiles; BL-acids, or as Lewis acids.
define the following:
- resistor
- galvanic cell
- electrolytic cell
- capacitors
- capacitance
A resistor is a device that impedes the flow of charge in a circuit.
A galvanic cell (battery) is a device that uses a spontaneous redox reaction to produce an electrical potential.
An electrolytic cell is a device that uses an electrical potential to drive a nonspontaneous redox reaction.
Capacitors have several medical applications (e.g. defibrillators) and are used to store charge and electrical potential energy, precluding the need for large batteries in electrical components. A basic capacitor consists of two metal plates separated by a layer of insulating material called a dielectric.
Capacitance is the ability to store charge and is calculated as C = ɛ0A/d, where A is the area of the plates and d is the distance between them.
how is body temperature regulated
thermoregulation via the anterior hypothalamus serves as the body’s “thermostat” to maintain body core temperature
Heat exchange is determined by convection, conduction, evaporation, and radiation.
The body can lose heat by increasing cutaneous blood flow and sweating, or by decreasing the basal metabolic rate through thyroid signaling.
Vs. It can gain heat by decreasing cutaneous blood flow, increasing muscular activity (through movement and shivering), increasing the basal metabolic rate through thyroid signaling, metabolizing brown adipose (in infants only), or triggering piloerection of the hair on the body (goosebumps).
forced change vs regulated
Forced change (in body temp): occurs when an environmental stress is sufficient to overcome the thermoregulatory systems of the body
Regulated change: when the hypothalamic “temperature setting” is shifted, as when a fever results from infection by a pathogen
what are structural proteins
Structural proteins: fibrous proteins that have an elongated shape and provide structural support for cells and organ tissues
Keratins: classified as soft or hard according to their sulfur content → low content becomes skin bc it is much more flexible than high content (eg nails); hair is a intermediate content example
Actin and Myosin proteins (of muscle tissue): interaction btwn the two form cross-linkages that allow the sliding of filaments over each other during muscle contraction via the sarcomere (the fundamental unit of all muscle fibers)
Collagen: found in tendons; forms connective ligaments within the body and provides the skin with extra support → forms by three proteins wrapped around each other in a triple helix; molecules of collagen are cross-linked together in the extracellular space to form collagen fibrils that provide structural support to the cell → flexible, elastic, and stretchy, thus allowing for spontaneous recoil
