Practice Test 1 Flashcards
Hypertonic
high concentration of solutes; if a cell is placed in an environment that contains a higher concentration of solutes than the interior of the cell
○ Water diffuse out of cell - cell shrink
Hypotonic
low concentration of solutes - dilute
○ Water diffuse into the cell -swell, burst, or lyse
Isotonic
an environment with the same solute concentration as the cell
_______________ can diffuse across cell membranes
Nonpolar and gases (often O2 and CO2)
Aquaporins
water can diffuse more rapidly in specialized water channels - transmembrane proteins
Notably present in the kidney, specifically the collecting ducts of nephrons
Adding salt to water causes:
○ the BP to increase -> requiring greater KE of liquid to produce vapor pressure equal to external pressure
○ MP to decrease = freezing point reduction
○ reduces vapor pressure of liquid - the more solute present, the lower the vapor pressure, and the higher the BP
○ BP = when vapour pressure = atmospheric pressure
Bent structure of water molecules ->
maximizes H-bonds that occur in solid phase -> hexagonal structure with large empty spaces
Less dense
Sulfate
SO4 (-2)
Sulfite
SO3 (-2)
Cation
+
Anion
-
Polyatomic ions
ions that contain multiple atoms ○ -ous =Ion with lesser charge § E.g. Fe2+ Iron(II) = ferrous ion ○ -ic = ion with greater charge § E.g. Fe3+ Iron(III) = ferric ion
Oxyanions
polyatomic anions that contain oxygen
○ -ite = fewer number of oxygen atoms
§ Chlorite (ClO(2-))
○ -ate = greater number of oxygen atoms
§ Chlorate (ClO(3-))
§ Carbonate (CO3 (2-))
§ HCO3- = hydrogen carbonate or bicarbonate
§ H2PO4- = dihydrogen phosphate
○ Hypo- = prefix added for oxyanions with one fewer oxygen than ite ions
§ E.g. hypochlorite (ClO-)
○ Per- = prefix added for ions with one more oxygen that -ate ions
Perchlorate (ClO(4-))
Gamma rays
form of electromagnetic radiation that consists of high-energy photons
○ Represents ionizing radiation
Beta-minus decay
neutron is converted to a proton, e-, and neutrino as an electron is emitted
○ Essentially an electron is emitted -> 1 more proton
element must be converted to an element with one additional proton
Alpha decay
an alpha particle containing 2 protons, two neutrons, and a 2+ charge is emitted
New isotopes are formed when …
an atom does not gain or lose any protons; only neutron count Is changed -> isotopes have different atomic mass
2H or deuterium (D)
used to track AA uptake in protein translation
Half life (t1/2)
time required for 1/2 of the parent isotopes in a sample to decay into daughter (radiogenic) isotopes
○ Determine how much sample is lost (1-1/2^n) or remains 1/2^n
Number of half-lives =n
Cancer
mutated DNA will disrupt the cell cycle over time for the cancer to be detectable
Chromatography
broad set of separatory techniques based on relative affinity or tendency for a compound to attract to a certain solvent or structure
Column chromatography = the stationary phase is a vertical column packed with an adsorbent can attract sample molecules based on charge, size, or affinity for specific ligands
Centrifugation
rapidly spinning apparatus to separate particles by density
○ The more dense particles (e.g. cells) gravitate towards the bottom of the spin tube
○ Less dense substance remain at the top in a liquid (supernatant)
Supernatant can be poured off and further separated or analysis
Boiling chip
provide nucleation sites that give the liquid a place to start forming bubbles to prevent superheating
Vacuum distillations
lowers the BP of the substances to be distilled
Distillation
component with lower BP boils off first
○ The types of bonds the compound has determines the BP
Acid has H-bonds that create vastly higher BP
Stereocenters
for a carbon, must be bonded to 4 different substituents
○ Can give rise to different stereoisomers
○ Chiral centre
Gravitational potential energy
PE = mgh
KE
KE = (1/2)mv^2
Law of conservation of energy
KEi +PEi = KEf +PEf
The preferred ion configuration of many elements is determined by
the electron configuration of the nearest noble gas (full octet)
Torque equation
τ = F∙d∙sin(θ)
- Perpendicularly applied force = 90-degrees = 1 = sin(90)
3 ways to increase the torque applied to an object:
- Increasing the force
- Increasing the distance at which the force is applied from the fulcrum
- Adjusting the angle at which the force is applied to make it as close as possible to perpendicular to the level arm
Torque - Equilibrium setups
objects are not moving
§ If the potential for rotational motion exists => clockwise and counterclockwise torques will balance out
§ Tcw = -Tccw
□ Clockwise torque = (-)
□ Counterclockwise torque = (+)
- Force acting at the pivot point - the length of the lever arm, r=0
§ Does not produce any torque
Titration - Analyte
the substance whose quantity or concentration is to be determined
Titration curve analysis
look for equivalence points - located halfway along the steep portions of the curve
For a monoprotic acid @ the equivalence point =
Mbase x Vbase = Macid x Vacid
§ M is molarity
§ V is volume
§ Diprotic = contains both a carboxylic acid group + thiol group
§ Equivalence point -> inflection point
§ The molar amount of NaOH (titrant) must be equal to the amount of analyte due to 1:1 ratio of NaOH and analyte to neutralize
Km
michaelis constant = substrate concentration at which enzyme catalysed reaction proceeds at 1/2 its maximum rate -> measure of [S] required for effective catalusis to occur
- Higher the Km the less sensitive to the substrate - Lower the Km the more sensitive to the substrate - less [S] needed for enzyme activity
Vmax
the maximum rate of enzyme catalyzed reaction when all active sites are saturated with substrate
- Changes with enzyme concentration - Vmax increases with increasing [E]
Kcat
- Kcat = Vmax/[E]
§ Standardized Vmax
Competitive inhibitor
Reversible inhibition
binds to active site and competes with the substrate
§ Common
§ Catalysis slowed
§ Increase Km (need more [S] to reach Vmax)
§ Vmax unchanged
Can be overcome by adding more substrate
Uncompetitive inhibitor
Reversible inhibition
inhibitor binds the ES, preventing formation of product
§ Decrease in Vmax (lowering functional enzymes)
§ Km decreased - enzymes more sensitive to substrate as there is no product being made
Noncompetitive inhibitor
Reversible inhibition
binds to allosteric site and alters enzyme
§ Product not formed
§ Cannot compete
§ Km does not change but Vmax decreases
□ Lower the number of functional enzymes
µ =
n =
p =
µ = x10^-6 n = x10^-9 p = x10^-12
Newtons Laws
- Inertia - constant velocity or rest unless force acts upon it
- Fnet = 0 at equilibrium- Defines forces - the total sum of forces acting on an object is equivalent F = ma
- Forces come in pairs - when body A exerts a force on body B, body B exerts an equal and opposite force on A
Fab = -Fba
- Frictional force is equal to the product of the appropriate coefficient of friction and the normal force: Ff = μFn- μ = coefficient of friction
- Fn = normal force
Diatomic Nitrogen (N2)
gas is relatively inert (unreactive) and can be used as the atmosphere in laboratory conditions to prevent unwanted side reactions
○ Makes up 80% of the air we breathe with no significant chemical reaction in the lungs or with anything other than nitrogen fixing plants
Good artificial atmosphere when working with reagents that might react with oxygen or other gases
Acetone
methyl -c-methyl
=o
120-degrees
Power equations developed from Ohm’s law
○ P = IV
○ P = I^2 x R
○ P = V^2/R
Resistance:
○ In parallel: 1/R-total = 1/R1 +1/R2 + 1/R4 +….
○ In series: R-total = R1 + R2 + R3 + R4…
LiAlH4
Reducing agent used in classic case of reduction - gain of bonds to hydrogen or the loss of bonds to oxygen (or other electron-withdrawing species)
O3
ozone takes part in ozonolysis which results in the oxidative cleavage of alkenes
Ozone could not be used to reduce retinal retinol
H2 with Pd
very strong catalytic reduction mechanism which would reduce this molecule to an alkane
KMnO4
strong oxidizing agent
Reagents which are rich in oxygen typically act as oxidizing agents
Reduction in organic chemistry:
○ Gain of electron
○ Decreased oxidative state
○ Formation of a C-H bond (alkene -> alkane)
○ Loss of a C-O or C-N bond (or any bond between carbon and an electronegative atom)
Oxygen-containing organic compounds exist on a spectrum of oxidation
Alcohols
most reduced/least oxidized
§ Primary alc Can be oxidized to an aldehyde by a mild oxidizing agent such as PCC
§ Primary alc can be oxidized to a carboxylic acid by a strong oxidizing agent such as NaCr2O7
□ Strong oxidizing agent can also oxidize an aldehyde to a carboxylic acid
§ Secondary alc can be oxidized to a ketone by either a mild or strong oxidizing agent
Oxygen-containing organic compounds exist on a spectrum of oxidation
Aldehydes/ketones
intermediate reduction/oxidation
§ Both mild and strong reducing agents can reduce aldehydes and ketones into primary and secondary alcohols respectively
Oxygen-containing organic compounds exist on a spectrum of oxidation
Carboxylic acids
least reduced/most oxidized
§ Can be reduce carboxylic acid to alcohol with a strong reducing agent such as LiAlH4
§ Special agent DIBAL can reduce carboxylic acid to an aldehyde when applied at a precise 1:1 ratio
Majority of steroid hormones have names that end in
“-one”, “-en”, “-ol”
○ 4 fused ring system of steroids
Transferase
move functional groups from one molecule to another (such as kinases that move phosphate groups onto their substrate)
○ Often donor is a cofactor that is charged with the group about to be transferred
○ E.g. kinases and phosphorylase
Lyase
break molecules into two smaller molecules without using water or redox reactions. Functional groups are added to break bonds in molecules or they can be used to form new double bonds or rings by the removal of functional group(s)
○ E.g. decarboxylase
Hydrolases
catalyze reactions that involve cleavage of a molecule using water (hydrolysis)
○ Usually involves the transfer of functional groups to water
○ E.g. amylase, protease/peptidase, lipases, and phosphatase
Ligases
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
Isomerase
converts a molecules from one isomer to another (including stereoisomers and constitutional isomers)
Oxidoreductase
catalyze oxidation-reduction reactions where electrons are transferred
○ Usually in the form of hydride ions or hydrogen atoms
○ When a substrate is being oxidized, it is the hydrogen donor
○ E.g. reductase, oxidases, dehydrogenase
Infrared IR spectroscopy
method used to identify specific functional groups present on an unknown molecule
○ Group frequencies = vibrations associated with certain functional groups
○ Relies on smaller energy absorbances (than UV-Vis spectroscopy) that occurs between various vibrational and rotational states
○ Only molecules with net change in dipole movement during motion can absorb IR radiation
○ Diatomic molecules do not return IR signals because there is no net change in the dipole movement
○ Molecules respond to the influx of energy by either stretching or bending
The most high-yield IR spectra are those of carbonyl group (C=O) and hydroxyl groups (OH)
Infrared IR spectroscopy
Stretching
a result of changing distances in a bond between two atoms on a molecule
Infrared IR spectroscopy
Bending
any change in the angle between two bonds on the molecule
Standard reduction potential
used to measure tendency for a species to spontaneously become reduced
○ Reduction potentials (E°) are measured in volts and are defined relative to the standard hydrogen electrode (2 H+ (aq) + 2 e- → H2(g)), which is set at 0 V.
○ The greater (+) the reduction potential , the more the substance wants to be reduced
○ The lesser (-) the reduction potential, the substance is not prone to reduction
Electron transport change: O2 serves as the final electron acceptor of the electron transport chain and must possess a standard reduction potential that is more positive than any other acceptor in the chain
anode
Electrode where oxidation happens
Ecell = E°cathode - E°anode
cathode
Electrode where reduction happens
Ecell = E°cathode - E°anode
Enzymes cannot alter the equilibrium of a reaction
○ Thus, they cannot change the spontaneity of a reaction - which is determined by the free energy change associated with the reaction
○ Enzymes change the activation energy and the reaction rate of reactions in which enzymes are involved
The presence of ATP hydrolyzing enzymes in the body could account for difference in reaction rates
Spontaneity =
○ ∆G < 0 : negative gibbs free energy = spontaneous
§ Spontaneity is associated with exothermic (∆H < 0) reactions and those that increase entropy (∆S > 0)
□ Spontaneous reaction can be endothermic as long as it is balanced sufficiently positive entropy
§ ∆G = ∆H – T∆S
○ Spontaneous reactions will lead to more products being present than reactants
§ Equilibrium constant (Keq = [P]^(stoichiometric coefficient)/[R]^(stoichiometric coefficient)) will be greater than 1 for spontaneous reactions
□ Keq varies in temperature - solid and pure liquids should not be include in the equilibrium expression
□ Products favoured = greater Keq; reactants favoured = lower Keq
§ ∆G°rxn = −RTlnKeq
Spontaneous reactions are associated with positive cell potentials (E° > 0) in the context of electrochemical cells
Start codon
AUG = methionine
Stop codon
UAA, UAG, UGA = nonsense codons because they do not code for an amino acid and instead signal the end of protein synthesis
1 mole
One mole of any substance must always be the same number of molecules
Le Chatelier’s principle
if an equilibrium is disturbed, it will shift to favour the direction of the reaction that best facilitates a return to equilibrium
○ Disturbance to equilibrium = temperature, [P], [S], temperature, pressure, volume
○ Reactions with gases:
§ Increase in volume (decrease in pressure) -> shift equilibrium to side with more moles of gas (and vice versa)
○ ∆H > 0:
§ Increase in temperature will shift equilibrium towards the products
§ Decrease in temperature will shift eq to the reactants
Opposite pattern when ∆H < 0
-∆H
+∆S
spontaneous?
always -∆G
+∆H
-∆S
spontaneous?
always +∆G
- ∆H
- ∆S
spontaneous?
Spontaneous at low temperature
+∆H
+∆S
spontaneous?
Spontaneous at high temperatures
Snell’s law and Index of refraction
• Propagation speed of a wave is specific to the medium that it is travelling through for sound, electromagnetic waves, and light
○ When a light wave goes from one medium to another, it changes speed/bends
• Speed of light in a vacuum = c = maximum speed at which normal matter can travel in the universe
○ 1 = n when v =c in vacuum and air
○ For all other materials n > 1
§ E.g. window glass n = 1.52
Refractive index
n =c/v = how much speed of light wave changes
Snell’s Law
n1sin(θ1) = n2sin(θ2)
○ Θ is with reference to the normal or a line that runs perpendicularly to the surface on which the wave is incident
Angle of incidence =
angle of reflection
Light entering a more dense medium will bend towards the ____
normal
Total internal reflection
can only result when a ray of light begins in a higher-index material and reaches a boundary with a lower-index one (e.g. starting in water and moving towards air)
○ The light ray started in air (n=1) and moved into water (n ~ 1.3), making total internal reflection impossible (III)
• When light moves into a medium with smaller index of refraction: n2>n1 (e.g. water to air)
○ The angle θ with the normal will increase; there will come a point where the angle of refracted ray θ2 reaches 90-degrees aka critical angle
If angle is increased beyond the critical angle, the light can no longer refract at all -> instead all the light rats are reflected within the original medium = Internal reflection
Orbital hybridization
• Electrons exist in the region around atom in characteristic shapes depending on the angular momentum quantum number of their subshells: s, p, d, or f
○ Spherical = s
Two lobes and a central node = p
When atoms combine to form a molecule, their atomic orbitals overlap to produce molecular orbitals
sigma (σ) bond
Single bond consisting of 2 electrons - between two atoms with overlapping region of electron density
Pi (π) bonds
Bonds that occur between two parallel p orbitals and are weaker than sigma (σ) bond
Double bonds
1 sigma bond and 1 pi bond
Hybridization
when orbitals combine
§ E.g. CH4 has 4 identical sp3 orbitals instead of separate s and p orbitals
To determine orbital hybridization of a molecule -> determine the number of regions of electron density around the atom (aka bond or a lone pair of electrons)
1 alpha helix turn
3.5 aa
• H-bonds -> high entropy/energetically favourable
• Aqueous environment with nonpolar residues create a highly ordered solvation shell to minimize interaction -> decrease in entropy = energetically unfavourable
Relative stabilization energy (RSE) :
the stabilizing effects of the substituents can be determined from this
○ The more negative the RSE -> the greater the stabilization
○ Carbocations are typically destabilizing due to their high concentration of positive charge
§ If the substituent can contribute some electron density to the carbocation, this positive charge will be balanced and the species stabilized
§ Electron withdrawing substituents pull even more electron density away from the carbocation, decreasing its stability
Fluorine is destabilizing and highly electronegative, it is electron withdrawing
Electron-rich molecules
tend to act as nucleophiles when a covalent bond is being made
○ Tend to act as Bronsted-Lowry bases when making a bond to an H+, or as Lewis bases when a coordinate bond is formed
○ E.g. amines are good nucleophiles due to the presence of a lone pair of electrons
Determining electron density -> look for C atoms bound or near to highly electronegative atoms (O,F,N) and for pi bonds which can undergo resonance allowing for molecules to be better nucleophiles
Electron-poor molecules
function as electrophiles in reactions that yield covalent bonds ○ As Bronsted-Lowry acids when making a bond to an H+ or as a Lewis acids when coordinate bonds are formed E.g. carbonyl groups (C=O) are electron poor - good electrophiles
Enthalpy
heat energy in a system
Exothermic reaction = -∆H = heat released
Endothermic reaction = +∆H = heat not released
• When reactants are converted into products, the overall enthalpy change is the same whether it is done as one step or multiple steps
Enthalpy of a substance can only be calculated relative to other substances => enthalpy does not approach 0 as temperature approaches 0 K (absolute zero)
Entropy
energy in a closed system that is unavailable to do work
Hess’s Law
ΔHrxn = Σ∆Hproducts - ΣΔHreactants
Ways to estimate entropy of a system
○ Reactions that increase the number of moles of substances in the system (or produce more gas particles) typically increase the entropy of the system
○ Entropy increases when a solid or liquid is dissolved in a solvent
○ Entropy increases when the solubility of a gas decreases and it escapes from a solvent
○ Entropy generally increases as molecular complexity increases (more elements in molecule) due to increased movement of electrons
○ Entropy increases with temperature as a material changes phase from solid to liquid to gas
Resistor
device that impedes the flow of charge in a circuit
Galvanic cell (battery)
a device that uses a spontaneous redox reaction to produce an electrical potential
Electrolytic cell
a device that uses an electrical potential to drive spontaneous redox reaction
Capacitor
when voltage applied, charge will accumulate on the plates (parallel-plate capacitor)
• E.g. defibrillators: used to store charge and electrical potential energy, precluding the need for large batteries in electrical components
Basic capacitors consists of 2 metal plates separated by a layer of insulating material called a dielectric
• Both plates eventually have equal and opposite charge, +Q and -Q
• When the capacitor is fully charged, it has a charge of Q
Once fully charged, the capacitor can discharge a current across the circuit until the capacitor is emptied of all the stored charge
Capacitance equation
• Capacitance = ability to store charge = C = ɛ0A/d
○ A = area of the plates
d = Distance between them
Q = VC
Charging when battery is connected (V is constant) or disconnected (Q is constant)
○ We can relate the charge, capacitance, and voltage across the plates using this equation
○ V = the maximum potential difference that can be applied before the insulation of the dielectric breaks down
Electrical potential stored in the capacitor can also be related via this equation
E = (1/2)QV = CV^2
Capacitors can be combined in series (common path) or parallel (common origin and destination, different path)
• In series: 1/Ceq = 1/C1 + 1/C2…
In parallel: Ceq = C1 + C2…
Vast majority of metal oxides are ____ at standard temperature
solid
dry heat
Dry heat feel cooler than humid heat because the increase evaporation from the skin helps to keep the body cool by sweating, and drying, and sweating more
Structural proteins
Fibrous proteins that have an elongated shape and provide structural support for cells and organ tissues
Keratins
form the skin, hair, nails, and are classified as soft or hard according to their sulfur content (i.e. the relative number of cysteine residues in their chain)
Low sulfur keratins of the skin are much more flexible than high sulfur hard keratins
Actin and myosin
proteins of the muscle tissue
○ Actin and myosin interact to form cross-linkages that allow the sliding of the filaments over each other in muscle contraction - which takes place through the contraction and relaxation of the sarcomere, the fundamental unit of all muscle fibers
○ When muscles contract, the actin and myosin filaments slide over each other and the H-zone (myosin only region), Z lines (sarcomere boundaries) and I-band (actin only region) all shrink, while the A-band (the entire myosin region) remains the same size.
The opposite occurs in muscle relaxation
Collagen
found in tendons, forms connective ligaments within the body and gives extra support to skin
○ Collagen is a triple helix formed by 3 proteins that wrap around one another
○ Many collagen molecules are cross-linked together in the extracellular space to form collagen fibrils to provide structural support for the cell
E.g. elastin polypeptide chains are cross linked together to form flexible, elastic fibers that five stretched tissues flexibility and the ability to recoil spontaneously as soon as the stretching force is relaxed
Microtubes
are used in transport of vesicles and the positioning of organelles within the cell
○ They form structures that assist in the transport of phagosomes (vesicles that contain particles that have been engulfed via phagocytosis( to the lysosomes of the cell, to which the phagosomes fuse (I)
Microtubes form the spindle apparatus that is an essential part of both mitosis and meiosis (II and III)
Ostentatious
pretentious display designed to attract notice
Paternalism
policy or practice on the part of people in positions of authority of restricting the freedom and responsibilities of those subordinate to them in the subordinates supposed best interest
Imperialism
policy of extending a country’s power and influence through diplomacy or military force
Albeit
although
Dichotomy
a division or contrast between two things that are or are represented as being opposed or entirely different
Chicanery
the use of trickery to achieve political, financial, or legal purpose
Anthropomorphism
the attribution of human characteristics or behavior to a god, animal, or object
Deity
a god or goddess; divine status, quality, or nature; the creator and supreme being
“some have suggested” signals that there have been challenges to the author’s argument
Ludology
the study of games and gaming, especially video games
Lobby
group of people seeking to influence politicians or public on a particular issue (n)
Seek to influence a politician or public official on an issue (v)
Scurvy
a disease caused by a deficiency in vitamin C, characterized by swollen bleeding gums and the opening of previously healed wounds
Hair cells
hearing; linear and rotational acceleration which also respond to the movement of fluid in the ear
Olfactory receptors
smell - respond to volatile compounds in the air
Osmoreceptors
water homeostasis - respond to the osmolarity of blood
Nociceptors
somatosensation - respond to painful stimuli
Photoreceptors
sight - respond to visual spectrum of electromagnetic waves
Taste receptor
respond to dissolved compounds in substances
§ broadly divided into:
□ exteroceptors -> respond to stimuli from the outside word
□ Interoceptors -> respond to stimuli generated within the body
Baroreceptor
measure pressure
Volatile
substance that is easily evaporated
Alcohol (drunk)
binds and activates GABA receptors (alcohol is a GABA agonist)
Glycine
inhibitory NT found in the spinal cord and brainstem that works in conjunction with GABA
Dopamine
used in reward and motor pathways - motivation
Endorphins
suppresses pain and can produce euphoria
○ Released from the anterior pituitary
○ Naturally block the release of certain NT at nociceptors
released from the anterior pituitary
Luteinizing hormone (LH) + follicle stimulating hormone (FSH) + growth hormone (GH)
Serotonin
regulates mood, appetite, and sleep in the brain with low levels associated with depressive mood disorders
○ Regulates intestinal movement in the GI tract
Acetylcholine
- NT can be active in the peripheral NS
activates muscle contraction at the neuromuscular junction - used in all autonomic outputs from the brain to autonomic ganglia, and in the parasympathetic NS for post-ganglionic connections
Epinephrine
used in post-ganglionic connections in the sympathetic divisions of the autonomic NS
Increases arousal and alertness and focuses attention
Muscle activation does require release of _____ from the sacroplasmic reticulum to cause a mechanical response in the muscle
calcium
Depolarization
Na+ influx into the neuron
- The mechanisms of action potentials involve the voltage potential difference across the neuronal cell membrane
Resting membrane potential
-70mV
○ Maintained by constant Na+/K+ pump => 3Na+ out, 2K+ in
○ Electrochemical gradient is also maintained by the hydrophobic core of the PM does not allow ions to easily diffuse back across
AP
- Threshold = -55mV ==> AP
- When inside the cell loses negative potential = depolarized > -70mV
○ +40mV peak in an AP - Less than -70mV = hyperpolarized when repolarization continues
○ Refractory period - AP begin at the axon hillock and move down the axon towards the synapse
This AP can either move slowly and smoothly along the cell membrane (if the cell is myelinated) or can jump very rapidly down the axon through nodes of ranvier (gaps in the myelin sheath present in myelinated neurons)
- When inside the cell loses negative potential = depolarized > -70mV
Cross sectional studies
investigate a population at single point in time, looking for perspective relationships among variables
§ Shows correlation but no causation (assessing changes over time is necessary to assess whether a cause and effect relationship is present
Qualitative research
focuses on analyzing experiences rather than the objective metrics
Negative controls
treatments that are known to have a certain effect
§ Can be used to assess whether the experimental methodology was sound
Double-blind design
neither the participant nor the researchers know who is receiving the treatment and who is receiving the control
§ Often in clinical contexts
Confounding variables
external variables affecting both the IV and DV
Sample size = N
number of data points developed in an experiment
§ Larger the N, the higher the statistical power of the experiment
Non-random sampling
can introduce important sources of bias -> limits the validity of the study
Cancer
abnormal gene expression
○ Stem cells have the ability to undergo self renewal => can resist chemotherapy, replicate, and then differentiate as needed
Oncogenesis + steps
cancer development
1. Tumour initiation - changes that allow a single cell to proliferate abnormally - Cell must develop the ability to bypass regulatory steps of the cell cycle that normally help to limit mitotic proliferation 2. Tumour progression occurs as a cell develops the ability to proliferate more 3. Malignant tumours often go through mutations that promote their own growth and the development of blood vessels to feed them (angiogenesis) - Oncogenesis is associated with mutations that occur by random chance (normal DNA repair machinery) or as a result of mutagenic compounds known as mutagens or carcinogens - Mutagens = UV light or chemicals such as reactive oxygen species - These mutations alter functionality of crucial genes in the cell 4. Oncogenesis is associated with dysregulation of gene expression - abnormally elevated expression of genes involved in growth and proliferation can help contribute to the development of a tumor
Tumour
abnormal proliferation of cells
§ Benign tumours remain localized
§ Malignant tumours can invade other organs and tissues in the body in a process called metastasis
Genes involved in oncogenesis can be divided into 2 groups
§ Oncogenes - function to promote abnormal growth and proliferation, leading to cancer
- Protooncogenes: Can arise from mutation of other genes
® If not mutated, protooncogenes do not promote cancer but certain mutations or inappropriately elevated gene expression can effectively turn them into oncogenes
§ Tumor supressor genes - function to prevent tumorigenic properties
peptide bonds
○ Amino acids are linked together by peptide bonds => formation of amide via the condensation of -COOH group of one amino acid with the -NH2 group of another
§ Condensation -> results water molecule product
○ Peptide bonds are stable in intracellular conditions
§ Due to resonance stabilization in addition to the form with a C=O double bond and a C-NH2 single bond
Due to resonance, peptide bonds are planar and do not rotate freely which helps contribute to the structural stability of 3D polypeptide structures
Peptide bond usually exists in trans conformation
Hydrolysis of peptide bonds
○ Peptide bonds are broken through hydrolysis - the reverse of the condensation reaction
§ Energetically favorable but extremely slow under physiological conditions
§ The breaking of peptide bonds (the destruction of primary structure of a protein) is generally accomplished by specific enzymes in living cells
Hypo- and Hypertonicity
○ The relative solute concentrations of different biological compartments are particularly relevant to osmosis or the simple diffusion of solvent molecules
○ MCAT = solvent is always water
○ Water, a polar molecule, cannot pass through the lipid-based plasma membrane as easily as similarly-sized nonpolar molecules can
§ But small enough to simply diffuse to some extent
○ The osmosis takes place in situations where water can diffuse through the membrane or other barriers but solutes cannot = semipermeable membrane
RNA Transcription
prokaryotes vs. eukaryotes
○ Only Eukaryotes have a 5’ GTP cap on their mRNA
○ Prokaryotic ribosomes differ from eukaryotic ribosomes
§ Prokaryotes have 70S ribosome consisting of 50S and 30S subunits, while eukaryotes have an 80S ribosome consisting of 60S and 40S subunits
In eukaryotes, each gene has its own transcription initiation site
mRNA is transported out of the nucleus in eukaryotes to the cytosol for translation into a protein
Monocistronic
one gene per transcript
Polycistronic
containing multiple genes in a single transcript
RNA polymerase
RNA synthesis enzyme that binds to the promoter region upstream of the start codon with the assistance of transcription factors, the most important of which is the TATA box
§ It travels along the template 3’-5’ direction, synthesizing an antiparallel complement in the 5’ -3’ direction
Template strand
antisense strand
RNA polymerization
a process by which nucleotides are strung together to form a single-stranded RNA strand, not the joining of 2 complementary strands
Elongation
polymerization - the adding of subunits to make a longer strand of macromolecule
Sense strand
opposite strand because it corresponds to the codons on the mRNA that is eventually exported to the cytosol for translation
Heterogeneous nuclear RNA (hnRNA)
immediate product of transcription in eukaryotes
§ Must undergo a set of post-translational modifications to become mRNA
3’poly-A tail
string of ~250 adenine (A) nucleotides added to the 3’ end of an hnRNA transcript to protect the eventual mRNA transcript against rapid degeneration in the cytosol
5’ cap
7-methylguanylate triphosphate cap placed on the 5’ end of the hnRNA transcript; it helps prevent the transcript from being degraded too quickly in the cytosol and prepares RNA complex for export from the nucleus
Splicing
noncoding sequences (introns) are removed and coding sequence (exons) are ligated together
§ Exons can have many combinations
§ Splicing explains why there are over 200,000 proteins in the human body but only 20,000 genes
Splicing is carried out by spliceosome - a combination of small nuclear RNAs (snRNAs) and protein complexes
Hybridization/annealing
Two single strands - both DNA, both RNA, or a DNA-RNA hybrid - can attach together
Denaturation
separating stands
§ Heating is most common
○ dsDNA is stable under typical physiological conditions, its strands can be separated by heating or certain chemical agents
Polymerase chain reaction, PCR
lab technique used to make larger number of copies of DNA sequence of interest - similar to man-made version of mass DNA replication
§ First, denature template DNA by heating the reaction mixture to around 95-degrees C => sufficient to disrupt the H-bonds between bases
§ Melting point for denaturation is higher for guanine-cytosine (GC) content since guanine and cytosine are held together by 3 H-bonds whereas adenine and thymine are attached by 2
§ Annealing/hybridization = takes place at lower temperatures (~68-degrees C)
§ Short stranded RNA molecules termed small interfering RNA (siRNA) can hybridize with mRNA in a process that induces gene silencing
§ The siRNA-mRNA hybrid is recognized as an abnormal double stranded RNA and is enzymatically cleaved preventing its translation
Carboxylic acids are ____ acids..
Carboxylic acids are weak acids: COOH groups are happy to give up an extra proton and exist as COO- even at relatively low pH values where there is a fair amount of H+ present
○ A huge amount of H+ must be available to force the carboxylate ions to accept a proton
For intermediate pH ranges, the carboxylic acid will be deprotonated
