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
Amine groups are ___ bases
weak; like being protonated
○ The pH must be quite high for it to be willing to give up its proton
○ For intermediate pH ranges, the amine group will be protonated (NH3+)
Immune system
complex set of mechanisms that the body uses to protect itself against foreign invaders and malfunctioning cells originating from the body itself
Adaptive immune system
directed against particular pathogens to which the body has been previously exposed
○ Pathogens are remembered by specialized cells, leading to a quicker response in the case of second exposure
○ Includes B cells and T cells - both lymphocytes that are produced in the bone marrow and mature in the lymphatic system
B cells
○ B cells recognize antigens and secrete large amounts of antibodies in response
§ 5 classes of antibodies in the human body: - differ in the details of their heavy chains
□ Immunoglobin (Ig) A
□ IgD
□ IgE
□ IgG
□ IgM
T cells
○ T cells correspond to the cell-mediated branch of adaptive immune system
§ T cells mature in the thymus
§ Recognize cells that were originally self but have been damaged by viral infections or have malfunctioned in ways likely to turn them into cancer cells
Innate immune system
nonspecific immune responses
○ Its responses provide general protection rather than protection against specific pathogens that have been previously encountered and remembered
○ Response to general non-specific threats
○ Inflammation is a function of the immune system as it serves a general response to infection or injury
○ Noncellular component includes - anatomical barriers and signaling molecules such as cytokines and complement proteins while cellular component includes a range of white blood cell types (leukocytes) that play various roles in responding to threats
○ White blood cells include neutrophils, lymphocytes, monocytes, eosinophils, basophils, and mast cells
Eosinophils
granulocytes or cells that contain small particles (granules) in their cytoplasm
○ Granulocytes include basophils and neutrophils - both involved in innate immunity
Erythrocytes (red blood cells)
- Do not contain DNA or membrane-bound nucleus, allowing the cells to have more space for oxygen-carrying hemoglobin molecules
- Hemoglobin - a polymer of 4 proteins and iron that binds oxygen
- Created in bone marrow in response to erythropoietin (EP), a hormone that is released form the kidney whenever erythrocyte levels are low
- During erythrocytes development - they lose their membrane bound organelles including their mitochondria and nucleus -> biconcave shape for more efficient travel and maximize surface area for gas exchange
- Only engage in anaerobic metabolism and have a limited lifespan of only 100 days
Erythrocytes are degraded by the spleen @ upper left quadrant
In eukaryotes, the residues that are most prone to phosphorylation are (3)
serine (S), tyrosine (Y), and threonine (T)
- PKA (protein kinase A) is stimulated by cAMP
Protein kinase A = adds phosphate group to its substrate
Aldosterone
Adrenal cortex secretes aldosterone which responds to changes in blood pressure and cortisol vaso
Aldosterone = steroid hormone (mineralocorticoids) released from adrenal cortex in response to low blood pressure -> increases sodium reabsorption in the distal tubule and collecting duct
- Upregulates the Na+/K+ pumps along the lining of the nephron = 3 Na+ out and 2 K+ in
- Increases passive water reabsorption NOT through regulation of aquaporin channels
- Drives water reabsorption through increased sodium absorption
Increases K+ and H+ excretion in to urine
- Aldosterone comes from the adrenal cortex
- Aldosterone adds sodium and potassium pumps to the walls of the DCT
® Exact same Na/K pumps found in neurons => they pump Na out and K in
® 321NOKIA: 3 Na out, 2 K in, and 1 ATP
® Chloride wants to leave due to electrochemical gradient
® Salts and water leave -> does not change saltiness levels (osmolarity) -> increases Blood Pressure/volume
Aldosterone causes salt and water reabsorption -> increases blood pressure/volume without changing the saltiness
Antidiuretic hormone (ADH)
peptide hormone aka vasopressin
- These 2 hormones have different mechanisms - ADH increases the permeability of the collecting duct to water - thereby increasing water reabsorption - Reduce the osmolarity of blood by increasing the amount of water present without changing the solute levels - Released in the posterior pituitary (and so is oxytocin)
Atrial natriuretic peptide (ANP aka atrial natriuretic factor ANF)
a hormone that the endocrine system uses to deal with the problem of excess blood volume
- Opposite of aldosterone - Released in response to high blood volume and decreases sodium reabsorption in the distal convoluted tubule and the collecting duct - Increases glomerular filtration rate and inhibiting aldosterone release
Apoptosis
programmed cell death
- In embryonic development, apoptosis plays a major role in defining the boundaries of organ and tissues
○ E.g. developing human embryo, fingers and toes are initially linked by webbed structures and apoptosis of the cells in those structures is what allows fingers and toes to become separate by the time of birth
Common causes of apoptosis:
○ Appropriate mitotic checkpoint
○ Cell-internal signaling after mitochondrial dysfunction
○ Lysosomes bursting (autolysis)
○ Various disease may dysregulate apoptosis - e.g. cancer
Necrosis
unplanned cell death
Sterilization
completely removing all living microorganisms and viruses from the surface of an inanimate object
- Most common method = autoclaving = subjecting a surface to saturated steam under high pressure at a temperature well over the boiling point of water
○ Will inactivate all bacteria, spores, fungi, and viruses, except prions (infectious misshaped proteins)
- Other methods include, UV radiation, heat, extremely noxious chemicals, and filtration
Disinfection
removal of most microorganisms especially pathogenic microorganisms
- Many disinfecting agents interfere with the cell walls of bacteria, although there are many different disinfecting agents with a wide range of mechanisms, most are a more effective to specific types of microorganisms - E.g. bleach, 70% ethanol (more effective than 90% ethanol)
Synaptonemal complexes
complexes made out of chromosomes
sex chromosomes
Females chromosomes = XX
Male chromosomes = XY
Mitochondria
organelles where citric acid cycle, beta-oxidation of fatty acids, and oxidative phosphorylation
- Mitochondrial matrix = place of the citric acid cycle
- oxidative phosphorylation takes place via the action of protein complexes embedded in the inner membrane of the mitochondrion
○ Electron transport chain causes the buildup of protons in the intermembrane space and the resulting proton gradient is used to power the activity of the ATP
- Self-replicating organelles
- Contain own DNA
Undergo binary fission
Endosymbiotic origin hypothesis
mitochondria derive from an original prokaryotic cell capable of aerobic metabolism that became engulfed in another cell -> endosymbiotic lineage
Sperm mitochondria
associated with ubiquitin protein which causes them to be target for destruction post fertilization
Embryology
- Fertilization takes place in the Fallopian tube, when a sperm cell encounters a secondary oocyte
- Sperm cells passes through the corona radiata (layer of the follicular cells surrounding the oocyte) and the zona pellucid (a layer of glycoproteins between the corona radiata and the oocyte)
- The secondary oocyte completes Meisosis II creating a second polar body and a mature ovum
- Haploid nuclei of the sperm cell and the ovum merge creating a diploid one-cell zygote
- The zygote travels to the uterus - it undergoes a series of mitotic cell divisions (cleavage)
- Once the zygote has cleaved into a mass of 16 cells (morula) by three to four days after fertilization
Acrosome reaction
digestive enzymes are released that allow the nucleus of the sperm cell to enter the egg
blastocytes
3 - 5 days after fertilization, the morula develops some degree of internal structure and becomes a blastocyst
○ has a fluid-filled cavity in the middle known as the blastocoel
○ Implants in the uterine endometrium and further differentiates into the gastrula
gastrula
has 3 layers: ectoderm, mesoderm, endoderm
○ These layers eventually go on to form specific organs and components in the body
Ectoderm -> NS and epidermis, hair, nails, sweat glands, linings of mouth, anus, and nostrils
○ Mesoderm -> generates many structures present within the body including the musculature, connective tissue (bone, blood, and cartilage), the gonads, kidneys, adrenal cortex
○ Endoderm -> interior lining of the body such as the GI tract, pancreas, and part of the liver, the urinary bladder, part of the urethra, and lungs
Neurulation
the process through which the NS is formed from the ectoderm
Mitosis
Takes 4 phases:
the process of asexual cell division in eukaryotes
1. prophase
2. metaphase
3. anaphase
4. telophase
○ Generates cells with 2 copies of each chromosome (diploid, 2n) that are essentially identical to their parent cell
Prophase
prepares for mitosis - DNA condenses such that distinct chromosomes becomes visible as sister chromatids (copies of given chromosomes) join at centromere
□ Kinetochore assembles on the centromere, and is the site where microtubule fibers that extend from the centrosome and form the mitotic spindle attach to pull the sister chromatids apart in later stages of mitosis
□ Asters (other microtubules) extend from the centrosome to anchor it to the cell membrane
□ Nuclear envelope and nucleolus disappear and mitotic spindle forms
Metaphase
the chromosomes line up at the middle of the cell along an imaginary line (metaphase plate)
Anaphase
the sister chromatids are separated and pulled to opposite sides of the cell by shortening of the microtubules attached to the kinetochores
Telophase
opposite of prophase - new nuclear envelope appears around each set of chromosomes and a nucleolus reappears within each of those nuclei
Meiosis
form of cell division that is essential for sexual reproduction
○ Germ cells (sex cells)
○ Forms 4 daughter cells - each has one copy of each chromosome (haploid, n)
○ 2 stages:
Prophase I, Metaphase I, Anaphase I, meiosis II
Prophase I
homologous chromosomes (I.e. the maternal and paternal copies of a given chromosome) pair up with each other in a process known as synapsis forming tetrads □ Cross over- exchange genetic info when paired -> results in recombinant DNA - source of variability □ Chiasmata = cross-over points
Metaphase I
homologous pairs (tetrads) line up at the metaphase plate □ Orientation of pairs is random in terms of which side of the metaphase plate the maternal or paternal copy of a given chromosome in a homologous pair winds up
Anaphase I
the homologous pairs are separated and one member of each pair is pulled to each side of the cell
Meisosis
the sister chromatids are split up into 2 haploid daughter cells
Troponin
complex of three proteins (troponin I, troponin C, and troponin T) required for muscle contraction in skeletal muscle and cardiac muscle
Skeletal muscles
innervated by the somatic NS - under conscious control
○ Striated - has extensive linear myofibrils that form striations when viewed with a microscope
○ Myocytes in skeletal muscles have multiple nuclei on the periphery of the cell - formed via the fusion of multiple precursor cells
2 different types of fibers within skeletal muscles:
- Red fibers (slow twitch fibers)
2. White fibers (fast-twitch fibers)
Red fibers (slow twitch fibers)
red fibers obtain their color from the presence of abundant reserves of myoglobin - rich in mitochondria
Prefer oxidative metabolism - present in many muscles that specialize in performing less intense actions over long periods of time
White fibers (fast-twitch fibers)
tend to mobilize glycogen for quick bursts of intense action followed by fatigue
Smooth muscle
innervated by the autonomic NS, unconscious control
○ Found in digestive tract - peristalsis, blood vessel walls, bladder, the uterus, and locations
○ Non-striated - does not contain well-organized, linear myofibrils (but contains actin and myosin filament that engage in contraction)
○ Contain ONE nucleus - found towards center of the cell
Cardiac muscle
shares some features of skeletal muscle and some features of smooth muscle and some unique features
○ Not under voluntary control
○ Tend to have 1 nucleus although some have two or more
○ Striated
○ Cells are connected by structures known as intercalated discs
§ Connect the cytoplasm of adjacent cardiac muscle cells, allowing ions to pass from cell to cell
Gap junctions
allow AP to pass rapidly from one cardiac muscle cell to another
Beta-oxidation
process in which fatty acids are broken down into acetyl-coA
- Generates electron carrriers NADH and FADH2, which produce energy in the electron transport chain
Beta carbon of each fatty acid is oxidized to carbonyl group (C=O) -> occurs in mitochondria in eukaryotic cells
- Easy with saturated fatty acid with an even number of carbons
- Special enzymes can handle fatty acid and odd numbers of carbons
- Beta-oxidation can produce very large amounts of ATP -> fats are a form of long-term energy storage in the body
- Beta-oxidation of palmitic acid (saturated fatty acid with 16 carbons) yields ~ 106 ATP
Beta-oxidation steps
- Step 1: forming C=C double bond between alpha and beta carbons of the carbonyl group at the head of the acyl-CoA molecule - coupled to the formation of FADH2
- Step 2: an -OH group is added to the beta carbon
- Step 3: The C-OH bond on the beta carbon is oxidized to C=O and NADH is formed
Step 4: the molecule is broken up, yielding an acetyl-coA group and a shorter acyl-coA group
Insulin
peptide hormone released by the beta cells of the pancreas in response to high blood glucose levels
○ Reduce blood glucose levels by promoting transport of glucose into cells via insulin receptors
○ Glucose is transported into the cell can be used immediately through glycolysis
○ Muscle and liver cells can store the glucose as glycogen and adipocytes (fat cells) can mobilize fatty acids to store downstream byproducts of glucose metabolism in the form of triglycerides - insulin upregulates these processes and protein synthesis
○ Glycogen synthesis = esterification of fatty acids
Glucagon
peptide hormone released by alpha cells of the pancreas
○ Released in response to low glucose levels and has the effect of increasing blood glucose levels by promoting glycogenolysis and gluconeogenesis in liver cells
Cortisol
(glucocorticoids from adrenal cortex): associated with long-term responses to stress and increases blood glucose levels
Epinephrine
released by adrenal medulla (as well as norepinephrine) plays a major role in the fight or flight response to immediate stress also raises blood glucose levels
Growth hormone
can increase blood glucose levels due to its antagonistic effect on insulin
Fatty acids
- Amphipathic: long hydrophobic chain and a hydrophilic head
- Saturated = no C=C
Unsaturated = 1 or more C=C pi bonds - lower melting points than saturated - Fatty acids are constituents of complex membrane lipids
- They are stored fat in the form of triglycerides (esters of 3 fatty acids joined together with glycerol, a 3-C triol)
- Saturated = no C=C
Most necessary fatty acids can be synthesized in the body EXCEPT ________cannot be synthesized from precursors in the body
linoleic acid and a-linolenic acid
Fatty acids
nomenclature
The site of unsaturation in a fatty acid is indicated by the symbol ∆ and the number of the first carbon of the double bond relative to the carboxylic acid group (–COOH), which is the highest priority carbon (i.e. #1).
○ E.g. oleic acid is a 16-carbon fatty acid with one degree of unsaturation between C9 and C10, and is labeled as 16:1Δ9
Base pairing
- A and G have 2 ring structures = purines
- C and T and U have 1 ring structures = pyrimidines
- C and G pair and A and T pair
Chargaff rule: a double-stranded DNA molecule A% =T% and C% = G%
Group selection
natural selection could act on the level of the group not the individual
Helps to explain altruistic behaviour
Stabilizing selection
occurs if both extremes are selected against, directional selection occurs if only one extreme phenotype is selected against and the other extreme is favored
Disruptive selection
the median phenotype is selected against
Hardy-Weinberg equilibrium
used to model stable gene pools that satisfy following assumptions
○ Organisms must be diploid and reproduce sexually
○ Mating is random
○ Population size is very large
○ Alleles are randomly distributed by sex
○ No mutations occur
No migration into or out of the population
Hardy-weinberg equation uses ____ _____ to predict the distribution of phenotypes in the population….
allele frequencies; ○ If p and q are the only 2 alleles of a gene present: p + q = 1
§ (p +q)^2 = 1^2 -> p^2 + 2pq + q^2 = 1
□ Allows us to connect genotypes and phenotypes
□ p^2 + q^2 => correspond to individuals homozygous for p and q
□ 2pq => frequency of heterozygotes
Genetic drift
role of chance in the absence of strong selective pressures in determining reproductive fitness of various alleles
When no strong pressure exists for a certain allele, it may randomly happen to be reproduced more or less often
Bottlenecks
occurs when external event dramatically reduces the size of a population in a way that is essentially random with regard to most if not all alleles - dramatically reduce diversity in a gene pool
Alveoli
where gas exchange takes place; sacs coated with surfactant film that reduces surface tension, allowing the alveoli to remain inflated when the lung is compressed during exhalation
○ Surrounded by tiny capillaries
- Oxygen and CO2 can simply diffuse down their respective concentration gradients
Negative pressure respiration
when the diaphragm (muscle at bottom of thoracic cavity that separates it from the abdominal cavity below) contracts, the thoracic cavity expands -> causing parietal pleura to expand, causing a pressure gradient that in turn causes the pulmonary pleura and lungs to expand
○ When lung expand, the pressure within decreases
passive exhalation
simple relaxation of diaphragm is enough to cause the lungs to contract, increasing pressure and expelling air
active exhalation
intercostal and abdominal muscles can be used to force out air more intensely and quickly; e.g. exercise
Glycolysis equation
glucose + 2NAD+ + 2 ADP + 2Pi -> 2 pyruvate + 2NADH + 2ATP + 2H2O
Glycolysis
- initial investment phase, consuming 2 ATP
- Payoff phase = generates 4 ATP -> net ATP =2
- Pyruvate has three-carbon alpha-keto acid that participates in multiple pathways
- Aerobic metabolism: pyruvate is converted to acetyl-coA and fed into the citric acid cycle
- NADH needs to be converted back to NAD+ for glycolysis to continue - can happen through the electron transport chain or through fermentation
glycolysis steps overview
- initial investment phase, consuming 2 ATP
- Payoff phase = generates 4 ATP -> net ATP =2
- Pyruvate has three-carbon alpha-keto acid that participates in multiple pathways
- Aerobic metabolism: pyruvate is converted to acetyl-coA and fed into the citric acid cycle
- NADH needs to be converted back to NAD+ for glycolysis to continue - can happen through the electron transport chain or through fermentation
glycolysis is upregulated when
the cell needs more ATP, as signaled by relatively high concentrations of AMP/ADP or an abundance of inorganic phosphate (Pi)
Glycolysis is down regulated when..
the cell does not need more ATP from high ATP levels and abundant NADH or high levels of citrate (product of first step in the citric acid cycle)
Negative regulation
certain products inhibit previous steps
G6P, the first product of glycolysis inhibits hexokinase (catalyzes the first step), the conversion of glucose to G6P
Lactic acid fermentation
often occurs in human muscles, pyruvate is converted to lactate by lactate dehydrogenase in a reaction coupled to the conversion of NADH to NAD+
Lactate is a product of fermentation
Trisomy
a chromosomal condition characterized by an additional chromosome
Cholesterol
- At moderate to high temperatures (including normal physiological temperature), cholesterol increases the rigidity of cell membranes by attracting adjacent phospholipid tails
A more rigid membrane appears to correlate with a higher incidence of trisomy 21
Prokaryotes
(bacteria and archaea): absence of a nucleus and membrane bound organelles
- Bacteria is ubiquitous and play a major role in maintenance of human health - They have cell wall containing peptidoglycan that encloses the cell membrane - Rotating flagella in single circular chromosome - Structural differences between eukaryotes and prokaryotes are often specifically targeted by antibiotics
Cocci
spherical shaped bacteria
Bacilli
Rod-shaped bacteria
Spirilli
spiral-shaped bacteria
Anaerobes
bacteria that do not require oxygen for metabolism
Obligate anaerobes
oxygen is toxic
Aerotolerant anaerobes
similar to obligate anaerobes in that they cannot engage in aerobic metabolism - but oxygen is not toxic for them
Facultative anaerobes
can exchange in either aerobic or anaerobic metabolism
Obligate aerobes
bacteria that require oxygen for metabolism
AA Buffer
- Amino acids that make up a protein may include many acidic or basic side chain groups
Those side chains can either release or absorb protons, allowing them to help buffer the blood through action as a Bronsted-Lowry acid or base
Henderson-hasselbach equation
pH = pKa + log[A-]/[HA]
○ HA = generic acid
○ A- = conjugate weak base
○ pH of buffer solution can be calculated using this equation
If we add a small to moderate amount of a strong acid or base to the buffered solution, it will …
it will entirely protonate or deprotonate some of the weak acid/ base
Bicarbonate buffer system
(CO2 + H2O ⇌ H2CO3 ⇌ HCO3− + H+)
○ Maintains pH of blood within the narrow range of roughly 7.35 -7.45 that is compatible with health
○ Encodes a key relationship for understanding the importance of respiration in the context of human metabolism
Analogous structures
structures that evolved independently to carry out the same function
E.g. wing of bee and wing of bird
Homologous structures
hose that similar evolutionary history arising from the same source even if now they have different functions
The forelimbs of mammals (human arm, walrus flipper, bat wing) would all be homologous despite their different functions
Mediating variable
process through which 2 variables are related
Moderating variable
affects the strength and direction of that relationship
withdrawal symptoms
Withdrawal from substances tend to produce the opposite effect of symptoms occurred while using the substances
Depressants
relaxation by reducing nervous system activity
○ E.g. alcohol - stimulates GABA - slows activity of frontal lobe reducing judgement and lowering inhibitions
GABA: inhibitory NT associated with reduced anxiety, dopamine
Opiates
derived from poppy plant
○ E.g. morphine and codeine - cause a sense of euphoria and decreased reaction to pain by binding to opioid receptors in the NS
○ Overdose can cause death when brain stops sending signals for respiration
After prolonged use, drugs can cause the brain to entirely stop producing endorphins - withdrawal are painful
Hallucinogens
e.g. LSD and ketamine - distort perception, enhance sensory experiences and cause introspection - heart rate + blood pressure + body temperature increase and dilate pupils
Marijuana
has qualities of stimulants, depressant, and hallucinogen
○ THC affect certain receptors in the brain
○ THC increases production of GABA and dopamine
THC can increase appetite, dry mouth, fatigue, eye redness, lowered blood pressure, and increased heart rate
Arousal
mental alertness, attentiveness, and general awakeness
○ Low arousal state: drowsiness, lack of focus, boredom, and low energy overall
High arousal state: awake, jitters, restlessness
Arousal theory
people behave in certain ways to maintain a level of optimal arousal
○ Optimal level of arousal can vary depending on the particular task or behavior
○ Highly cognitive actions like playing chess have lower optimal levels of arousal
More physical tasks like sports typically require higher level of arousal
Yerkes dodson law
performance of a behavior tends to be negatively impacted at high and low levels of arousal
U shaped function (x-axis =arousal ; y-axis = performance)
Drive-reduction theories
Drive-reduction theories suggest that depression stems from a reduction in the motivating forces of arousal
Limbic system structures
regulate emotion and memories
Hypothalamus
coordinate many hormones, some of which are involved in mood regulation
Mood disorders
characterized by the persistent, abnormal elevation and or lowering of one’s mood - sustained internal state of feeling or emotion
Somatic disorders
unified by somatic bodily symptoms (that can cause stress and impairment to the sufferer
○ Symptoms generally lack an identifiable physical cause
Individual may be impaired by irrational fears or developing or having a disease
Schizophrenia
psychotic disorder - delusions, disorganized thought and behavior, hallucinations, catatonia, and negative symptoms
Dissociative disorders
disruption or breakdown of perception, identity, memory, or awareness
○ Feel disconnected from reality
Unintentional escape from reality or barrier against stress from a life event
Personality disorder
characterized by long lasting, maladaptive patterns of behavior that can impair cognition, emotion, and interpersonal behavior and communication, and/or impulse control
Incidence
the number of new cases of disease during a specific time interval
Prevalence
how common - how many people (new and current) have MS within a certain amount of time
Risk ratio
compare the risk among one group with the risk among another group
Uneven distribution of risk factors across a population results in health disparities which can exist based on geography, gender, environment, socioeconomic status, ethnicity/race, and access to healthcare
Social epidemiology
societal factors that influence the distribution of health and illnesses across a population
Power of a study
ability of a study design to detect a real statistically significant effect
Larger samples and more effect size has more power
Primary socialization
learning of acceptable actions and attitudes during childhood by observing parents, siblings, friends, teachers, and other authority figures
Secondary socialization
process of learning acceptable and appropriate in small more focused section of society
Learning in school or the workplace
Anticipatory socialization
process by which we prepare for future changes that we anticipate
E.g. changing sleep schedule
Resocialization
process through which we get rid of old behaviors in order to take on new ones e.g. soldier military training
Symbolic interactionism
focuses on symbolic meaning that people develop and rely upon in the process of social interactions
E.g. smoking - meaning differs per group
Conflict theory
emphasizes the role of coercion and power in producing social order
Social order is maintained by those with the most power
Functionalism
system of interconnected parts that carry out specific role that enables them to cooperate to maintain social equilibrium for society as a whole
Sociobiology
some social differences are rooted in biology
Related concept of anomie
describes social instability caused by the breakdown of social bonds; e.g. social norms between individuals and communities
Rational choice theory
people make individualistic rational and calculated decisions about all things in their life
Game theory views
social interaction as a game in which there will be winners, losers, and proper wats to play in order to achieve victory
Social exchange theory
society as a series of interactions that are based on estimates of rewards and punishments
○ Interactions are determined by rewards or punishments that we receive from others
Key principles of gestalt perception
○ Proximity = objects that are close together will be perceived as forming a gorup
○ Similarity = objects that are similar to each other will be grouped together
○ Closure = people tend to infer complete shapes even if a shape is incompletely sketched out
Good continuation = we perceive intersecting objects as forming coherent wholes
Ethnocentrisms
world view in which one’s own culture and traditions are seen inherently superior to those of other people
Stereotypes
attitude + cognitive action - a prevalent but oversimplified idea or set of ideas about a certain group
Self-fulfilling prophecy
people fulfil their stereotype
Prejudice
attitude - preconceived notion about a person, group or thing
Actually seeing person and judging them
Cognitive biases
ways in which out perception and judgements systematically differ from reality
Avoid features of our cognitive system - may be adaptive
Heuristics
mental shortcuts or simplified iterations of principles that can help us make decisions or poor judgement
Representative heuristic
tendency to make decisions about actions or events based upon our standard representation of those events
Availability heuristic
tendency to make decisions about how likely an action or event is based upon how readily available similar information is in our memories
Belief Bias
tendency that people have to judge things based not upon sound logic but upon already held beliefs
Confirmation bias
tendency that people have to focus on information that is in agreement with the beliefs they already have
Fundamental attribution error
Fundamental attribution error Attribution theory = the ways in which people attempt to explain various behaviors and events
an individual’s tendency to attribute another’s actions to their character or personality, while attributing their behavior to external situational factors outside of their control
Actor-observer bias
tendency to blame our own actions on external situations but others actions on personality
Self-serving bias
tendency people have to credit their successes to themselves and their failures either to the actions of others or to situations
Distress
unpleasant and counterproductive stress
Eustress
positive form of stress
Cognitive stress response
hypothalamus releases corticotropin-releasing hormone (CRH) which stimulates the pituitary gland to produce adrenocorticotropic hormone (ACTH) - stimulated release of cortisol from the adrenal glands
Cortisol
maintains continuous supply of blood sugar needed to sustain a stress response by upregulating gluconeogenesis and mobilizing free fatty acids and amino acids from body stores to be metabolized
○ Brains only energy source is glucose
○ If cortisol release is chronic - the healthy functioning of white blood cells can be inhibited making the immune system weaker and this the body more susceptible to illness and infection
Classical conditioning
pavlov dog pairing unconditioned stimuli to neural stimuli to conditioned stimuli
Operant conditioning
using reinforcement to encourage behavior and punishment to discourage behaviour
○ Positive = adding stimulus
○ Negative = removing stimulus
in reinforcement schedules
Typical reinforcement schedules
§ Fixed ratio = behavior is reinforced after a specific number of responses
§ Variable ratio = behavior is reinforced after an average but unpredictable number of responses => considered most effective
§ Fixed interval = behavior is reinforced after a specific amount of time has passed
§ Variable interval = behavior is reinforced after an average but unpredictable amount of time has passed
Social loafing
tendency that people have to put in less effort in a group setting particularly if the group is being evaluated as a whole and not on an individual basis
Deindividuation
people lose their sense of self-awareness in a large group setting which provides a high degree of arousal and a low sense of responsibility
○ Anonymity, diffused responsibility, and group size are factors of deindividuation
Bystander effect
people do not offer to help the victim if there are other people present
The more bystanders, the less likely anyone is going to help
Group polarization
tendency that groups have to make decisions that are notably more extreme than the initial individual opinions of their members
Groupthink
a group of people has such a strong desire for harmony and individual conformity that the group makes irrational decisions
Internalization
occurs when an individual genuinely agrees with the values/behaviors/attitudes that he or she is conforming with and finds the behavior to be inherently rewarding
Identification
the acceptance of other people’s ideas without thinking critically about them
Compliance
an individual yields to social pressure (typically in response to a direct request) because he or she wishes to get a positive reaction from another individual or group or to avoid social disapproval by others
- when an individual changes his or her behavior in response to a direct request
Informational social influence
think other people’s opinions are correct when they are unsure
3 components of emotion
behavior (action), cognitive (mind), physiological (body)
Paul ekman’s 7 universal emotions
anger, contempt, disgust, fear, happiness, sadness, and surprise
James-Lange theory
a stimulus triggers a physiological response which then leads to the subjective conscious experience of emotion
○ But certain physiological states may be experienced as different emotions depending on the context
○ E.g. Timothy’s dog runs out of the house without his collar or leash. Timothy’s heart rate increases and he shouts for the dog to come home. His body’s cues and behavior lead him to understand that he is in a scary situation, and he feels afraid.
Cannon-Bard theory
cognitive and physiological responses to a stimulus occur simultaneously and independently of one another with a behavioral response following them
○ Lacks element of cognitive appraisal (continuous thought about how one’s situation may impact the emotions felt)
○ E.g. Annabel is holding her guinea pig on the couch and scratching its ears. As she does this, her brain releases hormones associated with reward. At the same time, she interprets the situation as happy and calm. She then smiles.
Schachter-Singer theory
a stimulus first leads to physiological arousal then a cognitive interpretation (cognitive appraisal + James lange theory) of the circumstances and finally the perception of emotion
○ E.g. As Julia pets her cat, her blood pressure decreases and her brain releases oxytocin. She then thinks of how much she loves her cat, and experiences happiness as a result.
Persuasion
form of social influence in which an individual or group (audience) is encouraged to adopt an idea, attitude, or course of action - non compulsory
○ Providing a favor, being likable, obtaining a written commitment of agreement
Coercive methods of persuasion
which actively threaten or intimidate the audience to achieve the desired goal
Cognitive dissonance
the unpleasant feeling a person experiences when holding two contradictory beliefs at the same time
Vision
light enters through the cornea (clear portion)
○ Cornea is highly curved and light is refracted as it passes through it
○ Light then passes through the pupil (controlled by autonomic NS)
Light then moves through the lens which can be precisely adjusted by the ciliary muscle to ensure that light is focused on the retina
Retina
part of the CNS and contains photoreceptors (cones and rods) that convert light into electrical impulses to be sent to the brain
Cones
perceive color and fine detail
Rods
allow for the perception of light and dark
optic chiasm
and vision representation in the brain
optic fibers from the nasal half of each retina cross paths
§ The temporal fibers do not cross paths
○ The fibers corresponding to the left visual field from both eyes are projected to the right side of the brain
○ The fibers corresponding to the right visual field from both eyes are projected to the left side of the brain
Inter-rater reliability
assessment by different people would generate similar results
Validity
how well a given experiment actually measures what it sets out to measure
Internal validity
the study has internally been well constructed - e.g. large random samples, safegaurd against confounding variables, reasonable and reliable processes and instruments
External validity
how generalizable the results are to other settings - must control any situational variables in the execution of the study
Construct validity
how well a given assessment (a survey, a test, etc.) actually measures what it claims to measure
Conflict theory
social class conflict
Absolute mobility
compares your income to parent’s income - if you are better off than your parents and your children are better off than you
Demographics can shift over time by changes in ..
birth rates, death rates, migration into and out of the society
Demographic transitions
specific category of demographic shifts accounting for changes in fertility and mortality rates as the country develops from a preindustrial to an industrial modern economic system
Urbanization
pattern of movement from rural to cities
Vertical mobility
movement from one social level to a higher one or a lower one by either changing jobs or marrying
Globalization
increasing amount of interaction and integration on the international scale through exchange of products services, ideas and information
Culture
languages, customs, beliefs, rules, arts, knowledge, and collective identities and memories developed by members of a given social group
Ethnocentrisms
bias that occurs when evaluation of other cultures is done with preconceptions that originate in the standards and customs of one’s own culture
Principle of cultural relativism
when analyzing the beliefs, values, and practices of a culture, it is best to do so from the viewpoint of that culture itself
symbolic or nonmaterial culture
Ideas, beliefs and symbols
Material culture
artifacts, buildings, and physical objects
Ingratiation
an attempt to get someone to like you in order to get them to comply with your request
Normative Influence
influence to conform with the expectations of others to gain social approval
Motivation
driving force or reasoning behind our actions and behaviors
○ Arousal describes how even when all instincts are fulfilled, people are still motivated to do things sometimes out of boredom or curiosity
Extrinsic motivation
created by external forces
Intrinsic motivation
created by internal forces including attitudes, ways of thinking, feelings about people, places, and things that are reflected in our actions and our behaviors
Instincts
innate, unlearned, and usually fixed patterns of behavior that are present in all members of species
Drive
urge to reach a goal or satisfy a need
○ Basic drives stem from physiological needs like hunger and thirst = primary drives -> body alerts that it is out of equilibrium
○ Secondary drives = learning and experiences -> feelings of love and aggression
Opponent-process theory
self destructive behaviors like drug addiction
Drive-reduction theory
examines the actions we take to fulfill (reduce) basic biological drives like hunger, thirst, or reproduction
Expectancy-value theory
the amount of motivation required to achieve a goal is affected both by a person’s expectation of reaching the goal and how much that person values reaching that goal
○ If a person reaches that goal highly, she will need less motivation to achieve it and vice versa
Norms
enforced by sanctions, which are punishments for deviations from the norm or rewards for acting in accordance with it
Formal norms
written, explicit, and generally enforced with penalties e.g. laws
Informal norms
generally understood but implicit, unwritten, and not associated with criminal or legal penalties
§ Mores = carry major importance for society and if broken can result in severe social sanctions
§ Folkways = less important; breaking a folkway usually brings with it less severe consequences than breaking more
Deviance
breaking a folkway or any other social norm
Identification
mechanism through which new ideas are spread but not necessarily - this influence factor may promulgate old or new ideas
Minority influence
new ideas are automatically minority opinion that can be spread through the influence of minority on others accepting the view
Conformity
identification takes place when individuals accept an influence or viewpoint without deep reflection in order to produce or maintain a desired and beneficial relationship to another person or a group
Social conflict model
society is unequal, and inequalities present give rise to conflicts and change
○ Social conflict involves interests
○ A person or groups interest is his or her attitude + strength => desired outcomes
○ Social conflict can then be seen as the opposition, balancing, and resolution of two or more competing interests
Approach-approach conflict
two options are both appealing
Avoidant-avoidant conflict
both options are unappealing
Approach-avoidant conflict
one option has both positive and negative aspects
Double approach-avoidant conflict
two options with both appealing and negative characteristics
Conflict theorists
seek to explain the workings and institutions of society as a result of competition over power resources or other forms of capital
Social functionalists
differentiation within society leads to order and stability
Weber’s Law
quantifies the perception of differences between stimuli
○ Examines the relationship between actual physical changes in a stimulus and the percieved changes
○ The perceivable change in stimulus intensity (I) is a constant or mathematically (If -Ii)/Ii = constant
Can be applied to sensory systems
Magnitude effect
phenomenon that the subjective perception of a linear difference between two stimuli progressively diminishes when the average magnitude of stimuli increases
related to Weber’s Law
Meritocracy
system under which individuals are rewarded on the basis of individual skill, talent or achievement
Oligarchy
system which a small number of individuals hold the majority of power
Spatial discrimination
one’s ability to distinguish between two points of contact with one’s skin
Renal cortex
300mOSM: most tissues and blood is somewhere around this
renal medulla
○ Very salty
○ 1200mOSM
○ Contains glomerulus inside the renal corpuscle
Connected to proximal convoluted tubule followed by the loop of Henle to the distal convoluted
Glomerulus
○ Net that is semipermeable § Lets small stuff through § Glucose can go through ○ Large particles such as cells and proteins cannot pass through the glomerulus Within the Bowman's capsule
Proximal convoluted tubule
○ The filtered “blood” = filtrate enters from the glomerulus
○ Pumps stuff we want back into the body
○ Pumps trash into the filtrate
Absorbed or secreted based on what we want
Filtrate
- Filtrate all the way until released from ureter -> urine
○ Stuff we want = glucose, ATP, etc.
Trash/HUNK = urea, ammonia (nitrogen), potassium, hydrogen
Loop of Henle
Descending limb
§ Salty - water wants to move outside of the loop
□ This is why we do not pee so much
§ Aquaporins let the water leave - happens passively without energy input
§ Really concentrated at the bottom of the loop of Henle due to all the water leaving the descending limb of LOH
Loop of Henle
Ascending limb
pulling out salt (reason why medulla is salty)
§ No aquaporins in the ascending limb of LOH to keep water out
§ Thin ascending limb
□ More salty inside the limb - salt wants to leave
□ Na+ and Cl- ion channels : The salt moves out
® passive
§ Thick ascending limb
□ Pump Na+ and Cl- out of the limb to be used in other parts of our body - active
® Used for AP and muscles, neurons
To get osmolarity to around 100mOSM
Countercurrent exchange multiplier
Loop of henle
§ Salt pulled out and outside gets saltier
§ Makes water want to leave
Positive feedback loop with water leaving and salt leaving
Distal convoluted tubule
○ Must reach around 100mOSM
○ Under normal conditions, nothing happens in the DCT or the collecting duct
○ Adjust what happens depending on what our condition is
Hypernatremic/Hyperosmotic
blood too salty
- When blood is too salty, we need to reabsorb more water and need more water
- If salt levels change - you are dead very quickly
○ Need Na+ for muscles, and neurons to fire
○ Too much salt - heart flutters, seizures from neurons firing too easily
- Hypothalamus tests blood - notices the posterior pituitary to release ADH
Hypernatremic/Hyperosmotic
- give what
- ADH: makes you pee less
○ Adds aquaporins to the collecting duct
○ Water leaves the collecting duct more - pulls out water and gets added to the blood
§ Same function of descending limb
§ Dilutes the blood - add more water to blood - main purpose
§ Increases blood pressure - more blood due to water added - side effect
§ Makes urine more salty and concentrated - more yellow
○ Reabsorb water alone - dilute blood and increase blood pressure
○ Peptide hormone = quick
ACE inhibitor
prevents angiotensin 1 from turning into angiotensin 2
- Stops aldosterone - does not increase BP
Atrial natriuretic peptide
makes you pee out salt and water
- Lowers blood pressure; when blood pressure is too high, the heart cannot pump properly - Natr- = sodium ; -uretic = pee
Osmole
concentration of solute (not specifically 1 type of solute)
Hypovolemic (low blood) or hypotensive (low BP)
- Not enough blood
- Juxtaglomerular: Cells next to the glomerulus
○ Technically part of artery
○ Notice if there is not enough blood (blood pressure)
○ Baroreceptors: pressure receptor
○ Secrete Renin (renin angiotensin aldosterone system : RAAS)
- Release of angiotensin 1 (doesn’t really do anything)
- Angiotensin 1 is converted to angiotensin 2 by angiotensin converting enzyme (ACE)
- Angiotensin 1 and 2 are isomers
- Juxtaglomerular: Cells next to the glomerulus
Angiotensin 2 causes
- Vasoconstriction: increases blood pressure because it makes all of the arteries squeeze blood
- When there isn’t in enough blood, squeeze all the arteries to push blood around to get blood to brain
- Fixes problem of low blood pressure
- Release of aldosterone
- Aldosterone causes salt and water reabsorption -> increases blood pressure/volume without changing the saltiness
- -one = steroid hormone and has a ketone, slow to get going
® Takes a while to kick in
- ADH release
Galvanic and voltaic cells are ______ ____
spontaneous reactions
Galvanic cell charges
there is an Ox (-) and a Red Cat (+)
Electrolytic cell charges
anode (+) and cathode (-)
Patterns are backwards for electrolytic cells because it is not spontaneous and requires a power source
Daltons
molecular weight
1 AA in Dalton
110 Da
Electrophoresis
- DNA, RNA or proteins can undergo electrophoresis and get separated by size (ideally) and charge
○ DNA - phosphate (-) backbone that wants to go to anode (+)
○ DNA and RNA = consistent m/z ratio
§ Where m = mass; z = charge
Proteins - no consistent m/z ratio or 3D shape due to a variety of amino acids
Agarose Gel Electrophoresis
gels with a lot of tiny pores that molecules are going to move by size and charge due to the power supply (Electrolytic cell)
○ Add samples to the gel
○ Smaller molecules navigate through the gel easier and get farther on the gel
○ Larger molecules will not migrate far
Want to get rid of charge to just separate by size
Electrophoresis with DNA and RNA
- DNA ladder - contains DNA of known lengths used for reference = control
- Separated based on size/weight because the m/z ratio is consistent in DNA and RNA
Electrophoresis with Proteins
Native Gel
completely folded
○ Samples of globular and filamentary are separated
○ Native gels will always give 1 band per protein (even if it has multiple subunits) -> all subunits run together
§ Give us the total weight of the protein
Electrophoresis with Proteins
SDS-PAGE
unfolded but contain disulfide bridges
○ SDS = detergent
§ denatures the protein Breaks all noncovalent linkages - unfolds
§ gives everything the same charge - gives uniform m/z ratio
§ 1 (-2) SDS will bind to 2 AAs and stabilizes them no matter what type they are
□ SDS is amphipathic: negatively charged head and nonpolar tail
§ SDS eliminates all bonds except peptide bonds and disulfide bridges
○ Subunits will migrate + form a band based on weight/size
○ Multiple proteins of the same weight/size will form the same band
Electrophoresis with Proteins
SDS-PAGE + BME
Unfolded with no disulfide bridges
○ BME = reducing agent that breaks disulfide bridges (reduction)
§ 1 band -> 2 bands
§ If it is the same weight => 2 bands combine to form 1 band
§ Peptide bonds are not broken
○ No intramolecular interaction = only primary structure remains
Isoelectric focusing
- Separate proteins by pI (isoelectric point)
- pI = pH at which the molecule will be neutral
- Add sample to the middle
- The molecules are going to migrate towards where they are neutral in the pH gradient
- Allows us to determine pI of each protein
- Separate AA/proteins by pI (charge) - separated on pH gradient
○ Molecules move until they are no longer charged - Tug a war/bidding war for hydrogens between molecules + environment
○ Protons will go to the highest bidder -> whoever has the highest value between pH and pKa - When there is 1 pKa, pKa = pI
Calculating pI
- Amino acids have at least 2 pKa
- Take the two closest pKa value and average them Higher pI = probably basic
- Lower pI = acidic
- pKa of histidine ~6
After Electrophoresis: Blotting
3 types of Blots:
- 3 types of Blots:
○ Southern -> DNA
○ Northern -> RNA
○ Western -> Protein
SNOW
DROP- Blotting is used to press proteins to a sheet and the fluorescent or radioactive label
- Blotting over goal = visualization and identification
- Radioactive antibody - only binds to proteins of interest and the decay will make it visible
Chromatography
- Separate based on affinity (desire to interact) with either stationary phase and mobile phase
- Polarity is common
- Stationary phase = doesn’t move; usually some polar material
- Mobile phase = moves; often a liquid or gas
- Eluent = fluid part of the mixture = mobile phase (solvent) + analyte
- Analyte = substances that we want to separate
Chromatography
Normal Phase
○ Mobile phase (MP): nonpolar
○ Stationary phase (SP): polar (e.g. silica; often solid)
○ Elution order: order by which you leave the column => nonpolar then polar
§ The nonpolar molecule wants to interact with mobile phase -> wants to leave first
§ The polar molecule wants to interact with stationary phase -> wants to not move
Chromatography
Reverse Phase
○ Mobile phase: polar
○ Stationary phase: nonpolar
○ Elution order: polar first then nonpolar
Column chromatography
goal + steps
- Goal is to let gravity do the work
- Step 1: load sample
- Step 2: add the mobile phase
- Step 3: watch the sample pass through and the speed at which they pass through
- Step 4: collect the separate samples that are separated in the column
High Performance/Pressure Liquid Chromatography (HPLC)
- Fancier column chromatography - works the same
- Uses high pressure -> better separation
- Not using gravity -> allows it to separate characteristically based on polarity
Thin Layer Chromatography (TLC)
- Work against gravity because the molecules travel upwards
- Elution time = distance travelled
- TLC plates are normally made of silica plates
- Rf value = distance molecule travelled/distance solvent traveled
○ Rf < 1 because the molecule cannot travel farther than the solvent
○ Higher Rf values => more distance travelled
○ No units for Rf values
Gas Chromatography (GC) AKA Gas-Liquid
- Used for separating compounds that can vaporize without decomposing
○ Cannot use proteins that would denature- Stationary phase: liquid
- Mobile phase: inert gas -> not interacting with sample but will act as a current
- Technically separates by boiling point and polarity but polarity does not have much of an effect unless BP are very close
- High BP -> remain in column longer
Lower BP -> move through column faster = favorable interactions with mobile phase will elute first
BP is based on the _____ interactions within the sample..
noncovalent; ○ Polar molecules = have stronger intermolecular forces = higher BP
○ Nonpolar molecules = have weaker intermolecular forces = lower BP
Size exclusion Chromatography AKA Gel Filtration
- Mixture between gel electrophoresis and chromatography
- Molecules have to travel through small pores
○ Pores are different sizes - Sorts/separates by size
- Smaller molecules will retain longer because they go through smaller pores for longer -> higher affinity for stationary phase (gel)
Elution order = larger molecules -> medium molecules -> smaller molecules
- Molecules have to travel through small pores
Affinity Chromatography
- Separates by: whether or not you are the molecule of interest
- Elution order: everything, THEN molecule of interest
- Fishing for one SPECIFIC molecule
For anything that can bind to a protein
Distillation Basics
- Distillation goal = purification
- Before = mixture of liquids
- After = boil and cool down vapors into a different flask (purified liquid)
Simple distillation
- Use when you have to separate liquids with very different boiling points
Fractional distillation
- If you have molecules that are very close in BP (<40-degrees)
- Add in fractionating column = allows vapors to condense and fall back down
○ The longer the column, the better the separation - There is more control = better separation
- Add in fractionating column = allows vapors to condense and fall back down
Vacuum distillation
- When boiling point is really high (>150-200-degrees C)
- Could decompose at such temperatures
- Vacuum added -> decreases atmospheric pressure to lower BP
- BP = point that the atmospheric pressure = the vapor pressure
Anion Exchange chromatography
- Anion Exchange: wanted negative charges
§ Cations first -> then anions
Buffers have positive charge
cation Exchange chromatography
- Cation Exchange: want positive charges because the bead is negatively charged
§ Anions first -> then cations
Buffers have negative charge
Ion Exchange Chromatography
- Separates by net charge for separation and purification of analyte (proteins, peptides, nucleic acids, poly-nucleotides, etc.)
- Stationary phase = ion exchanger
- Elution order: (named for what they attract)
- The repelled charged leave first as they do not higher affinity for the
NaCl added to kick off molecules with lower degrees of negative charges -> washing phase
