4.1-5.17 Flashcards
kind of independent variables
MANIPULATED
- age
- sex
- race
- SES
- standardized measures and scores
4 sampling biases
a NOT random sample. types of bias include
- special real area - people are selected in a physical space (the quad - this is not representative of all the students)
- self-selection bias - participant choose to participate
- advertising - only the advertised people
- healthy user bias - picking only healthy subjects (say, people who use the gym)
standard error
standard deviation / (sample size)^(1/2)
test-retest reliability
taking the MCAT multiple times should result in equivalent scores
inter-rater reliability
the degree to which two researchers or raters agree in; two doctors come up with the same diagnosis
validity
how well an experiment measures what it is trying to measure
internal validity
demonstrate a causal relationship between two variables (highly controlled), avoid confounding factors
external validity
results of study can be generalized to other situations and other people
construct validity
does the survey ask the question clearly?
liquid-liquid extraction
like dissolves like
organic compound is extracted with water; inorganic salts, acids/bases, and polar low-molecular weight compounds (alcohols, amines, carboxylic acids)
acid extraction
basic (amines) can be extracted from mixtures of organic compounds upon treatment by an acid
formation of a positively charged ion (cation), soluble in AQUEOUS solution and removed from organic compounds that remain dissolved in the organic phase
base extraction
converts carboxylic acids into anionic salt -> found in aqueous layer
NaHCO3 cannot extract phenols, but NaCl can
convert the acid into a SALT, which can be extracted away
chromatography
SEPARATE MIXTURES
“Chromatography involves the SEPARATION of colors”
thin layer chromatography (TLC)
“The polar ice caps are dangerously thin layered”
POLARITIES
more polar -> travels SLOWER (POLAR STATIONARY PHASE)
less polar -> travels FASTER
Rf = ratio (1/1 is extremely not polar)
good for small amounts
thin layer of absorbant (silica, SiO2) = POLAR STATIONARY PHASE
column (flash) chromatography
POLARITY - good for BULK
pour down a column, SiO2 slows down the polar, so you capture the non-polar first
Ion exchange chromatography
VARIOUS CHARGES
MIXTURES OF PROTEINS
a resin (anionic sulfate groups) captures positive charges, the negative and neutral charged particles are eluted first. Later, the positive charged species can be eluted afterward with sodium-containing solution
CATION exchange resin -> positively charged proteins with pI greater than pH elute elute SLOWLY (CATION exchange KEEPS positively charged) -> proteins with pI below pH pass through
anion exchange -> hold on to low pI, while high pI (positive charged) elute first
High performance liquid chromatography
reverse phase HPLC:
opposite of TLC; more polar compounds elute first (stationary phase is silica gel bonded to a non-polar group = NONPOLAR STATIONARY PHASE)
Mobile phase = POLAR
size exclusion chromatography
MOLECULAR SIZE
POROUS BEADS
BIG = FAST
affinity chromatography
PURIFY PROTEINS/macromolecules
Target is TRAPPED in the STATIONARY PHASE
ANTIGEN/ANTIBODY
Enzyme/Subtrate
Receptor/Ligand
Protein/Nucleic acid
trapping in a stationary phase, washing to remove unwanted components; target protein is released off the solid phase
affinity tags = His tags
Gas chromatography
DIFFERENT VOLATILITIES
MORE VOLATILE = carried away FASTER
distillation
raise temperature, overcome intermolecular forces, vapor is collected and condensed
SIMPLE -> salt water is boiled, removing the salt
Fractional distillation
when difference in boiling points is not large
remove something of a lower boiling point
spectroscopy (light)
SEEING structural features based on absorption patterns; light excites the molecules, energy is released
Mass spectroscopy
determines the MASS of compounds in a sample
ionized in a high vacuum, bombarded by high energy ELECTRONS, magnetic field, flight path of charged species alters
UV/VISIBLE light spectroscopy
conjugated systems = wavelength of maximum absorption increases
if a compound absorbs UV, all visible wavelengths will be reflected (white)
if a compound absorbs BLUE light, it is will appear ORANGE
MEMORIZE THIS:
RED - GREEN (725 nm - 525 nm)
Orange - blue (625 nm - 460 nm)
Yellow - violet (580 nm - 415 nm)
MORE CONJUGATED = ABSORBS LOWER FREQUENCY = more likely blue/violet
infrared spectroscopy (identify functional groups)
IR == STRETCH (“I REALLY need to STRETCH”)
IR (2.5 - 20 micrometers) can excite organic molecules
Wavenumber = 1/wavelength = 1/c * v (measured in reciprocal centimeters)
MEMORIZE THE STRETCH FREQUENCIES (p. 64)
carbonyl = 1700 cm-1
Alkene = 1650
triple bond = 2260-2100
hydroxyl -> 3600-3200
C-H for sp3 = 3000-2850
C-H for sp2 = 3150-3000
C-H for sp = 3300
NMR Spectroscopy (proton NMR)
look at unique hydrogens (group them)
peaks is number of neighboring hydrogens + 1
area is the number of protons (the integration)
if EN atom is in close proximity, decreases electron density and DESHIELD it, DOWNfield shift (goes LEFT)
AROMATIC proton = 6.5-8 ppm shift
ALKENE = 5-6 ppm shift
attached to O, N are DESHIELDED (2-5 ppm)
carboxylic acid = 10-13 ppm
alcohol = 2-5 ppm
ALKYL = 0-2 ppm
ELISA*
enzyme-linked antibodies
determines PRESENCE of ANTIGENS/PROTEINS/CYTOKINES/ANTIBODIES
LOOK AT PICTURE
“Enzyme-linked ANTIBODY” is the DETECTION enzyme, which leads to COLOR CHANGE
radioimmunoassay (RIA)*
measures RADIOACTIVITY in immune complexes via RADIOLABELED ANTIBODIES
measure radioactivity
determine amount of HORMONES or drugs
electrophoresis*
SEPARATION based on SIZE or CHARGE
acrylamide and agarose (GEL) form “nets” as they solidify
DNA is negatively charged
SMALL moves FASTER
NEGATIVE move FASTER
Southern blotting
blotting = transfer of DNA/proteins from electrophoresis to nitrocellulose
SPECIFIC SEQUENCES within a heterogenous sample of DNA -> isolate and purify target DNA sequences
filter is PROBED with radiolabeled NUCLEOTIDES that are complementary to portion of target DNA -> allows visualization
- Cleave DNA (endonuclease)
- Run on gel electrophoresis
- Add filter
Northern blotting
RNA is separated via gel electrophoresis, rather than DNA
determines if GENE PRODUCTS are being expressed
Western blotting
presence of certain PROTEINS, DIAGNOSTIC TOOL
an enzyme FLOURESCES when detecting a substrate, brightness is proportional to abundance
Use of PRIMARY/SECONDARY ANTIBODIES instead of nucleotides
restriction endonuclease
bacterial enzyme
RESTRICT the reproduction of hostile viruses
CUTS in the MIDDLE of DNA chain (exo cuts on the ends)
STICKY END is GOOD
plasmid
can have a gene for antibiotic resistance, and incorporate a gene of interest, and can survive while the other bacteria die
heating DNA can separate the strands
primers bond, then DNA pol adds nucleotides to the 3’ end
DNA fingerprinting depends on …
POLYMORPHISMS = 2-100 base pair stretches of repetitive DNA
- Restriction Fragment Length Polymorphism (10-100 base pairs) - RESTRICTION ENDONUCLEASE followed by GEL ELECTROPHORESIS
- Short tandem repeats - DNA obtained, PCR’d, and repetitive DNA in introns is analyzed via SOUTHERN BLOTTING
knocking down gene expression with …
RNA interference
- microRNA
- small interfering RNA
degrade mRNA
ddNTPs
dideoxynucleotide triphosphate
lack the 3’ hydroxyl group, cannot elogate
important for DNA sequencing (Sanger)
immunohistochemistry
specific for protein expression
Bradford Quantification
protein quantification
proteins bind to blue pigment
dna sequencing
ddNTPs
