Chemistry:
CHAPTER 1
● Charge of electron -1.6 x 10-19; Avogadro’s # 6 x 1023
● Mass number (A) on top of element, atomic number (Z) below
●
𝐸=
ℎ𝑐
𝜆
= −𝑅 [
1
𝑛𝑖 2
−
1
];
𝑛𝑓2
E = qV (energy = charge on e- x electron volts); c = fλ (c = 3 x 108)
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Heisenberg uncertainty – impossible to determine momentum and position simultaneously
Pauli exclusion – no electrons have same quantum #’s
Max e- in a shell 2n2, max e- in subshell 4l+2
o Possible values for l 0 to n-1, possible values for ml -l to +l
● S can hold 2 e-, p 6, d 10, f 14
● Aufbau principle (building up) – lowest n+l will fill first
● For anions add extra e-, for cations remove e- from subshells with highest n first
● Hund’s – half filled orbitals with parallel spins (bus seats)
● Paramagnetic – unpaired parallel spin e-, attracted to magnetic field
o Diamagnetic – paired e-, repelled by magnetic field
o Ferromagnetic – unpaired e-, randomly oriented dipoles, become magnetized in field
● A faraday is equal to one mole of electric charge
CHAPTER 2
● Z eff increases from left to right, constant up and down
● Ionic radius is smallest near metalloid line and increases out
● F is smallest, most EN, highest IE and EA; Cs is the largest and least EN
● Complex ions from transition metals associate with water to form hydration complexes
● Atomic radius has the opposite trend of all others
CHAPTER 3
● C, N, O, F, Na, Mg always abide by octet rule; H, He, Li, Be, B can have incomplete; period 3 or
higher can have expanded
● Coordinate covalent bond – both e- are contributed by one atom (lone pair attack, acid-base)
● Ionic EN difference greater than 1.7, polar covalent 0.5 to 1.7, nonpolar less than 0.5
o Ionic are stronger than covalent (which are both stronger than IM forces)
▪ Van der Waals occurs more with close proximity and large molecules
● Dipole moment p = qd
● Triple bonds are shorter and have more energy
● Major resonance contributor is more stable (less formal charge, negative on more EN atom)
o Formal charge = valence – nonbonding – ½ bonding
● Electron geometry is when bonding and lone are equal, molecular geo is when lone repel more
o 5 connections is trigonal bipyramidal, 6 is octahedral
● Bond length decreases with larger EN differences ; Ammonium is NH4+ and ammonia is NH3
CHAPTER 4
● Molecules use molecular weight (sum of atomic weights in molecule) but ionic compounds form
lattice instead of true molecules so they use formula weight (based on empirical formula)
● Gram equivalent weight (g of a compound that produces one equivalent) = molar mass/n
● Normality = equivalents/L
● Percent composition = mass of element/molar mass of formula
● Combustion reaction: hydrocarbon + oxygen carbon dioxide + water
● Double displacement (metathesis) ex: neutralization (acid + base salt + water)
● 1 mole of gas at STP = 22.4 L; 1 mole of a substance = 6 x 10^23 = its molar mass
● Percent yield = actual yield/theoretical yield
● -ous and -ic represent ions with less and greater charge; monatomic anions have -ide ending
o -ite and -ate is less and more oxygen; hypo- and hyper- for even less and more O
o HCO3- is bicarbonate
● Strong electrolytes dissociate completely; weak does not dissolve into ions completely
CHAPTER 5
● Rate determining step is slowest, rate of reaction is only as fast as this step
● Greater concentration of reactants will increase reaction rate for all but zero order
o Only temp/catalyst changes zero order
● Homogeneous catalyst is in same phase as reactants, heterogeneous is in different phase
●
𝛥[𝐴]
𝛥[𝐵]
Rate = − 𝑎𝛥𝑡 = − 𝑏𝛥𝑡 =
𝛥[𝐶]
𝑐𝛥𝑡
=
𝛥[𝐷]
𝑑𝛥𝑡
RATE LAW: Rate = k[A]x[B]y (overall order is x + y which are experimentally determined)
Zero order: k has units M/s, first order: s-1 (slope 0/1 = -k), second order: M-1s-1 (slope = k)
o Zero order has linear [A] vs t graph, first is linear for ln[A] vs t, second is 1/[A] vs t
CHAPTER 6
●
●
[𝐶]𝑐 [𝐷]𝑑
● Keq = [𝐴]𝑎[𝐵]𝑏
o Temperature dependent, larger value means equilibrium position is further to the right
o Kc is the equilibrium constant, equal to Keq for dilute solutions
o Do not include concentration of pure solids and liquids
● Q < Keq reaction proceeds forward to equilibrium (greater concentration of reactants, G < 0)
● Le Chatlier’s only reactions with a gaseous species will be affected by change in
●
pressure/volume (system will move towards side with less or more moles)
o If reaction is endothermic, heat is a reactant
At lower temp, kinetic product forms faster (less stable product)
o
At higher temp, thermodynamic product forms (requires more energy to form
transition state but results in more stable product)
CHAPTER 7
● Isolated system – no exchange of energy (heat/work) or matter, closed system – can exchange
only energy, open system – can exchange both energy and matter
● Zeroth law of thermo: objects are in thermal equilibrium (no heat flow) when at equal temp
● First law of thermo: ΔU = Q – W (U is internal energy, Q is heat added, W is work done by
system)
o Area under PV graph is work (pressure is y axis, volume is x axis)
● Second law of thermo: energy spontaneously disperses if unhindered, objects go to thermal eq.
● Isothermal (constant temp): internal energy is constant (U = 0)
o Adiabatic (no heat exchange): Q = 0
o Isobaric (constant pressure): horizonal line on graph
o Isovolumetric/isochoric (constant volume): no work performed, vertical line on graph
● Standard conditions – 298 K, 1 atm, 1 M
● Boiling point – temperature when vapor pressure of liquid is equal to ambient/external
pressure
● Sublimation is solid to gas, deposition is gas to solid
● Triple point - all phases in equilibrium, critical point - liquid and gas are indistinct (supercritical)
● Coffee cup is constant pressure calorimeter, bomb is constant volume calorimeter
● 1 cal = 4.184 J, q = mcΔT, q = mL during phase change since temp remains constant
o Specific heat of water = 1 cal/g K or 4.184 J/g K
● ΔHrxn = Hproducts - Hreactants = Hbb - Hbf (negative H means exothermic)
● ΔHf of an element in standard state is zero; breaking bonds is endothermic, making is
exothermic
o Endothermic/exothermic describes enthalpy, endergonic/exergonic describes Gibbs free
● ΔG = ΔH - TΔS ; ΔG = -RT ln Keq
CHAPTER 8
● STP is 273 K and 1 atm (1 atm = 760
mmHg
= 105 Pa)
● Ideal gas – molecules have no IM forces and occupy no volume, real deviates at high P/low
temp
𝑃1𝑉1
𝑃2𝑉2
𝑉1
𝑉2 𝑃1
𝑃2 𝑛1
𝑛2
● PV = nRT, 𝑇2 = 𝑇2 , P1V1 = P2V2, 𝑇1 = 𝑇2 , 𝑇1 = 𝑇2 , 𝑉1 = 𝑉2 , 𝑃𝑇 = 𝑃𝐴 + 𝑃𝐵 (PA = X*PT)
● Vapor pressure from evaporated particles above liquid surface, ↑gas pressure = ↑solubility
● Kinetic molecular theory negligible volume of particles, no IM forces, random motion, elastic
collisions; KE = 3/2kBT
● Heavier gases diffuse more slowly, effusion = gas particles flowing through small opening
CHAPTER 9
● Mixtures have molecules that do not interact chemically, solutions do
● When new interactions are stronger than original, solvation is exothermic (favored at low temp)
● Salts are soluble if they have a molar solubility above 0.1 M (sparingly soluble salts are below
this)
o Molar solubility (x) – molarity of solute in saturated solution (equilibrium)
▪ MX has Ksp = x2, MX2 4x3, MX3 27x4
● Ammonium, alkali metals (group 1), nitrate (NO3-) and acetate (CH3COO-) are soluble
o Ag, PB are common insoluble exceptions and ammonium/group 1 are soluble exceptions
● Complex ion/coordination compound = cation is bonded to at least one electron pair donor
● Molality – moles of solute/kg solution
● Solubility product constant (Ksp) = [C]c[D]d (no pure solids/liquids, no denominator only
products)
o Ion product shows where system is with respect to equilibrium
● Common ion effect – solubility is reduced if solution already contains ion (does not affect Ksp)
● Colligative properties are physical, depend on concentration of solute, not identity
o Vapor pressure depression, FP depression, BP elevation, osmotic pressure (sucking
pressure where water moves to higher solute iMRT)
CHAPTER 10
● Arrhenius acid/base – dissociates to form excess H+/OHo Bronsted Lowry acid/base – donate/accepts hydrogen ions
o Lewis acid/Lewis base – electron pair acceptor/donor
● Amphoteric can act as both an acid or base, amphiprotic can gain or lose a proton
● If anion ends in -ite (less oxygen), acid will be -ous acid; -ate (more oxygen) -ic acid
● Kw = [H3O+][OH-] = 10-14 (can only be changed by temperature of water)
o Contribution from autoionization of H2O is negligible if [HA] or [BOH] is greater than 10-7
● Log(n x 10m) = m – 0.n
● Strong acids (dissociate fully): HCl, HBr, HI, H2SO4 (HF = weak); strong base: NaOH, KOH (group
1)
o Ka < 1 = weak acid, conjugate of strong acid/base is always weak
● Induction (EN element near acidic proton) increases acid strength
● Indicators are weak acids/bases (must be weaker than acid or base being titrated)
o Ideal indicator has pKa value close to pH of reaction at equivalence point
● Strong acid + strong base = pH 7 equivalence pt. (half eq. pt. is first buffer region/horizontal
area)
● Buffer = weak acid or base and its salt (conjugate and anion), optimal within 1 pH unit of its pKa
[𝐻+][𝐴−]
●
Ka =
●
Henderson-Hasselbach equation: pH = pKa + log [
[𝐻𝐴]
; pKa = -log Ka; Strong acids have pKa below -2 (smaller pKa means stronger acid)
[𝐴−]
𝐻𝐴]
; 𝑝𝑂𝐻 = 𝑝𝐾𝑏 + 𝑙𝑜𝑔
[𝐵+]
[𝐵𝑂𝐻]
CHAPTER 11
● Oxidizing agent usually contains oxygen or another EN element, often nonmetals
o Reducing agent usually contains metal ions of hydrides (H-), often metals
● Oxidation number of a free element is zero, oxygen in free radical is -1/2
● To balance half reactions, balance all atoms except H and O; in acid add H2O and H+, in base add
H2O and OH-, use e- to balance charge; multiply reaction to have same e- and then add
reactions
● Complete ionic equation has spectator ions (retains charge throughout reaction)
o Net ionic equation only shows participating species (no spectators)
o Solid salts are kept together, aqueous compounds are split into ions
● Disproportionation is when same element undergoes both oxidation and reduction
● Redox titrations follow transfer of charge, can measure voltage using color indicator or
voltmeter
CHAPTER 12
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Anode is oxidized, cathode is reduced; e- flow from anode to cathode, current flows opposite;
cations are attracted to cathode, anions are attracted to anode
More positive the reduction potential = greater tendency to be reduced, don’t multiply by
moles
Galvanic (voltaic) cell: spontaneous (negative G means positive Ecell cell releases energy)
o Salt bridge made of inert salt dissipates charge gradient
o Includes concentration cells in which electrodes are chemically identical, different conc.
o Anode is negative and cathode is positive, anode is source of eo Cathode has more positive reduction potential
Electrolytic cell: nonspontaneous; 1 e- 1.6 x 10-19 C, 1 F = 105 C
o Anode is positive, cathode is negative; anode has more positive red potential (opposite)
Rechargeable battery – can function as both galvanic and electrolytic cell
Anode | anode solution (concentration) || cathode solution (concentration | cathode
Isoelectric focusing – AA are separated based on pI, positive AA (protonated at solution pH)
migrate to negative cathode, negatively charged AA (deprotonated) migrate to positive anode
o Gel electrophoresis has positive anode and negative cathode
0.0592
Eocell = Eored,cat - Eored,ano ∆G = -nFEocell Ecell = Eocell log Q ; G = -RT ln Keq ∆G = ∆Go + RT lnQ
𝑛
Biology:
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Operator is where repressor binds, promoter is where RNA pol binds
Inducible system needs inducer for transcription, repressible needs repressor to stop tran
9:3:3:1 phenotypic ratio for AaBb; plasmids that can be integrated = episomes
CHAPTER 1
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Cell theory: living things are made of cells, cell is basic functional unit, cells arise from pre
existing cells, cells carry and pass on genetic info
Prokaryotes have no nucleus/membrane bound organelles, no mitochondria, 30S/50S ribosome
rRNA is made in nucleolus, lysosomes use hydrolytic enzymes to break down waste,
mitochondria have own genes and replicate independently via binary fission, SER does lipid
synthesis/detox, peroxisomes use hydrogen peroxide to break down long chain FA/synthesize
phospholipids
Microfilaments made of actin, for protection and movement (cleavage furrow)
o Microtubules made of tubulin (9+2); motor protein pathways, cilia/flagella, centrioles
o Intermediate filaments withstands tension, cell-cell adhesion
Epithelial tissue lines cavities (functional part of organ), attaches to connective by basement
membrane (connective provides framework/stroma and secretes ECM with collagen/elastin)
Gram positive cell wall thick peptidoglycan layer with lipoteichoic acid (purple)
Gram negative thin peptidoglycan layer, lipopolysaccharides, has periplasmic space (pink)
Flagella consists of basal body connected to filament by hook
Obligate anaerobes cannot survive with oxygen, aerotolerant can
Transformation – integration of foreign genetic material into host genome
o Conjugation – sexual, form conjugation bridge, use fertility factor from donor (+)
o Transduction – uses vector (virus) to carry genetic info from one bacterium to another
Positive sense – directly translated to functional proteins by ribosomes of host cell
o Negative sense – must carry RNA replicase, require synthesis of a complementary
strand
Retrovirus – carries reverse transcriptase, DNA is integrated into host genome and replicated so
cell is infected forever
CHAPTER 2
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Diploid means 2 copies of each chromosome
G1 creates organelles/increases size, S ploidy does not change despite doubling of chromatid
number, G2 ensures there are enough organelles/cytoplasm to divide
o G1/S checkpoint if DNA is damaged, cell cycle arrests while p53 repairs
o G2/M checkpoint has cell achieved adequate size and organelles
o Cyclins (changing concentration) bind CDK’s to phosphorylate transcription factors for
genes required in next stage of cell cycle
Meiosis is 1 round replication, 2 rounds division (first reductional division then equational)
o Meiosis I makes haploid daughter cells, crossing over in prophase 1 (Mendel’s second
law of independent assortment); disjunction in anaphase 1 (Mendel’s 1st law of
segregation)
Meiosis II is similar to mitosis (interkinesis is rest period in between meiosis I and II)
Sperm head has DNA in nuclear envelope and acrosome, middle section has mitochondria
Testes have seminiferous tubules (where sperm are formed, nourished by Sertoli cells) and
interstitial cells of Leydig (secrete testosterone and androgens)
o SEVE(N) UP flagella gain mobility in epididymis, vas deferens raises/lowers testes
o
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Seminal vesicles nourish sperm with fructose, seminal vesicles and prostate gland give
fluid alkalinity, bulbourethral glands produce clear fluid to lubricate urethra/clear urine
o Spermatogonia primary spermatocyte (diploid, after S stage), secondary spermatocyte
(haploid, after meiosis I), spermatid (after meiosis II), spermatozoa (mature)
Ovaries produce estrogen/progesterone; made of follicles that protect ova
o All oogenia are formed in fetus; by birth they have undergone DNA replication so they
are primary oocytes (2n) arrested in prophase I
▪ One completes meiosis I per month (ovulated into fallopian tube/oviduct)
▪ Produces a secondary oocyte and polar body which remain in metaphase II
▪ Complete meiosis II upon fertilization (penetration of corona and zona)
Puberty hypothalamus releases GnRH (previously restricted)
o This triggers anterior pituitary to release FSH and LH
▪ FSH triggers Sertoli cells for sperm maturation, LH causes interstitial cells to
produce testosterone (negative feedback on hypothalamus/anterior pituitary)
▪ FSH estrogen (establishes endometrium); LH corpus luteum produces
progesterone (protects endometrium)
Follicular phase menses = low estrogen so GnRH increases to replenish estrogen and regrow
endometrium (FSH and LH)
Ovulation developing follicles secrete more estrogen, positive feedback (LH surge = ovulation)
Luteal phase rupture follicle forms corpus
luteum which secretes progesterone (and
estrogen) to maintain lining (progesterone
exerts negative feedback preventing ovulation
of multiple eggs)
Menstruation corpus luteum atrophies,
progesterone/estrogen decrease = menses
CHAPTER 3
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Fertilization occurs in the fallopian tube
o Acrosomal enzymes from sperm penetrate corona radiata/zona pellucida
o Cortical reaction (release Ca2+) upon membrane contact prevents polyspermy
▪ Forms impenetrable fertilization membrane
● Zygote travels to uterus for implantation, undergoing cleavage to form morula
o This forms blastula with inner cell mass and trophoblast cells
● Umbilical cord has oxygenated vein and two deoxygenated arteries
● Allantois – fluid exchange (yolk sac embryo), amnion – protective fluid, chorion – membrane
● Invagination (archenteron) creates blastopore opening for gastrulation
● Adrenal cortex is from mesoderm, adrenal medulla and mouth lining is from ectoderm
o Endoderm – pancreas, liver, thyroid, bladder, digestive and respiratory
o Mesoderm – gonads, kidney, musculoskeletal, circulatory
● Neural crest cells form sensory ganglia, autonomic ganglia, adrenal medulla, Schwann cells
● Specification – reversible, determination – irreversible, differentiation
● Paracrine – diffuses to local cells, juxtacrine – cell directly stimulates neighbor (no diffusion)
● Fetal hemoglobin has higher affinity for oxygen, higher PO2 in maternal blood
o Unlike in adults, right side of heart is at higher pressure in fetus
● Foramen ovale and ductus arteriosus shunt blood from lungs, ductus venosus for liver
CHAPTER 4
● PNS has nerves and ganglia, CNS has tracts and nuclei
●
Neurons are supported by glial cells/neuroglia: astrocytes form blood brain barrier and nourish
neurons, ependymal cells produce cerebrospinal fluid, microglia are phagocytic,
oligodendrocytes (CNS) and Schwann cells (PNS) produce myelin
● Resting membrane potential is -70 mV, inside of neuron is negative (K is -90, Na is 60)
● Na/K ATPase maintains resting potential, if depolarized to threshold (-50) AP is triggered
● Temporal summation is multiple signals in short period of time
o Spatial summation is additive effects based on number/location of signals
● Absolute refractory period means no AP can be fired; relative means strong stimulus needed
o Each segment becomes momentarily refractory so info flows in one direction
● Sodium flows into cell causing depolarization, potassium flows out causing repol/hyperpol
● Increased intensity of stimulus leads to increased frequency of firing not increased AP
● Between neurons, NT are used; within a neuron electricity is used to pass signal down axon
● When AP occurs, calcium flows into cell causing NT vesicles to fuse with membrane at synapse
o NT binds to ligand gated receptor (causes depolarization/hyperpolarization) or GPCR
(causes changed in cAMP or calcium levels) on postsynaptic membrane
● Sensory (afferent), motor (efferent) afferent ascend while efferent exit
o Sensory bring info from dorsal side, motor exit from ventral side
o Cell bodies of sensory neurons are found in dorsal root ganglia
● White matter has myelin, gray does not (white is outside spinal cord, inside brain)
● Acetylcholine from vagus nerve parasympathetic, acetylcholine then norepi sympathetic
● Monosynaptic reflex – only has sensory + motor, polysynaptic – has interneuron between
CHAPTER 5
● Peptide hormones – charged so bind extracellular receptor second messenger
o Rapid but short lived; ex: ADH, insulin (almost everything)
● Steroid (cholesterol) – nonpolar (intracellular receptor), binds to DNA to alter transcription
o Slower but long lived, carried by proteins in bloodstream; FROM ADRENAL CORTEX
● AA derivatives – catecholamines (epinephrine and norepinephrine) bind GPCR and thyroid
hormones bind intracellularly (SECRETED BY ADRENAL MEDULLA/THYROID)
● Peptide and AA derivatives = -ine and -in; steroids = -one, -ol, -oid
● Hypothalamus secretes compounds into hypophyseal portal system to anterior pituitary
o Anterior pituitary secretes FLAT PEG (FLAT are tropic, PEG are direct)
▪ GnRH FSH and LH testes (testosterone), ovaries (estrogen/progesterone)
▪ CRF ACTH adrenal cortex corticosteroids (sugar, salt, sex)
● Glucocorticoids (cortisol) raise blood glucose
● Mineralocorticoids (aldosterone) control salt/water balance
o Aldosterone increases sodium reabsorption in DCT and
collecting duct so water follows, increasing BP/blood volume
▪ Osmolarity is unchanged unlike with ADH
▪ Decreased BP renin angiotensin aldosterone
● Cortical sex hormones (androgens/estrogens)
▪ TRH TSH thyroid
● Follicular cells release T3 and T4 which control metabolism
● Parafollicular cells produce calcitonin which decreases plasma calcium
● Parathyroid glands release PTH which raises blood calcium using Vit D
▪ Dopamine/PIF from hypothalamus inhibits prolactin
▪ Endorphins are painkillers
▪ GHRH GH (promotes growth)
o Posterior pituitary releases hormones produced in hypothalamus (not using portal)
Releases oxytocin and vasopressin/ADH increases reabsorption of water in
collecting ducts during high osmolarity/low blood volume (decreases
osmolarity)
Pancreas has islets of Langerhans (alpha cells glucagon, beta cells insulin, delta cells
somatostatin which inhibits glucagon and insulin and decreases growth hormone)
Pineal gland melatonin, thymus thymosin (stimulate T-cell development)
Kidney erythropoietin during low O2 to increase RBC production from bone marrow
Heart releases ANP during excess BP/volume to excrete sodium/increase urine volume
▪ Antagonistic to aldosterone (lowers BP/volume without changing osmolarity)
▪
o
o
o
o
CHAPTER 6
● Nasal cavity pharynx (both food and air) larynx (only air, epiglottis shuts when swallowing) 
trachea bronchi/bronchioles alveoli (surfactant lowers surface tension, prevent collapse)
● Membranes called pleurae surround lungs, inhalation is active while exhalation may not be
o Inhalation: diaphragm contracts and external intercostals expand (negative pressure)
o Exhalation: both relax, decreasing volume to expel air; internal intercostals speed this
up
● Medulla oblongata controls breathing, bicarb buffer system (acidic blood increase respiration)
TLC is max volume, RV is min volume, VC is difference
between min and max, TV is normal breath, ERV is
volume from forcible exhalation, IRV is volume from
forcible inhalation
● Deoxygenated blood from right ventricles comes to capillaries through pulmonary arteries,
oxygenated blood comes from left atrium through pulmonary veins (opposite)
CHAPTER 7
● Atrioventricular valve: tricuspid (right), mitral/bicuspid (left), semilunar: pulmonary + aortic
valves
● SA node AV node (signal delay for complete ventricle filling) bundle of His Purkinje fibers
o No neural input needed (myogenic activity), parasympathetic can slow down via vagus
o Intercalated discs contain gap junctions for coordinated ventricular contraction
● CO = HR x SV; ΔP = CO x TPR (total peripheral resistance)
● Portal systems pass through 2 capillary beds in series: hepatic, hypophyseal, renal
● Erythrocytes lose nuclei, mitochondria once mature; use glycolysis and lactic acid fermentation
● Thrombocytes (platelets) = cell fragments from bone marrow called megakaryocytes
o Hematopoiesis in bone marrow is triggered by erythropoietin and thrombopoietin
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Antigens stimulate B-cells to make antibodies, people make antigens of own blood type and
antibodies against other blood type
●
Rh + does not make anti Rh antibody,
Rh- lacks the antigen and does make anti Rh antibody
● BP is expressed as systolic (ventricular contraction) to diastolic (ventricular relaxation)
● Largest pressure drop is over arterioles, capillaries in parallel leads to low resistance
● Cooperative binding – when one O2 binds, Hb goes from taut to relaxed (increased affinity)
● CO2 + H2O ---carbonic anhydrase-H2CO3 (carbonic acid) H+ + HCO3- (bicarb)
● Bohr effect increased CO2 decreases pH curve shifts right/down, reducing Hb affinity for O2
o Allows for more unloading of O2 at tissues during exercise
o Leftward shift is fetal Hb since it has higher affinity for O2
● Thrombin fibrin (network captures platelets/coagulation factor) clot (plasmin breaks down)
CHAPTER 8
● Bone marrow produces leukocytes (WBC’s) through hematopoiesis
o Granulocytes include neutrophils, eosinophils, basophils for inflammatory response
o Agranulocytes include macrophages, and B and T cells (adaptive, rest are innate)
o Mast cells release histamine, dendritic cells present antigens, NK destroy infected cells
● Defensins are found on skin/sweat, lysozyme in tears and saliva
● Complement system consists of proteins in blood for nonspecific defense
● Cells infected by virus produce interferons to prevent viral replication, upregulate MHC
o MHC I is present in all nucleated cells and MHC II is in antigen-presenting cells
● Cytokines stimulate inflammation and recruit immune cells
● Humoral immunity production of antibodies, also called Ig (made by plasma B-cells which
mature in bone marrow and are activated in spleen and lymph nodes)
o When antibody binds antigen it may be immediately phagocytosed (opsonization),
clump (agglutination) to be phagocytosed, neutralize pathogens, release histamine
o Antibodies have two identical heavy chains and two identical light chains connected by
disulfide linkages, the antigen binding region is at the variable region (tips of Y)
▪ 5 Ig isotypes, each B-cell makes one type; nonspecific targets constant region
● Cell mediated (cytotoxic) immunity T cells, mature in thymus (facilitated by thymosin)
o Helper T cells (CD4+) secrete lymphokines which recruit other immune cells
▪ Response to MHC II antigens (exogenous) bacteria, fungus, parasites
o Cytotoxic T cells (CD8+) directly kill or promote apoptosis
▪ Respond to MHC I antigens (endogenous) virus and intracellular bacteria
o Suppressor/regulatory T cells tone down response, memory T-cells are generated
● Self antigens are present on every cell (T and B cells are eliminated if they respond to self)
● Active immunity is developing own antibodies, passive immunity is being given them (transfer)
● B cells develop in lymph nodes which also transport fats from digestive system into bloodstream
CHAPTER 9
● ADH/aldosterone trigger thirst, glucagon from pancreas + ghrelin from stomach and pancreas
trigger hunger, leptin + cholecystokinin (CCK) trigger satiety
● Digestion starts in mouth (salivary amylase) and ends in duodenum of SI (pancreatic amylase)
o Salivary amylase starch into small sugars, lipase hydrolysis of lipids
● Pharynx (somatic swallowing) esophagus (no digestion, autonomic peristalsis) stomach
● Parasympathetic vagus nerve signals to gastric glands in stomach (also has pyloric glands)
o Mucous cells produce bicarb rich mucus to protect muscular wall from acidic pH
o Chief cells secrete pepsinogen (proteolytic) which is active as pepsin (works in stomach)
o Parietal cells secrete HCl (acidity activates pepsin to cleave peptide bonds near
aromatic AA for digestion) and intrinsic factor for absorption of vitamin B12
● Pyloric glands have G-cells secrete gastrin (signals for HCl production + stomach contraction)
● Stomach (and duodenum) digest, small intestine absorbs (jejunum and ileum)
o Duodenum: brush border enzymes break down molecules, secretes secretin (releases
pancreatic enzymes in duodenum and regulates pH through increase in bicarb, decrease
in HCl) and CCK when chime is present (triggers bile release to emulsify fats for lipase)
▪ Secretes enteropeptidase, which activates trypsin (pancreatic, digests proteins)
● Liverglucose/glucagon, stores fats as triacylglycerol/mobilizes them in lipoproteins, detox,
bile production (stored in gallbladder/secreted to duodenum), albumin/clotting factor
production
● Simple carbs/AA use secondary active transport or facilitated diffusion from epithelial cells of SI
into capillaries, nonpolar FA do not require transporters (larger triglycerides/cholesterols are
packaged into chylomicrons which enters lacteals in lymphatic system)
● Vitamins are absorbed in SI ADEK are fat soluble, B and C are water soluble
● Large intestine water (+ salt) absorption, feces concentration; includes cecum (bacteria),
colon, rectum (storage); internal anal sphincter is involuntary, external is voluntary
● Trypsin + carboxypeptidase A and B made in pancreas, enteropeptidase made in intestine
o Both function in the small intestine
CHAPTER 10
● Blood enters kidney through renal artery/afferent arterioles, passes through glomerulus, enters
efferent arterioles surrounding loop of Henle called vasa recta (portal system)
o Blood passes glomerulus, filtered into Bowman’s capsule filtrate (isotonic to blood)
▪ Small molecules (glucose) can pass through, large (proteins/blood cells) cannot
● Liver converts ammonia to urea which is secreted into nephron (dump the HUNK)
o Secretion (moves solutes from blood to filtrate, not through Bowman’s capsule)
excretes wastes that are too large for glomerulus pores
● AA, vitamins, glucose = always reabsorbed; ADH/aldosterone regulate amount of water
resorbed
● Horizontal segment is for identity of particles (what we need), vertical focus on concentration
● Bottom of loop and collecting duct = passive diffusion, tubules and top of loop = mostly active
● PCT – AA, glucose, vitamins, salts are reabsorbed with water; H+, urea, NH3+, K+ are secreted
● Loop – descending limb = permeable to water which flows out as you move down
(concentration)
o Vasa recta and nephron are in countercurrent system where flow of filtrate through
loop of Henle is opposite to direction of blood flow in vasa recta
o Ascending limb – only permeable to salts
▪ Higher up is thick part active transport to reabsorb sodium and chloride
● Only part where filtrate is hypotonic to blood (prevents overhydration)
DCT – responds to aldosterone Na+ reabsorption (water follows, concentrated urine)
Collecting duct – responds to aldosterone and ADH, increase reabsorption of water (last chance)
Hormones in ch 5: ADH (peptide hormone) makes collecting duct more permeable to water to
decrease high osmolarity, aldosterone responds to low BP (does not change osmolarity)
● Kidneys help with bicarb buffer system by excreting or resorbing H+/bicarb
● Skin layers: come, let’s get sun burned (lucidum is only on palms and foot soles)
● Langerhans cells are macrophages in stratum spinosum that present antigens to T-cells
● Meissner’s corpuscles = light touch, Ruffini endings = stretch, Pacinian = deep
pressure/vibration
CHAPTER 11
● Skeletal muscle: Red fibers = slow twitch, high myoglobin and mitochondria, aerobic (slow/long)
o White fibers = fast twitch, less myoglobin (contract and fatigue quickly), glycolysis/ferm.
● Smooth muscle: constant state of low-level contraction = tonus, myogenic (can contract
without nervous system input), cardiac: myogenic, intercalated discs with gap junctions
(coordination)
● During contraction, all sarcomere bands become smaller except A band (all of thick filament)
o Z is both ends of sarcomere, M is middle of myosin, I is thin filaments only, H is thick
only
● Sarcomeres myofibril muscle fiber/myocyte arranged in parallel makes muscle
● Motor unit = nerve terminal (motor end plate where acetylcholine is released) and its myocytes
o Cell membrane of myocyte = sarcolemma; AP travels into T-tubule, SR releases calcium
o Calcium binds troponin changes tropomyosin on actin to expose myosin binding sites
o Myosin carrying hydrolyzed ATP binds to site, release of ADP and P power stroke, new
ATP binds to myosin head to release it from actin, ATP is hydrolyzed to recock myosin
o Acetylcholinesterase degrades acet. to allow for repolarization, reuptake of Ca into SR
● Myocytes respond once threshold is reached, # of myocytes determines response strength
● Simple twitch = single muscle fiber, frequent stimulation summation, tetanus = unable to
relax
● Myoglobin reserves and creatine phosphate provides supplemental energy in muscle (aerobic)
o Once O2 runs out, anaerobic produces lactic acid converted to pyruvate (Cori cycle)
● Compact bone = strength, spongey bone = bone marrow (red is stem cells, yellow is fat)
● Epiphyseal plate (cartilaginous, vertical growth) closes during puberty
● Bone strength is due to matrix made of hydroxyapatite (inorganic ions); each structural unit is a
Haversian system/osteon which are vascular/innervated
● Osteoblasts build, osteoclasts chew; bone remodeling = ions are resorbed/added from blood
o Parathyroid hormone (and vit D) = bone resorption, calcitonin = bone formation
● Cartilage is made of chondrocytes,
hardening into bone = endochondral
ossification
CHAPTER 12
● Alleles = alternative forms of genes
(2 alleles for a gene are inherited
except sex chromosomes)
● Homologous chromosomes have a
locus for each gene; hemizygous = one allele like X in males
● Penetrance = proportion of people with a genotype who express the phenotype
● Expressivity = varying phenotypes despite identical genotypes
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
●
Mendel’s first law (of segregation) – alleles/homologues segregate during meiosis gametes
only carry one allele for a trait, expressed allele is dominant, silent is recessive (exceptions:
codominance = more than one dominant allele, incomplete = intermediate is expressed)
Mendel’s second law (of independent assortment) – inheritance of one gene does not affect
inheritance of another due to recombination (exception: linked genes)
Griffith: virulent/nonvirulent strains, smooth capsules could be acquired from dead bacteria
(transforming principle), Avery/McCarty: uses enzymes to degrade DNA = transforming
principle, Hershey/Chase confirmed using viruses with labeled phosphorus (found in DNA not
protein)
Silent mutation = no effect (third nucleotide degeneracy in AA code), missense = substituting
one AA for another, nonsense = substituting a stop codon, frameshift due to insertion/deletion
Transposon = jumping gene; deletion, duplication, inversion, translocation in chromosomes
Genetic leakage is flow of genes between species (mate to produce hybrid)
Genetic drift: changes in gene pool due to chance, more profound in small populations
o Founder effect (reproductive isolation), bottleneck (sudden population reduction), and
inbreeding cause reduction in diversity (reduces fitness)
Cross two heterozygotes 1:2:1 genotype, 3:1 phenotype, dihybrid hetero 9:3:3:1 phenotype
Test cross: cross unknown with homozygous recessive
Man can never pass sex-linked trait to his son. Heterozygous female = carrier
Recombination frequency is proportional to distance between genes, one map
unit/centimorgan = 1% chance of recombination occurring between two genes
Hardy Weinberg equilibrium: large population (no genetic drift), no mutations, random mating,
no migration, equal reproductive success; p + q = 1, p2 + 2pq + q2 = 1
Natural selection (mechanism for evolution): survival of fittest; populations evolve, not
individuals
Neo-Darwinism is updated with inclusive fitness/altruism, an alternative theory is punctuated
equilibrium (rapid bursts of evolution rather than steady over time)
Stabilizing selection selects against extremes and toward narrow middle phenotype, directional
is dominance of an extreme phenotype, disruptive is two extreme phenotypes over the middle
Species – largest group that can breed to form fertile offspring
Prezygotic mechanisms prevent formation of zygote completely, postzygotic allow for gamete
fusion but lead to nonviable/infertile offspring
Divergent evolution share common ancestor but become more different, convergent 
develop similar characteristics without common ancestor, parallel is similar evolution over time
Physics:
F = -kx, EPE = 1/2kx^2; SG = pobject/pwater; SG = weight/weight-apparent weight in water (or Fb)
● 1 A = 10-10 m, nm = 9, pm = 12, mm = 6; 1eV = 1.6 x 10-19 J
● Add vectors tip to tail, subtract by making negative vector point in opposite direction
● If angle is coming off x-axis, x = v cos(θ) and y = v sin (θ)
o Pythagorean theorem for magnitude of resultant, θ = tan-1(y/x) for angle
● Displacement vector is initial to final position, not path taken (distance is scalar path taken)
o Velocity vector uses displacement, speed uses distance
𝐺𝑚1𝑚2
● 𝐹 =
, Fg = mg, 0 ≤ fs ≤ μN?, fk = μN, (normal force is perpendicular to surface)
𝑟^2
● First law (of inertia) – body at rest/constant velocity will stay that way; Fnet = ma = 0
● Second law – acceleration occurs when sum of forces is nonzero; Fnet = ma
● Third law (action and reaction) – opposite but equal reaction; FAB = -FAB
● If air resistance is negligible, object would fall with constant acceleration (no terminal velocity)
o If air resistance is present, it opposes fall and increases as speed of object increases
o This drag force is eventually equal to weight of object constant terminal velocity
● Projectile motion has vy changing at rate of gravity but vx is constant
● Use mgsinθ for forces parallel to plane (gravity), and mgcosθ for perpendicular (normal force)
●
●
●
𝑚𝑣 2
Centripetal force points into circle; Fc =
𝑟
Translational equilibrium = constant or zero velocity (no acceleration/net force)
Rotational equilibrium = stationary or constant velocity rotation (no net torque)
o Torque = Fr sin (θ), greatest when force is applied perpendicular (zero when parallel)
CHAPTER 2
● Energy ability to do work; KE = 1/2mv2; PE = mgh; EPE = 1/2kx2 (k is spring constant)
● Total mechanical energy (E) = PE + KE (change in energy equals zero when energy is conserved)
o Conservation of mechanical energy (cannot be created/destroyed) = first law of thermo
● Non conservative forces dissipate mechanical energy (path dependent), conservative do not
● Work/heat measure energy transfer; when gas expands work is done by system (positive)
● W = Fd cos(θ), only force components parallel/antiparallel to displacement do work
● W = PΔV; P = W/t = ΔE/t; Wnet = ΔKE (work energy theorem: net work on object changes it’s KE)
CHAPTER 3 (general chemistry chapter 7 is very similar)
● Temp = KE of particles, heat = transfer of energy from hot to cold (natural process, irreversible)
● Third law of thermo: entropy of perfectly organized crystal at absolute zero is zero, ΔS = Q/T
9
● F = 5 𝐶 + 32; thermal expansion: ∆L = αL∆T
● State function is independent of path taken, process function depends on path (work/heat)
●
Entropy of universe is
increasing (2nd law), work is required
to concentrate energy
●
Conduction, convection (fluid
transfers energy), radiation (EM
waves)
CHAPTER 4
● mL and cm3 is the same, density of water 1 g/cm3 = 1000 kg/m3
● P = F/A, 1 Pa = 1 N/m2; 1 atm = 760 mmHg/torr = 105 Pa
● Atmospheric pressure changes with altitude, absolute/hydrostatic pressure is weight of water
on an object submerged in fluid (P = P0 + pgh where P0 is ambient, p is density of fluid, h is depth
of object), gauge pressure = P – Patm
●
●
Pascal’s principle – change in pressure is transmitted undiminished, Archimedes’ principle =
object in fluid will be buoyed up by force equal to weight of fluid displaced
𝐹1
𝐹2
o 𝐴1 = 𝐴2; W = F1d1 = F2d2 (larger area = larger force, but over smaller distance)
o Fbuoy = pfluidVfluid displacedg (two objects with same volume experience same buoyant force)
▪ Buoyant force is equal to weight of displaced fluid; weight = pVg
Energy is conserved for low viscosity fluids with laminar flow
●
Poiseuille’s Q =
𝜋𝑟 4 ∆𝑃
8𝜂𝐿
1
1
; Bernoulli’s  P1 + 2ρv12 + ρgh1 = P2 + 2ρv22 + ρgh2
● Continuity equation  Q = v1A1 = v2A2 (flow rate in closed system is constant despite area)
● Venturi effect faster flow = lower pressure (fluid in column is lower)
CHAPTER 5
𝑘𝑞1𝑞2
;
𝑟2
k = 9 x 109
𝑁∗𝑚2
𝐹
; (electric field) 𝐸 = 𝑞 =
𝑘𝑄
𝑟2
●
Coulomb's law --> (electrostatic force) Fe =
●
●
●
Test charge q is placed in the field and experiences Fe, source charge Q creates electric field
Field lines come away from positive charge and toward negative, equipotential lines are circles
o Field lines exit north pole and enter south pole
𝑘𝑄𝑞
𝑈
𝑘𝑄
𝐽
Electric potential energy U = 𝑟 ; electric potential V = 𝑞 = 𝑟 (1 V = 1 𝐶)
●
Magnetic field B (1 T = 1
𝑁∗𝑠
) is created by
𝐶∗𝑚
𝐶2
a moving charge
𝜇𝐼
●
●
𝜇𝐼
Field produced by current perpendicular to wire: B = 2𝜋𝑟; field in circular loop of wire: B = 2𝑟
Right hand rule: thumb is current, fingers wrap around wire (field); thumb is velocity, finger is
field, palm is force on positive charge
● Magnetic force is exerted on moving charge in a field: FB = qvB sinθ (charge must have
perpendicular component of velocity to field to experience a magnetic force)
o Force on a wire: FB = ILB sinθ
CHAPTER 6
● Current is flow of positive charge (but negative charges are actually moving)
● Conductors allow free flow of charge (metals, sea of electrons, charge is evenly distributed upon
a surface); insulator (nonmetal) does not distribute/transfer charge
𝜌𝐿
● Current (I is in amperes C/s) = Q/t; Ohm’s law V = IR; R = 𝐴 (p is resistivity, L is length)
● Direct current is one direction, alternating current changes direction
● Emf is the voltage when no charge is moving between two terminals at different potentials (V)
● Kirchoff’s rules: sum of current directed into a junction equals sum of current coming out, sum
of voltage sources is always equal to sum of voltage drops
●
●
𝑊
∆𝐸
𝑉2
𝑄
𝐴
𝑉
1
P = 𝑡 = 𝑡 ; P = 𝐼𝑉 = 𝐼 2 𝑅 = 𝑅 ; 𝐶 = 𝑉 = 𝜀0 (𝐷) ; 𝐸 = 𝑑 ; 𝑈 (𝑒𝑛𝑒𝑟𝑔𝑦 𝑝𝑜𝑡𝑒𝑛𝑡𝑖𝑎𝑙) = 2 𝐶𝑉 2
Capacitors can hold charge at a voltage, dielectric material is insulation between capacitor
plates
o Dielectrics increase capacitance by decreasing voltage
CHAPTER 7
● Transverse waves (EM waves) – oscillation is perpendicular to propagation, longitudinal waves –
oscillation is perpendicular to direction of propagation (sound waves, need deformable medium)
● Frequency is # of wavelengths passing per second, period is # of cycles per second
o T = 1/f ; v = f λ, human ear can hear 20-20,000 Hz
● Phase difference: amplitudes add in phase (crests/troughs line up) = constructive interference,
amplitude is zero when out of phase (crests lines up with trough) = destructive interference
● Traveling wave propagates toward fixed end, standing wave is when both ends are fixed
o Node remains at rest, antinode is fluctuation with max amplitude
● One frequency: pure tone, multiple natural frequencies (fundamental pitch and overtones) = full
tone
● Speed of sound is fastest in low density solid, slowest in dense gas; speed of sound in 20 C = 343 m/s
● Doppler effect – if source and observer are moving towards each other perceived frequency f’ is
(𝑣 ± 𝑣𝑜)
greater than actual frequency f; f' = f (𝑣 ∓ 𝑣𝑠) v is speed of sound, use top sign for moving towards
𝐼
𝐼0
𝑊
𝑚2
●
Intensity is in W/m^2 I = P/A ; β = 10 log ( ) threshold of hearing I0 1 x 10-12
●
String: λ = 𝑛 , 𝑓 = 2𝐿 ; fundamental frequency is lowest, n = 2 is 1st overtone/2nd harmonic which
has twice the frequency of 1st harmonic; strings attached at both ends # antinodes tells the
harmonic
2𝐿
𝑛𝑣
Open (on both ends) pipe: λ = 𝑛 , f = 2𝐿 ; # of node tells which harmonic
●
2𝐿
𝑛𝑣
4𝐿
𝑛𝑣
● One end closed pipe: λ = 𝑛 (n is always odd integer); f = 4𝐿 , λ is four times length of closed pipe
CHAPTER 8 (converging = positive f, diverging = negative f), object distance is always positive; image
distance is positive if on opposite side of lens as object or same side of mirror as object
● EM waves can travel through vacuum (unlike sound); visible spectrum: 400 (violet) - 700 nm (red)
o c = fλ; c = 3 x 108 m/s
● Incident angle = reflected angle, measured from normal (perpendicular to boundary of medium)
● Real image - light converges there, virtual doesn’t; f (focal length) is half of r (radius of curvature)
● Plane mirror parallel incidence rays remain parallel, creates virtual image, same distance (o=-i)
● Converging = concave mirror (positive f and r, in front of mirror) = convex lens (thick middle)
o Concave mirror: ray striking parallel is reflected through focal point, ray passing through focal
point is reflected back parallel, ray striking center is reflected back at same angle
▪ Where two of the above intersect is the tip of image, or extend them to other side
(virtual)
▪ Object beyond F real image, object at F no image, between mirror and F virtual
o
●
●
●
●
●
●
●
●
●
●
Convex lens: parallel ray refracts through focal point, ray through focal point refracts parallel,
ray hitting center continues straight with no refraction
Diverging = convex mirror (negative f and r, behind mirror) = concave lens (thin middle)
o Diverging/convex mirror only forms virtual, upright, reduced image (UV IR)
Changing magnetic field can cause change in electric field and vice versa
1
1
1
= 𝑜 + 𝑖 ; positive I real image (front of mirror), negative I virtual image (behind mirror)
𝑓
𝑖
m = − ; negative m inverted image, positive m upright; (m < 1 reduced image)
𝑜
Refraction – light bends from one medium to another; bends towards normal when entering higher
n
o Critical angle – results in 90 degree refraction, light passes along interface between two media
o Total internal refraction – incident light is reflected back into original medium, results from
angle of incidence greater than critical angle, occurs when light moves from higher refractive
index
n = c/v; n1 sinθ1 = n2 sinθ2 ; index of refraction for vacuum is 1 (greater than 1 for other mediums)
Lenses have a focal point on each side; real image on opposite side, virtual image on same side
Converging corrects farsightedness (hyperopia), diverging corrects nearsightedness (myopia)
Power is measured in diopters P = 1/f
o Multiple lenses: 1/f = 1/f1 + 1/f2; P = P1 + P2; m = m1 x m2 (image of one lens is object of another)
Plane polarized electric fields of waves are in same direction; polarizers allow light pointing
parallel to pass (2 polarizers lined up allows same light through, 2 polarizers perpendicular allows no
light)
CHAPTER 9
● Photoelectric effect - light reaching threshold frequency hits metal, causing it to emit eo Supports particle theory of light (acts as discrete bundles of energy called photons)
● E = hf (h = 6.6 x 10^-34); c = f λ (excess energy from above is converted to KE in ejected e-)
● E- can absorb photon with energy matching difference between two orbitals and jump to higher
level or emission of photon occurs when e- falls to lower energy level
●
●
●
Strong/weak nuclear forces keep protons +
neutrons together despite positive charge repulsion
Fusion is when small nuclei combine, fission is when large nuclei splits (non spontaneous)
Radioactive decay – spontaneous decay of nuclei accompanies by emission of particles
o Alpha – emission of alpha particle which has 2 protons, 2 neutrons
o Negative beta – emission of beta particle (electron), neutron proton (Z+1, A)
o Positive beta – emission of positron, proton neutron (Z-1, A)
o Gamma – emission of gamma rays, lowers energy of parent nucleus, no # changes
o Electron capture – similar to positive beta decay, (Z-1, A)
● Half life: asymptotically approaches zero; exponential decay: n = n0e-λt
CHAPTER 10
● Sig figs indicate certainty of measurement; all numbers between first and last nonzero digits are
significant, leading zeros are not significant, trailing zeros are significant only if there is a decimal
o M/D: after calculations round to # of sig figs that is the lowest in one of the factors
o A/S: answer should only have as many decimal digits as initial # with fewest digits
● Round in opposite directions for multiplication and same direction for division
𝑋𝐴
= 𝑋𝐴−𝐵 ; (𝑋 𝐴 )^𝐵B= 𝑋 𝐴∗𝐵 ; √2 = 1.4, √3 = 1.7 ; log (𝑛 ∗ 10𝑚 ) = 𝑚 + 0. 𝑛
●
𝑋 𝐴 ∗ 𝑋 𝐵 = 𝑋 𝐴+𝐵 ;
●
logA1 = 0; logAA = 1; log A x B = log A + log B; 𝑙𝑜𝑔 𝑙𝑜𝑔 ( ) =𝑙𝑜𝑔 𝑙𝑜𝑔 𝐴 −𝑙𝑜𝑔 𝑙𝑜𝑔 𝐵 ; log 𝐴𝐵 =
𝑋𝐵
𝐴
𝐵
𝐵 𝑙𝑜𝑔 𝑙𝑜𝑔 𝐴
CHAPTER 11
● FINER method: evaluates research question feasible, interesting, novel, ethical, relevant
● Positive control change in dependent variable when expected, negative control no change
when not expected (used to assess for placebo effect)
● Accuracy/validity – measure true value; precision/reliability – consistency
o Bias is systematic error (does not impact precision but impacts accuracy)
● Random error is overcome by large sample size, randomization is used to form sample
● Blinding – no info about which group subject is in; single blind = only subject or evaluator is
blinded, double bind = investigator, subject, and assessor do not know subject group
● Observational studies do not demonstrate causality, just look for relationships
o Cohort – longitudinal, subjects are grouped based on exposure; outcomes are measured
o Cross sectional – categorize patients into different groups at single point in time
o Case control – identify subjects with an outcome and look backwards to see exposures
● Hill’s criteria for causality requires temporality (independent variable comes before dependent)
● Selection bias: subjects are not representative of target population, detection bias: researchers
looking for confirming data, observation bias/Hawthorne effect: observation act differently
● Confounding – incorrect relationship found due to third party variables
● Four ethical tenets of medicine: beneficence, nonmaleficence, autonomy, justice
● Research uses Belmont report: beneficence (equipoise is nonmalificience), justice (morally
relevant differences), respect for persons (informed consent, vulnerable persons,
confidentiality)
● Parameter is info based on population; statistic is info based on sample (estimates population)
● Internal validity: research answers question; external: generalizable to external population
● Statistically significant: not due to random chance, clinical significance: notable change in
health
CHAPTER 12
● Mean: good for when values are close, largely affected by outliers; peaks represent modes
● Median: (number of data values + 1)/2; least susceptible to outliers, ^bimodal distribution
● Mean and median are far apart outliers/skewed distribution, close together symmetrical
● Normal distribution can be transformed into standard distribution with mean of zero, SD of 1
o All measures of central tendency are the same (bell curve)
● Negative skew has tail on left, mean < median; positive skew has tail on right, mean > median
● Range does not consider # of values or measures of central tendency, affected by outliers
●
●
●
●
●
●
●
●
●
o Q1 = n x ¼; Q3 = n x ¾ IQR = Q3 - Q1 (outlier < 1.5 x Q1 or > 1.5 x Q3)
Standard deviation can be approximated as ¼ of range; outlier lies more than 3 SD from mean
Independent events have unchanging probability, no effect on one another, dependent events
do
Mutually exclusive outcomes cannot occur at the same time
“and” P(A) x P(B) ; “or” P(A) + P(B) – P(A and B)
Null hypothesis says two populations are equal; alternative hypothesis says they are different
P-value is likelihood that statistic was obtained by random chance; if p-value is greater than a
significance level (alpha is the level of risk we accept for incorrectly rejecting null) then we fail
to reject null and there is not a statistically significant difference; (alpha is usually 0.5)
Type I error (alpha) is false positive; type II error (beta) is false negative, power is reporting a
difference when it exists and confidence is reporting no difference when one does not exist
Semi-log graphs make curved log graphs linear, log-log graph has both axes using constant ratio
Correlation coefficient of +1 indicates strong positive correlation (variables trend together), -1
indicates negative correlation (trend in opposite directions), 0 means no correlation
Organic Chemistry:
CHAPTER 1
● Germinal diols have hydroxyl on same carbon, vicinal have hydroxyl on adjacent carbon
● Aldehyde common names: formaldehyde, acetaldehyde, propionaldehyde
● List alkyl groups followed by “ketone”, acetone has 3 C (usually “acet” means 2)
● Carbon adjacent to carbonyl is alpha, then beta, gamma, delta
● Carboxylic acids are most oxidized (always highest priority)
o Esters (“oate”) hydroxyl replaced by OR (alkoxy group), amides have amino group (Ncontaining), anhydrides remove water from two carboxylic acids
CHAPTER 2
● Chiral – mirror image cannot be superimposed (lack internal plane of symmetry)
● Structural (constitutional) isomers = shared molecule formula, not same connectivity
● Stereoisomers = same connectivity, differ in spatial arrangement (wedge/dash)
o Conformational = differ in rotation around single bond
▪ Staggered – anti (big groups 180 degrees apart) or gauche (60 degrees)
▪ Eclipsed – groups are lined up (totally eclipsed if biggest groups are lined up)
▪ Ring strain arises from angle (deviation from ideal), torsional (eclipsed), or
nonbonded/steric (big groups compete for same space) strain
● Chair is most stable (axial = up/down, equatorial = to the side)
o Configurational = can only be interconverted by breaking bonds
▪ Enantiomers = non super imposable mirror images, same connectivity with
opposite configurations at every chiral center
● Same physical/chemical properties except rotation of light (D/+ vs. L/-)
(determined experimentally) and reactions in chiral environments
● Racemic mixture is when +/- are equal (no optical activity)
▪ Diastereomers = not related by mirror image, must have multiple chiral centers
of which some differ (n chiral centers means 2n stereoisomers)
● Different chemical/physical properties, rotate plane polarized light
● Include cis/trans (geometric isomers) – differ around immovable bond
● Epimer: type of diastereomer that differs at only one chiral center
o Meso compounds = has chiral centers + internal plane of symmetry (not optically active)
● Use E/Z nomenclature for polysubstituted bonds (identify highest priority on each side of
double bond, if they are on the same side Z, opposite sides E)
● Fischer projection: horizontal lines = wedges, vertical lines = dashes
CHAPTER 3
● Molecular orbitals form when two atomic orbitals combine (same
sign = lower energy bonding orbital, different sign = higher energy
less stable antibonding orbital)
● Sigma bond is head to head overlap, 2e- (stronger than pi bond)
● Pi bond is two p orbitals lining up (on top of sigma makes double
bond, 2 pi 1 sigma = triple bond)
o Cannot exist without sigma bond, weaker
● Merging 3 p orbitals with 1 s 4 identical Sp3 (25% s, 75% p)
CHAPTER 4
● Products should be weaker/more stable than reactants; more oxidized carbons = more reactive
● Acidity increases right and down the periodic table, size over EN (long bond = stronger acid)
o More positive charge = more acidic, inductive effects, resonance
● Acids: alcohols, aldehydes, ketones, carboxylic acids + derivatives; bases: amines, amides
●
●
●
●
●
●
More negative and EN = more nucleophilic, bulkiness and protic solvents = less nucleophilic
Leaving group retains e-, weak bases are good LG (replaced by strong base Nu)
SN1 prefers more subst. carbocation, SN2 prefers less hindered for backside attack inversion
PCC is weak oxidizing agent, CrO3 and Na2Cr2O7 are strong oxidizing agents
NaBH4 is weak reducing agent (cannot do acids/derivatives); LiAlH4 is strong reducing agent
Aldehydes/ketones can be protected by
reacting with diol or two alcohol equivalents to form unreactive acetal (C with R, two -OR
groups, and H)/ketal (C with two -OR groups, two R groups); they can be reverted to carbonyl
using aqueous acid
● SN2 is stereospecific, stereoselective is preferred (major product= less strain, conjugation)
● Acid/base reaction starts with protonation/deprotonation, nucleophilic reaction starts with
attack
CHAPTER 5
● Electron withdrawing substituents increase acidity, e- donating (like alkyl groups) decrease
acidity
● Primary alcohol aldehyde using PCC or to acid using any other oxidizing agent
o Secondary alcohol ketone using any oxidizing agent, tertiary alcohol to nothing
● OH groups are poor LG so they can be protonated or reacted to form better LG called mesylates
and tosylates (have sulfur), they also serve as protecting groups to prevent alcohol from
reacting
● Phenols are oxidized to quinones (which are e- acceptors) which are oxidized to
hydroxyquinones
o Ubiquinone is reduced to ubiquinol
CHAPTER 6
● Aldehyde is more reactive than ketone (less steric hindrance)
● Once carbonyl is attacked, O- will accept a proton from solvent to form hydroxyl; if there is a
good LG, carbonyl double bond will reform and push LG off
● Hydration: with H2O, aldehyde/ketone react to form geminal diol (acid/base speed it up)
● One equivalent of alcohol makes hemiacetal/ketal, second equivalent makes acetal/ketal
o
Hydroxyl of hemiacetal/hemiketal is protonated under anhydrous acid conditions and
lost as water forms carbocation which another alcohol equivalent attacks
● Imine is C=N, undergoes tautomerization of form enamine (C=C-N)
● Aldehyde/ketone can be reduced to alcohol with LiAlH4 (strong) or NaBH4 (mild)
CHAPTER 7
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●
●
●
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Alpha carbon is easily deprotonated, due
to acidity of alpha hydrogen aldehydes
and ketones exist in solution as isomers
called tautomers (enol has C=C while keto
has C=O and is favored);
THERMODYNAMIC IS REVERSIBLE, KINETIC
IS NOT
Michael addition is where carbanion attacks alpha, beta-unsaturated carbonyl compound
Kinetic product: formed rapidly, irreversible, less stable, low temp, (double bond to less sub C);
sterically hindered base removes less hindered H; thermodynamic: opposite, weak, small base
Enamines are tautomers of imines (enols are tautomers of carbonyls)
Aldol condensation – aldehyde/ketone act as both an electrophile (keto) and nucleophile
(enolate ion negatively charged so more nucleophilic); end result is formation of C=C
o Step 1: Aldehyde/ketone + base enolate aldol (contains aldehyde + alcohol groups)
o Step 2: Strong base and heat causes dehydration which kicks off water to form double
bond (alpha beta unsaturated carbonyl)
Aldol condensation is more useful with one type of aldehyde/ketone or product mixture forms
Retro aldol condensation breaks bonds between alpha and beta carbons of carbonyl to form
two aldehydes, two ketones, or one of each (reverse, catalyzed by aqueous base and heat)
CHAPTER 8
● Carboxylic acid is terminal, most oxidized (so carbonyl C is
always number 1)
o Acidic H, H bonding increases BP/MP, acidity due to
resonance (increased by EW groups)
▪ When one proton is removed, remaining acid is less acidic (second proton is
less)
o Dicarboxylic acid has acid groups on both ends -dioic acid
o Beta dicarboxylic acid has two carboxylic acids separated by alpha carbon
● Nucleophile attacks carbonyl, carbonyl reforms kicking off weak base LG (acidic/basic conditions)
o Forms amide if nucleophile is ammonia (NH3) or amine; cyclic amide = lactam (strain)
● Acyl derivative: molecule with carboxylic acid derived carbonyl; anhydride: condensation of 2 acids
● Acid + alcohol (under acidic conditions) ester + water (-oate
ending, cyclic ester = lactone)
● LiAlH4 is strong enough to reduce acids, NaBH4 is not
● Decarboxylation is loss of carboxyl group as carbon dioxide,
carboxyl group replaced with H
● Saponification – long carboxylic acid reacts with hydroxide cation to
form salt/soap (acid remakes FA)
CHAPTER 9
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Carboxylic acid undergoes dehydration reaction to form carboxylic acid derivatives
Acid/derivative + primary/secondary amine amide
o If they can H bond depends on # of alkyl groups so BP may be same or lower than acid)
Fischer esterification: acid/anhydride + alcohol ester (lack H bonding so lower BP than acids)
o Ex: triacylglycerols (fatty acid + glycerol); saponification is reverse
Anhydrides: formed by heating acids, stable 5-6 member rings, higher BP than acid due to
weight
o Most reactive toward Nu, then esters and acids, then amides (due to e- donating amine)
Increase acidity: EW (EN) groups, steric hindrance/size, conjugation, resonance, induction
(weak)
Anhydride cleavage: should be symmetric or else mixture of products will form
o NH3 + anhyd amide + acid; alcohol + anhyd ester + acid; anhyd + H2O 2 acids
Transesterification – alcohol is Nu and displaces esterifying group on ester (replace OR with OR)
Amide in acidic conditions is hydrolyzed: carbonyl O is protonated so water attacks carboxylic
acid + ammonia (can occur in base but O isn’t protonated, Nu is OH-, produces carboxylate
anion)
CHAPTER 10
● AA written N to C terminus, amphoteric (zwitterions) due to amino and carboxyl groups
o Undergo condensation to form peptide bonds, strong acid/base hydrolysis of bond
o Resonance gives C-N partial double bond character making it rigid/stable
● Strecker (aldehyde + amine) and Gabriel synthesis (ester and phthalimide) of AA
● Phosphoric acid 3 acidic H’s with their own pKa (pKa increases with loss of each progressive H)
o Makes it good buffer, H2PO4- and HPO4-2 predominate at physiological pH
o In acidic conditions H3PO4 (keeps getting deprotonated); in base PO4-3
CHAPTER 11
● IR measures vibrations in molecules with
net dipole moments to determine functional groups
● OH is wide at 3300 for alcohols and 3000 for carboxylic acid; NH is 3300 sharp, C=O is 1700
sharp
● UV: more conjugation = lower energy transition, long wavelength; pi/non bonding e- can be
excited to higher energy anti bonding orbital (easier if less difference between HOMO and
LUMO)
● NMR: proton or atom with nuclear spin (odd atomic/mass #); shift increases downfield (left)
o Equivalent protons have same peak (height represents # of protons)
▪ Nonequivalent protons on adjacent C within 3 bonds splitting (n+1 peaks)
o Close to more EN atom = proton peak further downfield (de-shielded); TMS = 0 ppm
CHAPTER 12
● Extraction separates
dissolved compounds
o Use two immiscible
solvents (nonpolar
organic phase and
polar aqueous
phase), shake to mix and allow them to separate 
desired compound in more similar phase
o Organic is usually on top so aqueous is released from
bottom; multiple extractions are more effective than
large volume
o Reverse is called wash solute extracts impurities rather than compound of interest
● Filtration isolates solid from liquid, solid residue is filtered out while liquid filtrate passes
through
o Gravity filtration solvent’s weight pulls it through filter, used when filtrate is of
interest
o Vacuum filtration vacuum forces solvent through filter, used if solid is desired product
● Recrystallization – product is dissolved in hot solvent, cool/recrystallize with impurities
excluded
● Distillation – BP difference to separate liquids (lower BP vaporizes, condenses into distillate)
o Simple – only used for liquids below 150 C and less than 25 degree difference
▪ Superheating – liquid is heated above BP without vaporization (gas bubbles)
o Vacuum – used if BP is above 150 C, vacuum lowers ambient pressure, decreasing BP
o Fractional – separates liquids w/ similar BP (<25 degrees apart), uses inert objects to
increase SA so lower BP compound vaporizes higher up on these surfaces
● Chromatography – compound more similar to its stationary phase/adsorbent sticks more
o Thin layer chroma. uses silica (polar) as stationary, mobile phase displaces/elutes
sample
▪ Rf = distance spot moved/distance solvent moved (larger value = moved more)
o Reverse phase chroma. uses nonpolar stationary phase
o Column uses silica beads and gravity moves solvent down column, drips out
▪ Ion exchange – charged beads, increases retention for opposite charge (salt
gradient elutes charged molecules stuck to column)
● Cation exchange means cations stick to negative beads, vice versa
▪ Size exclusion – beads have pores in which smaller compounds enter (slowed
down) so larger compounds travel faster
▪ Affinity – beads have receptor/antibody for protein/compound so it is retained
in column; eluted by using competing free receptor or disrupting pH/salinity
level
o Gas chromatography - gas eluent/polar adsorbent coiled in 30 ft. column and heated in
oven, inject mixture into column, vaporizes and travels through, adheres to dif. degrees
o High perform. liquid chrom. – like CC but computerized, eluent is liquid under pressure
Biochemistry:
CHAPTER 1 – AN AMINO ACID IS 110 Daltons
● AA have amino and carboxyl group bonded to chiral alpha carbon of carboxylic acid
o Glycine is not chiral (H side chain), all chiral AA are L and S except cysteine is R
o Tryptophan is largest AA, tyrosine is the only polar aromatic, serine/threonine have OH
side chains, asparagine/glutamine have amide side chains, cysteine has thiol (oxidation)
o Aspartate/glutamate: COO- side chains rather than amides, lys: terminal primary amino
group, arg: 3 N atoms, his: aromatic w/ 2 N (imidazole) one N is protonated at 7.4 pH
● pKa is the pH at which half the molecules are deprotonated (pH < pKa protonated)
o pKa 1 is for carboxyl group ~ 2; pKa 2 is amino group ~ 9-10; pKa 3 is side chain
o Vertical part of graph is pI (pH at which molecule is neutral), horizontal part is pKa
● Peptide bond forms when Nu amino group attacks carbonyl C and water is kicked off
o C-N partial double bond character/resonance, amide can be hydrolyzed with acid/base
● Primary structure is AA sequence with covalent peptide bonds between
● Secondary structure is alpha helices/beta pleated sheets from intramolecular H bonding
o Proline induces kinks so it is found only at turns of beta sheets or start of alpha helix
● Tertiary structure is 3D shape from hydrophilic/hydrophobic interactions, H bonding, salt
bridges (acid/base interactions between charged AA), disulfide bond between 2 cysteines
(creates loop)
● Quaternary structure: proteins with more than one polypeptide chain cooperativity/allosteric
● Conjugated proteins have covalently attached organic molecules/metal ions (prosthetic groups)
● Denaturation: loss of tertiary structure (therefore function), with high temp/disruptive solutes
CHAPTER 2:
𝑣 𝑚𝑎𝑥[𝑆]
𝐾𝑚+[𝑆]
; vmax = [E]kcat; kcat is s-1 (# substrate converted to product per enzyme per second)
●
v=
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●
●
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Catalytic efficiency of the enzyme: E = kcat/Km (large turnover or small Km --> high efficiency)
Enzymes: not changed during reaction, do not alter G or Keq (just rate), lower Ea by stabilizing T
Lyases: cleave single molecule into two without water; can also be synthase (2 1 molecule)
Ligase: addition/synthesis using ATP between large similar molecules
Hydrolase: break compound into two using water (peptidase, nuclease, lipase, phosphatase)
Oxidoreductase: redox reactions, cofactor acts as e- carrier (dehydrogenase, reductase, oxidase)
Transferase: movement of functional group (kinase); isomerase: rearranges bond
Lock and key: active site is already fit for substrate; induced fit: active site conforms after
binding
Prosthetic groups: cofactors (inorganic, metal ions, mineral) and coenzymes (organic, vitamins)
help enzymes by binding active site everything together = holoenzyme (w/o is apoenzyme)
As substrate is added, rate levels off until all active rates are occupied (saturation, vmax)
o The only way to increase vmax is by increasing [enzyme] (not by increasing substrate)
Km is the substrate concentration at half vmax (high Km means low affinity for enzyme)
LB is double reciprocal of MM; x-intercept = -1/Km, y-intercept = 1/vmax; slope = Km/vmax
Cooperative binding: sigmoidal curve; binding one substrate makes TR leading to more binding
o Hill’s coefficient > 1 positively cooperative binding; <1 negative; =1 none
Competitive can be overcome by adding more substrate, noncompetitive cannot
Mixed: if inhibitor binds to enzyme Km increases, if inhibitor binds to ES complex Km decreases
●
●
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●
Uncompetitive binds ES complex, locks substrate in enzyme (prevents release + increases
affinity)
CHAPTER 3
● Hybridization: joining complementary base pair sequences, PCR: uses hybridization to generate
●
●
●
●
●
●
●
lots of DNA copies, electrophoresis separates DNA molecules by size, southern blotting detects
presence/quantity of various DNA in sample (later probed w/ single strand DNA to find
sequence of interest), DNA sequencing: dNTP primer (lack 3’ OH) shows complementary
sequence on gel
o In electrophoresis, negative compounds migrate to positive anode, vice versa
▪ Smaller/charged particles pass through gel more easily
▪ Native PAGE analyzes protein in native state, SDS PAGE denatures non-covalent
bonds and separates by mass, reducing PAGE breaks disulfide bonds too
o Isoelectric focusing – acidic gel is at positive anode, basic is at negative cathode
▪ Positive protein migrates to cathode, protein halts when pH = pI (neutral)
o ELISA determines concentration of molecules using antibodies
Cytoskeleton – has proteins that anchor to membrane for structural support
o Collagen and elastin in ECM of connective tissue
o Actin = microfilaments and thin filaments in microfibrils (has positive and negative
ends)
o Tubulin forms microtubules (structure, chromosome separation, intracellular transport)
Myosin is motor protein, acts with actin; kinesin and dynein are associated with microtubules
CAMs are integral membrane proteins on cell surface, aid in binding to ECM
o Cadherins = calcium dependent cell adhesion, hold similar cell types together
o Integrins = alpha and beta chains span membrane, bind/communicate with matrix
o Selectins weakly bind to carbohydrate molecules on cell surface
Immunoglobulins (antibodies) have 2 identical light and heavy chains (constant region) linked
by disulfides; antigen binding region at tips of Y (variable) where only a specific sequence is
bound
o Opsonization – mark pathogen for destruction, agglutination – clump antigen/antibody
Ungated, voltage gated, ligand gated channels (Km and vmax apply to ion channels)
Enzyme linked receptors have membrane spanning domain, ligand binding domain, catalytic
domain second messenger cascade (ex: RTKs)
Ligand binds G protein coupled receptor; Gs stimulates adenylate cyclase to increase cAMP, Gi
inhibits cAMP, Gq activates phospholipase C PIP2 DAG and IP3 increases calcium in cell
o When G protein is active (GTP form), alpha dissociates to alter adenylate cyclase activity
● Edman degradation – cleaves and analyzes small proteins
● Bradford assay – protonated green/brown dye which turns blue after binding AA in proteins
CHAPTER 4
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-ose is sugar ending
Aldose/ketose is carbohydrate with aldehyde/ketone group
Aldehyde C participates in glycosidic linkages, makes disaccharides/ polysaccharides
On every monosaccharide, every carbon except carbonyl carries a hydroxyl group
All D sugars have hydroxide of their highest numbered chiral center on the right
To form acetal, hydroxyl group attacks carbonyl (O becomes member of ring)
o Carbonyl C becomes chiral and is called anomeric carbon bonded to 2 oxygens
▪ Alpha anomer has C1 OH group axial/down, beta has it equatorial/up
Water makes hemiacetal ring cycle between open and closed; in acid or base it switches
between alpha and beta mutarotation (creates mixture of both, alpha is less favored)
Hemiacetal ring can be oxidized to aldonic acid or reduced to alditol
Aldoses are reducing agents, reducing sugar = a monomer with hemiacetal ring
o To detect presence of reducing sugar (has free aldehyde/ketone, can mutarotate):
▪ Tollen’s reagent: produces silvery mirror in presence of aldehydes
▪ Benedict’s reagent: aldehyde on aldose is oxidized red Cu2O precipitate
o Ketoses are also reducing sugars and can give positive test results (cannot be directly
oxidized but can tautomerize under basic conditions to form aldoses)
All monosaccharides = reducing sugars, all disaccharides except sucrose b/c (1,2 glycosidic bond)
Hemiacetals/aldehydes are reducing sugars while acetals are not since OR, OR cannot be
oxidized
●
●
Hydroxyl group of carbohydrate can react with carboxylic acid/derivatives to form esters
When acetal forms, resulting C-O bond is glycosidic bond and acetal formed = glycoside
o Derived from furanose = furanoside, from pyranose = pyranoside
o Glycoside formation is dehydration so hydrolysis breaks glycosidic bond
● Cellulose is beta D glucose chains linked by beta 1,4 glycosidic bonds
● Starches (plant storage forms) are linked alpha D glucose monomers (amylose has alpha 1,4
glycosidic bonds while amylopectin also has alpha 1,6 bonds)
● Glycogen (animal storage) = more branching (alpha 1,6 bonds) more soluble/efficient
CHAPTER 5
● Membrane components are amphipathic (hydrophilic and hydrophobic)
o Phospholipid: phosphate and OH polar head, joined to FA tail by phosphodiester
linkage
▪ Glycerol is a 3C alcohol backbone, unsaturated FA double bonds (kinks, fluid)
● Glycerophospholipids/phosphoglycerides are a type of phospholipid with glycerol backbone
bonded by ester linkages to 2 FA and by phosphodiester linkage to polar group (any/no charge)
● Sphingolipids have sphingosine backbone, often used as cell-surface antigens
o Sphingomyelin/sphingophospholipids have head group with no charge, produce myelin
o Glycosphingolipids are glycolipids, sugar; not phospholipids (no phosphodiester bond)
o Gangliosides are sphingolipids/glycolipids with NANA polar head groups and (-) charge
o Sphingosine backbone is a long carbon chain attached to polar group
● Waxes: esters of long chain FA with long chain alcohols, solid at room temp., stabilize
membrane
● Terpenes: precursors to steroids, built from isoprene and have carbons grouped by multiples of
5
o Monoterpenes have 2 isoprene units, triterpenes have 6 and make cholesterol/steroids
● Steroids have 3 cyclohexane and 1 cyclopentane rings fused, nonpolar
● Cholesterol is an amphipathic steroid and mediates membrane fluidity
● Prostaglandins are 20 carbon unsaturated acids with one 5 carbon ring
● Vitamins must be consumed (cannot be synthesized), lipid soluble vitamins can accumulate in
stored fats (ADEK), water soluble are excreted through the urine
● Vitamin A (carotene) is in carrots, vitamin D (calcitrol) increases Ca2+ uptake for bone
production, vitamin E destroys free radicals/prevents oxidative damage, vitamin K is a clotting
factor
● Triacylglycerols: energy storage (carbons on FA are more reduced so they are energy dense,
triacylglycerols are hydrophobic so they do not draw water in which reduced weight), insulation
o AKA triglycerides, 3 FA bonded by ester linkages to glycerol; nonpolar, insoluble in
water
● Free FA are unesterified FA with free carboxylate group, micelles help absorb fat soluble
vitamins
● Saponification: ester hydrolysis of triacylglycerol w/ base (lye/hydroxide) glycerol + FA salt
o Soaps can act as surfactant to lower surface tension of liquid
CHAPTER 6 - Nucleoside: 5C sugar bonded to nitrogenous base (no phosphate)
o Nucleotide: phosphate attached to sugar, high energy, DNA (no OH on 2’ C)
▪ 5’ end has OH/phosphate on C5 while 3’ end has OH on C3
● Purines: A and G (2 rings, G has =O); pyrimidines: C, U, T (1 ring, C has 1 =O, U/T have 2 =O)
● Aromatic cyclic, planar, conjugated (sp2), 4n+2 pi electrons (Huckel’s rule)
o Stable, unreactive (heterocycles: rings with 2+ different elements like
purine/pyrimidine)
●
Watson-Crick: right handed double helix, complementary base pairs (Chargaff’s rule),
antiparallel strand polarity, structure; denaturation = no covalent bond breakage, only H
bond/base pairs
● In PCR, probe DNA (complimentary known sequence) is added to mixture with target DNA,
binding shows presence of gene of interest; DNA is denatured, replicated, cooled/reannealed
● DNA is wound around histones to form nucleosomes which make up chromatin, H1 stabilizes
● Heterochromatin: dark, dense, and transcriptionally silent; euchromatin: open, genetically
active
● Telomeres: high GC content, prevents unraveling; not replicated so shortened telomeres = aging
o Some can be replaced by telomerase; more rapidly dividing cells have more telomerase
● Centromere is connection in middle of chromosome; high GC content/heterochromatin
● Replisome assists DNA pol, helicase unwinds DNA at origin, replication forks go in both
directions
● Eukaryotes have faster DNA replication due to multiple origins of replication
● SSBP keep strands separated, topoisomerase induces negative supercoils to alleviate stain
● DNA pol reads 3’ to 5’ but synthesis, repair, transcription and translation occur 5’ to 3’
● First step: primase synthesizes RNA primer (one for each okazaki fragment, one for leading)
● Pol III (proks), a/d/e in euks synthesize; pyrophosphate released w/ forming of phosphodiester
o DNA pol I/RNase H remove RNA primer; DNA pol I/d fill in gap, ligase seals
o Gamma replicates mitochondrial DNA, beta and epsilon are for DNA repair
● Oncogenes: mutated genes that cause cancer (promote cell cycle), unmutated = proto oncogene
● Tumor suppressor genes inhibit cells cycle, mutation can no longer slow cell cycle/cancer
● Proofreading – unstable H bond is detected, incorrect base is excised from less methylated
strand
o G2 phase has mismatch repair for mutations missed in S phase
o Nucleotide excision repair eliminates large thymine dimers: first, excision
endonuclease removes the section and DNA pol fills in gap using undamaged strand as
template
● Base excision repair for smaller CU conversion (AP site removed by AP endonuclease)
● Recombinant DNA tech multiplies DNA fragments through gene cloning/PCR
o Cloning produces lots of desired sequence (ligate DNA of interest into vector with
antibiotic resistance which is transferred to host bacterium, rest can be killed)
▪ Processed by restriction enzymes to release cloned DNA from vector
● DNA libraries: known sequences, genomic libraries: exons + introns, cDNA: only exons
● Hybridization – joining of complementary base pair sequences
● Gel electrophoresis separates macromolecules by size/charge, DNA is negative (goes to anode)
● Western blot: detects presence of specific protein in sample using antibody
● Southern blot: detects presence/quantity of strands (DNA is cut with restriction enzymes,
electrophoresis, labelled probes), Northern blot detects presence of RNA
● Gene therapy uses gene delivery vectors (modified viruses) to deliver functioning gene
● Transgenic mice: altered at germ line by introducing cloned gene into ova/embryonic stem cells
o Transgene is passed onto offspring, knockout mice have gene deleted
CHAPTER 7
● mRNA is complementary and antiparallel to DNA template strand (transcribed by RNA pol)
o Euks: monocistronic mRNA (translated to only one protein product) and post trans mod
o With the help of transcription factors, RNA pol (II in euks) looks for promoter regions
and binds a site in there called TATA box
● Ribosome translates mRNA from 5’ 3’ and synthesizes protein from N to C terminus
●
●
Each tRNA has a 3 nucleotide anticodon, rRNA is made in nucleolus
64 codons, genetic code is unambiguous so each codon only specifies one AA
o AUG (methionine is start codon); UAA, UGA, UAG are stop codons
● DNA cannot leave the nucleus since it would be degraded, in transcription RNA pol reads from 3’
to 5’ but synthesizes from 5’ to 3’ (does not proofread its work unlike DNA pol)
o In replication, DNA is synthesized 5’ to 3’; in translation mRNA is read 5’ to 3’
● Template strand = noncoding = antisense = negative sense (need to be converted to positive)
● Non template strand = coding = sense = positive sense (identical to mRNA, can directly translate)
● Post transcriptional processing turns hnRNA into mRNA: splicing, 5’ G cap, 3’ poly A tail
o Alternative splicing: snRNPs in spliceosome remove introns (degrade lariat), ligate
exons
o 5’ cap is added during transcription and recognized by ribosome as binding site, protects
mRNA from degradation in cytoplasm; 3’ poly A tail protects against degradation
(longer)
● mRNA transcript exits via nuclear pores; ribosome has APE binding sites w/ 40S + 60S = 80 S
● Prokaryotes start translating before transcription is complete, eukaryotes separate both
o Initiation: small subunit binds Shine Dalgarno/5’ cap, tRNA binds Met, large subunit
joins
o Elongation: moves through APE sites, elongation factors assist, signal sequence added?
o Termination: stop codon in A site, release factor/termination factors, subunits
dissociate
● Post translational processing: chaperone proteins fold, may be cleaved to active form, subunits
join; phosphorylation (Ser, Thr, Tyr), carboxylation, glycosylation (signaling)
● Operon: genes transcribed in a group by sharing single promoter region (usually in proks)
● Structural gene codes; upstream are operator (binds repressor), promoter (binds RNA pol), and
regulator (codes for repressor); enhancer is far from promoter
o Inducible: repressor is bonded to operator (off), inducer binds repressor to remove it
o Repressible: system is on; repressor binds corepressor, both bind operator to turn off
▪ Negative control: protein binds DNA to stop transcription
● Lac operon is negative inducible, trp operon is negative repressible
▪ Positive control: protein binds DNA to increases transcription
● Acetylation opens DNA from histones transcriptionally active; methylation silences
CHAPTER 8
● Lipid rafts: attachment point for signaling molecules; flippases flip phospholipids in membrane
● Cells can up or down regulate receptors in membrane, saturated FA are solid/less healthy
● FA in the diet are transported as triacylglycerols in chylomicrons from the intestine
● Phospholipids spontaneously assemble into micelles (monolayer vesicles) or liposomes (bilayer)
● Sphingolipids do not contain glycerol, hydrophilic region + 2 FA tails, found in myelin
● Cholesterol: synthesizes steroids, has hydrophobic/hydrophilic regions, membrane fluidity
● Waxes provide membrane stability in plants, high MP, long chain FA + long chain alcohol
● Integral proteins: transmembrane proteins go through, embedded proteins are only associated
with one side; peripheral proteins are bound to other membrane components
● Carbohydrates: signaling/recognition, glycoproteins and water can form coat around cell
● Cell cell junctions are composed of cell adhesion molecules (CAMs)
o Gap junctions allow for direct communication/solute movement, formed from
connexins
o Tight junctions prevent solute from leaking between cells
o Desmosomes bind adjacent cells by anchoring their cytoskeletons
●
Passive transport (diffusion, facilitated, osmosis) increases with temp, active depends on ΔH
o Facilitated is for large, polar charged molecules, uses integral proteins (channel/carrier)
o Primary active uses ATP, secondary is coupled (symport vs antiport directions)
● Hypotonic – concentration of solutes inside cells is higher (will swell)
● Osmotic pressure is colligative property (depends on solutes) and sucks solutes into/out of cell
● Endocytosis uses vesicle coating proteins for invagination (such as clathrin)
● Resting membrane potential (-70 mV) is maintained by Na/K ATPase since leak channels ruin
o ATPase pumps 3 sodium out for every 2 potassium in, membrane is more permeable to
K
● Nernst equation (for body temp): E = 61.7/z log [ion outside]/[ion inside] z is charge of the ion
● Outer mitochondrial membrane is highly permeable, inner is not
CHAPTER 9
● Glucose needs sodium for absorption in digestive tract but enters cells via concentration
gradient
o GLUT 2 transports glucose in hepatocytes and pancreatic cells for storage (low affinity)
o GLUT 4 is in adipose and muscle, insulin stimulates more GLUT4 to uptake glucose
▪ Adipose requires glucose to form DHAP which is converted to glycerol
phosphate to store incoming FA as triacylglycerols
● Glycolysis: glucose 2 pyruvate, galactose; 1 oxidation, 2 substrate level phosphorylations
o NADH produced feeds into aerobic respiration (or just glycolysis for anaerobic)
● Hexokinase: all tissues, glucose glucose 6 phosphate (trapped inside cell); negative feedback
● Glucokinase: liver/pancreatic cells (in the liver, glucokinase is induced by insulin), low affinity
Rate limiting enzyme for each process:
o Glycolysis: PFK 1
o Fermentation: LDH
o Glycogenesis: glycogen synthase
o Glycogenolysis: glycogen phosphorylase
o Gluconeogenesis: F 1,6 BP
o PPP: glucose 6 phosphate DH
● PFK 1: glycolysis RDS; ATP, citrate, glucagon
inhibit, AMP and insulin (using PFK 2) activate
● No O2 = fermentation, LDH converts pyruvate
to lactate (replenishes NAD+ for GAPDH)
● Irreversible steps of glycolysis: (all kinases)
hexokinase/glucokinase, PFK 1, pyruvate kinase
● RBC’s lack mitochondria so glycolysis is the only
form of energy production (2 ATP per glucose)
o BPG mutase: 1,3 BPG from glycolysis 
2,3 BPG (decreases Hb affinity for O2)
o Rightward shift in dissociation curve
means more unloading at tissues
● Galactose/fructose can also feed into glycolysis
o Lactose is hydrolyzed to galactose and
glucose by lactase, galactokinase traps
it in cell, galactose 1 phosphate
uridyltransferase converts galactose 1
phosphate to glucose 1 phosphate
o Sucrase converts sucrose to fructose
and glucose, fructokinase traps
fructose in cell, aldolase B converts
fructose 1 phosphate to glyceraldehyde
and DHAP
● Pyruvate enters mitochondria, PDH
(irreversible) converts it to acetyl coA to enter
TCA cycle if energy is needed or FA synthesis if energy is sufficient (responds to insulin)
o Other fates of pyruvate: conversion to lactate by LDH, or to OAA by pyruvate
carboxylase
o
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PDH: inhibited by product (acetyl coA), buildup of acetyl coA in beta oxidation results in
pyruvate being converted into OAA to enter gluconeogenesis instead of more acetyl coA
Liver glycogen is broken
down to maintain
constant level of blood
glucose, muscle glycogen
is broken down during
exercise for muscle
contraction; glycogen is
stored in cytoplasm as granules
Glycogenesis: glycogenin core, glucose 6 phosphate is converted to G1P and added to UDP
o Glycogen synthase forms alpha 1,4 glycosidic bonds in the linear chain
▪ Stimulated by glucose 6 phosphate/insulin, inhibited by epinephrine/glucagon
o Branching enzyme makes alpha 1,6 linkages
Glycogenolysis: glycogen phosphorylase breaks 1,4 bonds using phosphate instead of water
o Releases glucose 1 phosphate which is converted to glucose 6 phosphate
▪ Activated by glucagon in liver, and AMP/epinephrine in muscle; inhibited by ATP
o Debranching enzyme transfers 1,4 bond and removes glucose at branch point (1,6)
Insulin lowers blood sugar, glucagon/epinephrine/cortisol/growth hormone raise blood sugar by
stimulating glycogenolysis and gluconeogenesis (done by liver to maintain blood glucose levels)
Gluconeogenesis uses glycerol 3 phosphate from triacylglycerols in adipose, lactate (from
anaerobic glycolysis), glucogenic AA(from muscles, include all except leucine and lysine)
o Lactate is converted to pyruvate through LDH, alanine is converted to pyruvate using
alanine aminotransferase, G3P is converted to DHAP by glycerol 3 phosphate DH
o Gluconeogenesis is basically the reverse of glycolysis, occurs in liver cytosol and mito
o Pyruvate carboxylase: pyruvate OAA which is converted to malate and leaves
mitochondria through malate-aspartate shuttle (turned back into OAA in cytoplasm)
▪
Activated by acetyl coA from beta oxidation (FA provide energy to make
glucose)
● Acetyl coA is needed for gluconeogenesis to activate PC and inhibit PDH
o PEPCK: OAA to PEP using GTP (pyruvate carboxylase and PEPCK bypass pyruvate kinase)
o F 16 bisphophatase: rate limiting step, reverses PFK 1 action by turning F16BP into F6P
▪ AMP/insulin inhibit (via increase F26BP, insulin ↑ PFK2?), ATP/glucagon activate
o Glucose 6 phosphatase: liver only (muscle glycogen can’t serve as blood glucose source)
▪ Glucose 6 phosphate free glucose (bypasses glucokinase)
● Gluconeogenesis does not serve as an energy source for the liver, liver uses FA beta oxidation
● Acetyl coA from FA can’t be converted to glucose but it can be made into ketone bodies for
brain
● PPP (fuel storage): cytoplasm of cells; makes NADPH + ribose 5 phosphate (nucleotide
synthesis)
o First part is glucose 6 phosphate 
ribulose 5 phosphate (irreversible,
produces NADPH and involves rate
limiting enzyme G6PDH -- activated by
insulin, inhibited by NADPH)
▪ NADPH: biosynthesis, immune
system, forms glutathione as
antioxidant
o Second part is reversible, ribulose 5
phosphate becomes ribose 5
phosphate and F6P, GAP are produced
to feed back into glycolysis (uses
transketolase/transaldolase)
CHAPTER 10
● TCA cycle occurs in mitochondrial matrix (glycolysis occurs in cytoplasm)
o Oxidizes acetyl coA to CO2 and H2O while producing NADH and FADH2
o First, PDH in matrix oxidizes/decarboxylates pyruvate to acetyl coA and CO2
(irreversible)
▪ PD complex has 5 enzymes and is inhibited by acetyl coA/NADH; coA = thiol (SH)
● PDH oxidizes pyruvate, creating CO2, requires TPP coenzyme and Mg2+
● Dihydrolipoyl transacetylase oxidizes using lipoic acid, forms acetyl coA
● Dihydrolipoyl dehydrogenase reoxidizes lipoic acid and forms FADH2
● Pyruvate dehydrogenase kinase phosphorylates PDH if ATP is high off
● Pyruvate dehydrogenase phosphatase removes phosphate on
● Acetyl coA can form from FA beta oxidation: fatty acyl cross inner membrane via carnitine
where 2 C fragments are removed from carboxyl end to make acetyl coA
● Amino acids lose amino group via transamination and carbon skeletons form ketone bodies
● Acetyl coA produces ketones if pyruvate dehydrogenase complex is inhibited (reverse can occur)
● Alcohol/acetaldehyde DH converts alcohol to acetyl coA (TCA is inhibited so FA synthesis
occurs)
● Acetyl coA + OAA starts TCA cycle, will not occur anaerobically since NADH will build up if no O2
● Citrate synthase does not require energy but succinyl-coA synthetase does
● High energy state of cell inhibits TCA cycle and there are 3 checkpoints:
o Citrate synthase, isocitrate DH, alpha ketoglutarate DH (first 4 steps except aconitase)
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NADH and FADH2 transfer e- to carrier proteins in inner membrane, given to O2 and water
forms
o Protons go from matrix to intermembrane space to make gradient (proton motive
force)
Forming of ATP is endergonic and electron transport is exergonic, O2 has high reduction
potential
H2O
●Complex I: uses iron/sulfur to transfer e- from NADH 
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FMN CoQ (4 PROTONS are moved)
Complex II: uses iron/sulfur to transfer e- from succinate FAD CoQ (NO PROTON pumping)
Complex III: iron/sulfur to transfer e- from CoQH2 heme (forms cytochrome c) 4 PROTONS
Complex IV: uses cytochromes and Cu2+ to transfer e- (H-) from cyt c to oxygen (2 PROTONS)
NADH cannot cross inner membrane so shuttle must be used
o Glycerol 3 phosphate shuttle: e- are transferred from NADH to DHAP to form glycerol 3
phosphate, these e- are transferred to FAD to form FADH2 (malate is more efficient)
o Malate aspartate shuttle: e- transferred from NADH to OAA to form malate which
crosses membrane and transfers e- to NAD+ to form NADH, aspartate goes back into
cytosol
Electrochemical gradient: low pH in intermembrane space as well as large voltage difference
F0 functions as ion channel and uses energy releases from gradient to convert ADP to ATP
o Chemiosmotic coupling; uncouplers prevent ATP synthesis but not ETC (heat release)
●
If O2 decreases, oxidative
phosphorylation decreases (energy
carriers build up, inhibiting TCA)
● CoQ transports 2 e-, cyt c transports 1
CHAPTER 11
● Lipids are emulsified in duodenum via
bile
● Pancreas secretes pancreatic lipase,
colipase, and cholesterol esterase to
hydrolyze lipid components to 2
monoacylglycerol, free FA and cholesterol
● Short FA are absorbed across intestine
into blood, transported via albumin
● Long FA are absorbed as micelles and
assembled into chylomicrons packaged
with apoproteins and fat soluble vitamins which enter lacteals and re enter blood stream via
thoracic duct
● Fall in insulin (post absorptive) or rise in cortisol/epinephrine activates hormone sensitive
lipase hydrolyzes triacylglycerols from adipocytes (go to liver for glycolysis/ gluconeogenesis)
o Lipoprotein lipase mobilizes lipids from lipoproteins, chylomicrons and VLDL
● Chylomicrons = soluble in blood, assembled in intestinal lining and transported to tissues
● VLDL is made in liver, transports to tissues; HDL moves accumulated cholesterol to liver/tissues
● Chylomicrons and VLDL mostly carry triacylglycerols while LDL and HDL carry cholesterol
● Cholesterol = synthesis of membranes, steroids, bile; insulin promotes cholesterol synthesis
o Made in liver using HMG-CoA reductase and citrate shuttle to carry mitochondrial
acetyl coA to cytoplasm where synthesis occurs, LCAT and CETP help
● C2 in the FA is the alpha carbon; linolenic
and linoleic acid are essential FA and
maintain membrane fluidity
● Omega naming represents last double bond
● FA synthesis occurs in liver, stored in adipose
o Acetyl coA carboxylase (biotin), FA
synthase (insulin/citrate stimulate)
▪ Carboxylase adds CO2 to
acetyl coA malonyl coA
o Synthesized in cytoplasm from acetyl
CoA transported out of mitochondria
o 2 reductions and dehydration,
repeated 8 times to form 16 C
palmitic acid (only one by humans)
▪ 8 acetyl CoA to make 1 palm
●
FA oxidation is reverse, occurs in mito after transport via carnitine
shuttle (carnitine acyltransferase is rate limiting, also uses FA coA
synthetase)
o Beta oxidation (stimulated by glucagon) involves oxidation to
form double bond, hydration of double bond to form hydroxyl,
oxidation of hydroxyl to form carbonyl, cleavage each cycle
releases 1 acetyl coA and reduces NAD and FAD for ETC
▪ Acetyl coA enters TCA or stimulates gluconeo by
activating pyruvate carboxylase
o Monounsaturated FA use enoyl coA isomerase and
polyunsaturated also need reductase
o Odd FA chains end with a propionyl coA which is converted to
succinyl coA to enter TCA (this is the only time FA can be
converted to glucose)
● Excess FA from beta oxidation in liver leads to ketogenesis in
mitochondria (used in brain, cardiac/skeletal muscle) during starvation
o Ketogenesis HMG coA synthase/lyase (acetone side
product)
o Ketolysis regenerates acetyl coA for energy use, liver lacks
enzyme to metabolize the energy it produces
● Protein digestion occurs in SI, body protein is catabolized mainly in
muscle and liver (AA are transaminated and carbon skeleton is used)
o Removed amino group are fed into urea cycle in liver for excretion
o AA metabolized during starvation via gluconeogenesis or ketone formation
▪ Glucogenic AA (all but leucine and lysine) can be converted to glucose,
ketogenic (leucine, lysine, isoleucine, phenylalanine, tryptophan, tyrosine,
threonine) can be converted into acetyl coA and ketone bodies = keto PLIT
CHAPTER 12
● In the body: ΔG = ΔG ° + RT ln(Q) no work performed in closed bio system (no change in P/V)
● ATP is a midlevel energy carrier (30 kJ/mol), formed from substrate level phos/ox phos
● Post prandial state is absorptive/well fed state after eating (more anabolism than catabolism)
o Insulin is a peptide hormone secreted by beta cells of pancreatic islets of Langerhans
o Insulin glycogen synthesis in liver/muscle; liver converts excess to FA/triacylglycerols
▪ Nervous tissue, beta cells, RBC’s = insensitive to insulin (nervous oxidizes
glucose to CO2 + water in well fed/normal state; RBC’s use glucose
anaerobically)
▪ Adipose/resting skeletal muscle require insulin for glucose uptake
▪ Insulin increases glucokinase/glycogen synthase (glycogenesis), decreases
glycogen phosphorylase/glucose 6 phosphatase (glycogenolysis)
● Counterregulatory hormones (to insulin): glucagon, cortisol, epinephrine, norepinephrine, GH
o Glucagon is peptide hormone secreted by alpha cells of islets of Langerhans
▪ Low blood glucose and amino acids promote secretion of glucagon
▪ Promotes pyruvate PEP conversion by pyruvate carboxylase and PEPCK,
promotes fructose 1,6 BP to fructose 6 P by fructose 1,6 bisphosphatase
● Flavoproteins are e- carriers derived from riboflavin (vitamin B2)
● Post absorptive (fasting) state – glycogenolysis (Immediate), hepatic gluconeogenesis (12 hr)
o Decrease in insulin AA from muscle and FA from adipose are released
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Prolonged fasting (starvation) state high glucagon/epinephrine, lipolysis makes acetyl coA for
synthesis of ketone bodies for brain, cells with mitochondria continue to depend on glucose
Glucocorticoids and catecholamines elevate blood glucose levels by mobilizing energy stores
Thyroid hormones increase basal metabolic rate
Well fed state: everything uses
glucose except cardiac muscle
Fasting: everything uses FA except
brain and RBC’s which use glucose
Roles of liver: maintain constant blood glucose, synthesize ketones when excess FA are oxidized
Glycogen/FA synthesis (released in blood as VLDL); lactate, glycerol, AA used for glucose
synthesis
● Elevated insulin = FA synthesis, low insulin = more HSL in fat cells release FA into blood
● Active muscle gets short lived energy (2-7 sec) from creatine phosphate (transfers P to ATP)
● Respiratory quotient = CO2 produced/O2 consumed; increase in mass increase in BMR
● Ghrelin increases appetite and produces orexin, orexin increases appetite and alertness
● Leptin is secreted by fat cells and decreases appetite by suppressing orexin; BMI = mass/height
Behavioral Sciences:
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∆𝐼
Weber’s Law (just noticeable difference)  𝐼 = 𝐾 ; I is initial stimulus intensity
Absolute threshold of sensation – minimum intensity needed to detect 50% of the time
o Subliminal – below this threshold, cannot detect 50% of the time
Semicircular canals detect positioning (proprioception), endolymph moves
o Utricle + saccule (otolithic organs) detect linear acceleration/head positioning (hair cells)
Bottom up processing (data driven) – stimulus influences perception, no preconceived ideas
o Top down processing (theory driven) – background knowledge influences perception
Rods detect light, located in periphery of retina; cones detect color in fovea (middle of retina)
All info from left visual field goes to right side of brain, nasal side info crosses chiasm
A delta fibers are fast (withdraw from hot stove), A beta fibers are medium (faster for fine touch,
slower for gross touch), C fibers are slow (lingering sense of pain)
Umami comes from glutamate, each taste bud has five receptors inside (one for each flavor)
Beta waves are for alertness (high frequency), alpha is daydreaming/light meditation/hypnosis,
theta is drowsiness/deep meditation
Sound wave hits outer visible part of ear (pinna), funneled into external auditory meatus, tympanic
membrane (eardrum) vibrates, hits incus, malleus, stapes, oval window vibrates, pushes fluid
inside cochlea to go around spiral
Retinal disparity and convergence are binocular cues
N1 N2 N3 N2 REM N1
o N1 is light sleep with hypnagogic hallucinations/hypnic jerks (theta waves)
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o N2 has K-complexes and sleep spindles which keep you asleep (theta)
o N3 has delta waves, sleep walking/talking
Activation synthesis hypothesis of dreaming interpreting random firing
Central sleep apnea (problem with brain = 5+ apneas/hour), obstructive apnea (problem with
airways (15+ per hour), problem to lungs = hypoventilation disorder
Depressants include alcohol and barbiturates like benzos (increase brain response to GABA)
Stimulants include amphetamines, cocaine, MDMA (ecstasy), nicotine, caffeine
Opiates = pain reducing depressants (increase endorphins), includes morphine, heroin, codeine
Hallucinogens increase dopamine and serotonin (body stops producing as much on its own leading
to withdrawal if you stop taking it)
Reward pathway: dopamine is produced in VTA and released during pleasurable experience
o Mesolimbic pathway (Hippo NAP): amygdala, hippocampus, nucleus accumbens (motor
control), prefrontal cortex; when dopamine goes up, serotonin goes down (satisfaction)
Cognitive behavior therapy – patients recognize bad thoughts, replace with coping strategies
Exogenous cues are things we don’t look for, endogenous require internal knowledge (cocktail)
Inattentional blindness – miss something while paying attention to something else; change
blindness is not noticing a change
Selective attention – focusing on certain info while ignoring other things
o Broadbent’s early selection theory (selective filter), Deutch late selection theory, Treisman’s
attenuation theory uses attenuator which weakens unimportant info
Spotlight model of attention and resource model (we have limited attention resources) say we are
not good at multitasking/divided attention
Sensory memory includes iconic (vision) and echoic (sound), echoic lasts longer
Working memory is what you are thinking in the moment (info processing)
Long term memory: explicit/declarative (semantic/episodic), implicit/nondeclarative (procedural)
Encoding through pneumonic devices and self-referencing is most effective
o Retrieval is pulling something from long term to working memory
o Free recall (without cues) is affected by serial position curve (primacy and recency)
Receiving misleading info after we encode can lead to retrieving false memories
o Source monitoring – keeping track of where info came from
Long term potentiation – connections between neurons strengthen
o Synaptic plasticity – ability of synapses to change their strength
Decay – neural connections becoming weaker over period of disuse
o Initial rate of forgetting is very high, levels off over time; faster rate of relearning
Retroactive interference – new piece of info impairs ability to remember something old
Proactive interference – old piece of info prevents you from learning something new
With age, episodic memory declines; implicit memory remains same; semantic memory, crystallized
intelligence (using experience), and emotional reasoning improves
Alzheimer’s results in amyloid plaques, Korsakoff’s results in memory loss/confabulation
Semantic network – concepts are organized in connected ideas
o Spreading activation – when you activate one concept, you pull up related concepts
PIAGET = 0-2 years sensorimotor stage: object permanence
o 2-7 years preoperational stage: egocentric, pretend play
o 7-11 years concrete operational: conservation, logic
o 12+ formal operational: abstract thinking
Assimilation is incorporating into old schemas, accommodation is changing schemas
Heuristic = mental shortcut; availability: examples from memory, representativeness: prototype
Belief perseverance - ignoring/rationalizing opposition, confirmation bias - seeking confirming facts
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Fluid intelligence – reasoning (decreases with age), crystallized = accumulated knowledge
Cognitive dissonance – discomfort from conflicting cognitions
Language/logic (+positive emotions) in left hemisphere which is usually dominant hemisphere
o Broca’s area is for speech (aphasia leads to broken speech)
o Wernicke’s area is for understanding speech (aphasia leads to trouble understanding)
o Both are connected by arcuate fasciculus (conduction aphasia cannot repeat things)
Universalism – thought determines language, Whorfian hypothesis – lang. determines thought
Nativist theory – innate ability to learn language through language acquisition device (LAD) during
critical/sensitive period, introduced by Chomsky
o Learning theory – language is acquired through reinforcement
o Interactionist theory – biological and social factors interact to learn language (Vygotsky)
Limbic system (HAT Hippo): thalamus = sensory relay station, hypothalamus = hormones for hunger,
thirst, sleep, sex; amygdala destroyed = Kluver Bucy: hypersexuality/no inhibitions
6 universal emotions (innate): happiness, sadness, anger, fear, disgust, surprise
James-Lange: event physiologic response interpretation of physiologic response emotion
o Canon-Bard: event physiologic response + emotion
o Schachter-Singer: event physio responseidentify event/response reasonemotion
Primary appraisal = initial evaluation, is this a threat? secondary = can I cope?
o General adaptation syndrome: alarm, resistance, exhaustion
Adrenal cortex releases cortisol, adrenal medulla releases catecholamines (epinephrine)
Brainstem: midbrain, pons, medulla (connect cerebrum to spinal cord, cerebellum is behind)
o Breathing, sleeping, heartbeat; reticular formation = alertness
o Cerebellum is voluntary movement, thalamus is sensory relay station
Afferent neurons carry info into CNS, efferent carry info away
o Motor unit is one lower motor neuron (efferent, PNS) and the skeletal muscle it contracts
▪ Upper motor neurons (in cerebral cortex) control LMN
Somatosensation: mechanoreceptors (touch), nociceptors (pain), thermoreceptors (temp)
o Brain hemisphere controls opposite side of body (contralateral), smell is ipsilateral
Sympathetic: short axon neuron in middle of spinal cord synapses with long axon neuron
Parasympathetic: long axon neuron in brainstem or bottom of spinal cord synapses w/ short axon
Frontal lobe has motor cortex and prefrontal (executive), parietal lobe has somatosensory cortex
and does spatial processing/orientation, occipital is vision and temporal is sound
o Broca’s = left frontal lobe, Wernicke’s = left parietal (right half is creativity, tone)
Basal ganglia – motor functions, cognition, emotion
Glutamate = excitatory, GABA/glycine = inhibitory, serotonin = sleep, dreams, mood, eating
Acetylcholine = voluntary muscle control in PNS, attention/arousal in CNS
o Sympathetic and para have acetylcholine in presynaptic neuron, para has it in post too
Norepinephrine functions in PNS (ANS), catecholamines are released from adrenal medulla
Dopamine is released from VTA/substantia nigra in midbrain, endorphins are painkillers
CAT/MRI = brain structure only, EEG = function (measures electrical activity of neurons), fMRI/PET
do both (fMRI measures active neurons using O2, PET measures neurons using glucose)
Rooting reflex = turning head toward something stroking cheek, Babinski = curling and uncurling
toes when bottom of foot is stroked, Moro = throwing arms out and bringing them back in (startle),
Palmar grasp = closing hand around object touching their palm
Epigenetics – adding something to gene to cause change/override DNA (like methylation)
Drive reduction – need/lack energizes a drive (aroused state) which reduces need
Optimum arousal theory – we want to reach full alertness which motivates us to do things
Maslow’s hierarchy of needs: physiological, safety (basic); love, self-esteem, self- actualization
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Incentive theory – rewarded after action, people are more likely to do positively received action
Lateral hypothalamus: hunger, ventromedial hypothalamus: full/stop, leptin: suppresses appetite
ABC model of attitude includes affect (emotion), behavior, cognition
Elaboration likelihood model (persuasion) central route = attitude change depends on quality of
argument, peripheral = superficial
Social psychology – how interactions shape behavior, (external situational attributions)
Libido: natural energy, id: unconscious immediate gratification, superego: morality, ego: mediator
o Life drive = eros, death drive = Thanatos
Humanistic theory – Rogers, people are good and motivated to self-actualize, self concept
o Biological theory – genes = personality
o Bandura social cognitive theory which includes attention, memory, imitation, motivation
o Behavioral theory – interaction with environment behavior (classical/operant)
o Trait theory uses patterns of behavior (traits) to describe personality (Big 5 = OCEAN)
Bobo doll = observational learning, learning performance distinction (can learn w/o doing)
Projection is attributing own thoughts to someone else, reaction formation is doing the opposite of
what you feel, sublimation is turning negative energy into positive
Personality disorders are outside cultural norms and cause distress in every day life: cluster A =
weird (paranoid, schizoid – emotionally detached, schizotypal – magical thinking), cluster B =
wild/emotional (anti social, borderline, narcissistic), cluster C = worried (avoidant, dependent, OCPD
- perfection/control over life, generalized anxiety disorder requires 6+ months in that state)
Dissociative disorders = abnormalities of identity/memory, multiple personalities
Schizophrenia = high dopamine, positive symptoms: delusions, negative: flat affect (lack emotion)
o Parkinson’s has low dopamine
Depression: decreased frontal lobe activity, increased limbic system activity
o Pessimistic attributional style (internal, stable, global); biopsychosocial model
o Bipolar I has full mania, may not have depressive episode; bipolar II has hypomania cycling
with depressive states
Somatic symptom – mental disorder manifests as physical symptoms, excessive worrying,
conversion disorder – neurological problems from traumatic event, unexplainable symptoms,
factitious disorder – patient wants to be sick
Informative influence – convinced, think group knows better; normative influence – not convinced
but go along with group to conform
Identification is going along with something/a group to be like a certain person, internalization is
conforming privately (integrating into own beliefs), compliance is agreeing but not convinced
Group polarization – group decision making amplifies original opinions, groupthink - when first
suggestion proposed by leader is adopted without considering outside opinions
Asch line experiment had perceived pressure to conform, Milgram study had teacher shocking
learner (compliance to authority if they take responsibility), Zimbardo prison study involved
internalizing roles, cognitive dissonance, situational effects, deindividuation
Ecological validity – mimics real world, demand characteristics - changing behavior to match what
you think is expected, Hawthorne effect - changing behavior due to being observed
Bystander effect increases with more people (diffusion of responsibility), deindividuation
Social facilitation: when you do better at familiar things, vice versa (social loafing = group work)
Folkways are common manners (no punishment), mores are moral (results in strong feelings)
Symbolic interactionist perspective – society is a product of interactions, primary deviance has few
consequences, secondary has lots; strain theory – people in difficult positions turn to deviance
Collective behavior: time limited, all can participate; group behavior: longer time, exclusive group
Shaping – gradually reinforcing behaviors that approximate target behavior, fixed action patterns
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Fixed ratio results in high rate of behavior, VR is strongest, FI has slower rate of response
Self concept – how someone thinks about themselves; includes existential self and categorical self
o Rogers is humanistic, believes self concept includes self image (what we believe we are), self
esteem (how much we value ourselves), and ideal self
o Self efficacy is the belief in one’s ability to succeed
Freud’s psychosexual development personality develops in early childhood
Erikson’s psychosocial development develop during lifetime, emphasized role of culture/society
Vygotsky’s sociocultural development
children learn actively
o Learn through interaction with
more knowledgeable other, zone
of proximal development is when
guidance should be given (includes what you can do at that age), info is transmitted via
language
Kohlberg’s moral development
o Preconventional: obedience vs punishment, self interest
o Conventional: societal norms, law and order
o Post conventional: social contract (law may not be right), universal ethical principles
Mead’s I and Me only certain people at certain times can influence our perception of ourselves
o Me = social self, how I believe others see me; I = response to social self, what I think about that
o Prep stage: imitation, play stage: pretend play, game stage: multiple roles, societal
expectations
Cooley: everyone we interact with influences our perception of self, looking glass self – our view of
ourselves comes from how we think we are being perceived by others
Covariation model of attribution: consistent = internal, distinctive and consensus = situational
o Fundamental attribution error is overattributing internal factors for others, self serving bias is
overattributing external factors to ourselves (both of these together is actor-observer bias)
Stereotype threat – people exposed to negative stereotypes surrounding a task have decreased
performance, stereotype = cognition, prejudice = affective/emotional, discrimination = action
Frustration aggression hypothesis – frustration may turn into aggression against minority groups
Hypothesis of relative deprivation – unrest when deprived of something you think you deserve
Halo effect – having a good overall impression makes you think everything about them is good
Just world hypothesis – rationalizes fortune/misfortune by overattributing internal causes
Ethnocentrism – judging own culture to be superior (in group favoritism/out group derogation)
o Cultural relativism – no right/wrong culture, all are different and valid
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Mere exposure effect – repeated exposure increases our liking for something
Retrograde amnesia = forgetting past; anterograde = things from past affect future memories
Harlow monkey experiment: monkey preferred contact comfort from cloth mother over wire
mother with food; served as a secure base where monkey could explore and return
Ainsworth (strange situation): secure attachment = explored, mother left (sad), returned (happy)
o secure: child is distressed when mother leaves, comforted upon her return
o ambivalent: child is distressed when mother leaves but not comforted when she returns
o avoidant: child doesn't care she left or when she returns
Reinforcement modeling – when parents deal with frustrating situations by yelling, child learns this
Altruism occurs due to kin selection, reciprocal altruism (so they help us), cost signaling (shows they
have resources, socially beneficial)
Emotional/esteem support, informational support = advice, tangible = $, material goods/ services
Ascribed status = born with it, does not change during life; achieved = earned by yourself
Role strain – pulled in different directions by one status, role conflict – between roles of 2+ statuses
Primary group: close, caring, not together for any purpose; secondary: temporary/formal, for a goal
Impression management/dramaturgy: multiple front stage selves depending on role, one
backstage
Individual discrimination is by one person, institutional could be intentional (law) or unintentional
Organizations have goals, utilitarian: members are paid for efforts (business, gov’t job, university),
normative: members have same purpose (religion); coercive = no choice, strict (prison, military)
Bureaucratization – laws increasing in organizations (iron rule of oligarchy: democracy few rulers)
o Characteristics: division of labor, hierarchy, written rules, impersonality (unbiased, equal
treatment), employment based on qualifications (peter principlepromoted until incompetent)
Mcdonalidization – policies governing fast food chains are implemented elsewhere (efficiency, etc)
Foraging behavior is determined by genetics/animal learning: solitary vs group foraging
(competition within group when resources are scarce but brings down large prey)
Macrosociology – large scale, affects populations; includes functionalism and conflict theory
o Functionalism – how societal institutions adapt/work together to keep society
stable/functioning
▪ Manifest functions are intended, latent functions are unintended
o Conflict theory – institutions benefit the powerful, create inequalities which are resolved
▪ Class consciousness = social unrest from realizing inequality
▪ False consciousness = unable to see oppression/exploitation
Microsociology – daily social interactions between people; includes symbolic interactionism
o Symbolic interactionism – different significance/meaning individuals assign to things/people
Social constructionism – we give things meaning through social agreement but these are not real
Capitalism = profit, private ownership, supply/demand market economy; socialism = common
ownership focused on human needs; functionalist = everyone has a responsibility/job in society
Medicalization is overdiagnosis, sick role, illness experience (how people cope with being sick)
Rational choice theory: people = rational, weight costs/benefits of actions to maximize personal
gain
o Actions can be ranked, follow transitive properties, alternative options do not change ranking
o Exchange theory: applied to social interactions (social approval encourages behavior, vice
versa)
Feminist theory is macro level, focuses on gender inequalities in patriarchal societies
Life course theory: aging is sociological, psychological, biological; no age based expectations?
Pluralism: encourages racial/ethnic dif; gender script (expectations), gender schema (stereotypes)
Growth rate = initial population + (births – deaths) + (immigration – emigration)
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o Fertility rate of 2 neither increases not decreases population size
Demographic transition – high birth/death rates to low birth/death rates (industrialization)
Globalization – interaction due to international trade, communication/transport/technology
advances
World systems theory: world functions as unit rather than individual countries, core countries are
more advanced while peripheral countries are not, semi periphery countries
o Modernization theory – all countries follow same path of development to become modern
o Dependency theory – periphery countries rely on core countries giving them power
Activist movements want to change an aspect of society, regressive are trying to resist change
Subculture is smaller community that distinguishes itself from larger society, microculture impacts
some aspects of peoples life during short periods of time, counterculture opposes dominant group
Culture lag: material culture changes faster than non material, culture shock (from unfamiliarity)
Horizontal movement – within same class, vertical movement – up/down social ladder
Caste system – position determined
by birth (no social mobility)
Class system – combination of
background and achievements
Meritocracy – based on abilities only
(lots of social mobility)
Intragenerational mobility is during
own lifetime, intergenerational is
across generations
Absolute poverty is a set line below
which survival is threatened, relative
poverty leads to exclusion for
society (if country grows richer,
absolute poverty line remains same
while relative poverty line increases)
Social reproduction – social inequality
replicates itself across generations
Social exclusion is not voluntary while social
isolation is
Intersectionality is experiencing
discrimination in multiple areas of life