Exam 2 Flashcards
Goldilocks of oral dose
Keep above minimum effective concentration but below toxicity level
Pharmacodynamics
What drug does to the body
Pharmacokinetics
What body does to the drug. ADME, absorption, distribution, metabolism, elimination
Absorption
Passage of drug molecules from admin site to the blood
Distribution
Passage of drug molecules from blood to tissues
Metabolism/biotransformation
Chemical mods of the molecule to typically make it more water-soluble and excreted
Elimination
Passage of molecules through the blood to the outside of the body via urine, bile, etc
Free drugs
Only the free drug can be moved around: no protein or plasma binding
Transport
Move molecules across concentration gradient. Both active and passive
Passive transport
Channel-mediated and carrier mediated with the concentration gradient
Active transport
Carrier protein. Against concentration gradient, requires ATP
Endocytosis
Requires ATP, bulk flow, moves in both directions
Filtration
Does not require ATP, moves with the gradient
Ionization: weak acid
Proton donor, easily absorbed/cross membranes from stomach: in an acidic environment
Ionization: weak base
Proton acceptor, not readily absorbed in stomach. Bases readily cross membranes in basic environment (increase stomach pH)
Ion trapping
Ability to trap compounds on one side of the membrane or if there is a pH gradient across the membrane (trapped in anionic form)
Henderson-Hasselbach
pH - pKa = log [nonprotonated]/[protonated]
HH for weak acids
A-/HA = [ionized]/[nonionized]
HH for weak bases
B/BH+ = [nonionized]/[ionized)
Ratio of protonated to nonprotonated in ionic trapping
Is the Rate limiting step. Ex: base in plasma (pH:7.4) is log 1, where in stomach (pH:1.4) is log 1/10^6
Ion trapping weak acids
Trapped in basic environments
Ion trapping weak bases
Trapped in acidic environments
Oral administration advantages
Easy, drug stable at room temp, cost, good patient compliance
Oral admin disadvantages
Destroyed in GI, 1st pass hepatic metabolism, variable rate, diet affects absorption rate
Bioavailability
How much drug makes it into the circulating plasma (absorption)
eqn: F = AUC.oral / AUC.iv where AUC is area under the curve and 0
Bioavailability of IV admin
100%
Things that affect drug distribution
1.) tissue perfusion rates
2.) plasma protein binding
3.) partitioning between plasma and tissues
Distribution: Perfusion Rate
Higher rate: faster equilibrium
Highest: kidney, liver, lung, brain
Intermediate: muscle
Slowest: adipose / fat tissue, bone
Distribution: plasma protein binding
Bound drugs are inert, do not cross membranes (ex. Albumin and a1-acid glycoprotein)
Albumin
Plasma protein that binds weak acids
a1-acid glycoprotein (AGP)
AGP binds many weak acids
Distribution: Plasma partitioning
Concentration of drug between plasma and tissue not equal from
1.) ion trapping
2.) tissue protein binding
3.) lipid solubility
Blood Brain Barrier
Tight endothelium junctions in capillary bed and glial cells. Astrocytes and glial cells also protect
VD : apparent volume of distribution
Total amount in body/ total concentration in a measured reference area (in L because g/g/L)
VD variation causes
1.) bodily accumulation of fat for lipid-soluble drugs
2.) accumulation of fluids for water-soluble drugs
VD increase/decrease
VD increase: things that cause drug to LEAVE plasma
VD decrease: things that cause drug to STAY IN plasma
Cofactor
Non-protein molecule that is a part of an enzymatic rxn. Organic material or metal ions.
Cofactors as substrates
Enzyme activity (particularly for apoenzymes) is dependent on cofactor concentration
Diet deficiency
Not enough of a cofactor or cofactor precursor in the diet (ex. Niacin, B12, etc)
Functional deficiency
No vitamin modification by cellular enzymes present OR inability of cofactor to bind to active site of enzyme
Prosthetic groups
Tightly, covalently bound cofactors to their enzymes: for lifetime of enzyme (ex. FAD). Cofactor modifications occur while still attached to enzyme
Transiently bound cofactor
Act like any other substrate or product. Bind for the rxn and release afterward. Separate rxn occurs to restore cofactor. (Ex. NAD for ADH)
Functions of redox reactions
1.) fuel oxidation: succinate dehydrogenase
2.) detoxification: alcohol dehydrogenase, cytochrome P450s
3.) biosynthesis: HMG CoA reductase
Redox potential
The willingness of molecules to accept electrons. Dictated by NERST eqn: deltaG0’ = -n F deltaE0’
Redox cofactors
NADH
NADPH
FAD(2H)
Ascorbic acid
Metals: Cu, Fe, etc
NADH and NADPH
Derived from niacin (B3 in diet). NADH is important for fuel oxidation. NADPH is important for biosynthesis and detoxification enzymes
Cytochrome P450s
Has NADPH as cofactor (and FAD, FMN, and Fe-heme) Fxn: add oxygen to chemicals to make them more soluble and easier to excrete
Cholesterol biosynthesis rate limiting step
NADPH oxidized by HMG-CoA reductase
Sources of Niacin (B3)
Meat, whole grains, fortified cereals, tryptophan (causes B6 deficiency)
Niacin deficiency
Causes: Pellegra Affects:
- pellegra - reliance on corn
- dermatitis - alcoholics
- diarrhea - sun exposed areas
- death
- glossitis
ADP Ribosylation
NAD+ is a substrate for enzymes that post-translationally modify arginine (glycosylation) residues on proteins. Nicotinamide is removed from NAD+ and the remaining portion is covalently linked to arginine.
- occurs by PARP1 when DNA is damaged and ADP ribosylation of histones initiates DNA repair
PARP1 inhibitors
Used in cancer treatments: cancer cells cannot signal repair for their DNA (ex. BRCA1 & BRCA2 genes)
Cholera toxin (CTA-1)
Uses NAD+ as substrate for ADP ribosylation of Arg AAs. This blocks GTPase activity resulting in constitutive activity (Cl- floods so H2O floods: diarrhea)
FMN and FAD
Derived from B2– riboflavin. Prosthetic groups for redox enzymes. They accept single e- (in the form of H) one at a time. They are involved in creating and destroying double bonds
Succinate dehydrogenase and FAD
FAD reduced to FAD(2H) by enzymes that convert single bonds to double bonds. TCA Cycle succ. Dehydrogenase does this
Dietary riboflavin, B2 (FAD and FMN)
Milk, eggs, organ meats, legumes, mushrooms
Riboflavin deficiency
- Cheilosis (mouth sores), and glossitis (swollen, beefy tongue)
- keratitis
- seborrheic dermatitis
- normochromic/normocytic anemia
- fatigue
Glutathione
Important antioxidant in cells, glutathione reductases use NADPH and FAD to transfer electrons to the sulfur atoms
Ascorbic acid (vitamin C) functions
A redox cofactor for
1.) hydroxylase enzymes (collagen synthesis, neurotransmitter synthesis, and oxygen sensing)
2.) a non-enzymatic anti-oxidant
Ascorbic radical
Vitamin C intermediate between L-ascorbate and Dehydro-L-ascorbic acid. Can gain/lose 2 e- which helps stabilize free radicals
Prolyl hydroxylases and Ascorbic acid
Vit. C is a redox cofactor helping w post-translational hydroxylation of lysine and proline for collagen synthesis
Lysyl hydroxylase and Ascorbic acid
Vit. C is redox cofactor. Post-trans mod hydroxylation of lysine and proline for collagen
Collagen
Important connective tissues. Every third AA is glycine, 3 collagen peptides form triple helix. Stabilized by hydrogen bonding of hydroxyproline and hydroxylysine
Ascorbic acid deficiency
Scurvy. Characterized by defects in connective tissue, slow wound healing, apathy, anemia, gingival lesions, petechiae, and enlargement of costochondral junctions
Metal electron conducting cofactors in redox rxns
Iron (Fe2+-> Fe3+) copper (Cu+-> Cu2+), cobalt (Co2+-> Co3+), manganese (Mn2+-> Mn3+), molybdenum (Mo4+-> Mo6+)
Activation transfer reactions
Move fxnal groups around
Examples: kinase, acyltransferase, acetyltransferase, aminotransferase, and pyrophosphatase
Kinase
Transfers phosphate group to and from ATP
Acyltransferase
Transfers carbon chains from one substrate to another *most common
Acetyltransferase
Transfers acetyl groups from one substrate to another
Aminotransferase
Transfers amine groups on amino acids
What other rxns do activation transfer reactions couple with?
Redox rxns, and lyase rxns
Pyruvate dehydrogenase complex
Links glycolysis with the TCA cycle and regulates the oxidation of carbon derived from glucose
Pyruvate dehydrogenase (PDH) and mitochondria
PDH is a gatekeeper that regulates glycolytic substrates’ complete oxidation in the mitochondria
PDH inactivated
Glucose is conserved and the TCA cycle is powered by fatty acid and amino acid catabolism
Multi subunit complex that catalyzes the oxidative decarboxylation of the three carbon Pyruvate
Pyruvate dehydrogenase
PDH complex rxn to create acetyl-CoA
-3 transfer and 2 redox cofactors
1.) decarboxylation (thiamine pyrophosphate)
2.) reduction and oxidation (FAD and NAD+)
3.) transfer acyl group (Lipoate and CoASH)
Thiamine pyrophosphate
TPP participates in decarboxylation rxns (including of Pyruvate, where the remaining 2 C covalently bond to TPP)
Thiamine
Vitamin B1 : meat, legumes, whole grains, fortified cereals. Heat labile
Phosphorylated to diphosphate form, and binds to decarboxylases creating an active apoenzyme
SLC19A transporter
Transports thiamine from diet into the cell
Thiamine deficiency occurs in what cases?
Malnutrition, alcoholism, and monotonous diet
Beriberi
Thiamine deficiency: headache, malaise, peripheral neuropathy, heart failure
Wet Beriberi
Cardiac problems
Dry beriberi
Neuropathy
Wernicke encephalopathy
Thiamine deficiency: confusion, AMS, nystagmus, ataxia
Karsokoff psychosis
Thiamine deficiency: amnesia, confabulation, evident in ~80% of people diagnosed with Wernicke
Thiamine responsive magaloblastic anemia syndrome
Inherited mutations in the thiamine transporter SLC19A2: anemia, deafness, non-type I diabetes
Lipoate
Forms covalent bond w lysine residue on transacylase subunits of alpha-keto acid dehydrogenase complexes
Cofactor for E2 subunit of pyruvate dehydrogenase
Accepts the 2 Cs from TPP and becomes lipoic acid
Lipoate in born errors
Epilepsy can occur. No deficiency ever seen
Coenzyme A (CoASH or CoA) action mechanism:
Covalently binds acyl groups through high energy thioester bond and transfers them
Coenzyme A dietary precursor
Pantothenic acid, B5 : no deficiency present
Coenzyme A and TCA cycle
Coenzyme A accepts the 2 Carbon acetates from lipoamide in PDH rxn to form acetyl CoA: used in TCA cycle
Biotin participates in what reactions?
Participate in carboxylation rxns.
Cofactor for: acetyl CoA carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, methylcrotinyl carboxylase
Acetyl CoA carboxylase
Fatty acid synthesis
Pyruvate carboxylase
Gluconeogenesis
Propionyl CoA carboxylase
Branched chain fatty acid metabolism
Methylcrotinyl CoA carboxylase
Branched chain amino acid metabolism
Biotin as a cofactor
Covalently bound to the app carboxylase to form a holocarboxylase
Biotin in the diet
Free or covalently bound to lysines in protein
Biotinidase
Removes free biotin from protein form
Biotin deficiency
From raw eggs: Avidin binds to biotin and makes in indigestible
Symptoms: scaly dermatitis, thinning hair, alopecia
Pyridoxal phosphate (PLP) function
A cofactor for enzymes that metabolize amino acids (ex. Transaminases)
Pyridoxal phosphate dietary precursors
Pyrodoxine, Pyridoxal, and Pyridoxamine. All considered vitamin B6 found in cereal, meat, bananas, etc
Phosphorylated by cellular kinases
Pyridoxal phosphate deficiency
Infants: seizures, diarrhea, EEG abnormalities
Adults: peripheral neuropathy
PLP as a cofactor
Converts tryptophan to niacin: double deficiency. The kynureninase requires PLP in trp —> niacin rxn
PLP Overdose
Symptoms: sensory neuropathy, ataxia
Pyridoxine oxidase deficiency/ antiquitin deficiency
Inborn errors of metabolism resulting in B6 deficiency symptoms in newborns
Cobalmin B12 functions
Transfers and rearranges methyl groups
2 forms in body: deoxyadenosylcobalmin and methylcobalmin
Methionine synthase cofactor
Methylcobalmin
Methylmalonyl CoA mutase cofactor
Adenosylcobalmin: essential for catabolism of branched chain AAs and fatty acids
Cobalmin B12 dietary groups
Produced by bacteria in animals. Animal products have B12. Vegans do not get B12
Cobalmin deficiency
Symptoms: Macrocyctic/megaloblastic anemia (failure to make nucleotides), weakness, fatigue, seizures, sensory defects, FTT
Homeostasis
Physiological control processes incorporating + and - feedback loops
Variability
Contributes to inter and intrapersonal differences in homeostasis
Homeostasis regulation steps
1.) detects changes in condition and operation
2.) control systems regulate responses
3.) mechanism to effect change in operational state
Physiological agonist
Effectors that work to return the system to the set point (return to homeostasis)
Physiological antagonist
Effectors that move conditions away from the set point
Negative feedback loop
Change in variable to return set point (homeostasis)
Positive feedback loop
Further from set point
Nested loop
When + amplifies a bigger - loop and vice versa
Mechanism for negative feedback loop
-stimulus changes variable
- sensor detects change and signals to controller
- controller activates/inactivated effector
-effector alters conditions so the variable is returned to set point
Mechanism for positive feedback loop
-change in variable to further change by the stimulus
- sensor detects change and signals controller
- controller activates/inactivates effector
- activated effectors alter conditions and the change is amplified
- regulator (required) stops the process
The 3 levels of control
Tissue, involuntary, and voluntary
Local homeostasis is maintained by:
Direct connections between tissue sensors and effectors
Info from local processes flows:
Up to a higher control system
The voluntary system receives:
Direct sensory input and info from lower centers
Voluntary system can directly and indirectly control effectors
Feedback
Positive and negative adjustment AFTER the regulated variable has changed
Feedforward
Adjustment occurs BEFORE changes in the regulated variable occur (ex HR before exam)
Autocrine signaling
The signal itself
Paracrine signaling
Signals nearby cells
Endocrine signaling
Signals distant cells via hormones secreted
Neurocrine signaling
Signal nearby OR distant cells via neurotransmission
Immune signaling
Inflammation during injury, etc
Translation
The conversion of info on RNA into proteins — in cytosol
64 3 nucleotide codons in mRNA encode 20 AAs
Direction of codon reading
5’ —> 3’ with the n-terminus containing AUG (met) for the start codon of translation
Stop codons
UAA, UAG, UGA
Reading frame
Starting the read at 5’ end either on the first, second, or third nucleotide causing frameshifting for formation of different polypeptide strands
Frameshift mutations
Insertion or deletion of nucleotides in anything besides multiples of 3
TRNA region that recognizes and binds to specific AA
Short, single stranded region on 3’ end of tRNA
Aminoacyl-tRNA synthetase
Recognize and attach correct AA to the tRNA covalently (different aa-tRNAs for each AA)
HIGH ENERGY BOND IN TRANSLATION
Synthetases use ATP hydrolysis to produce high energy bond between 3’ end of tRNA and AA: the energy of breaking this bond is used to link the AA covalently to the growing peptide chain
The two adapters that act one after another in translation
1.) Aminoacyl-transferase (couples AA and tRNA)
2.) tRNA molecule itself (anticodon forms base pair w appropriate codon on mRNA)
EPA sites
On ribosomes:
E: exit site
P: peptide bond (peptidyl-tRNA)
A: incoming site (aminoacyl-tRNA)
Prokaryotic ribosome
70s
^
50s 30s
^ ^
5s 23s 16s
Eukaryotic ribosome
80s
^
60s 40s
^ ^
5s 28s 5.8s 18s
Start of protein synthesis
-AUG (met) typically removed by protease later
- eukaryote: initiator tRNA loaded into small subunit (eIFs)
- small subunit binds to 5’ end of mRNA (recognized by 5’ cap bound to eIF4E and eIF4G)
- AUG found: initiation factors disperse, larger ribosomal unit binds
- tRNA occupies P-site
- A site available and ready for aminoacyl-tRNA
Shine Delgarno sequence
5’ AGGAGGU 3’ forms base pairs with the RNA 16S subunit in order to position the AUG start codon
Elongation factors for prokaryotes
EF-Tu and EF-G
Elongation factors for eukaryotes
eEF-1 and eEF-2
What do elongation factors do?
Speed up processes but also cause 2 pauses between codon-anticodon base pairing and peptide elongation to remove incorrectly bound tRNAs before they are added to the chain
Protein release factors: termination
Bind to ribosome w/ stop codon in the A site and this binding forces peptidyl transferase to add a water molecule instead of an AA to the peptidal-tRNA which frees the carboxyl end from its attachments to tRNA and the chain floats into cytoplasm & ribosome units are released
Tetracycline
Antibiotic: blocks binding of amino acyl-tRNA to the A site of the ribosome. Small ribosomal unit
Streptomycin
Antibiotic: prevents the transition from translation initiation to chain elongation and also causes miscoding. Small ribosomal subunit
Chloramphenicol
Antibiotic: Blocks the peptidyl transferase rxn on ribosome. Large ribosomal subunit
Erythromycin
Antibiotic: Blocks the exit channel of the ribosome and thereby inhibits elongation of the peptide chain. Large ribosomal unit
Rifamycin
Antibiotic:blocks initiation of RNA chains by binding to RNA polymerase (prevents RNA synthesis).
Presumptive diagnosis
Differential, vague
Definitive diagnosis
Specific: identifies causative microorganisms using diagnostic tests
Empiric treatment
Common, treats many diseases only okay
Definitive treatments
Specific: treats specific disease and targets specific organism
The gram stain
1.) heat fixed smear: all cells purple
2.) add iodine solution: all cells purple and fixes the gram + purple color
3.) decolonize w alcohol: gram + cells purple, gram - cells colorless
4.) counterstain w safranin: gram + cells purple, gram - cells pink/red
Antony Can Leeuwenhoek
1684: created first magnifying glass which had 200x magnification
Robert Hooke
1665: first to visualize bacteria in book minute bodies
Louis Pasteur
Work against spontaneous generation led to the development for controlling the growth of microorganisms. Sterile broth vs broth exposed to the air
Spontaneous generation
Hypothesis that live can generate from non-living matter
Robert Koch
-Germ Theory of Disease
- Koch’s postulates:
1.) the suspected pathogen must be present in ALL cases of disease and absent from healthy animals
2.) the suspected pathogen must be grown in pure culture
3.) cells from pure culture of pathogen must infect healthy animal
4.) pathogen must be reisolated and be the same as the original
Fredrick Griffith
1928: proved DNA is heritable w experiment w rough strain (non virulent) and smooth strain (virulent) disease
Virulence
The ability for microorganism to cause disease. Degree of pathology caused by organism (ex: toxins, surface coats, receptors, etc)
Mechanism of bacterial disease
1.) Toxin production: bacteria released toxin that causes illness
2.) host immune response
3.) bacterial proliferation and invasion
Mechanism of viral disease
1.) cytopathic effect: affects normal cell physiology
2.) host immune response
3.) tumorgenesis
Bioenergetics
Differences in potential energy between substrates and products of a rxn
Kinetics
The speed at which a rxn occurs — substrates converted to products
Enzymes:
Increase speed of rxn — do not alter bioenergetics
DeltaG
Release of free energy of the system.
DeltaG = deltaH - T•deltaS
DeltaH < 0
Exothermic, gives off heat/energy
DeltaH > 0
Endothermic, absorbs heat/energy
DeltaS
Entropy: amount of disorder
S >0 order decreases
S <0 order increases
Michaelis-Meten eqn
V= Vmax [S]/ Km + [S]
• measure the effects of pH
• compare different isoforms
• measure PTMs
• identify potency
Enzyme kinetics are dependent on pH because
1.) the ionization of AAs at the active site is dependent on pH
2.) some enzymes use protons (H+) as substrates or products
Lineweaver Burke
Creates linear model of michaelis Menten eqn
Competitive inhibitors
Increase the Km, Vmax unchanged
- adding more substrate will outcompete the competitor
Km
The concentration of substrate required to permit the enzyme to achieve half Vmax
Non competitive inhibitors
Lower Vmax, permanent, does not change Km
- no amount of additional substrate will fix this
Allosteric regulations
-taut (T) or relaxed (R) conformations
- inhibitors or activators bind at allosteric site and alter enzymes conformation and activity
Taut conformation
-tense, does not want to bind, low affinity for binding
Relaxed conformation
Binds substrate more readily, higher affinity
Activators of allosteric regulation
Make the curve more hyperbolic and reaches v max more quickly (left shift)
Inhibitors of allosteric regulation
Flattens the sigmoidal curve (right side U) (right shift)
Pasteurization
Process of using precisely controlled heat to reduce microbial load in heat sensitive liquids: does not sterilize
Nonionizing radiation
Causes abnormal bonds, thymine dimers are most common: 240-280nm is most lethal
Confidence intervals
CI = p +/- (coefficient)•SE
Coefficient of 95%: 1.96
Coefficient of 99%: 2.58
Membrane functions
•establish specialized environments
•scaffold to organize biochem rxns
•semi-permeable barrier (ion gradient)
•transport
Membrane organization is driven by what?
Amphipathic nature of phospholipids
Mobility types of membrane phospholipids
Lateral diffusion, flexion, rotation
- flip-flop is rare
Three major groups of membrane proteins:
• receptors
• transporters
• enzymes
Cytosolic leaflet
Faces the cytoplasm
Non-cytosolic leaflet
Faces the lumen (inside) of an organelle, or extra cellular environment (plasma membrane)
Phosphatidylserine
Negatively charged, affects electrochemical features of the membrane. Fxns include: apoptosis and blood clotting
*** concentrated in the cytosolic leaflet
Sphingomyelin
Enriched lipid rafts, can be GLYCOSYLATED to form glycolipids. Fxns include: cell identity, adhesion, and protection
*** extracellular space, on non-cytosolic leaflet
Gangliosides
- made from sphingomyelin
- prominently in neurons
- over accumulation= toxic to neurons
Ganglioside GM1
Cell surface receptor for bacterial toxin that causes cholera diarrhea (continuous Cl- flow)
Cholesterol
Interacts w fatty acid tails and modulates bilayer characteristics. Changes: fluidity, thickness, compressibility, water penetration, and intrinsic curvature
Phosphatidylinositol
EXTREMELY IMPORTANT:
1.) cell signaling pathways
2.) imparting organelle membrane identities
Turtle: inositol positions 3,4,5 can be Phosphorylated, where C1 holds onto diester phosphate linkage
Phosphotidylinositol functions
• cell signaling
• Ca2+ regulation
• enzyme activation
• gene regulation
• membrane identification
• seeding biochem rxns
Cardiolipin
Unique dimeric phospholipid w 4 fatty acyl chains in mitochondria — Fxns: chemiosmatic events associated w oxidative phosphorylation
Lipid rafts
Special membrane domains w a concentration of specific lipids and proteins. (Sphingolipids). Fxns: transport vesicle formation and signal transduction
Caveolae
Curved membrane domains— special lipid raft. Phospholipids w cholesterol + sphingolipids + CAV1 (caveolin)
Fxns: signal transduction, regulation of metabolism, reservoir membrane, and cancer
Membrane lipids formed in the ER
• Phosphotidylinositol
• phosphatidylserine
• phosphatidylcholine
• phosphatidylethanolamine
• cholesterol
Membrane lipids formed in the ER & Golgi A
• sphingomyelin
• glycolipids
Lipid membranes formed in mitochondria
Cardiolipin
The enzymes that assemble phospholipids are located on the:
Cyotplasmic surface of the ER membrane
Flippases
Translocate phospholipids from non-cytosolic to cytosolic
Floppases
Translocate phospholipids from cytosolic to non-cytosolic
Scramblases
Randomly flip phospholipids between leaflets
Fxns of phosphatidylserine on the non-cytosolic leaflet of plasma membranes: platelets
Platelets: externalized PS= platform where coagulation factors assemble
Fxns of phosphatidylserine on the non-cytosolic leaflet of plasma membranes: apoptotic cells
Apoptotic cells: externalized PS = EAT ME signal for phagocytic cells
Glycosylation and lipid membranes
• enzymes that glycosylate are in the ER LUMEN
• oligosaccharide chains are modified in golgi A
• Fxns: receptors, cell-cell recognition, modulating membrane stability
Where are sugars and oligosaccharides of glycolipids/proteins present?
SURFACE OF THE MEMBRANE
Integral membrane proteins
Anchored in lipid bilayer:
1.) polypeptide chain embedded/transversing membrane
2.) covalently bonded to lipid bilayer
Peripheral membrane protein
Associate w integral membrane proteins/ membrane lipids. Are easy to displace
Lipid modifications that anchor integral membrane proteins
1.) glycosylphosphatidylinositol anchors (GPI anchors)
2.) prenylation (farnesylation or geranyl-geranylation) include RAS superfamily of small G-proteins
RAS small G-proteins
Important regulators of cell division and cytoskeletal organization
Functions of glycoproteins
• modulation of membrane surface properties
• cell identification
• cell adhesion
Glycosylation
Glycosylation occurs in ER and modified by Golgi A
Glycocalyx function
Protection
- found commonly in intestinal epithelial cells
Membrane damaging conditions
Ca2+ serves as trigger to initiate repair mechanisms
RER function
• synthesis of integral membrane, luminal, and secreted proteins
• lipid synthesis
• Ca2+ signaling
SER function
• lipid synthesis (Steroids)
• detoxification rxns
• Ca2+ signaling
Vesicular transport
ER—>Golgi A—>lysosome—>plasma membrane
Signal Recognition Particles (SRPs)
Recognize polypeptides by their signal sequence, and bind to ribo-mRNA-polyp SRP complex to bring PP into ER
Lumenal proteins
Signal sequence is hydrophobic, gets immobilized in bilayer. Protein gets released into ER LUMEN and signal sequence is degraded.
Integral membrane proteins
Start/stop transfer sequence also immobilized in bilayer. Finished protein + sequence released into plane of MEMBRANE by lateral opening of transport complex
Glycosylation: N-linked and O-linked
N-linked: asparagine via Nitrogen (most common) in the ER
O-linked: serine and threonine via Oxygen in the Golgi A at the surface. sometimes ER
Chaperone proteins BiP/GRP78
Help proteins fold correctly
ERAD
ER-associated protein degradation. Proteins deglycosylated, ubiquitinated, and targeted by PROTEASOMES for destruction
Protein misfolding diseases
• Alzheimer’s disease
• Parkinson’s disease
• Huntington’s disease
• Cystic fibrosis
• Gaucher’s disease
• Creutzfeldt Jakob disease
unfolded protein response (UPR)
UPR- ATF6, IRE1, and PERK draw out BiP from its original position (keeping proteins inactive) which activates proteins and the UPR — Triggering ERAD
Remediation of protein misfolding
1.) suppresses overall translation except genes involved in the UPR to reduce processing load
2.) Increases the expression of chaperones, other folding mediators, and proteins of the ERAD system
3.) if not corrected UPR primes cells for apoptosis and autophagy 
MAMs
Mitochondrial associated membranes, specialized areas of ER – mitochondrial apposition involved in mutual lipid and ca2+ metabolism and signaling
SERCA (sarco-ER calcium ATPase)
Pumps Ca2+ out of the cytoplasm and into the ER lumen
IP3-gated and RyR channels
Open to release calcium into the cytosol under appropriate stimulation for multiple cell responses
Malignant hyperthermia
Mutation in RyRs that pump calcium out of ER. The ATP hydrolysis to pump calcium back into ER (out of cytosol) raise body temperature to fatal levels
Detoxification
— mostly in SER
— cytochrome p450
— oxidizing enzymes, make compound more hydrophilic so they enter bloodstream
— liver cells have good SER detox system
ER Stress diseases
Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis, type two diabetes, atherosclerosis, nonalcoholic fatty liver disease, HCV, HPV, alcoholic liver disease, cancer
CHOP
A transcription factor upregulated by the UPR that promotes apoptosis
Golgi apparatus function
• Modifies N- linked glycoproteins received from the ER
• Glycosylated O-linked glycoproteins and proteoglycans
• Participates in sphingomyelin and glycolipid synthesis
• Sorts and packages material for transport
COP- coat protein complex
Protein complexes involved in the secular trafficking 
COP-II
ER —> Golgi. including: Sar1
COP-I
Golgi—> ER. Including: Arf
KDEL sequence - brings proteins back to ER that shouldn’t have left
Monomeric G-proteins
• can bind GTP or GDP
• Have inherent GTPase activity
• Function as switches, ON when bound to GTP, OFF when bound to GDP

Rho family
Cytoskeleton G-proteins
Ran family
Nuclear transport G-proteins. Regulates directionality of nuclear-cytoplasmic transport
RAS family
Cell division, G-proteins
Sar/Arf and Rab family
Membrane trafficking G-proteins
GEF: Guanine nucleotide exchange factor
Turns G-proteins ON by exchanging GDP for GTP
GAP: GTPase Activating protein
Turns G-protein OFF by activating the GTPase activity, resulting in the hydrolysis of GTP—>GDP
GDI: Guanine dissociation inhibitor
Inhibits GDP dissociation, keeping a G-protein turned OFF
Processing events in Golgi A
1.) Oligosaccharide modification of N-linked glycol proteins made in the ER
2.) Formation of proteoglycans through O-linked glycosylation
3.) Addition of a phosphorylated mannose tag (M6P) to proteolytic enzymes destined for lysosomes
GAGs
Glycosaminoglycan: Long, unbranched polysaccharides with a repeating disaccharide structure. They help make up proteoglycans
COG: Conserved oligomeric Golgi
Keep different components of the glycosylation machinery and their correct cis-to-trans locations. Ensures correct sequence of glycosylation rxns
COG mutations (CDGs)
• severe neurological impairment
• Liver and muscle dysfunction
• infant lethality 
All bacteria have:
1.) cell membrane
2.) chromosome or nucleiod
3.) ribosomes
4.) cytoplasm
Two major systems for disposal in cells
Proteasomes and lysosomes
Lysosome:
Polymorphic membrane-enclosed compartments that are filled with hydrolytic enzymes and substrates in the process of being digested
Proteasomes
Digest protein molecule by molecule
Endocytosis
Primarily extracellular material taken up by the cell
Autophagy
Includes parts of the cell itself, from individual molecules and macromolecular arrays, to organelles and volumes of cytoplasm
Lysosomes contain about 40 enzymes:
Proteases, nucleases, glycosidases, lipases, phospholipases, phosphatases, and sulfatases
Acid hydrolases:
What make up Lysosomes, maximally active at low pH of 4.5-5.0
Specializations of the lysosomal membrane:
• lysosomal membrane proteins are highly glycosylated for protection
• Contain proton pumps (H+ ATPases) to create an acidic lumen for maximal activation of the acid hydrolases
• contain numerous transporters to shuttle material past the membrane in both directions (Substrates in, products out)
MP6 receptors in the trans Golgi concentrate what?
Lysosomal enzymes into vesicles
What does endocytosis use to digest?
1.) Pinocytosis
2.) receptor-mediated endocytosis
3.) chaperone-mediated autophagy
What does Autophagy use to digest?
1.) macroautophagy
2.) microautophagy
3.) chaperone-mediated autophagy
Pinocytosis (cell drinking)
Constitutive non-specific endocytosis that internalizes extracellular fluid and plasma membrane via small uncoated vesicles
Receptor-mediated endocytosis
Receptor-ligand binding and internalization of specific cargo molecules
Phagocytosis
Engulfment of large particles (bacteria, dead cells,etc) into large specialized and dissolves called phagosomes
Responsible for plasma membrane turnover and renewal. The entire area of plasma membrane engulfed every 30 to 60 minutes in some cells
Pinocytosis
Macropinocytosis
Engulfment of larger volumes via extensions of cytoplasm that fold over and fuse, entrapping extracellular fluid and associated material
Where is Pinocyted material routed to for lysosomal digestion?
Endosomes
Receptor-mediated endocytosis
Employs receptor-ligand interactions at plasma membrane to internalize SPECIFIC molecules
Clathrin
A coat protein similar to COPI and COPII, helps drive vesicle formation. Removal of coat helps vesicles fuse with target membrane
Triskelions
Formed by clathrin, self-assemble to form basket-like cage around forming vesicles
Steps in clathrin vesicle formation
1.) receptors bind to their specific ligands (cargo)
2.) Adapter proteins bind receptor-ligand complexes
3.) clathrin assembles onto the adapter proteins, deforming the membrane informing a coated pit
4.) vesicle invaginates as more clathrin added, DYNAMIN protein pinches off neck of vesicle
5.) uncoating ATPases remove clathrin coat, vesicle can fuse w target membranes
Hsp70 family
Uncoating ATPases
Familial hypercholesterolemia (FH)
Mutations in LDLR receptor for LDL particles or in apoplipoprotein B (ligand for LDLR)  Resulting in high circulating LDL/cholesterol levels
Endosomes
Collection of irregular and dynamic membrane bound compartments that receive both plasma membrane derived vesicles filled with endocided material and vesicles filled with acid hydrolases from Golgi a
Endosomes can be functionally subdivided into:
1.) early and recycling Endosomes
2.) late Endosomes/multivesicular bodies 
What can fuse with Endosomes?
• Receptor-mediated endocytotic vesicles
• Pinocytotic vesicles
• caveolae-originating vesicles
• macropinosomes
Transcytosis
Transfer of endocytosed material across the cell, which is then released, essentially unmodified, through exocytosis
Sorting signal for proteins to be degraded in lysosomes
Ubiquination
Intraluminal vesicles
Ubiquinated Cytoplasmic material can bind to specific endosomal subdomains causing INWARD pinch to form cargo-containing vesicles
ILVs transform Endosome regions into:
Multivesicular body (MVB)
ESCRT complexes
Endosomal sorting complexes required for transport: function to invaginate and endosomal membranes inward to form ILV’s within the lumen of the endosome
PH change during lysosomal maturation
PH decreases to 4.5 for acid hydrolase activity optimization
Phagosome
Formed by the formation of cytoplasmic extensions called pseudopods over the material desired
Process is driven by the actin cytoskeleton
Phagolysosome
When phagosomes fuse with lysosomes for digestion
Two classes of specialized phagocytes
Macrophages and neutrophils
Macroautophagy
Refers to self eating. The process by which a cell turns over its own components. Survival mechanism
Microautophagy
Formation and internalization of vesicles formed by invaginating lysosome membranes that entrap cytoplasmic material to be digested
Chaperone-mediated autophagy
Individual molecules in the cytoplasm can be transferred through the lysosome membrane to be digested.
Proteins are denatured by chaperones so they can be spooled through membrane transporters
Autophagosome
Formed by Cisterna of ER to wrap around an engulf material to be disposed. This double-membrane-bound structure than fuses with a lysosome
COP and Clathrin
 COP involved in trafficking between ER and Golgi. Clathrin is involved in receptor mediated endocytosis and lysosomal trafficking.
Both are protein coats required to be removed diffused with target membranes
Constitutive secretion
Vesicle contents not specifically segregated or concentrated by the Golgi, are released continuously in small vesicles.
Vesicle membrane itself is important cargo in terms of replenishing the plasma membrane
Regulated secretion
Secretary granules accumulate in cells and the granule content is released by exocytosis upon appropriate stimulation. 
Used for bio active compounds necessary for cell and tissue function
Exosomes
Released by ILVs outside of the cell by exocytosis of MVBs
What do exosomes do?
Signal and influence the behavior of other cells. 
Exosomes released from cancer cells can interact with potential metastatic tissue sites to make colonization by circulating tumor cells more likely
Microvesicle formation:
A direct outpouching and pinching off of cytoplasm-containing vesicles from the plasma membrane
Exosomes and mircovesicles may:
• fuse with plasma membrane of a target cell
• Be endocytosed by a target cell. Both endocytosis and fusion release vesicle contents into recipient cell cytoplasm
• bind to the target cell surface
• Open to release their contents in the extracellular environment

Function of microvesicles
Intercellular communication: which can include transfer of membrane, cytosolic proteins, lipids, and RNA
Phosphatidylinositol lipid markers
Marks organelles and membrane domains. This helps determine which adapter proteins bind to which cargo receptors throughout the endocytic and secretary pathways 
PI(4,5)P2 binds:
Adapter AP2
AP2 binds:
Cargo receptors
Assembles on PIP2-cargo receptor-AP2 complex and vesicle formation is initiated
Clathrin
RAB G-proteins
Regulate the motility and directionality of vesicle trafficking
V-SNARES and t-SNARES
Bind at the target site and wind around each other to draw vesicle and target membranes close enough to drive fusion
Where does intracytoplasmic vesicle transport take place?
Along tracks of microtubules
SNARE proteins
Mediate the final recognition and fusion of cargo carrying vesicles with target membranes/organelles
Lipofuscin granules
Indigestible residues from lysosomal activity that accumulate in the cell. Promoted by accumulation of glycosphingolipids
Age/wear and tear pigments
Fenton rxns
Production of reactive oxygen species (ROS) from iron ions concentrated in lipofuscin granules
Ferroptosis
A type of cell death triggered by ROS generation due to the buildup of iron ions.
Neurons are particularly sensitive to this process
Lysosomal storage diseases (LSDs)
Caused by genetic defects that affect one or more lysosomal hydrolases.
Results in the accumulation of undigested substrates in the lysosomes with severe pathological consequences, most often in the nervous system
I-cell disease (mucolipidosis II)
Autosomal recessive disorder resulting in a Deficiency in phosphotransferase activity, preventing M6–>M6P. Leads to the failure to route almost ALL lysosomal enzymes to lysosomes.
Mitochondria
• double membrane bound
• Inner membrane thrown into folds or tubules called cristae
• electron transport chain located on inner membrane 
Mitochondrial matrix contains:
Mitochondrial DNA, ribosomes, proteins and enzymes that facilitate the citric acid, urea cycles, and beta oxidation
Fission and fusion
Mitochondria continually undergo fission and fusion, which is necessary for optimal functioning.
Fission/fusion state
Depends in part on the respiratory activity of the mitochondria
Mitophagy
Autophagy of damaged mitochondria
Microtubules in mitochondria
Help organize mitochondria within the cell. And helps coupling with the ER
Location of mitochondria
Generally localized to where ATP is needed.
Muscle fibers, sperm flagellar anoxeme, salivatory glands, etc.
GRP75
Glucose regulated proteins
IP3R
Inositol triphosphate receptor
mCU
Mitochondrial calcium uniporter
MFN
Mitofusin 
MAMs Ca2+ transfer
Calcium from the ER to the mitochondria occurs at MAM‘s, via A linkage between ER inositol triphosphate receptor, and mitochondrial voltage dependent anion channel (VDAC)
MAMs phospholipid exchange
Phospholipid exchange proteins (PEPs) mediate exchange of membrane lipids between ER and mitochondria.  this is how mitochondria gets most membrane lipids, except cardiolipin
Mitochondrial genome
A circular chromosome containing about 40 genes. Includes 413 proteins that are important for the electron transport chain.
OXPHOS genes in mitochondria help with immediate transcriptional responsiveness to redox state of mitochondria
Heteroplasmy
Each mitochondrion contains multiple chromosome copies, so some of these copies may exhibit mutations but not all of them.
The more heteroplasmy, the worse the disease
Mitochondrial inheritance
Maternal in humans, resulting from the fact that sperm mitochondria degenerate after fertilization
Mitochondrial biogenesis
Input of two genetic systems: the mitochondrial and nuclear genomes.
Proteins encoded by mitochondrial genome are made in the mitochondrial matrix and then transported to correct location
Translocator complexes
TOM: trance locator of the outer mitochondrial membrane
TIM: translocator of the inner mitochondrial membrane
OXA: cytochrome oxidase assembly trans locator. Transports proteins synthesized in the matrix into the inner mitochondrial membrane
Anterograde signaling for mitochondria
Signals from nucleus—> Mitochondria
Mainly depends on nuclear-encoded transcription factors
Retrograde signaling in mitochondria
Signals from mitochondria—> Nucleus
This happens in response to perturbations within mitochondria such as proteostasis stress, ROS production increases, and energy deficiencies
Mitochondrial nuclear communication and aging
Mitochondrial DNA is more prone to damage and mutation, resulting in positive feedback loop where increased mitochondria damage leads to more ROS which leads to more damage. This place is central role in aging
Peroxisome
Involved in a variety of oxidation reactions, including the production and removal of hydrogen peroxide
Fxns include:
• Detoxification reactions
• Formation of myelin phospholipids
• breakdown of very long chain fatty acids and branched chain fatty acids (VLCFAs and BCFAs)
Specialized regions of chromosomes
1.) telomeres
2.) Origins of replication
3.) Centromere
4.) Heterochromatin
5.) Euchromatin
6.) Nucleolar organizing region
7.) Matrix attachment regions
Chromosome location
Chromosomes tend to occupy discreet territories in the nucleus.
Active regions of chromosomes can move to preferred nuclear locations during transcription
Fibrillarin
A component of snoRNPs and nucleoli
Nuclear speckles
Enriched in pre-mRNA splicing factors
Coilin
A component of cajal bodies
Nuclear pore complex
A few thousand pores per nucleus. Each pore is comprised of about 30 nucleoporins. Pores are semi-permeable 
• 5000 Da or less = Freely permeable
• Between 5000 and 60,000 Da = Permeable but at a slower rate
• Over 60,000 Da = Not freely permeable, must be actively transported

Determining directionality of nuclear cytoplasmic transport
Increase GDP and GAPs = cytosol
Increased GTP and GEFs = nucleus
RAN family G-proteins
LINC
Linker of nucleoskeleton and cytoskeleton
Adapter proteins (vincullin, talin) and integrins (IMPs) 
Physically connect the acting cytoskeleton to the extracellular matrix
Nuclear lamina
Underlays the nuclear envelope. A meshwork of filament serving as a physical support, and may also participate in regulating gene expression.
SUN/ Nesprin proteins
Connect the nucleus and cytoskeleton by binding to each other and spanning both the inner and outer membranes of the nuclear envelope.
 Nuclear plasmic portion binds to lamins, and cytoplasmic portion binds to microtubules in actin cytoskeletal elements
Mitchondria and ER linkage
Ca2+ dynamics
Nucleolus
A large aggregate of macromolecules including:
- rRNA genes
- precursor and mature RNA
-snoRNA
- ribosomal proteins
- partially assembled ribosomes
Imported nuclear proteins must:
Bind important receptors in the presence of GDP, and dissociate in the presence of GTP
Exported nuclear proteins must:
Bind export receptors in the presence of GTP and dissociate in the presence of GDP
Bayer
Developed sulfonamides. First antimicrobial material
Alexander Fleming
Created penicillin
Antibacterial spectrum
Range of activity of an antimicrobial against bacteria
Antimicrobial chemotherapy
The use of chemotherapeutic drugs to control infection
Antimicrobials
All inclusive term for an antimicrobial drug, regardless of what type of microorganism it targets
Bacteriacidal antibiotic
Antibiotic that kills bacteria
Bacteriostatic antibiotic
Antibiotic that inhibits the growth of bacteria but does not kill
Beta- lactamase
An enzyme that hydrolyzes the beta lactam ring in the beta lactam class of antibiotics, inactivating the antibiotic. Penicillincillinases, cephalosporinases, carbapenemases
Broad spectrum
Antibacterial drug that can inhibit a variety of gram-positive and gram-negative bacteria
Definitive therapy
Used to treat a patient where the micro organism has been identified
Empiric therapy
Used to treat a symptomatic patient where are the microorganism causing infection has not been identified
Minimum inhibitory concentration MIC
Determined by exposing a standardized suspension of bacteria to a series of anti-microbial delusions. The lowest antibiotic concentration that inhibits the growth of the bacteria is the MIC 
Narrow spectrum
Anti-bacterial drug that is active against a limited variety of bacteria
Prophylaxis
Use of a drug to prevent eminent infection of a person at risk
Suppressive therapy
After initial disease is controlled, therapy is continued to prevent recurrence
Kirby Bauer test
1.) inoculate plate with a liquid culture of a test organism
2.) Disks containing antimicrobial agents are placed on the surface
3.) Incubate for 24 to 48 hours
4.) Test organism shows susceptibility to some agents, indicated by inhibition of bacterial growth around discs
Zone of inhibition
Zone around antimicrobial disk in a Kirby Bauer test that shows susceptibility versus resistance
Selective toxicity
The ability to inhibit or kill a pathogen without affecting the host
Drug spectrum of activity
The narrow or extended ranges of a drugs ability to be an antibiotic effectively
Preemptive
Lab test indicate organism is present, but patient is not symptomatic
Problems with microbiota
Potential pathogen resistant to drug but held in check by other microbes. Drug destroys beneficial biota, and pathogen takes over
Two faces of drug distribution
1.) drug distributes to tissues with hyperfusion rates
2.) The drug later distributes to tissues with low perfusion rates. The drug is still present in the body, but it can’t be used
Areas in the body with high perfusion
Liver, kidney, heart
Areas in the body with low perfusion
Fat, muscle
Biotransformation
The chemical modification of compounds, typically to make them more polar, in order to activate and inactivate drugs 
Primary and secondary sources of biotransformation
Primary is the liver
Secondary is the G.I. tract
Third is kidney, followed by lungs and skin
Phase 1 reactions Biotransformation
• Add or expose functional groups
• oxidation most common reaction
Cytochrome P450s
Terminal oxidases, metabolize 75% of known drugs
Key CYPs: CYP3A, CYP2D6, CYP2C
Localized to smooth endoplasmic reticulum
Substances that induce cytochrome P450
• Saint johns wort (CYP3A4)
• Ethanol (CYP2E1)
• Cigarette smoking (CYP1A1,1A2,2E1)
• Antidepressants, antipsychotics
Substances that inhibit cytochrome P450
• grapefruit juice (CYP3A4)
• Drug-drug interactions
• pharmacogenomics 
Individuals as metabolizers
Ultra rapid metabolizer, extensive metabolizer, intermediate metabolizer, poor metabolizer
Biotransformation phase 2 reactions
Less reactive, conjugation with charged species. Glucuronidation Is most common, followed Acetylation, sulfate conjugation, methylation, glutathione conjugation causing INACTIVATION 
Glomerular Filtration rate
The flow rate of filtered fluid through the kidney: specifically through glomeri
Three modes of excretion in kidney
1.) filtration
2.) Reabsorption
3.) Secretion
Kidney filtration
Portion of blood flow in the kidneys is filtered through glomerular capillaries to remove compounds
Kidney reabsorption
Create concentration gradient in collecting tubule and compound diffuses back out. Facilitated or passive diffusion process
Kidney secretion
Active transporters along tubule selectively pore compounds from plasma and dump into the urine (ex. Too large but needs to leave the body)
Renal clearance (CIr)
The volume of plasma (mL) that is cleared of drug by the kidney per minute
GFR and CLR will be the same when
A solute is freely filtered and not reabsorbed or secreted
Filtered and reabsorbed in kidney
CLR < GFR
Many drugs have this
Filtered and secreted in kidney
CLR > GFR
P aminohippurate (PAH) has this
Biliary expression
Fecal excretion, process initiates in liver and passes through the gut until products are excreted along with waste. Typically avoids tissue and absorption entirely
Respiratory excretion
Gases can be blown out of the lungs and removed. Example: anesthetic gases
Where can gene expression be regulated?
• DNA structure
• when, where and how often a gene is transcribed
• How a transcript is spliced
• If mRNAs are transported out of the nucleus, and where in the cytosol they are localized
• which mRNAs are translated
• rate of mRNA degradation
• Control of the Pro Tien: activation or an activation, degradation, trafficking and compartmentalizing
Gene copy number
There are multiple copies and normal/abnormal copy number variation creates different levels of expression.
Example: allelic imbalance, gene duplication, or gene loss 
Translocation of genes
Can you put genes in a different context based on where they are located
Local alterations in chromatin structure or directed by:
Eukaryotic gene activator proteins
Cis-acting factors
Short stretches of DNA of defined sequences
Trans-acting factors
Gene regulatory proteins 
Transacting regulatory proteins factors
Act to modify activation from someplace else
What serves as recognition sites for a wide variety of regulatory proteins?
Short nucleotide sequences, usually less than 20nt, most commonly found in gene promoters
Mammals: Sp1, Oct1, GATA1, MyoD, p53
Homeobox protein NANOG
A key Jean regulatory proteins that helps embryonic stem cells maintain pluripotent see by suppressing self determination factors
Homeodomain proteins
Special subclass of helix-turn-helix proteins, and are key regulators of animal development. Contain an identical stretch of 60 amino acids
Zinc finger motif proteins
Important group of regulatory proteins that use one or more zinc atoms in their DNA finding motifs
Leucine zipper motif
In leucine zipper proteins two alpha-helices, one from each monomer, are joined together to form a short coiled-coil structure
The dimer grips DNA like a close pin on a clothesline
Helix-loop-helix motif
A short alpha-helix connected by a loop to a longer alpha-helix. Can create both homodimers and heterodimers
Heterodimerization does what?
Increases the variety of DNA sequences recognized by regulatory proteins. They are an example of combinatorial control
Lac operon
The lac operon is on when CAP is bound, but lac repressor is not bound.
+ lactose = repressor not bound
- glucose = CAP bound 
Enhancers
Regulatory sites that are distant from the promoter.
Domains of gene regulatory proteins
A structural motif: recognizes specific DNA sequences
Activation domain: accelerates transcription
Transcriptional synergy
Regulatory proteins when added together create MORE of an effect
Enhanceosome
A group of proteins that form together on an enhancer to regulate transcription at a distance. You need ALL of the proteins to have the right effect
Insulators
DNA sequences that prevent regulatory proteins from influencing distant sites. They divide the genome into independent domains
Epigenetics
Heritable, reversible changes in the genome that regulate gene expression, Most often resulting in gene silencing. Can be influenced by environment.
DNA methylation is a common example 
Mammalian X chromosome inactivation
Synthesis of XIST into XIC locus. Correlated with the condensation of the chromosome (bar body) 
De novo DNA methylation
Causes recruitment of metal binding proteins, that in turn causes chromatin condensation, resulting in gene silencing
Imprinting
Differential expression of a gene allele depending on parental origin; the purpose is to control gene dosage
Caused by 5-cytosine DNA methylation leading to chromatin condensation
IncRNA rare mechanism for imprinting
IncRNA acting on chromatin, imprinting gene located on intron 11 of a non-coding RNA
CTCF methylation rare mechanism for imprinting
Methylation of the CTCF insulator element activates and enhancer for the lgf2 gene 
Fragile X syndrome
Silence is FMR1 and messes up regulation of translation by irregulating the shuttle between the nucleus in the cytoplasm
Iron starvation
Cytosolic aconitase binds so that ferritin is NOT made, it also binds so that transferrin receptor is made
Excess iron
Iron binds to cytosolic acconitase so that it cannot bind to anything, so that ferritin is made and transferrin receptor is NOT made
