Exam 1 Flashcards
Vorinostat
- A histone deacetylase (HDAC) inhibitor
- In cancer, HDAC’s can be turned ON, and genome is turned OFF
- This can turn ON the genome, in particular tumor suppressor genes
Werner Syndrome
- Progeria syndrome (pre-mature aging)
- WRN mutation
- Helicase assoc. with telomere maintenance
Antimetabolites
- Type of anti-neoplastic agent
- Incorporated into growing DNA instead of dNTP’s
Topoisomerase inhibitors
- Type of anti-neoplastic agent
RNA Polymerases
mRNA - II miRNA - II tRNA - III rRNA (5.8S, 18S, 28S) - I rRNA (5S) - III snRNA and scRNA - II and III
Proteosomes
- 20S core (protein breakdown)
- 19S caps (targets poly-ubiquitin tags)
Ubiquitin Ligase
- find degredation signal on target protein
- Adds ubiquitin tag
Actin
- Most abundant cytoskeletal protein
- G actin = globular
- F actin = filament
- Polym. occurs at + end, depolym. at - end
Cell shape/movement
Actin forms cell processes - Microvilli - Filopodia - Pseudopodia Locomotion - Lamellipodia (+ end leads)
Spectrin
- Actin binding protein
- Assoc. with membrane lipids/proteins
- Anchors actin to membrane
Microtubules
- ALPHA and BETA (form tube)
- GAMMA (forms foundation)
- Polym. at + end, requires GTP
- Depolym. at - end
Microtubule Organizing Centers (MTOC)
- places in cells where microtubules start to form
Microtubule Basal Bodies
- part of MTOC
- found at base of cilium/flagellum
- allow for whip-like, unidirectional motion
Motorproteins
- walk along microtubules
- kinesins: walk to +, away from nuc, can push OR pull
- dyneins: walk to-, towards nuc, can ONLY pull
Intermediate filaments types
mechanical strength
assoc. with membranes and cytoskel.
types
- keratins (synth. by epithelium)
- neurofilaments (support long, thin axons)
- lamins (undelying all nuc membranes)
Intermediate filament assembly
- homodimers (two together)
- protofilaments (two of those)
- filaments (eight of those)
Desmosomes
- cell-cell junctions
Hemidesmosomes
- cell-ECM junctions (at basement membrane)
Basement membrane
- Basal Lamina + Reticular Layer
- a fibrous EC layer
Glucosaminoglycans (GAG)
- sugars with sulfate groups
- (-) charged, trap + ions and water
- part of proteoglycan (protein + GAG)
Propyl hydroxylase
- resident ER protein
- forms hydroxy-Proline from Proline
- needed for collagen
- REQUIRES Vitamin C (Scurvy)
Collagen
- 31 kinds
- Sequence is Gly-Pro-hydroxyPro
- makes triple helixes (tropocollagen)
- important in wound healing
Elastin
can stretch and recoil
made of
- elastin (randomly coiled and hydrophobic, covalently cross-linked to each other)
- fibrillin (a surrounding network of microfibrils)
Lysyl oxidase
- enzyme that does the cross-linking of elastin molecules to create elastin fibrils from tropoelastin
Fibronectin
principle adhesion protein in conn. tissue contains multiple adhesion domains - collagen - GAG (part of ground substance) - integrin (cell surface protein)
Laminin
- principle adhesion protein of basal lamina
Integrins
- cell surface receptors
- bind to ECM (collagen, fibronectin, laminin)
- anchor to cytoskel.
Focal adhesions
- attach motile cells to ECM
- anchor to actin skel.
Scurvy
defective collagen formation
- impaired wound healing
- capillary hemorrhage
- vit C deficiency (ascorbic acid)
Kinetochore microtubules
- attach to sister chromatids
- depolymerize
Astral microtubules
- attach to membrane
- polymerize
Cell cycle: Restriction point
- late G1
- controls cell cycle and entry into DNA duplication
- Is environment favorable?
Cell cycle: G2/M checkpoint
- during G2
- is all DNA copied?
- Is environment favorable?
Cell cycle: Metaphase-to-anaphase checkpoint
- During M
- Are all chromosomes attached to spindle?
Cell cycle: DNA damage checkpoints
Found in
- G1
- S
- G2
Cyclin dependent kinases
Phosphorylate proteins that regulate cell cycle
G1/S cyclin
- trigger progression through restriction point
- peaks in G1
S cyclin
- trigger chr duplication
- Peaks through S and G2
M cyclin
- trigger process through G2/M checkpoint
- Peaks in M
Regulation of Cyclin-Cdk complex
- Cdk-activating kinase
- Wee1
- Cdc25
- Cdk Inhibitor proteins (CKI)
Cdk-activating kinase (activates complex by P active site)
Wee1 (inhibits complex by P inhibition site)
Cdc25 (actiates complex by de-P inhibition site)
Cdk Inhibitor proteins (CKI)
- creates Cyclin-Cdk-CKI complex
- inhibits Cyclin-Cdk activity
- ex: p27, p21, p16
Securin
- hold sister chromatids together
APC/C
- anaphase promoting complex/cyclosome
- actived by Cdc20
- ubiquitin ligases target securin (hold sister chr together) for degradatin ——-> anaphase
Origin replication complexes
- complexes found at origins of replication
- remain assoc. with origins throughout cell cycle
- include DNA helicases
- these are Phosphorylated to initiate replication
Cohesins
- ring-like structures around sister chr to keep them together
- cleaved by separase
M phase control
M-Cdk Phosph. targets
- Condensin (promotes chr condensation) - Mitotic spindle - Nuclear pore complexes - Nuclear lamina - APC/C
[Glucose] in cell
- 5mM
- 90 mg/dL
Phosphofructokinase
- 3rd step of Glyc.
- F6P ——> F-1,6-BP
- Activated: AMP, F-2,6-BP
- Inhibited: ATP, citrate
Hexokinase (I and IV)
Commitment step of Glyc. Glu -----> G6P Inhibited by G6P (product) Hexokinase I - high affinity, low Km - NOT super specific for Glu - Inhibited by its product Hexokinase IV - "Glucokinase" - In liver and pancrease - NOT inhibited by G6P - Larger Km, though - highly specific for Glu - Acts as a sensor for B-cells in pancrease (high Glu --> more HK IV activity --> insulin secreted)
Pyruvate Kinase
- 10th step of Glyc.
- PEP —–> Pyruvate
- Activated: AMP, F-1,6-BP
- Inhibited: ATP, Acetyl-CoA
Arsenic
Found in
- Rat poison
- Herbicides
- Industrial cleaners
Inhibits Pyruvate Dehydrogenase (Pyruvate —> A-CoA)
“Garlic smell” = PDH deficiency = lactic acidosis
Carboxylases
Require ABC - ATP - Biotin - CO2 Pyruvate carboxylase (gluconeogen.) Acetyl-CoA carboxylase (FA synth.) Propionyl-CoA carboxylase (Prop. acid pathway)
TLCFN
TLCFN - TPP (thiamin, Vit B1) - alpha-Lipoiic Acid - CoA - FAD (riboflavin, Vit B2) - NAD+ (nicain, Vit B3) 3 enzymes require - Pyruvate DH (pyruv ---> A-CoA) - a-ketoglutarate DH (a-KG ---> succinyl CoA) - branched chain ketoacid DH (Val/Iso/Leu ---> Propionyl CoA) "maple syrup urine disease"
Hutchinson-Gilford Progeria Syndrome
normal dev. 3-6 months LMNA mutation - Lamin A, of nuc. lamina fragile nuclei, genomic instability mean death 13.5 years
Beriberi
Thiamine deficiency (Vit B1) Need TPP for TLCFN enzymes - Pyruvate DH - a-Ketoglutarate DH Loss of neural function
Fluoroacetate
- Inhibits aconitase of TCA cycle
- metabolizes to fluorocitrate
- in some acacia trees in Australia/Africa
Tyrosine-Kinase Associated Receptors
act through CYTOplasmic tyr. kinases soluble tyr. kinases in cytosol associate with activvated receptor ligands - cytokines - interleukins - integrins
Receptor Tyrosine Kinase
aka "Tyrosine-linked receptors" contain intracellular tyrosine kinase domain two monomers cross-Phosph. each other ligands - growth factors
Philadelphia chr
- chromosomal translocation
- Bcr-Abl fusion protein
- Abl is always ON (it’s a Tyr Kinase)
- chronic myeloid leukemia
- treated by Imatinib (Gleevac)
PDGFR
platelet derived growth factor receptor stimulated mitogenic activity (MAPK/PI3K) oncogenic mutation - chronic myeloid leukemia - GI stromal tumors
GSD Type 1
von Gierke's Glu-6-Phosphatase symptoms - severe hypoglycemia - hepatomegaly - hyperlipidemia
GSD Type 2
Pompe's acid a-glucosidase (a1-4 linkages) symptoms - cardiomegaly - death by 2 y/o
GSD Type 3
Cori glycogen debranching enzyme/glycogen phosphorylase symptoms - mild hypoglycemia - hepatomegaly
GSD Type 4
Andersen Glycogen branching enzyme Symptoms - cirrhosis - failure to thrive - hypotonia - death by 2 y/o
GSD Type 5
McArdle's Muscle glycogen phosphorylase Symptoms - muscle weakness - cramps on exercise - rhabdomyolysis
GSD Type 6
Hers
Liver glycogen phosphorylase
Symptoms
- hepatomegaly
Ion Flow (Na, Ca, H, K, Cl, HCO3)
In - Na - Ca - H Out - K - Cl - HCO3
Wernicke-Korsakoff Disease
brain syndrome cause by lack of Vit B1 (thiamine)
transketolase has low affinity for TPP due to point mutation (part of HMP Shunt)
symptoms
- ataxia
- psychosis
- confusion
Also, alcohol inhibits thiamine absorption
Citrate synthase
A-CoA + Oxaloacetate ---> Citrate (Krebs) Inhibited - citrate - succinyl-Coa - NADH - ATP (this can be reversed by AMP)
Pyruvate DH
Pyruvate ---> Acetyl-CoA TLCFN Activated: - NAD+ - CoA - Ca (in muscle only) Inhibited - A-CoA - ATP - NADH
Complex 1 (ETC)
- NADH-ubiquinone oxidoredutase
ETC/OP Inhibitors (I - 2, IV - 3, OP - 2)
- “Br-cac, DO”
Complex I - Barbiturates - Rotenone (fish poison) Complex IV - Cyanide (Fe3+) - CO (Fe2+) - Azide ATPase - Oligomycin (antibiotic, plugs opening of F0) - DCCD
Chylomicrons
- packages of fat from diet
- Ride on Apoprotein B48
VLDL
- very low density lipopotein
- it is made of excess Glucose from diet
- Glu –> Pyruvate –> A-CoA –> fatty A –> fat (then exit liver)
- drop off FA at adipose, return glycerol-P to liver
lipoprotein lipase
- cuts the FA’s off of the fat in VLDL
- drops off FA at adipose tissue for storage, glycerol will return to liver
GLUT4
- Glu transporter
- found in muscle and adipose
- stays in vesicles, waiting for insulin to arrive at cell, then it’s on surface
Main source of fuel, 4 hours after eating
Liver glycogen
Main source of fuel, `8 hours after eating
Fatty acids (adipose tissue
Main source of fuel, 5 days after eating
Ketone bodies
- Adipose tissue fat –> (b-ox) –> fatty a –> fatty a albumins –> Liver –> A-CoA –> ketone bodies
4 main starvation adaptations
- fat hydrolysis in adipose
- gluconeogenesis in liver and kidney
- ketogenesis in liver
- protein degridation in muscle
CTD Tail
C-terminal end of RNA Pol II
Must be phosph. to initiate transcription
DNA Methylation
Done at CpG islands (C’s that proceed G’s)
Transcriptional REPRESSION
Heritable (epigenetic)
siRNA
- small interfering RNA
- can induce transcriptions silencing
- usually exogenous (artifically introduced)
miRNA
- micro RNA
- an regulate mRNA degredation by base pairing with existing mRNA, targets it for destruction
- usually endogenous
GLUT2
Found in Liver and Pancreatice B-cells
Uptake and release of Glu (liver)
Glu-sensing (B cells)
- GLUT2 –> ATP:ADP ratio –> membrane depolarization –> open Ca channel –> Ca enters –> Insulin vesicles secreted
3 different hemolytic anemias
1st most common
Sickle cell
- Hb has mutation –> distorts RBC –> RCB life expectancy drops –> RBC lysis
2nd most common
Pyruvate kinase deficiency
- Back up of Glyc. –> no ATP –> RBC has no other source of ATP –> can’t power Na-K pumps –> cell hypotonic –> swells –> lysis
G6PD deficiency
- No entry into HMP Shunt –> can’t make NADPH (reduced glutathione) –> oxidative damage to RBC –> lysis
MetHb
- Methemoglobin
- Heme group has Fe3+ not Fe2+
- Cannot carry O2
- Reverted to Hb by MetHb reductase, which requires NADPH
- “methemoglobinuminia”
Heinz bodies
Small budding dots on RBC’s
Found in G6PD hemolytic anemia, but not PK
2,3-BPG
- Part of Glycolysis
- Binds to Heme groups in Hb and lowers O2 affinity
- Necessary for dumping O2 in tissue
- It binds the B subunit of Hb and “kicks off” the O2 there
- HbF (fetal) has alpha and gamma subunits, so unaffected by 2,3-BPG
Pyruvate Dehydrogenase
- Pyruvate to A-CoA
- Inhibited by Arsenic (rat poison, herbicides, moonshine)
- TLCFN
Thiamine deficiency
- common in alcoholics (alcohol inhibits absorption of thiamine)
- and IV solution of glucose can kill alcoholics because lactic acidosis
Cell response to hypertonicity (in surroundings)
Activate Na-H exchanger (Na in, H out) —> This activates Cl-HCO3 exchanger —> Cl enters
Net uptake of Na and Cl —> water follows
Cell response to hypotonic (in surroundings)
Activate solute efflux (either Cl and/or K channels) —> Water exits
Idiogenic osmolytes
Some cells can increase tonicity by producing these
Response to long-term hyperosmolality
OR because Na and Cl can interrupt cell processes
Na-H exchanger
“acid extruder”
- Uses Na gradient to move H out
- activated by intracellular metabolic acidosis
- inhibited by very high pH
- induces Cl-HCO3 exchanger by creating high pH
Cl-HCO3 exchanger
“acid loader”
- uses Cl gradient to move HCO3 out
- activated by intracellular metabolic alkalosis
- inhibited by very low pH
- induces Na-H exchanger by creating low pH
Intracellular respiratory acidosis
high E CO2 pushes CO2 into cell
low pH in cell
CO2 + H20 —> H + HCO3 (carbonic anhydrase)
Activate Na-H exchanger
Protein sorting signals
encoded in aa sequence
usually at N-terminus
or can be “signal patches”, not near each other in aa sequence, but in 3d are near each other
no signal = destined for cytosol
Importins
Recognize nuclear localization signals on proteins
Brings them to/through nuclear pore complex
Have two binding sites
- nuclear localization signal
- nuclear pore complex
Exportin
Recognizes nuclear export signal
RanGTPase binds the protein-exportin complex and exits the nuclear pore with them
- RanGTPase used to dissociate the complex in the cytosol
Vesicle coats from different sources
Clathrin-coated (from plasma membrane)
COP I-coated (from Golgi)
COP II-coated (from ER)
ER retrieval signal
KDEL
Usually at C-terminus
Proteins can only leave ER after this sequence has been cleaved
SNARE
v-SNARE (vesicle)
t-SNARE (target)
Need SNARE-SNARE interaction for vesicle fusion
Co-translational import
rER “catches” the protein as it’s coming out of the ribosome
SRP recognizes the early budding protein, brings it to SRP receptor on ER
Two types of proteins are usually co-translated
- transmembrane proteins
- water soluble protein (for secretion)
Lysosome maturation
Endocytotic vesicle —> Early endosome —> Late endosome (mildly acidi pH 6, zymogens) —> Endolysosome (fusion with pre-existing lysosome, activates zymogens, pH 4.5-5) —> lysosome
Mannose-6-P
Signals lysosomal proteins for lysosomes
M6P receptors are on the inside of Trans-Golgi
UDP-glucose phosphorylase
G1P —> UDP-Glu (to be added to glycogen)
Required UTP
Glycogen synthase
UDP-Glu —> Glycogen (a1-4 linkages)
Activated by Insulin
Works alongside Glycogen branching enzyme (a1-6 linkages, every 8-14 residues)
Gluconeogenesis
Mainly in liver/kidneys (only places with G6Pase)
E to power gluconeogenesis comes from triacylglycerides (TG)
Hormone Sensitive Lipase (HSL) breaks fat —> FA + Glycerol
Cori cycle
LIVER
Lactate —> Pyruvate —> Glu (gluconeogenesis)
BLOOD
Transport
MUSCLE
Glu —> Pyruvate —> Lactate
- this cycle produces lactic acidosis
Glucose-Alanine Cycle
LIVER
Alanine —> Pyruvate —> Glu (alanine transaminase)
Urea excreted
BLOOD
Transport
MUSCLE
Glu —> Pyruvate —> Alanine (alanine transaminase)
Transketolase
Part of HMP Shunt
Requires TPP (but not the rest of TLCFN)
Wernicke-Korsakoff Disease (mut in TK gene, enzyme won’t bind TPP)
- treat with increased thiamine in diet (Vit. B1)
G6PD deficiency
Most common enzymatic deficiency in world
X-linked recessive
10-14% of African-American males have it
- Immunodeficiency
- In neutrophil, no NADPH made - Heinz bodies
- Hb denaturation in RBC’s because oxidative damage because no reduced gultathione because no NADPH - Hemolytic anemia
Trophic factors
Cells require these signals to “keep living”
Cell signaling dessensitization
Receptor sequestration
Receptor down-regulated
Receptor inactivated
Inhibitor protein production
Mitogen
Signaling molecules that stimulate cell division
Activate G1/S-Cdk activity
Intracellular receptors
- Steroids
- hydrophobic enough to diffuse in to cell
- intracellular receptors dimerize and then go to nuc as TF’s - Nitric Oxide
- gas, small enough to diffuse
- acts locally, short half life
- Activates guanylyl cyclase (GTP —> cGMP)
Eicosanoid
Lipids that bind cell surface recptors
Short half life, act locally
Induce clotting and inflammation
Ion-channel-coupled
“Ionotropic”
Rapid signaling in electrically-excitable cells
Action: opens/closes ion channels to change excitability state of cell
Ligands: Neurotransmitters
G Protein coupled receptors
GPCR
7TM (7 pass transmembrane proteins)
Ligands: eicosanoids, neurotransmitters, peptide hormones
Special senses: smell, sight, taste
Coupled to three protein inside
alpha (binds GTP)
beta-gamma (they stay together)
alpha subunit will be activated and will activate/inhibit adenylyl cyclase
Gs (activates) vs. Gi (inhibits)
Receptor serine/threonine kinases
Ligands: TGF-beta
Action: form heterodimers –> one chain activates other –> activates Smad pathway
Notch
- Do Not Work For HP
Receptor for direct cell-cell signaling
Ligand: Delta
Action: Delta induces proteolytic cleavage of cystolic tail of Notch —> to nuc as TF
Frizzled
- Do Not Work For HP
Receptor
Ligand: Wnt
It stops the bully from phosphorylating and ubiquinating beta-catenin
Patched
- Do Not Work For HP
Receptor
Ligand: Hedgehog
Actions: Activated smoothened —> inhibits phosphorylation of Ci —> Ci becomes TF
Death receptors
Ligands: cytokines, growth factors, pathogen assoc. molecular patters (MAMP)
Action: binding of one ligand induces clustering of cytosolic Death Domains
Ex: Caspase
Inegrins
At cell-matrix junctions (focal adhesions, hemidesmosomes)
Induce proliferation, gene expression, survival
cAMP
A secondary messenger
Activates protein kinase A
PIP2
Cleaved by phopsholipase C into IP3 + DAG (two secondary messengers)
IP3 - activated ligand-gated Ca channels
DAG - activates protein kinase C
PI3 Kinase
Phosphorylates PIP2 to PIP3
This activate Akt, a kinase that influences cell survival and protein synth.
A secondary messenger
JAK/STAT
JAK - cytokine receptor - non-receptor protein Tyr kinase - phosphorylates nearby STAT's ---> STAT's dimerize ---> TF's STAT - The secondary messenger
NF-kB
regulates proliferation and survival
activates through death receptors
Ligands: Cytokines, growth factors, pathogen assoc. molecular patters (MAMP) (this is same as death receptors)
Action: Receptor activates 1kB kinase —> phosphorylates and ubiquinates 1kB (which had been covering a NF-kB dimer) —> free NF-kB dimer —> TF
It’s a secondary messenger
Rho (secondary messenger)
Regulates cytoskeletal changes
Activated through integrins, growth factor receptors
Promotes actin growth, and phosphorlationg of myosin
Sickle Cell Disease
HbS
Affects shape/life span of RBC’s
Mutation in B chain, non-polar Val for Glu
Creates hydrophobic knobs that aggregate and pcpt
Sickle Cell Symptoms
Anemia
Growth failure
- long term effect of anemia
Infection
- reduced splenic function
Vaso-occlusive events
- local vessel obstruction, further promotion of hypoxia/acidosis
- causes extreme pain
Organ failure
- long term effect of hemolysis and clogging
Sickle Cell Treatment
Hydroxyurea
- stimulates HbF production
- mechanism noe 100% known but…
- Activates NOS
- ribonucleotide reductase
Ionotropic
receptor class
- ligand-gates ion channels
- typically fast neurotransmitters
Metabolic
receptor class
- G protein coupled
- coupled with effector protein, ion channel, or TF
Enzyme-linked
receptor class
- act on TF’s
- cell growth, differentiation, division, apop., inflammtion
Nuclear receptors (receptor class)
- act directly as TF’s
- located in cytosol/nucleus, ligand must diffuse in
